gifterreference atlas
Database 2026.39.1 · schema 9

Reference atlas

A browsable compilation of the gifter reference database: every curated GIFT, how its genomic support is evaluated, and where its definition came from.

gifter infers genome-inferred functional traits (GIFTs) from the markers observed in a genome. Each GIFT is a biologically defined capability with an explicit completeness model, and this atlas renders the curated database behind those calls, from the trait down to the accepted markers.

The database at a glance

163GIFTscurated capabilities
156Anchorsdeclared boundary molecules
233Alternativesroutes and implementations
606Systemsenzymes and machinery
770Componentsjointly required proteins
1,576Markersaccepted identifiers

Layers by GIFT type

TypeGIFTsAlternativesRequirementsSystemsComponentsMarkers
Metabolic143210routes440reactions505enzyme systems6071,252
Structural911architectures58functions61systems110184
Regulatory45circuits11functions14systems2023
Defense77mechanisms16functions26systems3396

Each type evaluates five Boolean layers: a GIFT is supported by any complete alternative (a route, architecture, circuit or mechanism), an alternative requires all of its reactions or functions, each of those is met by any complete system, a system requires all of its components, and a component is supported by any accepted marker. Reactions, functions and markers are counted once however many GIFTs share them, and a marker may serve more than one type.

Metabolic GIFTs by mode

  • Catabolic69
  • Anabolic67
  • Interconversion4
  • Transport3

Anchors by compartment

  • Unspecified138
  • Extracellular11
  • Cytoplasmic7

Markers by namespace

  • KO903
  • CAZY520
  • NCBIFAM145
  • TIGRFAM5
  • EC2
  • PFAM1

How the atlas is organised

19 presetsFrames

The sets of GIFTs over which quantitative traits are computed, with the analyses each supports. 4 are bounded, so coverage fractions are interpretable.

163 GIFTsGIFTs

The catalogue. Each GIFT has its own page with its boundaries, alternatives, reactions or functions, systems, components, markers and curation evidence.

144 changesChanges

Every change to the biological content, why it was made, its evidence, and the GIFTs it affects.

344 boundary linksNetwork overview

Every GIFT and its declared anchors drawn as one network, recoloured by curated metadata. GIFTs connect only through declared anchors.

37 tablesData model

Primary keys, foreign keys and the normalized tables behind the evaluation model.

8,749 rowsTables

Every compiled row, searchable, for inspecting exact values.

This release

Database version
2026.39.1
Schema version
9
Build date
2026-10-04
Rhea release
142
ChEBI release
254
KEGG release
2026-10-04
Source commit
unreleased

A positive call indicates that the markers support at least one complete curated route, architecture, circuit or mechanism. It does not indicate expression, activity, physiological state or phenotype.

Declared anchors

Network overview

Every GIFT with its declared boundaries. GIFTs connect only through anchors, never through metabolites shared inside routes.

Hover a dot for its detail · click a GIFT to open it
Acetyl-CoA and acetate interconversion · acetate_interconversionPyruvate to (R)-acetoin · acetoin_formationAcetyl-CoA and oxaloacetate to isocitrate · acetyl_coa_to_isocitrateIMP to AMP · adenylate_biosynthesisPyruvate to L-alanine · alanine_biosynthesisAllantoin to glyoxylate and urea · allantoin_degradationAmmonium and 2-oxoglutarate to glutamate · ammonium_assimilationAnthranilate to catechol · anthranilate_degradation_catecholL-arabinose to D-xylulose 5-phosphate · arabinose_degradationL-arabinose uptake · arabinose_uptake_abcArabinoxylan to xylan and L-arabinose · arabinoxylan_debranchingArchaellum machinery · archaellumL-ornithine to L-arginine · arginine_biosynthesisL-arginine to L-ornithine and ammonium · arginine_deiminase_pathwayL-aspartate to L-asparagine · asparagine_biosynthesisOxaloacetate to L-aspartate · aspartate_biosynthesisAspartate chemoreception · aspartate_chemoreceptionAspartate to aspartate 4-semialdehyde · aspartate_semialdehyde_biosynthesisSulfate to hydrogen sulfide · assimilatory_sulfate_reductionBenzoate to catechol · benzoate_degradation_catecholBeta-lactam detoxification · beta_lactam_detoxificationGlycine betaine to sarcosine · betaine_demethylationPimeloyl-CoA to biotin · biotin_biosynthesisAcetyl-CoA and acetate to butanoate · butyrate_formationL-carnitine to trimethylamine · carnitine_degradation_trimethylamineL-carnitine to glycine betaine · carnitine_to_betaineCatechol to 2-oxopent-4-enoate by meta cleavage · catechol_meta_cleavageCatechol to 3-oxoadipate by ortho cleavage · catechol_ortho_cleavageChemotaxis signal transduction · chemotaxis_signal_transductionChitin to N-acetyl-D-glucosamine · chitin_degradationChloramphenicol detoxification · chloramphenicol_detoxificationCholine to glycine betaine · choline_to_betainePhosphoenolpyruvate and erythrose 4-phosphate to chorismate · chorismate_biosynthesisCitrate to pyruvate and acetate · citrate_fermentationAdenosylcobinamide phosphate and dimethylbenzimidazole to cobalamin · cobamide_nucleotide_loop_assemblyCobyrinate a,c-diamide to adenosylcobinamide phosphate · cobinamide_biosynthesisCollagen to collagen peptides · collagen_cleavageUroporphyrinogen III to cobyrinate a,c-diamide · corrin_ring_biosynthesisCreatinine to sarcosine and urea · creatinine_degradationSerine and homocysteine to cysteine · cysteine_biosynthesis_homocysteineSerine and sulfide to cysteine · cysteine_biosynthesis_sulfideL-cysteine to hydrogen sulfide and pyruvate · cysteine_degradation_sulfideUTP to CTP · cytidylate_biosynthesisL-aspartate 4-semialdehyde to meso-diaminopimelate · dap_biosynthesisDiglucosyldiacylglycerol-anchored poly(glycerol-phosphate) lipoteichoic acid · diglucosyl_diacylglycerol_anchored_lipoteichoic_acidChorismate to 2,3-dihydroxybenzoate · dihydroxybenzoate_biosynthesis3-(2,3-Dihydroxyphenyl)propanoate to 2-oxopent-4-enoate and succinate · dihydroxyphenylpropanoate_degradationFMNH2 to 5,6-dimethylbenzimidazole · dmb_biosynthesis_aerobicAspartate semialdehyde to ectoine · ectoine_biosynthesisL-ectoine to L-2,4-diaminobutanoate · ectoine_degradation2,3-Dihydroxybenzoate and serine to enterobactin · enterobactin_biosynthesisAcetyl-CoA to ethanol · ethanol_formationFlagellar apparatus · flagellar_apparatusGTP and 4-aminobenzoate to tetrahydrofolate · folate_biosynthesisL-fucose to dihydroxyacetone phosphate and (S)-lactaldehyde · fucose_degradation_isomeraseFumarate and oxaloacetate interconversion · fumarate_oxaloacetate_interconversionbeta-D-galactose to alpha-D-glucose 1-phosphate · galactose_degradation_leloirD-galacturonate to 2-dehydro-3-deoxy-D-gluconate · galacturonate_degradationN-acetyl-D-glucosamine to beta-D-fructose 6-phosphate · glcnac_degradationD-glucuronate to 2-dehydro-3-deoxy-D-gluconate · glucuronate_degradationL-glutamate to 4-aminobutanoate · glutamate_decarboxylation_gabaL-glutamate and ammonium to L-glutamine · glutamine_biosynthesisSerine to glycine · glycine_biosynthesisGlycine to acetyl phosphate and ammonium · glycine_reduction_sticklandIsocitrate and acetyl-CoA to succinate and malate · glyoxylate_bypassIMP to GMP · guanylate_biosynthesisUroporphyrinogen III to heme b · heme_b_biosynthesisPRPP and L-glutamine to L-histidine · histidine_biosynthesisL-histidine to L-glutamate and ammonium · histidine_degradation_glutamateAIR to the thiamine pyrimidine · hmp_phosphate_biosynthesisAspartate 4-semialdehyde to homoserine · homoserine_biosynthesisL-ectoine to 5-hydroxyectoine · hydroxyectoine_biosynthesis3-(3-Hydroxyphenyl)propanoate to 3-(2,3-dihydroxyphenyl)propanoate · hydroxyphenylpropanoate_hydroxylationL-tryptophan to indole-3-acetate · indole_3_acetate_biosynthesisIsocitrate to 2-oxoglutarate · isocitrate_to_oxoglutarate2-oxobutanoate to L-isoleucine · isoleucine_biosynthesis2-dehydro-3-deoxy-D-gluconate to pyruvate and D-glyceraldehyde 3-phosphate · kdg_degradationPyruvate to (S)-lactate · lactate_formation(S)-lactaldehyde to (S)-lactate · lactate_formation_lactaldehyde(S)-lactate and (R)-lactate interconversion · lactate_racemisation3-methyl-2-oxobutanoate to L-leucine · leucine_biosynthesisLpt lipopolysaccharide export apparatus · lpt_lipopolysaccharide_export_apparatusmeso-diaminopimelate to L-lysine · lysine_biosynthesis_dap(S)-malate to (S)-lactate · malolactic_fermentationChorismate to menaquinone · menaquinone_biosynthesisMercury detoxification · mercury_detoxificationHomoserine and sulfide to methionine · methionine_biosynthesis_sulfhydrylationHomoserine and cysteine to methionine · methionine_biosynthesis_transsulfurationL-methionine to methanethiol and 2-oxobutanoate · methionine_degradation_methanethiolMethylamine to ammonium · methylamine_degradationGlutathione-dependent methylglyoxal detoxification · methylglyoxal_detoxificationMucin O-glycan to L-fucose · mucin_fucose_releaseMucin O-glycan to N-acetyl-D-galactosamine · mucin_galnac_releaseMucin O-glycan to N-acetylneuraminate · mucin_sialic_acid_releaseNicotinate D-ribonucleotide to NAD · nad_biosynthesis_namnQuinolinate to nicotinate D-ribonucleotide · namn_biosynthesis_quinolinateNicotinate to nicotinate D-ribonucleotide · namn_salvage_nicotinateN-acetylneuraminate to beta-D-fructose 6-phosphate · neuac_degradationNitrate to ammonium · nitrate_assimilationDinitrogen to ammonium · nitrogen_fixationL-glutamate to L-ornithine · ornithine_biosynthesis3-Oxoadipate to 3-oxoadipyl-CoA · oxoadipate_activation3-Oxoadipyl-CoA to succinyl-CoA and acetyl-CoA · oxoadipyl_coa_thiolysisPyruvate to 2-oxobutanoate · oxobutanoate_biosynthesis_citramalate2-oxoglutarate to succinate · oxoglutarate_to_succinatePyruvate to 3-methyl-2-oxobutanoate · oxoisovalerate_biosynthesis2-Oxopent-4-enoate to pyruvate and acetyl-CoA · oxopentenoate_degradationChorismate to 4-aminobenzoate · paba_biosynthesis2-oxoisovalerate and L-aspartate to pantothenate · pantothenate_biosynthesisPectin to 2-dehydro-3-deoxy-D-gluconate by beta-elimination · pectate_lyase_degradationPectin to D-galacturonate · pectin_degradationPhenol to catechol · phenol_hydroxylationPhenylacetate to 3-oxoadipyl-CoA · phenylacetate_degradationChorismate to L-phenylalanine · phenylalanine_biosynthesis3-Phenylpropanoate to 3-(2,3-dihydroxyphenyl)propanoate · phenylpropanoate_dihydroxylationPhosphate starvation response · phosphate_starvation_responseErythrose 4-phosphate and DXP to pyridoxal 5-phosphate · plp_biosynthesis_dxpRibose 5-phosphate and glyceraldehyde 3-phosphate to pyridoxal 5-phosphate · plp_biosynthesis_r5pL-glutamate to L-proline · proline_biosynthesisL-proline to 5-aminopentanoate · proline_reduction_stickland(S)-lactaldehyde to (S)-propane-1,2-diol · propanediol_formation(R)-lactate to propanoate · propionate_formation_acrylate(S)-propane-1,2-diol to propanoate · propionate_formation_propanediolPRPP to IMP · purine_core_biosynthesisGlutamine and PRPP to UMP · pyrimidine_core_biosynthesisPyruvate to acetyl-CoA · pyruvate_to_acetyl_coaL-aspartate to quinolinate · quinolinate_biosynthesis_aspartateL-rhamnose to dihydroxyacetone phosphate and (S)-lactaldehyde · rhamnose_degradationPoly(ribitol-phosphate) wall teichoic acid · ribitol_phosphate_wall_teichoic_acidGTP and D-ribulose 5-phosphate to riboflavin · riboflavin_biosynthesisChorismate to salicylate · salicylate_biosynthesisSarcosine to glycine · sarcosine_demethylation3-phosphoglycerate to serine · serine_biosynthesisSerine chemoreception · serine_chemoreceptionL-serine to pyruvate and ammonium · serine_deaminationUroporphyrinogen III to siroheme · siroheme_biosynthesisSiroheme to heme b · siroheme_to_heme_bStarch to D-glucose · starch_degradationSuccinate and fumarate interconversion · succinate_fumarate_interconversionComplete superoxide detoxification · superoxide_detoxificationTaurine to sulfite through sulfoacetaldehyde · taurine_degradation_sulfoacetaldehydeTaurine to sulfite · taurine_desulfonation_aerobicTaurine uptake · taurine_uptake_abcThiamine pyrimidine and thiazole to thiamine phosphate · thiamine_phosphate_biosynthesisThiamine precursor salvage to the activated moieties · thiamine_precursor_salvageDXP to the thiamine thiazole · thiazole_phosphate_biosynthesisHomoserine to threonine · threonine_biosynthesisL-threonine to 2-oxobutanoate and ammonium · threonine_deaminationChorismate and L-glutamine to L-tryptophan · tryptophan_biosynthesisL-tryptophan to indole, pyruvate and ammonium · tryptophan_degradation_indoleType I-E CRISPR-Cas machinery · type_i_e_crispr_cas_machineryType I restriction-modification · type_i_restriction_modificationType II secretion system · type_ii_secretion_systemType III secretion injectisome · type_iii_secretion_injectisomeType IVa pilus machinery · type_iva_pilusType VI secretion apparatus · type_vi_secretion_apparatusChorismate to L-tyrosine · tyrosine_biosynthesisUrate to allantoin · urate_degradationUrea to ammonium · urea_hydrolysis3-methyl-2-oxobutanoate to L-valine · valine_biosynthesisXylan to D-xylose · xylan_degradationD-xylose to D-xylulose 5-phosphate · xylose_degradation_isomeraseD-xylose uptake · xylose_uptake_abcacetyl-CoA · ACETYL_COAacetate · ACETATEpyruvate · PYRUVATE(R)-acetoin · ACETOINoxaloacetate · OXALOACETATED-threo-isocitrate · ISOCITRATEinosine 5'-monophosphate(2-) · IMPadenosine 5'-monophosphate(2-) · AMPL-alanine · ALANINE(S)-allantoin · ALLANTOINglyoxylate · GLYOXYLATEurea · UREAammonium · AMMONIUM2-oxoglutarate · OXOGLUTARATEL-glutamate · GLUTAMATEanthranilate · ANTHRANILATEcatechol · CATECHOLL-arabinose · ARABINOSE_IND-xylulose 5-phosphate · XYLULOSE_5PL-arabinose · ARABINOSE_EXarabinoxylan · ARABINOXYLANxylan · XYLANL-ornithine · ORNITHINEL-arginine · ARGININEL-aspartate · ASPARTATEL-asparagine · ASPARAGINEL-aspartate 4-semialdehyde · ASAsulfate · SULFATEhydrogen sulfide · SULFIDEbenzoate · BENZOATEglycine betaine · BETAINEsarcosine · SARCOSINEpimeloyl-CoA · PIMELOYL_COAbiotin · BIOTINbutanoate · BUTYRATE(R)-carnitine · CARNITINEtrimethylammonium · TRIMETHYLAMINE2-oxopent-4-enoate · OXOPENTENOATE3-oxoadipate · OXOADIPATEchitin · CHITINN-acetyl-D-glucosamine · GLCNACcholine · CHOLINEphosphoenolpyruvate · PEPD-erythrose 4-phosphate · E4Pchorismate · CHORISMATEcitrate · CITRATEadenosylcobinamide phosphate · ADENOSYLCOBINAMIDE_P5,6-dimethylbenzimidazole · DMBnicotinate D-ribonucleotide · NAMNadenosylcobalamin · COBALAMINcob(II)yrinate a,c diamide · COBYRINATE_DIAMIDEcollagen · COLLAGENcollagen peptides · COLLAGEN_PEPTIDESuroporphyrinogen III · UROGEN_IIIcreatinine · CREATININEL-serine · SERINEL-homocysteine · HOMOCYSTEINEL-cysteine · CYSTEINEuridine 5'-triphosphate(4-) · UTPcytidine 5'-triphosphate(4-) · CTPmeso-2,6-diaminopimelate · MESO_DAP2,3-dihydroxybenzoate · DIHYDROXYBENZOATE_2_33-(2,3-dihydroxyphenyl)propanoate · DHPPsuccinate · SUCCINATEFMNH2 · FMNH2L-ectoine · ECTOINEL-2,4-diaminobutanoate · DABAenterobactin · ENTEROBACTINethanol · ETHANOLGTP · GTP4-aminobenzoate · PABA(6S)-5,6,7,8-tetrahydrofolate · THFL-fucose · FUCOSEdihydroxyacetone phosphate · DHAP(S)-lactaldehyde · LACTALDEHYDEfumarate · FUMARATEbeta-D-galactose · GALACTOSEalpha-D-glucose 1-phosphate · GLUCOSE_1Paldehydo-D-galacturonate · GALACTURONATE2-dehydro-3-deoxy-D-gluconate · KDGbeta-D-fructose 6-phosphate · FRUCTOSE_6PD-glucuronate · GLUCURONATE4-aminobutanoate · GABAL-glutamine · GLUTAMINEglycine · GLYCINEacetyl phosphate · ACETYL_PHOSPHATE(S)-malate · MALATEguanosine 5'-monophosphate(2-) · GMPheme b · HEME_B5-phospho-alpha-D-ribose 1-diphosphate · PRPPL-histidine · HISTIDINE5-amino-1-(5-phospho-beta-D-ribosyl)imidazole · AIR4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine · HMP_PPL-homoserine · HOMOSERINE5-hydroxyectoine · HYDROXYECTOINE3-(3-hydroxyphenyl)propanoate · HPPL-tryptophan · TRYPTOPHAN(indol-3-yl)acetate · INDOLE_3_ACETATE2-oxobutanoate · OXOBUTANOATEL-isoleucine · ISOLEUCINED-glyceraldehyde 3-phosphate · GAP(S)-lactate · LACTATE_L(R)-lactate · LACTATE3-methyl-2-oxobutanoate · OXOISOVALERATEL-leucine · LEUCINEL-lysine · LYSINEmenaquinone · MENAQUINONEL-methionine · METHIONINEmethanethiol · METHANETHIOLmethylammonium · METHYLAMINEmucin O-glycan · MUCIN_O_GLYCANN-acetyl-D-galactosamine · GALNACaceneuramate · NEUACNAD(+) · NADquinolinate · QUINOLINATEnicotinate · NICOTINATEnitrate · NITRATEdinitrogen · NITROGEN3-oxoadipyl-CoA · OXOADIPYL_COAsuccinyl-CoA · SUCCINYL_COA(R)-pantothenate · PANTOTHENATEpectin · PECTINphenol · PHENOLphenylacetate · PHENYLACETATEL-phenylalanine · PHENYLALANINE3-phenylpropanoate · PHENYLPROPANOATE1-deoxy-D-xylulose 5-phosphate · DXPpyridoxal 5'-phosphate · PLPD-ribose 5-phosphate · RIBOSE_5PL-proline · PROLINE5-aminopentanoate · AMINOPENTANOATE(S)-propane-1,2-diol · PROPANEDIOLpropanoate · PROPIONATEuridine 5'-monophosphate(2-) · UMPL-rhamnopyranose · RHAMNOSED-ribulose 5-phosphate · RIBULOSE_5Priboflavin · RIBOFLAVINsalicylate · SALICYLATE(2R)-3-phosphoglycerate · PG3siroheme · SIROHEMEstarch · STARCHD-glucose · GLUCOSEtaurine · TAURINE_INsulfite · SULFITEtaurine · TAURINE_EX4-methyl-5-(2-phosphooxyethyl)-thiazole · THZ_Pthiamine phosphate · TMP4-amino-5-hydroxymethyl-2-methylpyrimidine · HMP5-(2-hydroxyethyl)-4-methylthiazole · HETL-threonine · THREONINEindole · INDOLEL-tyrosine · TYROSINEurate · URATEL-valine · VALINED-xylose · XYLOSE_EXD-xylose · XYLOSE_IN
GIFT
Anchor
Quantitative analysis

Frames

A frame is the set of GIFTs over which a quantitative trait is computed. It defines the comparison set for counts and breadth and, when the set is bounded, the denominator for proportions. Every trait reported by gifter states the frame in which it was computed.

Membership defined by curated metadata

A frame is defined by filters on curated metadata: GIFT type, metabolic mode, facets such as substrate class, and the derived GIFT profile. It does not store a list of GIFT identifiers. Membership is therefore resolved against each database release, and a newly curated GIFT is included in every frame whose filters it satisfies. Frames are not mutually exclusive; a GIFT may belong to several.

Open and bounded frames

An open frame contains the GIFTs currently curated for a capability, which is not the full extent of that capability in microbial genomes. Open frames support counts and breadth, and no proportion of the frame is reported. A bounded frame represents a biologically closed set that curation intends to cover completely, so the proportion of its members supported by a genome is interpretable. 4 of the 19 presets are bounded: Amino-acid autonomy, Biomass-essential anabolic GIFTs, Cofactor autonomy, Nucleotide autonomy.

Analysis scales

Genome metrics describe the repertoire encoded by a single genome, such as richness, breadth across a facet and, in bounded frames, coverage. Community metrics describe how these capabilities are distributed across genomes, with abundance reported separately from presence. Network metrics describe potential handoffs between organisms, which are inferred only through anchors curated as extracellular. Each preset lists recommended metrics for every scale it supports.

Preset, custom and default frames

The presets listed below are used with reference_frame(preset = "…"). Custom frames are built from the same filters, for example reference_frame(mode = "catabolic"), and are open unless declared bounded. When no frame is supplied, the trait functions report a default set: all curated GIFTs, each GIFT type, each metabolic mode, each resource strategy, and the biomass-essential anabolic frame.

Traits computed in any frame describe genomic capability. They do not indicate expression, activity, flux, substrate availability or phenotype.

Choosing a frame

1Define the biological question

Select the frame whose scope corresponds to the comparison of interest, rather than selecting by metric name.

2Match the unit of analysis

Genome metrics describe a single encoded repertoire; community metrics describe its distribution across genomes; network metrics require compatible extracellular boundaries.

3Check the denominator

Open frames support counts and breadth. Coverage fractions are interpretable only for frames curated as bounded.

Show questions for
19 framesSelect a frame to open its definition, members and recommended analyses
FrameCoversGIFTsAnalysis scalesDenominator
Amino-acid autonomyamino_acid_autonomyBiomass-essential anabolic GIFTs in the amino-acid substrate class.22GenomeCommunitybounded · coverage valid
Aromatic catabolismaromatic_catabolismGIFTs that activate, cleave or funnel aromatic rings toward central metabolism.12GenomeCommunityNetworkopen · counts and breadth
Biomass-essential anabolic GIFTsbiomass_essential_anabolismAnabolic GIFTs whose declared output is a curated biomass-essential anchor.44GenomeCommunitybounded · coverage valid
Carbohydrate degradationcarbohydrate_degradationCatabolic GIFTs acting on polysaccharides, neutral monosaccharides, amino sugars or uronates.18GenomeCommunityopen · counts and breadth
Carbon acquisitioncarbon_acquisitionGIFTs that convert an acquired substrate into central carbon metabolism.36GenomeCommunityopen · counts and breadth
Chemical detoxificationchemical_detoxificationDefense GIFTs implementing a complete curated chemical-detoxification mechanism.5GenomeCommunityopen · counts and breadth
Cofactor autonomycofactor_autonomyBiomass-essential anabolic GIFTs in the cofactor substrate class.15GenomeCommunitybounded · coverage valid
Extracellular processing outputsextracellular_public_goodsMetabolic GIFTs derived as consuming and releasing extracellular anchors.3GenomeCommunityNetworkopen · counts and breadth
Fermentation productsfermentation_productsGIFTs that form a curated terminal fermentation product.11GenomeCommunityopen · counts and breadth
Host glycan foraginghost_glycan_foragingGIFTs acting on host-derived glycans or the sugars released from them.7GenomeCommunityopen · counts and breadth
Nitrogen acquisitionnitrogen_acquisitionGIFTs whose curated role makes nitrogen available from inorganic or organic sources.20GenomeCommunityopen · counts and breadth
Nucleotide autonomynucleotide_autonomyBiomass-essential anabolic GIFTs in the nucleotide substrate class.4GenomeCommunitybounded · coverage valid
Nutrient uptakenutrient_uptakeMetabolic GIFTs derived as moving an extracellular anchor to a cytoplasmic anchor.3GenomeCommunityNetworkopen · counts and breadth
Plant fibre utilisationplant_fibre_utilisationGIFTs curated with a fibre-degradation role, including polymer processing, uptake and intracellular catabolism of released sugars.13GenomeCommunityNetworkopen · counts and breadth
Released bioactive productsreleased_bioactive_productsGIFTs whose chemistry forms a product curated as potentially bioactive when released.5GenomeCommunityopen · counts and breadth
Shikimate-derived biosynthesisshikimate_derived_biosynthesisBiosynthetic GIFTs whose product carbon skeleton is derived from the shikimate pathway.10GenomeCommunityopen · counts and breadth
Short-chain fatty acidsshort_chain_fatty_acidsGIFTs whose curated substrate or product class is a short-chain fatty acid.4GenomeCommunityopen · counts and breadth
Sulfur acquisitionsulfur_acquisitionGIFTs whose curated role makes sulfur available from inorganic or organic sources.4GenomeCommunityopen · counts and breadth
Vitamin biosynthesisvitamin_biosynthesisGIFTs participating in curated vitamin and cofactor biosynthetic capabilities.20GenomeCommunityopen · counts and breadth
No matching frames.
Biological hierarchy

GIFTs

A genome-inferred functional trait (GIFT) is a biologically defined capability whose genomic support is evaluated through an explicit, curated completeness model. Each GIFT receives a Boolean call from the markers observed in a genome, and every call can be traced back to the markers and genes that support it.

GIFT types

Each GIFT declares a type, which selects its completeness model. A metabolic GIFT describes a directed capability between curated molecular anchors. A structural GIFT describes the machinery that builds a defined cellular structure, a regulatory GIFT the machinery that senses a signal and executes a response, and a defense GIFT the machinery that executes a defined defense mechanism. The catalogue currently contains 143 metabolic, 9 structural, 4 regulatory and 7 defense GIFTs.

Evaluation logic

A metabolic GIFT is supported when any of its curated routes is complete. A route requires all of its reactions, a reaction is catalysed by any complete enzyme system, a system requires all of its components, and a component is supported by any accepted marker. Structural, regulatory and defense GIFTs follow the same alternation through architectures, circuits or mechanisms, functions, systems and components.

Boundaries and composition

A metabolic GIFT is bounded by declared input and output anchors, and GIFTs connect to one another only through these anchors; metabolites shared inside routes do not create links. Larger capabilities are composed from GIFTs that share anchors rather than by repeating their reactions. Machinery GIFTs declare no anchors.

Reading the catalogue

Each row lists a GIFT with its boundaries or structure, its class, the number of alternatives (routes or implementations), requirements (reactions or functions) and systems. Selecting a row opens its routes or implementations, reactions or functions, systems, components and accepted markers.

A positive call indicates that the markers support at least one complete curated route, architecture, circuit or mechanism. It does not indicate expression, activity, physiological state or phenotype.

Catalogue

163 curated GIFTsSelect a row to open its routes and reactions
01Acetyl-CoA and acetate interconversionacetate_interconversionACETYL_COA↔ACETATEshort_chain_fatty_acid122curatedView detail→
02Pyruvate to (R)-acetoinacetoin_formationPYRUVATE→ACETOINneutral_fermentation_product122curatedView detail→
03Acetyl-CoA and oxaloacetate to isocitrateacetyl_coa_to_isocitrateACETYL_COAOXALOACETATE→ISOCITRATEcentral_metabolite124curatedView detail→
04IMP to AMPadenylate_biosynthesisIMP→AMPnucleotide122curatedView detail→
05Pyruvate to L-alaninealanine_biosynthesisPYRUVATE→ALANINEamino_acid223curatedView detail→
06Allantoin to glyoxylate and ureaallantoin_degradationALLANTOIN→GLYOXYLATEUREAureide255curatedView detail→
07Ammonium and 2-oxoglutarate to glutamateammonium_assimilationAMMONIUMOXOGLUTARATE→GLUTAMATEinorganic_nitrogen455curatedView detail→
08Anthranilate to catecholanthranilate_degradation_catecholANTHRANILATE→CATECHOLaromatic_compound112curatedView detail→
09L-arabinose to D-xylulose 5-phosphatearabinose_degradationARABINOSE_IN→XYLULOSE_5Pmonosaccharide133curatedView detail→
10L-arabinose uptakearabinose_uptake_abcARABINOSE_EX→ARABINOSE_INmonosaccharide112curatedView detail→
11Arabinoxylan to xylan and L-arabinosearabinoxylan_debranchingARABINOXYLAN→XYLANARABINOSE_EXpolysaccharide111curatedView detail→
12Archaellum machineryarchaellumstructural architecturecell_surface_appendage178curatedView detail→
13L-ornithine to L-argininearginine_biosynthesisORNITHINE→ARGININEamino_acid133curatedView detail→
14L-arginine to L-ornithine and ammoniumarginine_deiminase_pathwayARGININE→ORNITHINEAMMONIUMamino_acid133curatedView detail→
15L-aspartate to L-asparagineasparagine_biosynthesisASPARTATE→ASPARAGINEamino_acid222curatedView detail→
16Oxaloacetate to L-aspartateaspartate_biosynthesisOXALOACETATE→ASPARTATEamino_acid111curatedView detail→
17Aspartate chemoreceptionaspartate_chemoreceptionregulatory circuitchemosensory_pathway144curatedView detail→
18Aspartate to aspartate 4-semialdehydeaspartate_semialdehyde_biosynthesisASPARTATE→ASAamino_acid122curatedView detail→
19Sulfate to hydrogen sulfideassimilatory_sulfate_reductionSULFATE→SULFIDEinorganic_sulfur469curatedView detail→
20Benzoate to catecholbenzoate_degradation_catecholBENZOATE→CATECHOLaromatic_compound122curatedView detail→
21Beta-lactam detoxificationbeta_lactam_detoxificationdefense mechanismchemical_detoxification114curatedView detail→
22Glycine betaine to sarcosinebetaine_demethylationBETAINE→SARCOSINEmethylated_amine344curatedView detail→
23Pimeloyl-CoA to biotinbiotin_biosynthesisPIMELOYL_COA→BIOTINcofactor255curatedView detail→
24Acetyl-CoA and acetate to butanoatebutyrate_formationACETYL_COAACETATE→BUTYRATEshort_chain_fatty_acid155curatedView detail→
25L-carnitine to trimethylaminecarnitine_degradation_trimethylamineCARNITINE→TRIMETHYLAMINEmethylated_amine111curatedView detail→
26L-carnitine to glycine betainecarnitine_to_betaineCARNITINE→BETAINEmethylated_amine133curatedView detail→
27Catechol to 2-oxopent-4-enoate by meta cleavagecatechol_meta_cleavageCATECHOL→OXOPENTENOATEaromatic_compound255curatedView detail→
28Catechol to 3-oxoadipate by ortho cleavagecatechol_ortho_cleavageCATECHOL→OXOADIPATEaromatic_compound145curatedView detail→
29Chemotaxis signal transductionchemotaxis_signal_transductionregulatory circuitchemosensory_pathway158curatedView detail→
30Chitin to N-acetyl-D-glucosaminechitin_degradationCHITIN→GLCNACpolysaccharide133curatedView detail→
31Chloramphenicol detoxificationchloramphenicol_detoxificationdefense mechanismchemical_detoxification112curatedView detail→
32Choline to glycine betainecholine_to_betaineCHOLINE→BETAINEmethylated_amine466curatedView detail→
33Phosphoenolpyruvate and erythrose 4-phosphate to chorismatechorismate_biosynthesisPEPE4P→CHORISMATEaromatic_compound1716curatedView detail→
34Citrate to pyruvate and acetatecitrate_fermentationCITRATE→ACETATEPYRUVATEorganic_acid123curatedView detail→
35Adenosylcobinamide phosphate and dimethylbenzimidazole to cobalamincobamide_nucleotide_loop_assemblyADENOSYLCOBINAMIDE_PDMBNAMN→COBALAMINcofactor144curatedView detail→
36Cobyrinate a,c-diamide to adenosylcobinamide phosphatecobinamide_biosynthesisCOBYRINATE_DIAMIDE→ADENOSYLCOBINAMIDE_Pcofactor133curatedView detail→
37Collagen to collagen peptidescollagen_cleavageCOLLAGEN→COLLAGEN_PEPTIDESprotein111curatedView detail→
38Uroporphyrinogen III to cobyrinate a,c-diamidecorrin_ring_biosynthesisUROGEN_III→COBYRINATE_DIAMIDEcofactor22325curatedView detail→
39Creatinine to sarcosine and ureacreatinine_degradationCREATININE→SARCOSINEUREAmethylated_amine122curatedView detail→
40Serine and homocysteine to cysteinecysteine_biosynthesis_homocysteineSERINEHOMOCYSTEINE→CYSTEINEamino_acid244curatedView detail→
41Serine and sulfide to cysteinecysteine_biosynthesis_sulfideSERINESULFIDE→CYSTEINEamino_acid122curatedView detail→
42L-cysteine to hydrogen sulfide and pyruvatecysteine_degradation_sulfideCYSTEINE→SULFIDEPYRUVATEAMMONIUMamino_acid111curatedView detail→
43UTP to CTPcytidylate_biosynthesisUTP→CTPnucleotide111curatedView detail→
44L-aspartate 4-semialdehyde to meso-diaminopimelatedap_biosynthesisASA→MESO_DAPamino_acid41111curatedView detail→
45Diglucosyldiacylglycerol-anchored poly(glycerol-phosphate) lipoteichoic aciddiglucosyl_diacylglycerol_anchored_lipoteichoic_acidstructural architectureenvelope_structure133curatedView detail→
46Chorismate to 2,3-dihydroxybenzoatedihydroxybenzoate_biosynthesisCHORISMATE→DIHYDROXYBENZOATE_2_3aromatic_compound136curatedView detail→
473-(2,3-Dihydroxyphenyl)propanoate to 2-oxopent-4-enoate and succinatedihydroxyphenylpropanoate_degradationDHPP→OXOPENTENOATESUCCINATEaromatic_compound122curatedView detail→
48FMNH2 to 5,6-dimethylbenzimidazoledmb_biosynthesis_aerobicFMNH2→DMBcofactor111curatedView detail→
49Aspartate semialdehyde to ectoineectoine_biosynthesisASA→ECTOINEcompatible_solute133curatedView detail→
50L-ectoine to L-2,4-diaminobutanoateectoine_degradationECTOINE→DABAcompatible_solute122curatedView detail→
512,3-Dihydroxybenzoate and serine to enterobactinenterobactin_biosynthesisDIHYDROXYBENZOATE_2_3SERINE→ENTEROBACTINaromatic_compound111curatedView detail→
52Acetyl-CoA to ethanolethanol_formationACETYL_COA→ETHANOLneutral_fermentation_product124curatedView detail→
53Flagellar apparatusflagellar_apparatusstructural architecturecell_surface_appendage21010curatedView detail→
54GTP and 4-aminobenzoate to tetrahydrofolatefolate_biosynthesisGTPPABA→THFcofactor177curatedView detail→
55L-fucose to dihydroxyacetone phosphate and (S)-lactaldehydefucose_degradation_isomeraseFUCOSE→DHAPLACTALDEHYDEmonosaccharide133curatedView detail→
56Fumarate and oxaloacetate interconversionfumarate_oxaloacetate_interconversionFUMARATEOXALOACETATE→FUMARATEOXALOACETATEcentral_metabolite235curatedView detail→
57beta-D-galactose to alpha-D-glucose 1-phosphategalactose_degradation_leloirGALACTOSE→GLUCOSE_1Pmonosaccharide144curatedView detail→
58D-galacturonate to 2-dehydro-3-deoxy-D-gluconategalacturonate_degradationGALACTURONATE→KDGuronate134curatedView detail→
59N-acetyl-D-glucosamine to beta-D-fructose 6-phosphateglcnac_degradationGLCNAC→FRUCTOSE_6PAMMONIUMamino_sugar244curatedView detail→
60D-glucuronate to 2-dehydro-3-deoxy-D-gluconateglucuronate_degradationGLUCURONATE→KDGuronate133curatedView detail→
61L-glutamate to 4-aminobutanoateglutamate_decarboxylation_gabaGLUTAMATE→GABAamino_acid111curatedView detail→
62L-glutamate and ammonium to L-glutamineglutamine_biosynthesisGLUTAMATEAMMONIUM→GLUTAMINEamino_acid111curatedView detail→
63Serine to glycineglycine_biosynthesisSERINE→GLYCINEamino_acid111curatedView detail→
64Glycine to acetyl phosphate and ammoniumglycine_reduction_sticklandGLYCINE→ACETYL_PHOSPHATEAMMONIUMamino_acid111curatedView detail→
65Isocitrate and acetyl-CoA to succinate and malateglyoxylate_bypassISOCITRATEACETYL_COA→SUCCINATEMALATEcentral_metabolite122curatedView detail→
66IMP to GMPguanylate_biosynthesisIMP→GMPnucleotide122curatedView detail→
67Uroporphyrinogen III to heme bheme_b_biosynthesisUROGEN_III→HEME_Bcofactor71010curatedView detail→
68PRPP and L-glutamine to L-histidinehistidine_biosynthesisPRPPGLUTAMINE→HISTIDINEamino_acid11013curatedView detail→
69L-histidine to L-glutamate and ammoniumhistidine_degradation_glutamateHISTIDINE→GLUTAMATEAMMONIUMamino_acid144curatedView detail→
70AIR to the thiamine pyrimidinehmp_phosphate_biosynthesisAIR→HMP_PPcofactor122curatedView detail→
71Aspartate 4-semialdehyde to homoserinehomoserine_biosynthesisASA→HOMOSERINEamino_acid222curatedView detail→
72L-ectoine to 5-hydroxyectoinehydroxyectoine_biosynthesisECTOINE→HYDROXYECTOINEcompatible_solute111curatedView detail→
733-(3-Hydroxyphenyl)propanoate to 3-(2,3-dihydroxyphenyl)propanoatehydroxyphenylpropanoate_hydroxylationHPP→DHPParomatic_compound111curatedView detail→
74L-tryptophan to indole-3-acetateindole_3_acetate_biosynthesisTRYPTOPHAN→INDOLE_3_ACETATEaromatic_compound123curatedView detail→
75Isocitrate to 2-oxoglutarateisocitrate_to_oxoglutarateISOCITRATE→OXOGLUTARATEcentral_metabolite222curatedView detail→
762-oxobutanoate to L-isoleucineisoleucine_biosynthesisOXOBUTANOATE→ISOLEUCINEamino_acid144curatedView detail→
772-dehydro-3-deoxy-D-gluconate to pyruvate and D-glyceraldehyde 3-phosphatekdg_degradationKDG→PYRUVATEGAPcentral_metabolite122curatedView detail→
78Pyruvate to (S)-lactatelactate_formationPYRUVATE→LACTATE_Lorganic_acid111curatedView detail→
79(S)-lactaldehyde to (S)-lactatelactate_formation_lactaldehydeLACTALDEHYDE→LACTATE_Lorganic_acid111curatedView detail→
80(S)-lactate and (R)-lactate interconversionlactate_racemisationLACTATE_L↔LACTATEorganic_acid111curatedView detail→
813-methyl-2-oxobutanoate to L-leucineleucine_biosynthesisOXOISOVALERATE→LEUCINEamino_acid157curatedView detail→
82Lpt lipopolysaccharide export apparatuslpt_lipopolysaccharide_export_apparatusstructural architecturesecretion_machine133curatedView detail→
83meso-diaminopimelate to L-lysinelysine_biosynthesis_dapMESO_DAP→LYSINEamino_acid111curatedView detail→
84(S)-malate to (S)-lactatemalolactic_fermentationMALATE→LACTATE_Lorganic_acid111curatedView detail→
85Chorismate to menaquinonemenaquinone_biosynthesisCHORISMATE→MENAQUINONEcofactor21518curatedView detail→
86Mercury detoxificationmercury_detoxificationdefense mechanismchemical_detoxification146curatedView detail→
87Homoserine and sulfide to methioninemethionine_biosynthesis_sulfhydrylationHOMOSERINESULFIDE→METHIONINEamino_acid466curatedView detail→
88Homoserine and cysteine to methioninemethionine_biosynthesis_transsulfurationHOMOSERINECYSTEINE→METHIONINEamino_acid699curatedView detail→
89L-methionine to methanethiol and 2-oxobutanoatemethionine_degradation_methanethiolMETHIONINE→METHANETHIOLOXOBUTANOATEAMMONIUMamino_acid111curatedView detail→
90Methylamine to ammoniummethylamine_degradationMETHYLAMINE→AMMONIUMmethylated_amine111curatedView detail→
91Glutathione-dependent methylglyoxal detoxificationmethylglyoxal_detoxificationdefense mechanismchemical_detoxification122curatedView detail→
92Mucin O-glycan to L-fucosemucin_fucose_releaseMUCIN_O_GLYCAN→FUCOSEpolysaccharide111curatedView detail→
93Mucin O-glycan to N-acetyl-D-galactosaminemucin_galnac_releaseMUCIN_O_GLYCAN→GALNACpolysaccharide111curatedView detail→
94Mucin O-glycan to N-acetylneuraminatemucin_sialic_acid_releaseMUCIN_O_GLYCAN→NEUACpolysaccharide111curatedView detail→
95Nicotinate D-ribonucleotide to NADnad_biosynthesis_namnNAMN→NADcofactor233curatedView detail→
96Quinolinate to nicotinate D-ribonucleotidenamn_biosynthesis_quinolinateQUINOLINATEPRPP→NAMNcofactor111curatedView detail→
97Nicotinate to nicotinate D-ribonucleotidenamn_salvage_nicotinateNICOTINATEPRPP→NAMNcofactor111curatedView detail→
98N-acetylneuraminate to beta-D-fructose 6-phosphateneuac_degradationNEUAC→FRUCTOSE_6PAMMONIUMamino_sugar155curatedView detail→
99Nitrate to ammoniumnitrate_assimilationNITRATE→AMMONIUMinorganic_nitrogen445curatedView detail→
100Dinitrogen to ammoniumnitrogen_fixationNITROGEN→AMMONIUMinorganic_nitrogen222curatedView detail→
101L-glutamate to L-ornithineornithine_biosynthesisGLUTAMATE→ORNITHINEamino_acid266curatedView detail→
1023-Oxoadipate to 3-oxoadipyl-CoAoxoadipate_activationOXOADIPATE→OXOADIPYL_COAaromatic_compound111curatedView detail→
1033-Oxoadipyl-CoA to succinyl-CoA and acetyl-CoAoxoadipyl_coa_thiolysisOXOADIPYL_COA→SUCCINYL_COAACETYL_COAaromatic_compound111curatedView detail→
104Pyruvate to 2-oxobutanoateoxobutanoate_biosynthesis_citramalatePYRUVATE→OXOBUTANOATEamino_acid144curatedView detail→
1052-oxoglutarate to succinateoxoglutarate_to_succinateOXOGLUTARATE→SUCCINATEcentral_metabolite467curatedView detail→
106Pyruvate to 3-methyl-2-oxobutanoateoxoisovalerate_biosynthesisPYRUVATE→OXOISOVALERATEamino_acid133curatedView detail→
1072-Oxopent-4-enoate to pyruvate and acetyl-CoAoxopentenoate_degradationOXOPENTENOATE→PYRUVATEACETYL_COAaromatic_compound137curatedView detail→
108Chorismate to 4-aminobenzoatepaba_biosynthesisCHORISMATE→PABAcofactor124curatedView detail→
1092-oxoisovalerate and L-aspartate to pantothenatepantothenate_biosynthesisOXOISOVALERATEASPARTATE→PANTOTHENATEcofactor145curatedView detail→
110Pectin to 2-dehydro-3-deoxy-D-gluconate by beta-eliminationpectate_lyase_degradationPECTIN→KDGpolysaccharide177curatedView detail→
111Pectin to D-galacturonatepectin_degradationPECTIN→GALACTURONATEpolysaccharide133curatedView detail→
112Phenol to catecholphenol_hydroxylationPHENOL→CATECHOLaromatic_compound111curatedView detail→
113Phenylacetate to 3-oxoadipyl-CoAphenylacetate_degradationPHENYLACETATE→OXOADIPYL_COAaromatic_compound188curatedView detail→
114Chorismate to L-phenylalaninephenylalanine_biosynthesisCHORISMATE→PHENYLALANINEamino_acid133curatedView detail→
1153-Phenylpropanoate to 3-(2,3-dihydroxyphenyl)propanoatephenylpropanoate_dihydroxylationPHENYLPROPANOATE→DHPParomatic_compound122curatedView detail→
116Phosphate starvation responsephosphate_starvation_responseregulatory circuittwo_component_system244curatedView detail→
117Erythrose 4-phosphate and DXP to pyridoxal 5-phosphateplp_biosynthesis_dxpE4PDXP→PLPcofactor166curatedView detail→
118Ribose 5-phosphate and glyceraldehyde 3-phosphate to pyridoxal 5-phosphateplp_biosynthesis_r5pRIBOSE_5PGLUTAMINE→PLPcofactor111curatedView detail→
119L-glutamate to L-prolineproline_biosynthesisGLUTAMATE→PROLINEamino_acid135curatedView detail→
120L-proline to 5-aminopentanoateproline_reduction_sticklandPROLINE→AMINOPENTANOATEamino_acid122curatedView detail→
121(S)-lactaldehyde to (S)-propane-1,2-diolpropanediol_formationLACTALDEHYDE→PROPANEDIOLcentral_metabolite111curatedView detail→
122(R)-lactate to propanoatepropionate_formation_acrylateLACTATE→PROPIONATEshort_chain_fatty_acid133curatedView detail→
123(S)-propane-1,2-diol to propanoatepropionate_formation_propanediolPROPANEDIOL→PROPIONATEshort_chain_fatty_acid144curatedView detail→
124PRPP to IMPpurine_core_biosynthesisPRPP→IMPnucleotide81416curatedView detail→
125Glutamine and PRPP to UMPpyrimidine_core_biosynthesisGLUTAMINEPRPP→UMPnucleotide3810curatedView detail→
126Pyruvate to acetyl-CoApyruvate_to_acetyl_coaPYRUVATE→ACETYL_COAcentral_metabolite335curatedView detail→
127L-aspartate to quinolinatequinolinate_biosynthesis_aspartateASPARTATE→QUINOLINATEcofactor233curatedView detail→
128L-rhamnose to dihydroxyacetone phosphate and (S)-lactaldehyderhamnose_degradationRHAMNOSE→DHAPLACTALDEHYDEmonosaccharide133curatedView detail→
129Poly(ribitol-phosphate) wall teichoic acidribitol_phosphate_wall_teichoic_acidstructural architectureenvelope_structure288curatedView detail→
130GTP and D-ribulose 5-phosphate to riboflavinriboflavin_biosynthesisGTPRIBULOSE_5P→RIBOFLAVINcofactor1711curatedView detail→
131Chorismate to salicylatesalicylate_biosynthesisCHORISMATE→SALICYLATEaromatic_compound126curatedView detail→
132Sarcosine to glycinesarcosine_demethylationSARCOSINE→GLYCINEmethylated_amine223curatedView detail→
1333-phosphoglycerate to serineserine_biosynthesisPG3→SERINEamino_acid133curatedView detail→
134Serine chemoreceptionserine_chemoreceptionregulatory circuitchemosensory_pathway144curatedView detail→
135L-serine to pyruvate and ammoniumserine_deaminationSERINE→PYRUVATEAMMONIUMamino_acid113curatedView detail→
136Uroporphyrinogen III to sirohemesiroheme_biosynthesisUROGEN_III→SIROHEMEcofactor137curatedView detail→
137Siroheme to heme bsiroheme_to_heme_bSIROHEME→HEME_Bcofactor244curatedView detail→
138Starch to D-glucosestarch_degradationSTARCH→GLUCOSEpolysaccharide133curatedView detail→
139Succinate and fumarate interconversionsuccinate_fumarate_interconversionSUCCINATEFUMARATE→SUCCINATEFUMARATEcentral_metabolite113curatedView detail→
140Complete superoxide detoxificationsuperoxide_detoxificationdefense mechanismchemical_detoxification126curatedView detail→
141Taurine to sulfite through sulfoacetaldehydetaurine_degradation_sulfoacetaldehydeTAURINE_IN→SULFITEorganosulfonate233curatedView detail→
142Taurine to sulfitetaurine_desulfonation_aerobicTAURINE_IN→SULFITEorganosulfonate111curatedView detail→
143Taurine uptaketaurine_uptake_abcTAURINE_EX→TAURINE_INorganosulfonate111curatedView detail→
144Thiamine pyrimidine and thiazole to thiamine phosphatethiamine_phosphate_biosynthesisHMP_PPTHZ_P→TMPcofactor111curatedView detail→
145Thiamine precursor salvage to the activated moietiesthiamine_precursor_salvageHMPHET→HMP_PPTHZ_Pcofactor133curatedView detail→
146DXP to the thiamine thiazolethiazole_phosphate_biosynthesisDXP→THZ_Pcofactor233curatedView detail→
147Homoserine to threoninethreonine_biosynthesisHOMOSERINE→THREONINEamino_acid122curatedView detail→
148L-threonine to 2-oxobutanoate and ammoniumthreonine_deaminationTHREONINE→OXOBUTANOATEAMMONIUMamino_acid111curatedView detail→
149Chorismate and L-glutamine to L-tryptophantryptophan_biosynthesisCHORISMATEGLUTAMINE→TRYPTOPHANamino_acid157curatedView detail→
150L-tryptophan to indole, pyruvate and ammoniumtryptophan_degradation_indoleTRYPTOPHAN→INDOLEPYRUVATEAMMONIUMamino_acid111curatedView detail→
151Type I-E CRISPR-Cas machinerytype_i_e_crispr_cas_machinerydefense mechanismcrispr_cas133curatedView detail→
152Type I restriction-modificationtype_i_restriction_modificationdefense mechanismrestriction_modification133curatedView detail→
153Type II secretion systemtype_ii_secretion_systemstructural architecturesecretion_machine155curatedView detail→
154Type III secretion injectisometype_iii_secretion_injectisomestructural architecturesecretion_machine178curatedView detail→
155Type IVa pilus machinerytype_iva_pilusstructural architecturecell_surface_appendage178curatedView detail→
156Type VI secretion apparatustype_vi_secretion_apparatusstructural architecturesecretion_machine188curatedView detail→
157Chorismate to L-tyrosinetyrosine_biosynthesisCHORISMATE→TYROSINEamino_acid244curatedView detail→
158Urate to allantoinurate_degradationURATE→ALLANTOINureide244curatedView detail→
159Urea to ammoniumurea_hydrolysisUREA→AMMONIUMureide111curatedView detail→
1603-methyl-2-oxobutanoate to L-valinevaline_biosynthesisOXOISOVALERATE→VALINEamino_acid111curatedView detail→
161Xylan to D-xylosexylan_degradationXYLAN→XYLOSE_EXpolysaccharide133curatedView detail→
162D-xylose to D-xylulose 5-phosphatexylose_degradation_isomeraseXYLOSE_IN→XYLULOSE_5Pmonosaccharide122curatedView detail→
163D-xylose uptakexylose_uptake_abcXYLOSE_EX→XYLOSE_INmonosaccharide112curatedView detail→
No matching GIFTs.
Curation history · database 2026.39.1

Database changes

Every change to the biological content, why it was made, the evidence behind it, and the traits it affects. Package and API changes are tracked separately.

144 recorded changes across 48 releasesSelect a change to open its rationale, evidence and effect, or a GIFT identifier to open the trait it refers to
ReleaseRecordedScopeChangeCallsGIFTs affected
2026.39.12026-10-0417:39 UTCmarkercorrectionNCBIfam and CAZy assignments are checked against their own releases, and eight with no matching EC number are reported as putativeDBC-20261004-FAMILY-MARKER-BASISnone
2026.38.12026-10-0416:32 UTCanchorcorrectionSixteen anchors now carry the ChEBI entity Rhea writes at pH 7.3DBC-20261004-ANCHOR-CHEBI-FORMSnone
2026.38.12026-10-0416:32 UTCreactioncorrectionReaction cross-references that Rhea does not record are corrected, removed or explainedDBC-20261004-REACTION-XREFSnone
2026.38.12026-10-0416:32 UTCschemaadditionSchema 9 pins Rhea, ChEBI and KEGG records and checks the source tables against themDBC-20261004-REFERENCE-VERIFICATIONnoneNo GIFT affected
2026.38.12026-10-0416:32 UTCreactioncorrectionThree reactions keyed by a bidirectional Rhea identifier now use the masterDBC-20261004-RHEA-MASTER-IDSnone
2026.38.12026-10-0416:32 UTCrouteclarificationTwenty-five places where a route does not literally reach its anchors or chain in Rhea are recordedDBC-20261004-ROUTE-CHEMISTRY-EXCEPTIONSnone
2026.38.12026-10-0416:32 UTCroutecorrectionFour route steps were oriented against the direction the route runsDBC-20261004-ROUTE-ORIENTATIONnone
2026.38.12026-10-0416:32 UTCmarkercorrectionThirty KO assignments with no checkable support are reported as putativeDBC-20261004-UNSUPPORTED-MARKER-CONFIDENCEnone
2026.37.12026-10-0411:41 UTCenzyme_systemcorrectionSerine deamination requires a complete single-chain enzyme or both split SdaAA and SdaAB subunitsDBC-20261004-SERINE-DEAMINATION-SYSTEMSmixed
2026.36.12026-10-0404:33 UTCanchorclarificationFour CoA and acyl-carrier thioester boundaries are declared cytoplasmicDBC-20261004-ACYL-CARRIER-COMPARTMENTnone
2026.35.22026-10-0403:51 UTCgiftclarificationCRISPR-Cas defense class definition matches the machinery-only claimDBC-20261004-CRISPR-CLASS-DEFINITIONnone
2026.35.12026-10-0402:09 UTCgiftadditionBeta-lactam hydrolysis and chloramphenicol acetylation become defense GIFTsDBC-20261004-ANTIMICROBIAL-DETOXbroadens
2026.35.12026-10-0402:09 UTCgiftadditionChallenge class separates the target of a defense mechanism from how it worksDBC-20261004-CHALLENGE-CLASSnone
2026.35.12026-10-0402:09 UTCgiftadditionTsr-equivalog serine chemoreception becomes a regulatory GIFTDBC-20261004-SERINE-CHEMORECEPTIONbroadens
2026.34.12026-10-0312:10 UTCschemaadditionEvery GIFT now records the curation documents, analysis scripts and result tables behind its definition, linked to the source repositoryDBC-20261003-GIFT-EVIDENCEnoneNo GIFT affected
2026.33.22026-10-0309:20 UTCschemaclarificationThe biomass_essential_anabolism preset label is capitalised as Biomass-essential anabolic GIFTsDBC-20261003-FRAME-LABELnoneNo GIFT affected
2026.33.12026-10-0306:58 UTCgiftadditionThe type II secretion system becomes a structural GIFT, and the shared-component rule it waited on is settledDBC-20261003-T2SSbroadens
2026.32.12026-10-0305:45 UTCgiftadditionThe archaellum becomes a structural GIFT with one core architecture of five required functions and two lineage-restricted accessory functionsDBC-20261003-ARCHAELLUMbroadens
2026.31.12026-10-0305:40 UTCgiftadditionType VI secretion and the non-flagellar type III secretion injectisome become structural GIFTs with one curated architecture eachDBC-20261003-SECRETION-SYSTEMSbroadens
2026.30.12026-10-0219:44 UTCgiftadditionDiglucosyldiacylglycerol-anchored poly(glycerol-phosphate) lipoteichoic acid becomes a structural GIFT with one three-function architectureDBC-20261002-GLC2DAG-LTAbroadens
2026.29.12026-10-0217:22 UTCgiftadditionPoly(ribitol-phosphate) wall teichoic acid becomes a structural GIFT with separate Staphylococcus-type and W23-type complete architecturesDBC-20261002-RIBITOL-WTAbroadens
2026.28.12026-10-0211:29 UTCgiftadditionA structural GIFT now reports a complete canonical LptA--G lipopolysaccharide export apparatus as three jointly required machine functionsDBC-20261002-LPT-APPARATUSbroadens
2026.27.12026-08-2716:30 UTCmarkeradditionK28205 is admitted as a second orthology group for RHEA:14329 with confidence ambiguous, the only marker the serine investigation found for the step that carries the shortfallDBC-20260827-PHOSPHOSERINE-TRANSAMINASE-ARCHAEALbroadens
2026.27.12026-08-2716:00 UTCanchorclarificationGLYCINE is not declared as an input anchor of serine_biosynthesis, RHEA:15481 is not curated forward, and glycine_biosynthesis stays anabolic rather than becoming an interconversion GIFTDBC-20260827-SERINE-GLYCINE-DIRECTIONnone
2026.26.12026-08-2713:30 UTCmarkeradditionTen NCBIfam equivalogs are admitted on the three amino sugar steps orthology under-covers, including NF046059.1 nagB-II for a deaminase family K02564 does not nameDBC-20260827-AMINO-SUGAR-NCBIFAM-MARKERSbroadens
2026.26.12026-08-2713:00 UTCrouteadditionA second route into glcnac_degradation enters through the phosphoenolpyruvate-dependent PTS, so the capability no longer requires a cytoplasmic kinase most of its users do not encodeDBC-20260827-GLCNAC-PTS-ROUTEbroadens
2026.25.12026-08-2709:00 UTCmarkeradditionNine NCBIfam equivalogs are admitted on the two histidine steps that orthology splits across unrelated familiesDBC-20260827-HISTIDINE-PHOSPHATASE-MARKERSbroadens
2026.24.12026-08-2314:30 UTCgiftadditionThe Ahb route from siroheme to heme b is curated as siroheme_to_heme_b, the first capability that depends on the NCBIFAM namespaceDBC-20260823-SIROHEME-TO-HEME-Bbroadens
2026.23.12026-08-2310:00 UTCmarkeradditionNCBIFAM is admitted as a marker namespace, and 53 equivalog-grade profiles join 25 enzyme components as OR alternatives beside the KEGG orthologs already thereDBC-20260823-NCBIFAM-NAMESPACEnone
2026.22.12026-08-2219:20 UTCgiftadditionEctoine degradation is curated as the ectoine-specific pair of ring hydrolysis and deacetylation, ending at L-2,4-diaminobutanoateDBC-20260822-ECTOINE-DEGRADATIONbroadens
2026.22.12026-08-2219:20 UTCgiftadditionEctoine hydroxylation to 5-hydroxyectoine is curated as a capability separate from ectoine biosynthesisDBC-20260822-HYDROXYECTOINEbroadens
2026.22.12026-08-2219:20 UTCgiftadditionLactaldehyde oxidation to (S)-lactate is curated as the second fate of the lactaldehyde branchpointDBC-20260822-LACTALDEHYDE-OXIDATIONbroadens
2026.21.32026-08-2120:40 UTCgiftadditionPectin degradation by beta-elimination is curated as a capability separate from the hydrolytic routeDBC-20260821-PECTATE-LYASEbroadens
2026.21.32026-08-2120:10 UTCanchorcorrectionThe hexuronate routes are cut at 2-dehydro-3-deoxy-D-gluconate and the shared Entner-Doudoroff tail becomes its own capabilityDBC-20260821-KDG-ANCHORmixed
2026.21.22026-08-2117:30 UTCgiftadditionHydrolytic pectin saccharification is curated as endo- plus exo-polygalacturonaseDBC-20260821-PECTIN-DEGRADATIONbroadens
2026.21.12026-08-2109:05 UTCschemacorrectionA handoff out of extracellular chemistry through an unsplit anchor is recorded as compartment-inexactDBC-20260821-EXTRACELLULAR-HANDOFFnoneNo GIFT affected
2026.21.12026-08-2109:00 UTCmarkercorrectiondbCAN-sub clusters whose EC agreement is below half are withdrawn as markersDBC-20260821-CAZY-AGREEMENT-FLOORnarrows
2026.21.12026-08-2109:00 UTCgiftadditionChitin saccharification is curated as endo-acting chitinase plus exo-acting hexosaminidaseDBC-20260821-CHITIN-DEGRADATIONbroadens
2026.21.12026-08-2109:00 UTCgiftadditionMucin O-glycan foraging is curated as three parallel exo-glycosidase capabilitiesDBC-20260821-MUCIN-O-GLYCANbroadens
2026.20.22026-08-2012:04 UTCgiftclarificationPolyhydroxybutyrate biosynthesis is refused at the current marker specificityDBC-20260820-PHB-REFUSEDnone
2026.20.22026-08-2012:03 UTCgiftadditionTwo complete chemical-detoxification mechanisms are added for methylglyoxal and superoxideDBC-20260820-CHEMICAL-DETOX-EXPANSIONbroadens
2026.20.22026-08-2012:02 UTCgiftadditionEnterobactin biosynthesis is split at 2,3-dihydroxybenzoate into a reusable catecholate head and a complete assembly GIFTDBC-20260820-ENTEROBACTIN-SPLITbroadens
2026.20.22026-08-2012:01 UTCgiftadditionHeme b biosynthesis is curated from the uroporphyrinogen III branchpoint through classical and coproporphyrin routesDBC-20260820-HEME-Bbroadens
2026.20.22026-08-2012:00 UTCgiftadditionEctoine biosynthesis and choline-to-betaine oxidation are curated as bounded compatible-solute chemistryDBC-20260820-COMPATIBLE-SOLUTESbroadens
2026.20.42026-08-2011:35 UTCschemaadditionNineteen named reference frames expose recurring genome and community questions through curated metadata filtersDBC-20260820-NAMED-FRAMESnoneNo GIFT affected
2026.20.32026-08-2010:07 UTCmarkerclarificationSiroheme-to-heme b remains refused because KO K22225 cannot prove both AhbA and AhbBDBC-20260820-AHB-DECARBOXYLASE-REFUSALnone
2026.20.32026-08-2010:06 UTCgiftadditionSiroheme biosynthesis is curated from uroporphyrinogen III through multifunctional or split enzyme systemsDBC-20260820-SIROHEME-BIOSYNTHESISbroadens
2026.20.12026-08-2005:32 UTCgiftadditionAssimilatory sulfate reduction is curated as four explicit APS/PAPS and NADPH/ferredoxin routesDBC-20260820-SULFATE-ASSIMILATIONbroadens
2026.20.12026-08-2005:31 UTCgiftadditionNitrogen fixation is curated as dinitrogen-to-ammonium chemistry with complete Mo and V nitrogenase architecturesDBC-20260820-NITROGEN-FIXATIONbroadens
2026.20.12026-08-2005:30 UTCgiftcorrectionThe upper oxidative TCA segment is cut at isocitrate and the glyoxylate bypass is curated without duplicated reactionsDBC-20260820-ISOCITRATE-RECUTmixed
2026.19.12026-08-1912:40 UTCgiftadditiondefense_class gains chemical_detoxification, named for the mechanism rather than for the metal or the phenotypeDBC-20260819-CHEMICAL-DETOXIFICATION-CLASSnone
2026.19.12026-08-1912:40 UTCmarkerclarificationNF033555, the InterPro accessions and merD are refused as mer evidenceDBC-20260819-MER-EVIDENCE-REFUSALSnone
2026.19.12026-08-1912:40 UTCgiftadditionMercury detoxification curated as a defense GIFT, with MerA-dependent reduction the only required functionDBC-20260819-MERCURY-DEFENSEbroadens
2026.19.12026-08-1910:11 UTCgiftclarificationNine ring-hydroxylating dioxygenase traits are refused on marker specificity, and five more on evidence availabilityDBC-20260819-AROMATIC-REFUSALSnone
2026.19.12026-08-1910:10 UTCgiftclarificationThe aromatic_compound substrate class now covers ring-cleavage products as wellDBC-20260819-AROMATIC-CLASSnone
2026.19.12026-08-1910:09 UTCenzyme_systemadditionTwo alternative acylating acetaldehyde dehydrogenase systems added to RHEA:23288DBC-20260819-ACETALDEHYDE-SYSTEMSnone
2026.19.12026-08-1910:08 UTCenzyme_componentclarificationShared ferredoxin and reductase subunits are deliberately not curated as components of Rieske oxygenase systemsDBC-20260819-RIESKE-COMPONENTSnone
2026.19.12026-08-1910:07 UTCmarkerclarificationK07104 is refused as evidence of catechol 2,3-dioxygenase; K00446 and NCBIfam TIGR03211 are accepted insteadDBC-20260819-META-CLEAVAGE-MARKERnone
2026.19.12026-08-1910:06 UTCgiftclarificationFour KEGG module boundaries were cut differently, because a module ORs substrates or duplicates a shared segmentDBC-20260819-AROMATIC-CUTSnone
2026.19.12026-08-1910:05 UTCgiftadditionTwelve aerobic aromatic ring catabolism GIFTs, built around the catechol and 3-oxoadipyl-CoA convergence nodesDBC-20260819-AROMATIC-LAYERbroadens
2026.19.12026-08-1905:20 UTCanchorcorrectionL-aspartate and L-glutamine are marked as biomass building blocksDBC-20260819-ASPARTATE-GLUTAMINE-ESSENTIALnone
2026.19.12026-08-1904:40 UTCanchoradditionAcetyl phosphate declared as an anchor, because glycine reductase has no other product to declareDBC-20260819-ACETYL-PHOSPHATE-ANCHORnone
2026.19.12026-08-1904:40 UTCgiftadditionThe fifteen remaining proteinogenic amino acids curated as eighteen composable biosynthesis GIFTsDBC-20260819-AMINO-ACID-BIOSYNTHESISbroadens
2026.19.12026-08-1904:40 UTCgiftadditionTen amino acid degradation and transformation capabilities curated, including the first Stickland contentDBC-20260819-AMINO-ACID-CATABOLISMbroadens
2026.19.12026-08-1904:40 UTCanchorclarificationThe amino donor of a transamination is never declared as an anchor; the nitrogen source of an assimilation isDBC-20260819-AMINO-DONOR-RULEnone
2026.19.12026-08-1904:40 UTCmarkeradditionThe final transamination of phenylalanine and tyrosine biosynthesis accepts the aspartate and branched-chain aminotransferasesDBC-20260819-AROMATIC-TRANSAMINASE-WIDENEDbroadens
2026.19.12026-08-1904:40 UTCmarkerclarificationCysteine desulfidation is evidenced by dedicated desulfidases only, and is knowingly under-calledDBC-20260819-CYSTEINE-SULFIDE-UNDERCALLEDnone
2026.11.12026-08-1823:59 UTCmarkeradditionCAZy subfamily markers curated from the dbCAN-sub HMM library, with confidence from measured EC dominanceDBC-20260818-CAZY-SUBFAMILIESbroadens
2026.11.12026-08-1823:59 UTCgiftadditionGIFTs and anchors carry a registered facet vocabulary, and a derived profile is exposed alongside itDBC-20260818-FACET-CLASSIFICATIONnone
2026.18.12026-08-1823:45 UTCgiftclarificationPhenylethylamine and hypotaurine degradation are refused on marker specificityDBC-20260818-NITROGEN-REFUSALSnone
2026.18.12026-08-1823:44 UTCgiftcorrectionThe carnitine dehydrogenase route makes glycine betaine, not trimethylamine, and is a separate GIFTDBC-20260818-CARNITINE-SPLITnarrows
2026.18.12026-08-1823:43 UTCanchoradditionGlcNAc and sialic acid degradation now declare the ammonium their deaminase liberatesDBC-20260818-AMINOSUGAR-AMMONIUMnone
2026.18.12026-08-1823:42 UTCgiftclarificationCapabilities requiring an external terminal electron acceptor are out of scopeDBC-20260818-ELECTRON-ACCEPTOR-SCOPEnone
2026.18.12026-08-1823:41 UTCanchorclarificationAmmonium is an anchor only where a reaction exists to liberate or assimilate itDBC-20260818-NITROGEN-ANCHOR-RULEnone
2026.18.12026-08-1823:40 UTCgiftadditionFourteen nitrogen, methylamine and organosulfonate catabolism GIFTs curatedDBC-20260818-NITROGEN-LAYERbroadens
2026.10.32026-08-1823:00 UTCgiftcorrectionThe curator note for polymer saccharification no longer claims that the exo-acting enzyme cannot release a monosaccharide on its ownDBC-20260818-EXO-ACTIVITY-CLAIMnone
2026.17.12026-08-1822:20 UTCgiftadditionA biosynthetic_family facet is registered and shikimate_derived_aromatic assigned to five GIFTsDBC-20260818-BIOSYNTHETIC-FAMILY-FACETnone
2026.17.12026-08-1822:18 UTCgiftclarificationGallate biosynthesis from 3-dehydroshikimate is refused and not curatedDBC-20260818-GALLATE-REFUSEDnone
2026.17.12026-08-1822:16 UTCrouteclarificationOnly the indole-3-acetamide route to the auxin is curated; the indole-3-pyruvate, tryptamine, indole-3-acetonitrile and side-chain oxidase routes are refusedDBC-20260818-IAA-ROUTES-REFUSEDnone
2026.17.12026-08-1822:14 UTCenzyme_systemadditionPchA and the bifunctional salicylate synthases are curated as enzyme systems of the existing isochorismate synthase reaction, not as a second route to salicylateDBC-20260818-SALICYLATE-SYNTHASE-SYSTEMSbroadens
2026.17.12026-08-1822:12 UTCrouteclarificationThe shikimate dehydrogenase step of the shikimate pathway is curated as not requiredDBC-20260818-SHIKIMATE-SDH-ORPHANbroadens
2026.17.12026-08-1822:10 UTCgiftadditionShikimate-derived aromatic biosynthesis curated as three composable GIFTs: chorismate, salicylate and indole-3-acetateDBC-20260818-SHIKIMATE-AROMATIC-LAYERbroadens
2026.16.12026-08-1821:30 UTCgiftadditionOxidative citric acid cycle chemistry curated as four composable segment GIFTs, reversing the earlier finding that the cycle cannot be anchoredDBC-20260818-CENTRAL-CYCLE-LAYERbroadens
2026.10.22026-08-1821:00 UTCgiftcorrectionPolysaccharide degradation is curated per substrate capability rather than per enzymatic stepDBC-20260818-SUBSTRATE-LEVEL-GIFTSmixed
2026.15.12026-08-1820:00 UTCanchorclarificationA co-substrate is not declared as an anchor merely because the reaction consumes itDBC-20260818-COSUBSTRATE-ANCHORSnone
2026.15.12026-08-1819:55 UTCgiftclarificationCobalamin uptake is refused as a transport GIFT, so the layer reports no cross-feeding outputDBC-20260818-VITAMIN-UPTAKE-REFUSEDnone
2026.15.12026-08-1819:50 UTCanchorclarificationGTP is declared as an input-only anchor and no GIFT is curated to link it to GMPDBC-20260818-GTP-LINK-OPENnone
2026.15.12026-08-1819:45 UTCgiftclarificationNAD biosynthesis is cut at nicotinate D-ribonucleotide so that de novo synthesis and pyridine salvage share the trunk instead of duplicating itDBC-20260818-NAD-CUT-AT-NAMNnone
2026.15.12026-08-1819:40 UTCmarkerclarificationThe corrin ring capability is curated with a known recall limit caused by gene fusion, and no domain marker is accepted to repair itDBC-20260818-CORRIN-RING-RECALLnone
2026.15.12026-08-1819:35 UTCmarkerclarificationEntC is accepted for the isochorismate synthase reaction of menaquinone biosynthesisDBC-20260818-ENTC-ACCEPTEDbroadens
2026.15.12026-08-1819:30 UTCenzyme_componentclarificationThe ThiS and ThiF sulfur carrier is not a required component of thiazole synthaseDBC-20260818-THIS-THIF-NOT-REQUIREDbroadens
2026.15.12026-08-1819:25 UTCmarkerclarificationA generic alkaline phosphatase is refused as evidence of the folate dihydroneopterin monophosphatase step, and the step is left uncuratedDBC-20260818-ALKALINE-PHOSPHATASE-REFUSEDnone
2026.15.12026-08-1819:20 UTCanchorclarificationA cofactor may be declared an anchor only where the reaction consumes it, and cofactor activation steps are not curatedDBC-20260818-COFACTOR-ANCHOR-RULEnone
2026.15.12026-08-1819:15 UTCgiftclarificationThe lower ligand is curated as its own capability, because a cobamide without dimethylbenzimidazole is not vitamin B12DBC-20260818-DMB-LOWER-LIGANDnarrows
2026.15.12026-08-1819:10 UTCgiftclarificationA single cobalamin biosynthesis trait is refused; corrin ring, cobinamide arm and nucleotide loop are curated as three capabilitiesDBC-20260818-B12-SPLITnarrows
2026.15.12026-08-1819:05 UTCrouteclarificationFour reactions that no marker identifies at the specificity of the step are curated as not requiredDBC-20260818-ORPHAN-STEP-RULEbroadens
2026.15.12026-08-1819:00 UTCgiftadditionVitamin biosynthesis curated as twenty GIFTs covering B1, B2, B3, B5, B6, B7, B9, B12 and K2DBC-20260818-VITAMIN-LAYERbroadens
2026.14.12026-08-1818:25 UTCrouteclarificationThe acetolactate synthase step of acetoin_formation is curated but not requiredDBC-20260818-ACETOIN-SYNTHASE-NOT-REQUIREDnone
2026.14.12026-08-1818:20 UTCmarkerclarificationD-lactate formation is deferred, and the (R)-lactate anchor is reached through the racemase insteadDBC-20260818-D-LACTATE-DEFERREDnone
2026.14.12026-08-1818:15 UTCanchorclarificationFormate formation is refused on the per-GIFT anchor rule rather than on evidenceDBC-20260818-FORMATE-REFUSEDnone
2026.14.12026-08-1818:10 UTCanchorclarificationCitric acid cycle intermediates are refused as output anchors, and succinate, fumarate and citrate formation are refused as traitsDBC-20260818-TCA-NOT-ANCHORABLEnone
2026.14.12026-08-1818:05 UTCgiftclarificationlactate_formation is the first fermentation end product whose direction is evidenced rather than assertedDBC-20260818-LACTATE-DIRECTIONnone
2026.10.12026-08-1818:00 UTCmarkeradditionCAZy families accepted as markers, with confidence derived from measured family polyspecificityDBC-20260818-CAZY-CONFIDENCEnone
2026.10.12026-08-1818:00 UTCenzyme_systemclarificationA CAZy family and a KEGG orthologue are alternative markers of one catalytic role, not alternative enzyme systemsDBC-20260818-CAZY-ONE-SYSTEMnone
2026.14.12026-08-1818:00 UTCgiftadditionOrganic acid and neutral fermentation product formation curated as six GIFTs, and the citric acid cycle refused as a source of anchorsDBC-20260818-ORGANIC-ACID-LAYERbroadens
2026.10.12026-08-1818:00 UTCgiftadditionArabinoxylan and starch depolymerisation and saccharification curated as separate tiersDBC-20260818-POLYSACCHARIDE-TIERSbroadens
2026.13.12026-08-1815:00 UTCschemaadditionThe interconversion mode gains a boundary contract the source validator enforcesDBC-20260818-INTERCONVERSION-CONTRACTnone
2026.13.12026-08-1814:25 UTCenzyme_componentclarificationThe electron-transfer flavoprotein is not a required component of the butanoyl-CoA dehydrogenase systemDBC-20260818-BCD-ETF-NOT-REQUIREDnone
2026.13.12026-08-1814:20 UTCgiftclarificationacetate_interconversion is declared mode = interconversion and declares both of its boundaries in both roles, the first use of that mode valueDBC-20260818-ACETATE-INTERCONVERSIONnone
2026.13.12026-08-1814:15 UTCgiftclarificationThe succinate (Wood-Werkman) route to propionate is refused and the refusal recordedDBC-20260818-PROPIONATE-SUCCINATE-REFUSEDnone
2026.13.12026-08-1814:10 UTCrouteclarificationThe butyrate kinase route is refused and the refusal recordedDBC-20260818-BUTYRATE-KINASE-REFUSEDnone
2026.13.12026-08-1814:05 UTCmarkeradditionThe butyrate terminal step is evidenced by NCBIfam TIGR03948, the first non-KO, non-CAZy marker in the metabolic layerDBC-20260818-BUTYRATE-MARKER-NAMESPACEbroadens
2026.09.42026-08-1814:00 UTCanchorcorrectionThe pentose anchors use the generic sugar rather than a single anomerDBC-20260818-PENTOSE-ANCHOR-IDENTITYnone
2026.09.42026-08-1814:00 UTCgiftadditionD-xylose and L-arabinose uptake curated, and their anchors split by compartmentDBC-20260818-PENTOSE-UPTAKEbroadens
2026.13.12026-08-1814:00 UTCgiftadditionShort-chain fatty acid formation curated as five GIFTs, with a sixth connecting them to existing catabolic contentDBC-20260818-SCFA-LAYERbroadens
2026.09.42026-08-1814:00 UTCgiftclarificationUptake GIFTs are curated only where transporter markers are substrate-specific and the translocation has a verified reaction identityDBC-20260818-UPTAKE-LICENCEnone
2026.12.12026-08-1812:00 UTCgiftadditionCollagen cleavage curated as the first protein-degradation GIFT, with a protein substrate class and a host tissue degradation roleDBC-20260818-COLLAGEN-CLEAVAGEbroadens
2026.12.12026-08-1812:00 UTCgiftclarificationTrait specificity may not exceed marker specificity, and seven candidate protein-degradation traits are refused under that ruleDBC-20260818-EVIDENCE-SPECIFICITYnone
2026.12.32026-08-1811:40 UTCgiftadditionType I-E CRISPR-Cas curated as an encoded-machinery claim, not an interference claimDBC-20260818-CRISPR-ARRAY-LIMITbroadens
2026.12.32026-08-1811:30 UTCgiftadditionType I restriction-modification added as the first defense GIFTDBC-20260818-TYPE-I-RMbroadens
2026.12.32026-08-1811:20 UTCgiftadditionPhosphate starvation response added with two cognate-pair circuitsDBC-20260818-PHO-TWO-CIRCUITSbroadens
2026.12.32026-08-1811:10 UTCregulatory_componentadditionLigand-specific chemoreception curated as a separate claim with separate evidenceDBC-20260818-CHEMOTAXIS-SPECIFICITYnarrows
2026.12.32026-08-1811:05 UTCgiftadditionCore chemotaxis signal transduction added as the first regulatory GIFTDBC-20260818-CHEMOTAXIS-COREbroadens
2026.09.32026-08-1810:00 UTCrouteclarificationAldose 1-epimerase is optional in the Leloir routeDBC-20260818-GALM-OPTIONALbroadens
2026.09.32026-08-1810:00 UTCmarkerclarificationThe bifunctional biosynthetic enzyme GNE is not accepted as evidence for N-acetylmannosamine kinaseDBC-20260818-GNE-EXCLUDEDnarrows
2026.09.32026-08-1810:00 UTCgiftadditionNine monosaccharide and uronate degradation GIFTs added as the first catabolic contentDBC-20260818-SUGAR-DEGRADATIONbroadens
2026.12.22026-08-1809:30 UTCgiftadditionType IVa pilus machinery added as a second structural GIFTDBC-20260818-TYPE-IVA-PILUSbroadens
2026.12.22026-08-1809:25 UTCstructural_componentclarificationProton- and sodium-driven flagellar apparatus refused at KO evidence levelDBC-20260818-FLAGELLAR-ION-COUPLINGnone
2026.12.22026-08-1809:20 UTCgiftadditionFlagellar apparatus added as the first structural GIFTDBC-20260818-FLAGELLAR-APPARATUSbroadens
2026.12.22026-08-1809:10 UTCschemaadditionGIFT becomes an umbrella concept with an explicit gift_typeDBC-20260818-GIFT-TYPEnoneNo GIFT affected
2026.09.22026-08-1721:30 UTCschemaadditionAnchors carry a molecule key and a two-state compartment qualifierDBC-20260817-SCHEMA-4-ANCHOR-COMPARTMENTnoneNo GIFT affected
2026.09.22026-08-1721:30 UTCschemaadditionGIFTs declare a mode and composition cycles are checked within a modeDBC-20260817-SCHEMA-4-GIFT-MODEnoneNo GIFT affected
2026.09.22026-08-1721:30 UTCschemaadditionReactions carry a stable reaction_id and an optional Rhea masterDBC-20260817-SCHEMA-4-REACTION-IDENTITYnoneNo GIFT affected
2026.09.12026-08-1720:10 UTCgiftadditionNine serine, glycine, aspartate-family, cysteine and methionine biosynthesis GIFTs addedDBC-20260817-AMINO-ACID-BATCHbroadens
2026.09.12026-08-1720:10 UTCgiftadditionThe aspartate-to-homoserine trunk is curated once instead of twiceDBC-20260817-ASPARTATE-TRUNKnone
2026.09.12026-08-1720:10 UTCschemaadditionGIFTs can be linked to related external pathways with an explicit set relationDBC-20260817-GIFT-PATHWAY-LINKSnoneNo GIFT affected
2026.09.12026-08-1720:10 UTCanchorclarificationL-homocysteine is declared as an input anchor only, and methionine biosynthesis is not split at itDBC-20260817-HOMOCYSTEINE-INPUT-ONLYnone
2026.09.12026-08-1720:10 UTCgiftadditionM00338 and the cysteine-forming tail of M00609 merged; the SAM-cycle steps of M00609 excludedDBC-20260817-M00609-REDUCTIONbroadens
2026.09.12026-08-1720:10 UTCgiftadditionDirect sulfhydrylation added as a methionine biosynthesis capability absent from KEGG M00017DBC-20260817-METHIONINE-SULFHYDRYLATIONbroadens
2026.08.32026-08-1718:05 UTCschemaadditionCuration history recorded inside the database and published in the atlasDBC-20260817-CHANGE-HISTORYnoneNo GIFT affected
2026.08.22026-08-1717:45 UTCenzyme_systemcorrectionAspartate carbamoyltransferase no longer requires the PyrI regulatory subunitDBC-20260817-ATCASE-PYRIbroadens
2026.08.22026-08-1717:45 UTCenzyme_systemcorrectionNAD-dependent dihydroorotate oxidation now requires the PyrK electron transfer subunitDBC-20260817-DHOD-PYRKnarrows
2026.08.22026-08-1717:45 UTCmarkerclarificationMarker layer audited against KEGG orthology; no orthologs missingDBC-20260817-MARKER-AUDITnone
2026.08.12026-08-17giftadditionInitial curated release of five nucleotide biosynthesis GIFTsDBC-20260817-INITIAL-CURATIONnone
No matching changes.
Curation history

Expansion attempts

Every investigation that set out to add GIFTs, and whether its candidates were implemented, deferred or refused.

Every bounded request, screen or investigation that set out to add GIFTs to the catalogue is registered before new evidence is collected, and closed with what came of it. Investigations that added nothing are listed too: a deferral or a refusal is a curation result, and recording it keeps a later curator from repeating the same search or admitting the same over-broad evidence under another name.

Implemented

The GIFTs the attempt added or redefined. Each links to its page in the atlas, where its curation evidence and change history are listed.

Deferred or open

Candidates with a standing blocker, such as missing evidence, an unresolved boundary or a marker that is not yet specific enough. The deferral register states what would reopen each one.

Refused or superseded

Claims that could not be supported without exceeding the specificity of the genomic evidence or breaking the ontology, and candidates replaced by a better-bounded definition.

This view renders the catalogue-expansion attempt log (inst/doc/catalogue-expansion-attempts.tsv) shipped with gifter 0.7.3. Outcomes are recorded per attempt, so a candidate deferred by one attempt and implemented by a later one appears in both. The documents linked from each attempt hold the full argument.

38Attemptsregistered investigations
163ImplementedGIFTs added or redefined
166Deferredcandidates left open
142Refusedclaims refused or superseded
Show attempts that
38 attemptsSelect an attempt to open its candidates, outcomes and sources
AttemptPeriodGIFT typesOutcomeResult
Screen of unsupported calls in the 696-genome GTDB phylogenetic panel for GIFT definitions to re-read: near misses by missing requirement, rarely supported GIFTs and lineages below the genome-size expectationGEA-20261004-GTDB-NEAR-MISS-SCREEN2026-10-04metabolicstructuralregulatorydefense16 deferred or open3 refused or superseded
No database content changed. The screen produced an open to-do list of GIFT definitions to re-read: one marker-specificity review, eight single-step alternatives in long pathways, fifteen two-requirement GIFTs, two boundary checks, sixteen rarely supported GIFTs and four lineages. None has been assessed, and a near miss is never support.
Reassess the split iron-sulfur serine ammonia-lyase as an alternative system of serine_deamination and audit K01752 specificityGEA-20261004-SERINE-DEAMINATION-REVISION2026-10-04metabolic1 deferred or open2 refused or superseded
Corrected existing serine_deamination in database 2026.37.1: retired K01752 as completing evidence, added separate single-chain and two-subunit NCBIfam systems, and kept K17989 as a separate single-protein alternative. A stratified 122-genome gene-level audit supported 120 on the audited proteins or K17989 and showed two KO-assigned genomes without complete audited profile evidence. KO-only frame exposure is quantified, but the exact frame-wide mixed-input call delta is not measured.
Reassessment and expansion of regulatory circuits and defense mechanismsGEA-20261004-REGULATORY-DEFENSE2026-10-04regulatorydefense3 implemented3 deferred or open3 refused or superseded
One regulatory and two defense GIFTs were added in database 2026.35.1; challenge_class now labels five defense mechanisms. PhoQ/PhoP, OxyR/PerR and additional CRISPR-Cas machinery remain deferred on specific evidence gaps.
Curation of the type II secretion system once the shared-component rule was settledGEA-20261003-T2SS2026-10-03structural1 implemented2 deferred or open3 refused or superseded
Implemented in database 2026.33.1 with five required functions and twelve components. The blocker was settled as a general rule rather than per candidate: a protein serving two machines is a shared component, accepted on both GIFTs, carrying no specificity to either, and not a reason for structural GIFTs to compose. 1,319 of the 1,536 complete frame architectures reach the peptidase role through PilD alone, so refusing the shared accession would have discarded most of the capability. GspC stays required because its 335 misses are spread over 108 genera rather than blinding a clade. Vibrio cholerae N16961 is correctly incomplete: its epsD region carries an authentic frameshift.
Curation of the archaellum as a structural GIFT, or a documented refusal, following the recommendation of the 2026-10-03 prevalent-machine screenGEA-20261003-ARCHAELLUM2026-10-03structural1 implemented3 deferred or open6 refused or superseded
Implemented archaellum as one core architecture of five required functions (archaellin, class III signal peptidase, FlaF/FlaG stator, FlaI/FlaH motor, FlaJ platform) with the FlaC/D/E switch complex and the FlaX ring accessory, database 2026.32.1. An exact screen of 5,093 KO-assigned proteins showed that K07332 and K07333 also collect archaeal type IV pilus and bindosome ATPases and platforms, so both are accepted only inside the conjunction at putative confidence; the FlaI and ArlJ equivalogs pass a protein in 252 and 253 of 256 core genomes and are high-confidence. K07991 covers FlaK and PibD and merges EppA in Methanococcales without affecting any frame call; bacterial K02654 is a putative alternative peptidase for archaellum-encoding Chloroflexota. K07325 assignments are archaellins, never bacterial FlgA. Prevalence: 253 of 470 archaea and 2 of 10,143 bacteria (both Chloroflexota); 25 archaea are one function short, 17 on the stator. M. maripaludis S2, S. acidocaldarius DSM 639 and H. volcanii DS2 complete; E. coli K-12 and B. subtilis 168 do not. No stored reference frame changes denominator.
Initial assessment of nine prevalent cell-surface and intracellular machines as structural GIFT candidates; assessment only, no implementation in this attemptGEA-20261003-STRUCTURAL-MACHINES2026-10-03structural12 deferred or open6 refused or superseded
Initial assessment only; no GIFT was added and the database was not rebuilt. Archaellum (256 of 470 archaea), diderm Tad pilus (1,631 bacteria), type II secretion (1,571) and curli (252) have a specific KO for every required function and are recommended for curation, type II secretion and Tad conditional on the shared-homologue rule still pending in GEA-20261003-SECRETION-T3-T6. Gas vesicles are deferred on five unmarked required proteins. BAM, and the chaperone-usher, type IV secretion and microcompartment classes are refused at that breadth; the beta-carboxysome (160 genomes) is the one narrowed design recommended. The screen also found that the stored frame flags 1,290 eukaryotes as prokaryotic.
Re-argument of type III and type VI secretion systems as structural GIFTs using system-specific KO and NCBIfam equivalog evidence without locus contextGEA-20261003-SECRETION-T3-T62026-10-03structural2 implemented6 deferred or open4 refused or superseded
Both systems were implemented in database 2026.31.1. The co-localisation objection did not survive testing: every required role has a system-specific KO or equivalog, the three flagellated controls encoding neither machine support no role of either architecture, and 4,399 genomes complete the flagellar export apparatus without supporting one injectisome role. TssJ and the SctL stator were made accessory or excluded because their markers do not reach reference genomes that build the machine, and the divergent type VI and injectisome families remain explicit under-calls.
Dedicated reassessment of lipoteichoic-acid and peptidoglycan-sacculus construction as independent structural GIFTsGEA-20261002-LTA-PEPTIDOGLYCAN2026-10-02structural1 implemented7 deferred or open4 refused or superseded
Implemented only the narrow diglucosyldiacylglycerol-anchored LTA architecture in database 2026.30.1; broader LTA designs and every peptidoglycan-sacculus boundary retain explicit marker and architecture blockers.
Admission of the two marker-resolved poly(ribitol-phosphate) wall teichoic acid architectures despite rarityGEA-20261002-RIBITOL-WTA-ADMISSION2026-10-02structural1 implemented1 deferred or open1 refused or superseded
Implemented one chemistry-specific structural GIFT with alternative Staphylococcus and W23 architectures in database 2026.29.1 under the explicit biological-importance exception; retained every required role and left 168-type glycerol WTA deferred on marker specificity.
NCBIfam-compatible prevalence and 168-type TagF marker retrigger for the separated wall teichoic acid candidatesGEA-20261002-WTA-NCBIFAM2026-10-02structural3 deferred or open2 refused or superseded
No GIFT was added: the exact two-profile screen resolves 48 Staphylococcus-type ribitol architectures, the W23 architecture remains at 22, and NCBIfam 20.0 contains no equivalog that separates the 168-type TagF polymerase from the W23 non-WTA homologue.
Dedicated curation of wall teichoic acid construction and peptidoglycan attachment as a structural GIFTGEA-20261002-WALL-TEICHOIC-ACID2026-10-02structural3 deferred or open1 refused or superseded
No GIFT was added: the glycerol-phosphate proxy fails chemistry specificity, the Staphylococcus ribitol-phosphate architecture cannot be quantified with its safe NCBIfam discriminator in the KO-only frame, and the W23 ribitol-phosphate architecture reaches 22 genomes.
Dedicated curation of the LptA--G lipopolysaccharide export apparatus as a structural GIFTGEA-20261002-LPT-APPARATUS2026-10-02structural1 implemented1 deferred or open3 refused or superseded
Implemented the canonical seven-role apparatus in database 2026.28.1 with KO and equivalog-grade NCBIfam evidence; preserved the experimentally reported LptE-independent Neisseria implementation as an explicit under-call pending discriminating evidence.
S-layers and other cell-wall or cell-envelope structures as possible structural GIFTsGEA-20261002-CELL-ENVELOPE-STRUCTURES2026-10-02structural6 deferred or open4 refused or superseded
No GIFT was added. The current structural model can express the candidates; Lpt is ready for a dedicated curation pass, S-layers require lineage-resolved architectures, other named polymers retain explicit blockers, and generic envelope claims were refused.
Candidate GIFT and route changes suggested by phenotype under-callsGEA-20260827-PHENOTYPE-LEADS2026-08-27metabolic1 deferred or open1 refused or superseded
No new GIFT was created: GlcNAc gained a route, histidine gained marker coverage, and proposed serine entries were declined or left blocked.
Whether gene neighbourhood can unblock context-dependent catalogue candidatesGEA-20260827-GENOMIC-CONTEXT2026-08-27metabolicstructuralregulatorydefense3 deferred or open7 refused or superseded
No GIFT was added; co-localisation was recommended only as a separate corroborating system-level axis and refused as Boolean or marker-specificity evidence.
Discovery pass for new capabilities exposed by NCBIfam equivalogsGEA-20260825-NCBIFAM-DISCOVERY2026-08-25metabolicstructuralregulatorydefense7 deferred or open3 refused or superseded
The pass found no new ready-to-curate GIFT; it recorded one biological refusal and durable follow-up candidates.
Capabilities giving output-only anchors a defensible fateGEA-20260822-ANCHOR-FATES2026-08-22metabolic3 implemented5 deferred or open1 refused or superseded
Three anchor fates were curated and five candidates retained with explicit blockers.
Antimicrobial detoxification and CARD as a possible evidence sourceGEA-20260822-ANTIMICROBIAL-DETOX2026-08-22defense4 deferred or open7 refused or superseded
Two defense GIFTs were recommended but not implemented; two families were deferred and outcome-level resistance mechanisms refused.
Reassessment of electron-acceptor respiration as GIFT contentGEA-20260822-RESPIRATION2026-08-22metabolicrespiratory2 deferred or open1 refused or superseded
No new GIFT was added; the assessment retained the refusal pending a completeness contract for a possible respiratory type.
Re-read catalogue deferrals after admitting NCBIfamGEA-20260822-NCBIFAM-RETRIGGER2026-08-22 → 2026-08-23metabolicstructuralregulatorydefense1 implemented8 deferred or open2 refused or superseded
The namespace unblocked the Ahb route, left several refusals intact, and made secretion-system evidence require a fresh argument.
Compatible solutes heme enterobactin and chemical detoxificationGEA-20260820-COMPATIBLE-HEME-ENTEROBACTIN-DETOX2026-08-20metabolicdefense8 implemented1 deferred or open1 refused or superseded
Eight capabilities were curated; PHB was refused and the Ahb tail was left for marker-specificity resolution.
Nitrogen fixation sulfate assimilation glyoxylate bypass and non-metabolic expansion candidatesGEA-20260820-NEXT-RELEASE2026-08-20metabolicstructuralregulatorydefense3 implemented8 deferred or open2 refused or superseded
The metabolic candidates were implemented; the non-metabolic candidates were explicitly assessed and deferred rather than silently skipped.
Systematic MetaCyc catalogue-expansion reconnaissanceGEA-20260820-METACYC-RECONNAISSANCE2026-08-20metabolicdefense22 deferred or open6 refused or superseded
A ranked reconnaissance assessed the full candidate families; later rows record the candidates that advanced to separate curation passes.
Aerobic aromatic degradation and mercury detoxificationGEA-20260819-AROMATIC-DEGRADATION2026-08-19metabolicdefense13 implemented2 deferred or open15 refused or superseded
Twelve metabolic GIFTs and one defense GIFT were curated; fourteen candidates were refused and two deferred.
Remaining proteinogenic amino-acid biosynthesis and selected transformationsGEA-20260819-AMINO-ACID-EXPANSION2026-08-19metabolic28 implemented12 deferred or open8 refused or superseded
Twenty-eight GIFTs were added; the source retains the full refused and deferred candidate inventory.
Nitrogen-compound catabolism methylamine and organosulfonate capabilitiesGEA-20260818-NITROGEN-CATABOLISM2026-08-18metabolic14 implemented3 deferred or open7 refused or superseded
Fourteen bounded capabilities were curated and respiratory or marker-unspecific alternatives remained outside the catalogue.
Shikimate-derived aromatic biosynthesisGEA-20260818-SHIKIMATE-AROMATICS2026-08-18metabolic3 implemented1 deferred or open3 refused or superseded
Three composable GIFTs were curated; three auxin alternatives and gallate were not supportable as named.
Atomic oxidative citric-acid-cycle segments and derived cycle topologyGEA-20260818-CENTRAL-CYCLES2026-08-18metabolic5 implemented3 deferred or open1 refused or superseded
Five atomic GIFTs were curated and the oxidative cycle became a derived graph result rather than a bundled GIFT.
Vitamin and cofactor biosynthesisGEA-20260818-VITAMINS2026-08-18metabolic20 implemented2 deferred or open5 refused or superseded
Twenty bounded capabilities replaced broad vitamin labels; unsupported precursor and activation claims were refused.
Organic-acid and neutral fermentation-product formationGEA-20260818-ORGANIC-ACIDS2026-08-18metabolic6 implemented2 deferred or open7 refused or superseded
Six informative capabilities were curated; generic central-metabolism product claims and a bundled cycle were refused at this stage.
Short-chain fatty-acid formationGEA-20260818-SCFA2026-08-18metabolic6 implemented5 refused or superseded
Six capabilities were curated; direction-blind and substrate-indistinguishable alternatives were refused.
Substrate-specific extracellular protein cleavageGEA-20260818-PROTEIN-DEGRADATION2026-08-18metabolic1 implemented1 deferred or open7 refused or superseded
Only collagen cleavage had substrate-resolving genomic evidence; seven named-substrate claims were refused.
First defense mechanisms and CRISPR claim boundaryGEA-20260818-DEFENSE2026-08-18defense2 implemented2 deferred or open3 refused or superseded
Two encoded-machinery defense GIFTs were curated without claiming interference or phenotypic defense.
First regulatory circuits and ligand-specific chemoreceptionGEA-20260818-REGULATORY2026-08-18regulatory3 implemented3 deferred or open2 refused or superseded
Three circuits were curated and ligand specificity was bounded by receptor-resolving evidence.
Monosaccharide uptake and degradation plus substrate-specific polysaccharide and mucin-glycan capabilitiesGEA-20260818-SUGAR-AND-POLYSACCHARIDE2026-08-18 → 2026-08-21metabolic21 implemented4 deferred or open2 refused or superseded
The pass produced the sugar and curated glycan layer, while preserving specificity refusals and context-dependent deferrals.
First structural GIFT catalogue and rejected structural specialisationsGEA-20260818-STRUCTURAL2026-08-18structuralprogrammatic2 implemented4 deferred or open3 refused or superseded
Two structural GIFTs were curated; coupling-ion claims were refused and sporulation was deferred outside the structural model.
Serine glycine aspartate-family cysteine and methionine biosynthesisGEA-20260817-AMINO-ACID-CORE2026-08-17metabolic9 implemented2 deferred or open1 refused or superseded
Nine composable amino-acid biosynthesis GIFTs were curated; alternative serine entry remains blocked by evidence and boundary problems.
Initial nucleotide-biosynthesis catalogueGEA-20260817-NUCLEOTIDE-BASELINE2026-08-17metabolic5 implemented
Five bounded nucleotide GIFTs established the initial catalogue.
No matching attempts.
SQLite · schema 9

Data model

Primary keys, foreign keys, and normalized tables behind the evaluation model.

metabolic giftORgift_routeANDreactionORenzyme_systemANDenzyme_componentORmarker
structural giftORgift_architectureANDstructural_functionORstructural_systemANDstructural_componentORmarker
▦

gift

163 rows
  • gift_pkPKINTEGER
  • gift_idTEXT
  • gift_typeTEXT
  • nameTEXT
  • descriptionTEXT
  • modeTEXT
  • statusTEXT
  • versionTEXT
  • notesTEXT
▦

anchor

156 rows
  • anchor_pkPKINTEGER
  • anchor_idTEXT
  • moleculeTEXT
  • compartmentTEXT
  • nameTEXT
  • chebi_idTEXT
  • descriptionTEXT
  • chebi_nameTEXT
▦

gift_anchor

344 rows
  • gift_pkPKFKINTEGER
  • anchor_pkFKINTEGER
  • rolePKTEXT
  • ordinalPKINTEGER
▦

gift_xref

214 rows
  • gift_pkPKFKINTEGER
  • namespacePKTEXT
  • accessionPKTEXT
  • nameTEXT
  • relationTEXT
  • notesTEXT
▦

gift_route

210 rows
  • route_pkPKINTEGER
  • gift_pkFKINTEGER
  • route_idTEXT
  • nameTEXT
  • descriptionTEXT
  • statusTEXT
  • oxygen_requirementTEXT
▦

route_reaction

633 rows
  • route_pkPKFKINTEGER
  • reaction_pkPKFKINTEGER
  • orientationTEXT
  • step_orderINTEGER
  • requiredINTEGER
▦

reaction

440 rows
  • reaction_pkPKINTEGER
  • reaction_idTEXT
  • rhea_masterTEXT
  • nameTEXT
  • descriptionTEXT
  • equationTEXT
▦

reaction_xref

764 rows
  • reaction_pkPKFKINTEGER
  • namespacePKTEXT
  • accessionPKTEXT
  • notesTEXT
▦

enzyme_system

505 rows
  • system_pkPKINTEGER
  • reaction_pkFKINTEGER
  • system_idTEXT
  • nameTEXT
  • descriptionTEXT
▦

enzyme_component

607 rows
  • component_pkPKINTEGER
  • system_pkFKINTEGER
  • component_idTEXT
  • nameTEXT
  • descriptionTEXT
▦

gift_architecture

11 rows
  • architecture_pkPKINTEGER
  • gift_pkFKINTEGER
  • architecture_idTEXT
  • nameTEXT
  • descriptionTEXT
  • statusTEXT
▦

architecture_function

73 rows
  • architecture_pkPKFKINTEGER
  • function_pkPKFKINTEGER
  • ordinalINTEGER
  • requiredINTEGER
▦

structural_function

58 rows
  • function_pkPKINTEGER
  • function_idTEXT
  • nameTEXT
  • descriptionTEXT
▦

structural_system

61 rows
  • system_pkPKINTEGER
  • function_pkFKINTEGER
  • system_idTEXT
  • nameTEXT
  • descriptionTEXT
▦

structural_component

110 rows
  • component_pkPKINTEGER
  • system_pkFKINTEGER
  • component_idTEXT
  • nameTEXT
  • descriptionTEXT
▦

structural_component_marker

188 rows
  • component_pkPKFKINTEGER
  • marker_pkPKFKINTEGER
  • evidence_typeTEXT
  • confidenceTEXT
  • sourceTEXT
  • notesTEXT
  • basisTEXT
  • referenceTEXT
▦

gift_circuit

5 rows
  • circuit_pkPKINTEGER
  • gift_pkFKINTEGER
  • circuit_idTEXT
  • nameTEXT
  • descriptionTEXT
  • statusTEXT
▦

circuit_function

19 rows
  • circuit_pkPKFKINTEGER
  • function_pkPKFKINTEGER
  • ordinalINTEGER
  • requiredINTEGER
▦

regulatory_function

11 rows
  • function_pkPKINTEGER
  • function_idTEXT
  • nameTEXT
  • descriptionTEXT
▦

regulatory_system

14 rows
  • system_pkPKINTEGER
  • function_pkFKINTEGER
  • system_idTEXT
  • nameTEXT
  • descriptionTEXT
▦

regulatory_component

20 rows
  • component_pkPKINTEGER
  • system_pkFKINTEGER
  • component_idTEXT
  • nameTEXT
  • descriptionTEXT
▦

regulatory_component_marker

25 rows
  • component_pkPKFKINTEGER
  • marker_pkPKFKINTEGER
  • evidence_typeTEXT
  • confidenceTEXT
  • sourceTEXT
  • notesTEXT
  • basisTEXT
  • referenceTEXT
▦

gift_mechanism

7 rows
  • mechanism_pkPKINTEGER
  • gift_pkFKINTEGER
  • mechanism_idTEXT
  • nameTEXT
  • descriptionTEXT
  • statusTEXT
▦

mechanism_function

16 rows
  • mechanism_pkPKFKINTEGER
  • function_pkPKFKINTEGER
  • ordinalINTEGER
  • requiredINTEGER
▦

defense_function

16 rows
  • function_pkPKINTEGER
  • function_idTEXT
  • nameTEXT
  • descriptionTEXT
▦

defense_system

26 rows
  • system_pkPKINTEGER
  • function_pkFKINTEGER
  • system_idTEXT
  • nameTEXT
  • descriptionTEXT
▦

defense_component

33 rows
  • component_pkPKINTEGER
  • system_pkFKINTEGER
  • component_idTEXT
  • nameTEXT
  • descriptionTEXT
▦

defense_component_marker

96 rows
  • component_pkPKFKINTEGER
  • marker_pkPKFKINTEGER
  • evidence_typeTEXT
  • confidenceTEXT
  • sourceTEXT
  • notesTEXT
  • basisTEXT
  • referenceTEXT
▦

marker

1576 rows
  • marker_pkPKINTEGER
  • namespaceTEXT
  • accessionTEXT
  • nameTEXT
  • descriptionTEXT
▦

component_marker

1405 rows
  • component_pkPKFKINTEGER
  • marker_pkPKFKINTEGER
  • evidence_typeTEXT
  • confidenceTEXT
  • sourceTEXT
  • notesTEXT
  • basisTEXT
  • referenceTEXT
▦

reference_frame

19 rows
  • frame_pkPKINTEGER
  • frame_idTEXT
  • labelTEXT
  • descriptionTEXT
  • boundedINTEGER
  • interpretationTEXT
▦

reference_frame_filter

31 rows
  • frame_pkPKFKINTEGER
  • filter_keyPKTEXT
  • valuePKTEXT
▦

reference_frame_metric

71 rows
  • frame_pkPKFKINTEGER
  • scopePKTEXT
  • metric_idPKTEXT
  • rationaleTEXT
▦

database_change

144 rows
  • change_pkPKINTEGER
  • change_idTEXT
  • releasedTEXT
  • changed_atTEXT
  • layerTEXT
  • categoryTEXT
  • call_effectTEXT
  • summaryTEXT
  • rationaleTEXT
  • evidenceTEXT
  • effectTEXT
▦

change_gift

474 rows
  • change_pkPKFKINTEGER
  • gift_pkPKFKINTEGER
▦

database_release

1 rows
  • release_pkPKINTEGER
  • gifter_db_versionTEXT
  • schema_versionINTEGER
  • build_dateTEXT
  • rhea_releaseTEXT
  • chebi_releaseTEXT
  • kegg_releaseTEXT
  • source_commitTEXT
  • source_repositoryTEXT
▦

gift_evidence

203 rows
  • gift_pkPKFKINTEGER
  • evidence_kindTEXT
  • locationPKTEXT
  • descriptionTEXT
No matching schema entities.
Complete snapshot

Table browser

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gift163 rows · 9 columns
gift_pkgift_idgift_typenamedescriptionmodestatusversionnotes
1purine_core_biosynthesismetabolicPRPP to IMPEncodes de novo assembly of IMP, the common purine branchpoint that supplies both adenylate and guanylate biosynthesis and supports nucleotide production without relying solely on purine salvage.anaboliccurated1Atomic GIFT corresponding to the biologically bounded PRPP-to-IMP capability derived from KEGG M00048.
2adenylate_biosynthesismetabolicIMP to AMPEncodes the adenylate-specific branch from IMP through adenylosuccinate to AMP, supplying the precursor of adenine nucleotides used in nucleic acids, energy transfer, and many cofactors.anaboliccurated1Atomic branch derived from KEGG M00049; ends at AMP because shared nucleotide phosphorylation is intentionally excluded.
3guanylate_biosynthesismetabolicIMP to GMPEncodes the guanylate-specific branch that oxidizes IMP to XMP and aminates XMP to GMP, supplying the precursor of guanine nucleotides used in nucleic acids and GTP-dependent cellular processes.anaboliccurated1Atomic branch derived from KEGG M00050; ends at GMP because shared nucleotide phosphorylation is intentionally excluded.
4pyrimidine_core_biosynthesismetabolicGlutamine and PRPP to UMPEncodes de novo assembly of UMP, the common precursor of uridine and cytidine nucleotides needed for RNA production, DNA precursor synthesis, and activated-sugar metabolism.anaboliccurated1Atomic GIFT corresponding to KEGG M00051; alternative dihydroorotate oxidation chemistries are separate routes.
5cytidylate_biosynthesismetabolicUTP to CTPEncodes CTP synthase-mediated amination of UTP to CTP, establishing cytidine nucleotide production for RNA synthesis and formation of activated intermediates in phospholipid and glycan biosynthesis.anaboliccurated1Atomic cytidylate-forming capability derived from KEGG M00052; shared UMP/UDP phosphorylation and CTP/CDP interconversion are intentionally excluded.
6serine_biosynthesismetabolic3-phosphoglycerate to serineEncodes de novo synthesis of L-serine from the glycolytic intermediate 3-phosphoglycerate, supplying the amino acid that also feeds glycine and both cysteine biosynthesis capabilities.anaboliccurated1Boundaries of KEGG M00020 retained. The phosphoserine phosphatase step is kept required even though a fifth of serA/serC genomes carry no recognised phosphatase orthologue; the chemistry is required and the missing reaction is reported rather than silently scored away.
7glycine_biosynthesismetabolicSerine to glycineEncodes serine hydroxymethyltransferase-mediated formation of glycine from L-serine, the dominant route to glycine and the main one-carbon donor reaction of the cell.anaboliccurated1No KEGG module covers this capability. Threonine aldolase is deliberately excluded as a route because it would require L-threonine as an input anchor and adds only 133 KEGG genomes beyond those carrying glyA.
8aspartate_semialdehyde_biosynthesismetabolicAspartate to aspartate 4-semialdehydeEncodes activation and reduction of L-aspartate to L-aspartate 4-semialdehyde, the branchpoint metabolite shared by the lysine, diaminopimelate, threonine and methionine branches of the aspartate family.anaboliccurated1Shared head of KEGG M00018 and M00017, cut out so that neither module duplicates it. Anchored at the semialdehyde so the lysine and diaminopimelate branch can attach without re-cutting this GIFT.
9homoserine_biosynthesismetabolicAspartate 4-semialdehyde to homoserineEncodes homoserine dehydrogenase-mediated reduction of L-aspartate 4-semialdehyde to L-homoserine, the step that commits aspartate carbon away from lysine and towards threonine and methionine.anaboliccurated1Single-reaction GIFT shared by KEGG M00018 and M00017. It is not merged into the upstream GIFT because homoserine dehydrogenase is precisely where the lysine branch is left behind.
10threonine_biosynthesismetabolicHomoserine to threonineEncodes phosphorylation of L-homoserine and its conversion to L-threonine, establishing threonine identity after the aspartate family branchpoint.anaboliccurated1Tail of KEGG M00018; the aspartate-to-homoserine head is curated separately and composed through the homoserine anchor.
11methionine_biosynthesis_transsulfurationmetabolicHomoserine and cysteine to methionineEncodes methionine synthesis in which the sulfur is donated by L-cysteine through a cystathionine intermediate, the route used by organisms that assimilate sulfur into cysteine first.anaboliccurated1Tail of KEGG M00017. Separated from the sulfhydrylation capability because the two consume different sulfur substrates, and anchors are declared per GIFT rather than per route. L-homocysteine is deliberately internal here; see database_changes.
12methionine_biosynthesis_sulfhydrylationmetabolicHomoserine and sulfide to methionineEncodes methionine synthesis in which acylated homoserine reacts directly with inorganic sulfide, bypassing cysteine and cystathionine entirely.anaboliccurated1Absent from KEGG M00017 although 3910 KEGG genomes complete methionine biosynthesis this way and no other. gifter curation, not a KEGG import.
13cysteine_biosynthesis_sulfidemetabolicSerine and sulfide to cysteineEncodes cysteine synthesis by acetylation of L-serine followed by sulfide incorporation, the principal route of sulfur assimilation into amino acids.anaboliccurated1Boundaries of KEGG M00021 retained; the sulfide requirement is declared explicitly as an input anchor so the capability can compose with assimilatory sulfate reduction.
14cysteine_biosynthesis_homocysteinemetabolicSerine and homocysteine to cysteineEncodes reverse transsulfuration, in which sulfur held in L-homocysteine is transferred through cystathionine onto a serine backbone to give L-cysteine.anaboliccurated1KEGG M00338 and the cysteine-forming tail of M00609 merged into one capability with two routes; their enzyme sets share no KEGG genome, which makes them alternatives rather than separate traits. The four SAM-cycle steps of M00609 are excluded.
15xylose_degradation_isomerasemetabolicD-xylose to D-xylulose 5-phosphateEncodes isomerase-dependent catabolism of D-xylose to the pentose phosphate pathway, the route by which most gut and soil bacteria obtain carbon from hemicellulosic xylose.cataboliccurated1No KEGG module covers this capability. The oxidative Weimberg and Dahms routes end at different central metabolites and are therefore different capabilities, not alternative routes of this one.
16arabinose_degradationmetabolicL-arabinose to D-xylulose 5-phosphateEncodes catabolism of L-arabinose released from arabinan and arabinoxylan side chains, converging on the same pentose phosphate entry point as xylose.cataboliccurated1Convergence on D-xylulose 5-phosphate is why arabinofuranosidase side-chain release composes with this GIFT rather than needing its own downstream chemistry.
17fucose_degradation_isomerasemetabolicL-fucose to dihydroxyacetone phosphate and (S)-lactaldehydeEncodes isomerase-dependent catabolism of L-fucose, a deoxyhexose abundant in host mucin O-glycans, making it a marker of mucin foraging and cross-feeding in the gut.cataboliccurated1The oxidative dehydrogenase route yields different products and is a separate capability. Anchors are declared per GIFT, so the two cannot be routes of one trait.
18rhamnose_degradationmetabolicL-rhamnose to dihydroxyacetone phosphate and (S)-lactaldehydeEncodes catabolism of L-rhamnose, the deoxyhexose of pectic rhamnogalacturonan, through the same aldol cleavage chemistry as fucose but with distinct enzymes.cataboliccurated1Shares product anchors with fucose degradation but no reactions; the two isomerase, kinase and aldolase families are non-homologous.
19galactose_degradation_leloirmetabolicbeta-D-galactose to alpha-D-glucose 1-phosphateEncodes the Leloir pathway, the dominant route for galactose released from lactose, plant galactans and host glycans.cataboliccurated1Boundaries of KEGG M00632 retained. Aldose 1-epimerase is optional because mutarotation also proceeds spontaneously; UDP-glucose 4-epimerase is required because without it the pathway cannot turn over catalytically.
20glcnac_degradationmetabolicN-acetyl-D-glucosamine to beta-D-fructose 6-phosphateEncodes catabolism of N-acetyl-D-glucosamine released from chitin, peptidoglycan and host glycans into glycolysis.cataboliccurated1Ends at fructose 6-phosphate, the point at which amino sugar carbon becomes indistinguishable from glycolytic carbon. Two curated routes differ only in how the cell reaches N-acetylglucosamine 6-phosphate: a cytoplasmic ATP-dependent kinase, or the phosphoenolpyruvate-dependent PTS that phosphorylates the sugar during transport. The input anchor stays N-acetylglucosamine and stays compartment-unspecified, because the two entries genuinely start in different compartments -- the PTS substrate is outside the cell, while the kinase also serves N-acetylglucosamine recovered from the organism's own peptidoglycan inside it.
21neuac_degradationmetabolicN-acetylneuraminate to beta-D-fructose 6-phosphateEncodes catabolism of sialic acid released from host mucin O-glycans, a capability tightly associated with gut colonisation and with cross-feeding on sialidase-producing neighbours.cataboliccurated1Shares the deacetylase and deaminase reactions with GlcNAc degradation but is not a composite of it: the shared intermediate is N-acetyl-D-glucosamine 6-phosphate, which is internal to both and is deliberately not an anchor.
22galacturonate_degradationmetabolicD-galacturonate to 2-dehydro-3-deoxy-D-gluconateEncodes the galacturonate-specific head of hexuronate catabolism: isomerisation to keto-D-tagaturonate, reduction to D-altronate and dehydration to 2-dehydro-3-deoxy-D-gluconate, the Entner-Doudoroff branchpoint. A positive call means the genome can commit pectin backbone carbon to central metabolism; kdg_degradation is the shared segment that finishes it.cataboliccurated2Re-cut at 2-dehydro-3-deoxy-D-gluconate in release 2026.21.3. The final two reactions were shared verbatim with glucuronate_degradation and are now kdg_degradation; what remains is the uronate-specific head, which the previous note already said was what the capability is about.
23glucuronate_degradationmetabolicD-glucuronate to 2-dehydro-3-deoxy-D-gluconateEncodes the glucuronate-specific head of hexuronate catabolism: isomerisation to keto-D-fructuronate, reduction to D-mannonate and dehydration to 2-dehydro-3-deoxy-D-gluconate, the Entner-Doudoroff branchpoint. A positive call means the genome can commit glucuronate from glucuronoxylan and host glycosaminoglycans to central metabolism; kdg_degradation is the shared segment that finishes it.cataboliccurated2Re-cut at 2-dehydro-3-deoxy-D-gluconate in release 2026.21.3, so the boundaries are no longer those of KEGG M00061; the cross-reference is downgraded to subset_of.
24xylose_uptake_abcmetabolicD-xylose uptakeEncodes ATP-dependent import of D-xylose, the step that separates a genome able to consume xylose released by others from one that merely encodes the catabolic enzymes.transportcurated1Curated because D-xylose has both substrate-specific transporter markers and a Rhea master for the translocation. Sugars moved mainly by promiscuous carriers are deliberately left without an uptake GIFT.
25arabinose_uptake_abcmetabolicL-arabinose uptakeEncodes ATP-dependent import of L-arabinose, distinguishing an arabinose cross-feeder from a genome carrying only the catabolic enzymes.transportcurated1As for xylose. The dual-specificity XacGHI system is accepted for both pentoses because it is characterised on both.
26xylan_degradationmetabolicXylan to D-xyloseEncodes saccharification of xylan to free D-xylose: endo-acting cleavage of the beta-1,4-xylose backbone followed by exo-acting release of the monosaccharide. A positive call means the genome can liberate usable xylose from the dominant hemicellulose of a plant-based diet.cataboliccurated1Endo- and exo-acting chemistry are both required for this curated saccharification capability. Endo-1,4-beta-xylanase depolymerises the xylan backbone and generates additional chain ends and xylo-oligosaccharides, while beta-xylosidase releases D-xylose successively from non-reducing termini. Although beta-xylosidase can in principle release xylose directly from xylan termini, exo activity alone is not treated here as sufficient evidence for complete polymer saccharification. Xylo-oligosaccharide is an internal intermediate, not an anchor: it would become one only if an oligosaccharide importer could be evidenced, which would make the selfish-foraging route independently meaningful.
27arabinoxylan_debranchingmetabolicArabinoxylan to xylan and L-arabinoseEncodes removal of alpha-L-arabinofuranosyl decorations from arabinoxylan, releasing free L-arabinose and exposing the xylan backbone to the enzymes of xylan degradation.cataboliccurated1Kept separate from xylan degradation because L-arabinose is itself an anchored fermentable sugar, so the same arabinose GIFTs serve arabinoxylan, arabinan and arabinogalactan without triplicate curation. One reaction, but a complete capability with its own product.
28starch_degradationmetabolicStarch to D-glucoseEncodes saccharification of starch to free D-glucose: endo-acting cleavage of the alpha-1,4-glucan backbone followed by exo-acting release of the monosaccharide.cataboliccurated1Endo- and exo-acting chemistry are both required for this curated saccharification capability. Alpha-amylase depolymerises the alpha-1,4-glucan backbone and generates additional chain ends and malto-oligosaccharides, while alpha-glucosidase releases D-glucose successively from non-reducing termini. As for xylan, the exo-acting enzyme can in principle act on polymer termini directly, but exo activity alone is not treated here as sufficient evidence for complete polymer saccharification. Debranching is accessory rather than required: amylose carries no alpha-1,6 branch points, so a genome without pullulanase still degrades starch, less completely. Malto-oligosaccharide is an internal intermediate for the same reason as xylo-oligosaccharide.
29collagen_cleavagemetabolicCollagen to collagen peptidesEncodes cleavage of native triple-helical collagen, releasing collagen-derived peptides outside the cell. A positive call means the genome encodes a microbial collagenase of MEROPS family M9, the activity that degrades the intact helix; it does not mean the organism assimilates the peptides.cataboliccurated1One required reaction, but a complete capability with its own product, as for arabinoxylan debranching. Substrate specificity rests on mechanism rather than on a family name: EC 3.4.24.3 is defined by digestion of native collagen in the triple-helical region, which generic endopeptidases cannot perform because the intact helix resists them. Broadly proteolytic enzymes such as pseudolysin are deliberately excluded even though they hydrolyse collagen among other host proteins, because accepting them would equate this trait with generic proteolysis. The product anchor is substrate-specific rather than a shared peptide pool; a shared oligopeptide tier and peptide uptake are deferred behind transporter evidence.
30flagellar_apparatusstructuralFlagellar apparatusEncodes the structural and assembly machinery of a bacterial flagellum: the type III export apparatus, basal body, C ring, hook, filament and stator of at least one curated flagellar architecture. A positive call means the genome encodes that machinery. It does not mean the organism is motile, that the flagellum is expressed, or that it rotates under any particular condition.NULLcurated1Ion coupling is deliberately not claimed. KEGG assigns the sodium-driven PomA/PomB stator of Vibrio cholerae to K02556/K02557, the same orthologues as the proton-driven MotA/MotB stator of Escherichia coli, so KO evidence cannot separate proton- from sodium-driven motors. Separate proton_driven_flagellar_apparatus and sodium_driven_flagellar_apparatus GIFTs are therefore refused at this evidence level; see inst/doc/proposal-structural-gifts.md. Transcriptional regulators (FlhDC, FliA, FlgM) are excluded because they are regulatory, not structural.
31type_iva_pilusstructuralType IVa pilus machineryEncodes the machinery required to assemble a type IVa pilus: prepilin processing, a major pilin, an extension ATPase, the inner membrane platform, the PilMNOP alignment subcomplex and the PilQ secretin. A positive call means the genome encodes that machinery; it does not establish twitching motility, natural competence, or adhesion to any particular surface, none of which follow from the assembly machinery alone.NULLcurated1Scoped to the type IVa system because the alignment subcomplex markers (PilM/N/O/P) are specific to it; type IVb and Tad pili are different architectures and are not covered. Retraction is curated as an accessory function: a pilus can be assembled without PilT.
32chemotaxis_signal_transductionregulatoryChemotaxis signal transductionEncodes the core chemotaxis signal-transduction machinery: a chemoreceptor, the CheA histidine kinase with its CheW coupling protein, the CheY response regulator, and the CheR/CheB adaptation cycle. A positive call means the genome encodes that pathway. It does not mean the cell is chemotactic, that the pathway is expressed, or that the organism responds to any particular compound: which chemoeffectors are detected depends on receptor sensing domains this claim says nothing about.NULLcurated1The reception function accepts either a generic methyl-accepting chemotaxis protein (K03406) or any characterised chemoreceptor. Both are needed: Escherichia coli K-12 carries no K03406 orthologue at all, its four receptors being assigned to the characterised groups, while Pseudomonas aeruginosa carries 21 K03406 genes and Vibrio cholerae 34. Signal termination is accessory and has three non-homologous implementations (CheZ, CheC, CheX). CheV is not accepted as a CheW substitute. See inst/doc/proposal-regulatory-gifts.md.
33aspartate_chemoreceptionregulatoryAspartate chemoreceptionEncodes the machinery to detect L-aspartate and transduce it into the chemotaxis pathway: the Tar aspartate chemoreceptor together with the shared chemotaxis kinase, response-regulator and adaptation functions. A positive call means the genome encodes an aspartate-responsive chemosensory input. It does not mean the cell swims toward aspartate, which additionally requires expression, a working flagellar motor, and a gradient.NULLcurated1This GIFT exists to keep the core pathway honest. Its reception function accepts K05875 (Tar) only. The generic chemoreceptor accession K03406 is deliberately refused here: it identifies the conserved cytoplasmic signalling domain shared by every chemoreceptor and cannot single out an aspartate sensor, so accepting it would let any chemotactic genome claim aspartate sensing. The three downstream functions are the same curated rows the core circuit uses.
34phosphate_starvation_responseregulatoryPhosphate starvation responseEncodes a phosphate-starvation two-component regulatory system: the PhoR sensor histidine kinase paired with a cognate phosphate-regulon response regulator. A positive call means the genome encodes the signalling machinery. It does not mean the regulon is induced, that the cell is phosphate-limited, or that any particular gene is regulated.NULLcurated1Two curated circuits share the PhoR sensor and differ in the response regulator: PhoB (K07657) in enterobacteria, pseudomonads and vibrios, PhoP (K07658) in Bacillus and relatives. Across the reference genomes checked on 2026-08-18 the sensor is single-copy where present and the two regulator groups are mutually exclusive, which is what licenses orthology as evidence of a cognate pair here. K07660, the response regulator of the magnesium-sensing PhoP/PhoQ system, shares the gene name and is a different protein; it is not accepted. The PstSCAB-PhoU complex is accessory because it is independently a transport capability.
35type_i_restriction_modificationdefenseType I restriction-modificationEncodes a complete type I restriction-modification system: the HsdS specificity subunit, the HsdM methyltransferase that protects the host's own target sites, and the HsdR subunit that translocates and cleaves unmethylated DNA. A positive call means the genome encodes that mechanism. It does not mean the organism resists any particular phage, which depends on the invader's anti-restriction counter-measures and on defences this GIFT does not describe.NULLcurated1All three subunits are required. A genome carrying only HsdM and HsdS has a methylation capability, which is real biology and common as an orphan methyltransferase, but it defends against nothing and is correctly called incomplete here. The target sequence the system recognises is deliberately not claimed: HsdS specificity comes from variable target recognition domains that the orthology group does not resolve.
36type_i_e_crispr_cas_machinerydefenseType I-E CRISPR-Cas machineryEncodes the protein machinery of a type I-E CRISPR-Cas system: the five-subunit Cascade surveillance complex and the Cas3 nuclease-helicase, with Cas1-Cas2 spacer acquisition accessory. A positive call means the genome encodes those proteins. It does not mean the system can interfere with anything, because interference additionally requires a CRISPR array to supply guide RNAs, and an array is a repeat-spacer locus detected by structure rather than a protein annotation.NULLcurated1The claim is deliberately narrowed to the encoded machinery. gifter's evidence layer is an annotation accession, which cannot express 'a CRISPR array was detected in this genome', and no Cas protein accession is evidence that an array is present. Broadening the evidence model to genomic features was considered and deferred to a second demonstrated need; see inst/doc/proposal-defense-gifts.md.
37pyruvate_to_acetyl_coametabolicPyruvate to acetyl-CoAEncodes decarboxylation of pyruvate to acetyl-CoA, the step that connects every sugar and amino acid catabolism GIFT ending at pyruvate to acyl-CoA chemistry and to short-chain fatty acid formation.cataboliccurated1No KEGG module covers this capability as a unit. Three non-homologous routes are curated because they are not interchangeable: the dehydrogenase complex is the aerobic route, the ferredoxin oxidoreductase and formate-lyase routes are oxygen-sensitive, and 10961 of 11856 KEGG organisms complete at least one. The dehydrogenase reaction carries two alternative systems because the fused E1 of Escherichia coli (K00163) and the alpha/beta E1 of Bacillus (K00161 with K00162) are different architectures; requiring either alone would call roughly 4800 genomes negative for chemistry they have.
38acetate_interconversionmetabolicAcetyl-CoA and acetate interconversionEncodes the two-step interconversion of acetyl-CoA and acetate through acetyl phosphate, the substrate-level phosphorylation that yields ATP when it runs towards acetate. A positive call means the genome encodes that chemistry. It does not mean the cell excretes acetate, and it cannot mean that: the same two enzymes run the reaction towards acetyl-CoA in genomes assimilating acetate, and no marker distinguishes the directions.interconversioncurated1Declared interconversion rather than catabolic because the node is near-equilibrium and physiologically bidirectional, and because a catabolic declaration would place any future acetate-activation GIFT in a within-mode cycle with this one. Boundaries of KEGG M00579 retained. 6582 of 11856 KEGG organisms complete it, so a positive call carries little discriminating power on its own; it is curated because it is the boundary the butyrate transferase route consumes.
39butyrate_formationmetabolicAcetyl-CoA and acetate to butanoateEncodes condensation and reduction of acetyl-CoA to butanoyl-CoA followed by CoA transfer onto acetate, releasing butanoate. A positive call means the genome encodes that route. It does not mean butyrate is produced, excreted, or ecologically consequential, and it says nothing about the amount.cataboliccurated1Absent from KEGG, and not curatable from KEGG orthology: the four core enzymes are chain-length-generic and the transferase shares K01034 and K01035 with the acetoacetate degradation transferase of Escherichia coli, so a KO-evidenced route calls Faecalibacterium prausnitzii, Roseburia intestinalis and Agathobacter rectalis negative and Bacillus subtilis positive. The terminal step is therefore evidenced by NCBIfam TIGR03948, corroborated by InterPro IPR023990 and HAMAP MF_03227. The butyrate kinase route is deliberately refused because Ptb and Buk are shared with Bacillus branched-chain acyl-CoA metabolism at KO and at TIGRFAM level alike. See inst/doc/proposal-scfa-biosynthesis.md.
40propanediol_formationmetabolic(S)-lactaldehyde to (S)-propane-1,2-diolEncodes reduction of the (S)-lactaldehyde released by deoxyhexose aldol cleavage to (S)-propane-1,2-diol, the step that converts fucose and rhamnose carbon into a diol that fermentation can carry to propionate.cataboliccurated1One reaction, but a complete capability with its own product, as for arabinoxylan debranching. Curated separately from the propionate route because propane-1,2-diol is itself a documented boundary metabolite: genomes carrying the propanediol utilisation operon frequently acquire the diol rather than making it, and 87 of the 232 such genomes carry no lactaldehyde reductase at all.
41propionate_formation_propanediolmetabolic(S)-propane-1,2-diol to propanoateEncodes dehydration of propane-1,2-diol to propanal, its oxidation to propanoyl-CoA, and substrate-level phosphorylation to propanoate. A positive call means the genome encodes that route, not that propionate is produced or released.cataboliccurated1No KEGG module covers this capability. 168 of 11856 KEGG organisms complete it and they are the propanediol utilisation operon of the Enterobacteriaceae: Salmonella (51), Klebsiella (46), Citrobacter (24), Yersinia (18) and Escherichia (9). The dehydratase is adenosylcobalamin-dependent; gifter models no cofactor availability, so the call does not assert that B12 is present.
42propionate_formation_acrylatemetabolic(R)-lactate to propanoateEncodes the acrylate pathway: CoA transfer onto lactate, dehydration to acryloyl-CoA, and reduction to propanoyl-CoA, with propanoyl-CoA regenerated as the CoA donor so that lactate is the net substrate and propanoate the net product.cataboliccurated1The most substrate-specific and least prevalent capability in this layer. All 13 KEGG organisms carrying propionate CoA-transferase with both lactoyl-CoA dehydratase subunits are characterised acrylate-pathway producers, among them Anaerotignum propionicum, Megasphaera elsdenii and Pseudocoprococcus catus, and no genome outside that group carries the set. The acryloyl-CoA reductase K20143 is assigned in only 4 of those 13, so most are reported incomplete with the reductase named as the missing reaction rather than having the step scored away; this follows the serine phosphatase precedent. The lcdC activator subunit has no orthology group and is not required.
43lactate_formationmetabolicPyruvate to (S)-lactateEncodes NAD-dependent reduction of pyruvate to (S)-lactate, the terminal disposal of reducing equivalents in homofermentative and mixed-acid fermentation. Unlike every other fermentation end product curated so far, the direction of this claim is evidenced rather than asserted: forming lactate is a cytoplasmic NADH-consuming reduction and consuming it feeds electrons to a quinone or a cytochrome, and KEGG assigns those to different orthology groups.cataboliccurated1K00016 is present in 4143 of the 11855 KEGG organisms examined and the quinone-dependent lldD group K29125 in 3388, but only 573 carry both. Every lactic acid bacterium checked carries the forming group and not the consuming one, and Escherichia coli, Salmonella Typhimurium and Pseudomonas aeruginosa are the reverse. The quinone- and cytochrome-dependent groups K29125, K00101, K03777 and K00102 are deliberately not accepted as markers, because they evidence the opposite direction. D-lactate formation is not curated: K03778 is specific to the right chemistry but its leading genera are Pseudomonas, Streptomyces and Burkholderia, which run the reaction oxidatively, and the (R) anchor is reached through lactate_racemisation instead.
44lactate_racemisationmetabolic(S)-lactate and (R)-lactate interconversionEncodes lactate racemase, which interconverts the two lactate enantiomers. A positive call means the genome can supply either enantiomer from the other. It does not mean the cell prefers a direction, and it cannot mean that: a racemase has no direction to prefer.interconversioncurated1Declared interconversion rather than catabolic because a racemase is the purest instance of that mode: acetate_interconversion is reversible as a matter of physiology, LarA as a matter of definition. It resolves a defect the SCFA layer left behind. propionate_formation_acrylate consumes (R)-lactate and nothing produced it, and of the ten KEGG genomes behind that route eight carry K22373 while only two carry a D-lactate dehydrogenase, so the racemase is how those organisms actually reach the anchor.
45malolactic_fermentationmetabolic(S)-malate to (S)-lactateEncodes malolactic enzyme, the direct decarboxylation of (S)-malate to (S)-lactate without a free pyruvate intermediate. This is the only capability in the database that takes a citric acid cycle metabolite as a boundary, and it takes it as an input.cataboliccurated1K22212 is present in 337 organisms and the set is Streptococcus, Lacticaseibacillus, Enterococcus, Lactococcus, Limosilactobacillus, Lactiplantibacillus, Lactobacillus and Leuconostoc almost without exception. The step releases CO2 and is therefore irreversible, which is why malate may be a boundary here while fumarase and malate dehydrogenase license no malate-forming trait.
46citrate_fermentationmetabolicCitrate to pyruvate and acetateEncodes fermentative cleavage of citrate: the holo-citrate lyase complex splits citrate to oxaloacetate and acetate, and oxaloacetate is decarboxylated to pyruvate. A positive call means the genome encodes the chemistry, not that it expresses it; the classic aerobic citrate-utilisation phenotype is a transport and regulation phenotype that gifter does not model.cataboliccurated1The lyase with its activating ligase is complete in 912 of 11855 organisms and adding an oxaloacetate decarboxylase gives 369, led by Salmonella, Streptococcus, Klebsiella, Lacticaseibacillus and Enterococcus. Bacillus subtilis, Bacteroides thetaiotaomicron and Pseudomonas aeruginosa are negative. Oxaloacetate is an internal intermediate and is deliberately not an anchor. The citrate transporter is not required evidence: Escherichia coli K-12 carries CitT and is aerobically Cit-negative because the gene is not expressed under oxygen, so requiring it would look like a phenotype claim without being one.
47ethanol_formationmetabolicAcetyl-CoA to ethanolEncodes the bifunctional acetaldehyde/alcohol dehydrogenase route from acetyl-CoA to ethanol, in which one protein carries both reductions. A positive call means the genome encodes that chemistry; AdhE is reversible and is used in the ethanol-oxidising direction by some genomes, and no marker distinguishes the two.cataboliccurated1K04072 is present in 2519 organisms, led by Streptococcus, Vibrio, Bacillus, Escherichia, Clostridium and Bifidobacterium. The route deliberately does not cover Zymomonas mobilis or Saccharomyces cerevisiae, which decarboxylate pyruvate through K01568 with a separate alcohol dehydrogenase; that route is complete in 258 organisms, is fungus-dominated, and its bacterial tail is Acetobacter and Gluconobacter, which oxidise ethanol rather than form it. It is left for a later pass rather than curated as an equal alternative.
48acetoin_formationmetabolicPyruvate to (R)-acetoinEncodes condensation of two pyruvate to (2S)-2-acetolactate and its decarboxylation to (R)-acetoin, the neutral fermentation route that the Voges-Proskauer test detects. The trait rests on the decarboxylase, which has no other role.cataboliccurated1K01575 is present in 1649 organisms, led by Streptococcus, Bacillus, Corynebacterium, Staphylococcus, Klebsiella, Enterobacter, Listeria, Enterococcus and Lactococcus. The synthase step is curated but not required, because its orthology group K01652 is the anabolic branched-chain amino acid synthase ilvB/ilvG/ilvI and carries no acetoin-specific information; requiring it changes the call in 50 of 1649 genomes and imports a marker that means something else. Butane-2,3-diol is one step further and is not curated.
49riboflavin_biosynthesismetabolicGTP and D-ribulose 5-phosphate to riboflavinEncodes de novo synthesis of riboflavin (vitamin B2) from GTP and D-ribulose 5-phosphate: ring opening and reduction of the GTP-derived pyrimidinedione, condensation with the four-carbon unit to give dimethylribityllumazine, and dismutation to riboflavin. A positive call means the genome encodes that route. It does not mean riboflavin is exported or available to anything else.anaboliccurated1Boundary ends at riboflavin. The flavin kinase and FMN adenylyltransferase that make FMN and FAD are shared housekeeping, complete in every reference genome including those that cannot make riboflavin, and are deliberately not curated.
50paba_biosynthesismetabolicChorismate to 4-aminobenzoateEncodes synthesis of 4-aminobenzoate from chorismate through 4-amino-4-deoxychorismate. A positive call means the genome can make the aromatic half of folate for itself; a negative one identifies a genome that must acquire 4-aminobenzoate, which is a documented dependency of several gut lineages.anaboliccurated1Cut from folate biosynthesis because the two halves are separately lost: 4099 KEGG bacteria complete both branches, 1799 only the pterin branch and 989 only this one.
51folate_biosynthesismetabolicGTP and 4-aminobenzoate to tetrahydrofolateEncodes de novo synthesis of tetrahydrofolate (vitamin B9) from GTP and 4-aminobenzoate: pterin ring formation, coupling to 4-aminobenzoate, glutamylation and reduction. A positive call means the genome encodes that route; it says nothing about how much folate is made or whether any leaves the cell.anaboliccurated1Two dephosphorylation steps between the pterin triphosphate and dihydroneopterin are not gating. The pyrophosphatase is curated as not required because its orthology is Proteobacteria-biased; the residual monophosphatase step is not curated at all, because the only marker offered for it is a generic alkaline phosphatase that would fire in every genome.
52hmp_phosphate_biosynthesismetabolicAIR to the thiamine pyrimidineEncodes de novo synthesis of the thiamine pyrimidine moiety: radical SAM rearrangement of the purine intermediate AIR into hydroxymethylpyrimidine phosphate, and its phosphorylation to the diphosphate that thiamine phosphate synthase requires.anaboliccurated1AIR is declared as an input anchor only. Purine core biosynthesis does not declare it as an output, so no composition edge is created from an internal purine intermediate.
53thiazole_phosphate_biosynthesismetabolicDXP to the thiamine thiazoleEncodes de novo synthesis of the thiamine thiazole moiety from 1-deoxy-D-xylulose 5-phosphate and an imine donor. A positive call means the genome encodes thiazole synthase together with an enzyme that supplies 2-iminoacetate.anaboliccurated1ThiS and ThiF are not required components. ThiF is homologous to MoeB and ThiI also serves tRNA thiolation, so neither marker adds thiamine specificity, while requiring them would reduce the trait from 5396 to 1554 bacterial genomes.
54thiamine_phosphate_biosynthesismetabolicThiamine pyrimidine and thiazole to thiamine phosphateEncodes condensation of the two thiamine moieties into thiamine phosphate (vitamin B1). A positive call means the genome encodes thiamine phosphate synthase; combined with the two branch GIFTs it means de novo thiamine synthesis, and combined with the salvage GIFT it means the genome can build thiamine from acquired precursors.anaboliccurated1The boundary stops at thiamine phosphate rather than the diphosphate. ThiL is absent from the KEGG annotation of ten of eighteen reference genomes that certainly make TPP, so requiring it would turn an annotation gap into an auxotrophy call.
55thiamine_precursor_salvagemetabolicThiamine precursor salvage to the activated moietiesEncodes phosphorylation of the free thiamine pyrimidine and thiazole acquired from the environment, giving the same two activated moieties that de novo synthesis produces. A positive call identifies a genome that can build thiamine from precursors made by something else.anaboliccurated1Curated as a separate capability that composes with thiamine phosphate biosynthesis through the HMP_PP and THZ_P anchors, so that ThiE is curated once rather than duplicated into a salvage route.
56pantothenate_biosynthesismetabolic2-oxoisovalerate and L-aspartate to pantothenateEncodes de novo synthesis of pantothenate (vitamin B5): hydroxymethylation and reduction of the branched-chain 2-oxo acid to pantoate, decarboxylation of L-aspartate to beta-alanine, and their ligation. A positive call means the genome encodes that route.anaboliccurated1The boundary stops at pantothenate. The five steps that convert it to coenzyme A are shared housekeeping and are not curated. KEGG M00119 defines completeness without PanC or PanD and therefore never reaches pantothenate.
57plp_biosynthesis_r5pmetabolicRibose 5-phosphate and glyceraldehyde 3-phosphate to pyridoxal 5-phosphateEncodes the DXP-independent route to pyridoxal 5-phosphate (vitamin B6): a single PdxS/PdxT synthase complex builds the pyridine ring from a pentose phosphate, a triose phosphate and the amide nitrogen of glutamine. A positive call means the genome encodes that complex.anaboliccurated1Separate from the DXP-dependent capability because the input boundaries differ, following the precedent of the two methionine biosynthesis GIFTs. The two routes are near-disjoint across bacteria and together cover 4199 genomes.
58plp_biosynthesis_dxpmetabolicErythrose 4-phosphate and DXP to pyridoxal 5-phosphateEncodes the DXP-dependent route to pyridoxal 5-phosphate (vitamin B6), in which erythrose 4-phosphate is oxidised and transaminated to 4-phosphohydroxy-L-threonine, decarboxylated, condensed with 1-deoxy-D-xylulose 5-phosphate to pyridoxine 5-phosphate, and oxidised to the aldehyde.anaboliccurated1Shares phosphoserine aminotransferase with serine biosynthesis. The marker is accepted for this reaction, not as evidence of vitamin B6 synthesis on its own; the other five reactions carry the claim.
59biotin_biosynthesismetabolicPimeloyl-CoA to biotinEncodes assembly of the biotin bicyclic ring from a pimelate thioester: condensation with L-alanine, transamination, ring closure to dethiobiotin, and sulfur insertion by biotin synthase. A positive call means the genome encodes that route.anaboliccurated1The precursor supply that makes the pimelate thioester is deliberately not curated: BioC/BioH, BioI, BioW and BioU are non-homologous solutions and no marker set spans them. The thioester carrier is not distinguished by the BioF marker, so the claim covers both the CoA and the acyl-carrier-protein forms.
60quinolinate_biosynthesis_aspartatemetabolicL-aspartate to quinolinateEncodes de novo formation of the pyridine ring of NAD from L-aspartate and dihydroxyacetone phosphate. A positive call means the genome can build the ring rather than depending on an exogenous pyridine.anaboliccurated1Cut at quinolinate so that de novo ring formation and pyridine salvage are separate claims that share no reactions.
61namn_biosynthesis_quinolinatemetabolicQuinolinate to nicotinate D-ribonucleotideEncodes phosphoribosyl transfer onto quinolinate with decarboxylation, giving nicotinate D-ribonucleotide. This is the step at which de novo pyridine synthesis joins the shared nucleotide chemistry that both salvage and cobamide lower-ligand attachment also use.anaboliccurated1Curated as its own GIFT so that the de novo and salvage capabilities can share the downstream adenylylation and amidation without duplicating them.
62nad_biosynthesis_namnmetabolicNicotinate D-ribonucleotide to NADEncodes adenylylation of nicotinate D-ribonucleotide and amidation of the resulting deamido-NAD to NAD. A positive call means the genome completes the shared trunk that both de novo synthesis and pyridine salvage feed.anaboliccurated1Shared by the de novo and salvage capabilities, which is why it is curated once rather than repeated in both.
63namn_salvage_nicotinatemetabolicNicotinate to nicotinate D-ribonucleotideEncodes recovery of an exogenous pyridine ring: nicotinate phosphoribosyltransferase converts acquired nicotinate into nicotinate D-ribonucleotide, which the shared trunk carries to NAD. A positive call means the genome can live on niacin; it does not mean the genome can make the ring.anaboliccurated1The layer separates being able to use vitamin B3 from being able to make it. 6921 KEGG bacteria carry this salvage together with the trunk, against 6398 that can form quinolinate from aspartate.
64corrin_ring_biosynthesismetabolicUroporphyrinogen III to cobyrinate a,c-diamideEncodes construction of the cobalt-loaded corrin ring from the tetrapyrrole branchpoint, by either the aerobic or the anaerobic route. A positive call means the genome encodes de novo corrin synthesis, which is the step that separates a corrinoid producer from a corrinoid salvager.anaboliccurated1Recall is limited by gene fusion: Propionibacterium freudenreichii carries cysG_cbiX and a cobJ_cbiE_cbiG_cbiH fusion that KEGG assigns to none of the component orthology groups, so the industrial B12 producer is called incomplete with three named missing reactions. Pfam PF00590 covers every cobalt-precorrin methyltransferase and cannot resolve the individual steps, so no domain marker rescues it.
65cobinamide_biosynthesismetabolicCobyrinate a,c-diamide to adenosylcobinamide phosphateEncodes adenosylation of the corrin ring, amidation of its remaining carboxylates, and attachment of the aminopropanol arm, giving the adenosylcobinamide phosphate that lower-ligand assembly requires.anaboliccurated1Curated separately from the ring because the two are separately present: 4428 KEGG bacteria carry this chemistry against 1081 that also complete a corrin ring.
66cobamide_nucleotide_loop_assemblymetabolicAdenosylcobinamide phosphate and dimethylbenzimidazole to cobalaminEncodes assembly of the cobamide nucleotide loop: guanylylation of adenosylcobinamide phosphate, transfer of the lower ligand onto nicotinate D-ribonucleotide, dephosphorylation, and joining of the two halves to give adenosylcobalamin. A positive call means the genome can attach a lower ligand; with 5,6-dimethylbenzimidazole as the ligand the product is vitamin B12, and 3044 bacteria carrying this capability encode no corrin ring at all, so a positive call is not evidence of production.anaboliccurated1Declares nicotinate D-ribonucleotide as an input anchor because CobT consumes it, which is what connects the cobamide layer to NAD metabolism. The CobU kinase half of the bifunctional marker is what lets a salvager enter this capability from imported cobinamide.
67dmb_biosynthesis_aerobicmetabolicFMNH2 to 5,6-dimethylbenzimidazoleEncodes the oxygen-dependent BluB route to 5,6-dimethylbenzimidazole, the lower ligand that makes a cobamide into vitamin B12. A negative call does not establish that the genome cannot make the ligand: the anaerobic bza route has no orthology group and is not curated.anaboliccurated1FMNH2 is declared as an input-only anchor. BluB destroys the flavin to build the benzimidazole ring, which is the one case in this layer where a cofactor is a substrate rather than a recycled participant.
68menaquinone_biosynthesismetabolicChorismate to menaquinoneEncodes synthesis of menaquinone (vitamin K2) from chorismate, by either the classical men route or the futalosine route. A positive call means the genome encodes one complete route to the prenylated, methylated naphthoquinone.anaboliccurated1Two orphan steps are curated as not required: MenH, whose elimination also proceeds without a dedicated enzyme, and the DHNA-CoA thioesterase, which has several non-homologous replacements and no orthology group covering them. Requiring both would reduce the classical route from 3109 to 1355 bacterial genomes.
69acetyl_coa_to_isocitratemetabolicAcetyl-CoA and oxaloacetate to isocitrateEncodes condensation of acetyl-CoA with oxaloacetate to citrate and isomerisation to isocitrate by citrate synthase and aconitase. Isocitrate is exposed as the branchpoint between oxidative decarboxylation and the glyoxylate bypass. A positive call means this upper central-carbon segment is encoded; it does not mean either downstream fate or either derived cycle is complete.cataboliccurated1Re-cut from acetyl_coa_to_oxoglutarate so that the oxidative and glyoxylate branches do not duplicate citrate synthase and aconitase. K01659 remains accepted at ambiguous confidence because it contains genuine citrate synthases as well as 2-methylcitrate synthases. K01681, K01682 and K27802 remain alternative aconitase markers. Full assessment in inst/doc/proposal-central-metabolic-cycles.md.
70oxoglutarate_to_succinatemetabolic2-oxoglutarate to succinateEncodes the oxidative conversion of 2-oxoglutarate to succinate by any of three alternative implementations: the 2-oxoglutarate dehydrogenase complex, the ferredoxin-dependent 2-oxoglutarate oxidoreductase, or the 2-oxoglutarate decarboxylase bypass through succinate semialdehyde. Succinyl-CoA and succinate semialdehyde are internal intermediates.cataboliccurated1The dehydrogenase complex is complete in 6902 organisms, the ferredoxin oxidoreductase in 3288 and the decarboxylase bypass in 1420; 8932 complete at least one. The bypass is the actinobacterial substitution that makes Mycobacterium tuberculosis and Corynebacterium glutamicum positive although both lack the E1o component. Direction is claimed for the GIFT as a whole and is honest for the dehydrogenase and decarboxylase routes, both of which release CO2 irreversibly; the ferredoxin route is the reductive citric acid cycle enzyme and is genuinely reversible, so its direction is a route-level claim the markers do not independently support. Making mode route-scoped is recorded as open question Q2 of inst/doc/proposal-central-metabolic-cycles.md. Succinyl-CoA synthetase is curated as one reaction with two enzyme systems rather than as separate ADP- and GDP-forming reactions, because K01899 and K01900 carry both EC numbers and no marker separates them.
71succinate_fumarate_interconversionmetabolicSuccinate and fumarate interconversionEncodes the quinone-dependent interconversion of succinate and fumarate. The mode is interconversion and not a direction, because succinate dehydrogenase and fumarate reductase are the same orthology group in most bacteria. A positive call states that the genome encodes the couple, not which way it runs, and it is not a claim about fumarate respiration.interconversioncurated1K00239 is named by KEGG sdhA, frdA and K00240 sdhB, frdB: one group for both enzymes, present in 8047 organisms. The dedicated frdAB group K00244/K00245 exists in 1059, almost all Enterobacteriaceae, and 943 of the 1041 genomes carrying frdABCD also carry sdhABCD, so the split is a paralogue duplication within one clade rather than a functional partition. Two opposed directional GIFTs would therefore be complete on identical markers in 8047 genomes. Only the catalytic flavoprotein and iron-sulfur subunits are required; requiring the cytochrome b anchor K00241 as well would call a further 402 genomes negative on a poorly conserved membrane subunit. The generic quinone reaction RHEA:40523 is curated rather than the ubiquinone, menaquinone or rhodoquinone forms, because no marker distinguishes them; resolving that is the trigger recorded for splitting this GIFT.
72fumarate_oxaloacetate_interconversionmetabolicFumarate and oxaloacetate interconversionEncodes hydration of fumarate to (S)-malate and oxidation of (S)-malate to oxaloacetate, or the reverse. Malate is an internal intermediate of this GIFT and remains an input-only boundary elsewhere. The mode is interconversion because fumarase is a hydratase at equilibrium and NAD-dependent malate dehydrogenase runs towards malate in every genome using the reductive branch.interconversioncurated1Fumarase is present in 10618 organisms and malate dehydrogenase or malate:quinone oxidoreductase in 9752; 9533 carry both. Rhea writes RHEA:12460 as (S)-malate = fumarate + H2O, so the traversal curated here records the hydratase step as reverse. Only malate:quinone oxidoreductase is effectively unidirectional towards oxaloacetate and it is one alternative system out of four, which is why the GIFT as a whole may not claim a direction. Splitting this GIFT at malate was assessed and deferred until a better-evidenced malate producer exists; see open question Q5 of inst/doc/proposal-central-metabolic-cycles.md.
73chorismate_biosynthesismetabolicPhosphoenolpyruvate and erythrose 4-phosphate to chorismateEncodes the shikimate pathway, the seven-step condensation and reduction sequence that builds chorismate from two central carbon intermediates. Chorismate is the branchpoint at which aromatic metabolism leaves central metabolism: phenylalanine, tyrosine, tryptophan, 4-aminobenzoate, menaquinone, salicylate and the enterobactin aryl group all descend from it, which is why the capability ends there rather than at any one of them.anaboliccurated1Boundaries chosen independently of KEGG M00022, which shares them. The archaeal route to 3-dehydroquinate from 6-deoxy-5-ketofructose 1-phosphate and aspartate semialdehyde is deliberately outside this GIFT: it consumes different precursors, so it cannot be a route between these anchors.
74salicylate_biosynthesismetabolicChorismate to salicylateEncodes the isochorismate-dependent formation of salicylate from chorismate. In bacteria salicylate is a siderophore building block rather than an end product, and the capability stops at the free acid because the ligases that commit it to pyochelin, yersiniabactin or mycobactin are separate, siderophore-specific chemistry.anaboliccurated1One route of two reactions. PchA/PchB and the bifunctional salicylate synthases MbtI, Irp9 and YbtS run the same two transformations, so they are curated as alternative enzyme systems rather than as alternative routes.
75indole_3_acetate_biosynthesismetabolicL-tryptophan to indole-3-acetateEncodes the indole-3-acetamide route from tryptophan to the auxin indole-3-acetate. Cut at tryptophan rather than at chorismate because tryptophan is a branchpoint and a building block in its own right, and bundling aromatic amino acid biosynthesis into an auxin trait would make two independently useful capabilities inseparable.anaboliccurated1Only the IAM route is curated. The indole-3-pyruvate, tryptamine, indole-3-acetonitrile and tryptophan side-chain oxidase routes are refused for want of markers that discriminate the activity; see inst/doc/proposal-shikimate-aromatics.md.
76urate_degradationmetabolicUrate to allantoinEncodes oxidative opening of the purine ring of urate to allantoin: hydroxylation of urate to 5-hydroxyisourate and its hydrolysis and decarboxylation to (S)-allantoin. A positive call means the genome can begin mineralising host purine nitrogen. It does not mean the nitrogen is released as ammonium, which needs two further capabilities.cataboliccurated1NULL
77allantoin_degradationmetabolicAllantoin to glyoxylate and ureaEncodes hydrolysis of allantoin to glyoxylate and urea, by either the allantoicase route or the allantoate deiminase route. A positive call means the genome can consume allantoin whether or not it can make it: 774 of the 893 bacteria completing this capability carry no uricase of any kind, so this is a consumer trait as often as a continuation of urate catabolism.cataboliccurated1Route-specific nitrogen fate: the deiminase route additionally releases two ammonium, the allantoicase route none. AMMONIUM is therefore not a declared output, because a GIFT anchor must hold for every route.
78urea_hydrolysismetabolicUrea to ammoniumEncodes urease-mediated hydrolysis of urea to ammonium and hydrogencarbonate. A positive call means the genome encodes the nickel-dependent urease catalytic core. It does not mean urea is available, nor that the ammonium is assimilated, nor that the pH rise urease causes is physiologically relevant.cataboliccurated1The UreD, UreE, UreF and UreG maturation proteins are deliberately not curated as components of the catalytic system. They perform nickel insertion rather than catalysis, and requiring all four drops the capability from 3725 to 2741 bacteria.
79nitrate_assimilationmetabolicNitrate to ammoniumEncodes assimilatory reduction of nitrate to ammonium: nitrate to nitrite by an assimilatory nitrate reductase, then nitrite to ammonium by a ferredoxin- or NAD(P)H-dependent nitrite reductase. A positive call means the genome can use nitrate as a nitrogen source. It is not a claim about nitrate respiration, denitrification or dissimilatory reduction, none of which gifter models, because gifter models no electron acceptors.anaboliccurated1Mode is anabolic on the SULFIDE precedent: assimilable inorganic nutrients enter gifter as inputs to anabolic capabilities. A fifth assimilatory mode was considered and deferred.
80betaine_demethylationmetabolicGlycine betaine to sarcosineEncodes oxidative demethylation of glycine betaine to sarcosine through N,N-dimethylglycine. Every curated route is aerobic, because the first step is a Rieske monooxygenase that consumes molecular oxygen. A positive call means that chemistry is encoded; the anaerobic betaine reductase route to trimethylamine is a different capability and is not curated.cataboliccurated1NULL
81sarcosine_demethylationmetabolicSarcosine to glycineEncodes demethylation of sarcosine to glycine, by the oxygen-dependent sarcosine oxidases or by the ferredoxin-dependent dehydrogenase. This is the shared tail of betaine and creatinine catabolism, curated once and reached from both by composition rather than duplicated in either.cataboliccurated1NULL
82creatinine_degradationmetabolicCreatinine to sarcosine and ureaEncodes hydrolysis of creatinine to creatine and its cleavage to sarcosine and urea. A positive call requires both enzymes: 2431 bacteria carry the creatininase fold and only 194 also carry creatinase, so the first enzyme alone would over-call the capability more than tenfold.cataboliccurated1The creatinine deiminase route is refused: K01485 is a cytosine/creatinine deaminase, one accession for two activities, and the cytosine activity is the common one.
83carnitine_degradation_trimethylaminemetabolicL-carnitine to trimethylamineEncodes carnitine monooxygenase, the Rieske oxygenase that cleaves L-carnitine to trimethylamine and a four-carbon aldehyde. A positive call means the genome encodes that chemistry. It does not mean trimethylamine is produced or released, and it says nothing about host trimethylamine N-oxide, which requires a host flavin monooxygenase gifter does not model.cataboliccurated1NULL
84carnitine_to_betainemetabolicL-carnitine to glycine betaineEncodes the dehydrogenase route from L-carnitine to glycine betaine: oxidation to 3-dehydrocarnitine, acetyl-CoA-dependent retro-Claisen cleavage to betainyl-CoA, and thioester hydrolysis. This route releases no trimethylamine, which is why it is a separate capability from carnitine monooxygenase rather than a second route of it.cataboliccurated1The betainyl-CoA thioesterase step is curated with required = 0. Its only marker, K27497, is a bifunctional protein that also carries the first step, and requiring it drops the capability from 944 to 256 bacteria.
85methylamine_degradationmetabolicMethylamine to ammoniumEncodes methylamine dehydrogenase, the tryptophan-tryptophylquinone enzyme that oxidises methylamine to formaldehyde and ammonium. Both subunits are jointly required. Formaldehyde is left as an internal product: it is a transient the cell detoxifies immediately and gifter has no consumer for it.cataboliccurated1The N-methylglutamate route is deferred: its four jointly required subunits complete in 46 bacteria, where single missing annotations would dominate the call.
86taurine_desulfonation_aerobicmetabolicTaurine to sulfiteEncodes taurine dioxygenase, the 2-oxoglutarate-dependent enzyme that releases the sulfonate sulfur of taurine as sulfite. A positive call means the genome can obtain sulfur from taurine. It leaves the nitrogen on aminoacetaldehyde and makes no nitrogen claim, and it is not a claim that hydrogen sulfide is formed.cataboliccurated1NULL
87taurine_degradation_sulfoacetaldehydemetabolicTaurine to sulfite through sulfoacetaldehydeEncodes removal of the taurine amino group by transamination or dehydrogenation and cleavage of the resulting sulfoacetaldehyde to acetyl phosphate and sulfite. A positive call means the genome encodes that chemistry. It is emphatically not a claim that hydrogen sulfide is produced: reducing sulfite to sulfide is dissimilatory sulfite reduction, which is respiration and out of scope.cataboliccurated1The nitrogen fate differs by route -- L-alanine from the transaminase, ammonium from the dehydrogenase -- so neither is a declared output and the GIFT makes no nitrogen claim. Acetyl phosphate is left internal rather than declared.
88taurine_uptake_abcmetabolicTaurine uptakeEncodes ATP-dependent import of taurine by the TauABC periplasmic-binding-protein-dependent transporter, the step that separates a genome able to consume taurine released by bile-salt hydrolysis from one that merely encodes the desulfonation enzymes.transportcurated1NULL
89ammonium_assimilationmetabolicAmmonium and 2-oxoglutarate to glutamateEncodes assimilation of ammonium into glutamate, by the glutamine synthetase/glutamate synthase cycle or by glutamate dehydrogenase. A positive call is uninformative on its own, since 9482 of 10151 bacteria have it; the informative call is the negative one, which identifies genomes dependent on preformed amino acids. The capability exists in gifter so that ammonium is a boundary with a consumer rather than a terminal one.anaboliccurated1NULL
90benzoate_degradation_catecholmetabolicBenzoate to catecholEncodes ring dihydroxylation of benzoate and decarboxylating rearomatisation to catechol, the entry most aerobic peripheral aromatic routes use to reach the ring-cleavage node. A positive call means the genome encodes one complete curated route. It does not mean the compound is encountered, taken up, degraded in situ, or degraded at any rate. The benzoate 1,2-dioxygenase orthologues KEGG names benA and benB are benzoate/toluate enzymes: the call is honest for benzoate, which is within the enzyme's range, and for that reason no separate methylbenzoate or xylene-derived GIFT may be curated on the same markers, since the two traits would be indistinguishable.cataboliccurated1The markers are orthology groups for the substrate-determining subunits; the shared ferredoxin and ferredoxin reductase components of the same system are deliberately not required, because they are interchangeable between systems and are annotated two to three times less often than the subunits they serve, so requiring them would report an annotation gap as a missing capability.
91anthranilate_degradation_catecholmetabolicAnthranilate to catecholEncodes oxidative deamination and decarboxylation of anthranilate to catechol in one step, a second peripheral entry into the ring-cleavage node. Anthranilate is a kynurenine-pathway catabolite of tryptophan in host and microbe alike rather than an industrial compound. A positive call means the genome encodes one complete curated route. It does not mean the compound is encountered, taken up, degraded in situ, or degraded at any rate.cataboliccurated1The markers are orthology groups for the substrate-determining subunits; the shared ferredoxin and ferredoxin reductase components of the same system are deliberately not required, because they are interchangeable between systems and are annotated two to three times less often than the subunits they serve, so requiring them would report an annotation gap as a missing capability. Two alternative systems are curated, the antAB and andAcAd oxygenases, because they are non-homologous solutions annotated to different orthology groups.
92phenol_hydroxylationmetabolicPhenol to catecholEncodes hydroxylation of phenol to catechol by the multicomponent phenol 2-monooxygenase. Phenol is a product of microbial tyrosine fermentation as well as an industrial compound. A positive call means the genome encodes one complete curated route. It does not mean the compound is encountered, taken up, degraded in situ, or degraded at any rate. KEGG module M00548 attaches the same marker set to benzene oxidation as well; that claim is not made here, because the enzyme is a phenol hydroxylase and gifter has no marker that evidences benzene as the substrate.cataboliccurated1All six subunits of the dmp/pox/tom system are jointly required. Unlike the Rieske systems in this layer, these components are the enzyme rather than interchangeable electron carriers.
93catechol_ortho_cleavagemetabolicCatechol to 3-oxoadipate by ortho cleavageEncodes intradiol cleavage of catechol between the hydroxyls and conversion of the muconate through two lactones to 3-oxoadipate: the beta-ketoadipate pathway. A positive call means the genome encodes one complete curated route. It does not mean the compound is encountered, taken up, degraded in situ, or degraded at any rate. Ortho and meta cleavage are curated as separate GIFTs rather than alternative routes of one, because they produce different compounds and reach central metabolism at different points.cataboliccurated1The lactone hydrolysis step carries two alternative systems, the standalone pcaD hydrolase and the fused pcaL protein that also decarboxylates.
94oxoadipate_activationmetabolic3-Oxoadipate to 3-oxoadipyl-CoAEncodes CoA transfer from succinyl-CoA onto 3-oxoadipate, the activation step that commits the ortho-cleavage product to thiolysis. A positive call means the genome encodes one complete curated route. It does not mean the compound is encountered, taken up, degraded in situ, or degraded at any rate.cataboliccurated1Curated as its own GIFT because 3-oxoadipyl-CoA is where the ortho-cleavage funnel and the aerobic phenylacetate route converge, and duplicating either segment inside the other would break composition through declared anchors.
95oxoadipyl_coa_thiolysismetabolic3-Oxoadipyl-CoA to succinyl-CoA and acetyl-CoAEncodes thiolytic cleavage of 3-oxoadipyl-CoA, the single step that delivers aromatic carbon into central metabolism. A positive call means the genome encodes one complete curated route. It does not mean the compound is encountered, taken up, degraded in situ, or degraded at any rate.cataboliccurated1The thiolase orthologue is shared with the phenylacetate route, which is why it is curated once here rather than inside each upstream GIFT.
96catechol_meta_cleavagemetabolicCatechol to 2-oxopent-4-enoate by meta cleavageEncodes extradiol cleavage of catechol adjacent to the hydroxyls and conversion of the resulting semialdehyde to 2-oxopent-4-enoate, by either the hydrolytic or the 4-oxalocrotonate branch. A positive call means the genome encodes one complete curated route. It does not mean the compound is encountered, taken up, degraded in situ, or degraded at any rate.cataboliccurated1K07104 is deliberately refused as evidence of catechol 2,3-dioxygenase. It is assigned in 2081 KEGG genomes dominated by Bacillus, Streptococcus, Staphylococcus and Listeria, only 276 of which carry any lower meta pathway gene, and accepting it would put an over-broad marker in reach of every future GIFT that declares this activity. K00446 is used instead, corroborated by NCBIfam TIGR03211.
97oxopentenoate_degradationmetabolic2-Oxopent-4-enoate to pyruvate and acetyl-CoAEncodes hydration, retro-aldol cleavage and acylating oxidation of 2-oxopent-4-enoate to pyruvate and acetyl-CoA. This is the common lower route of meta cleavage, shared by catechol, dihydroxyphenylpropanoate and, where their evidence permits, the biphenyl, cumate and xylene routes. A positive call means the genome encodes one complete curated route. It does not mean the compound is encountered, taken up, degraded in situ, or degraded at any rate.cataboliccurated1Curated once as an atomic GIFT rather than duplicated inside every upper route that ends here, which is what composition through declared anchors is for. Two alternative system sets are curated per step, the mhp and the bph/xyl/tes enzymes.
98phenylacetate_degradationmetabolicPhenylacetate to 3-oxoadipyl-CoAEncodes the aerobic CoA-dependent route: activation of phenylacetate to its CoA thioester, epoxidation of the ring, isomerisation to the oxepin, hydrolytic ring opening, and beta-oxidation to 3-oxoadipyl-CoA. Phenylacetate is a phenylalanine fermentation product, which makes this the entry into the layer that host-associated genomes most often carry. A positive call means the genome encodes one complete curated route. It does not mean the compound is encountered, taken up, degraded in situ, or degraded at any rate.cataboliccurated1Ends at 3-oxoadipyl-CoA so that the terminal thiolysis is not duplicated: oxoadipyl_coa_thiolysis carries it once for this route and for the ortho-cleavage funnel alike. The route's last three steps use chain-generic beta-oxidation orthologues, one of which is already curated for butyrate formation; the specificity of the claim rests on paaK and the epoxidase, not on the tail.
99phenylpropanoate_dihydroxylationmetabolic3-Phenylpropanoate to 3-(2,3-dihydroxyphenyl)propanoateEncodes ring dihydroxylation of 3-phenylpropanoate and dehydrogenation of the diol to the catecholic phenylpropanoid. A positive call means the genome encodes one complete curated route. It does not mean the compound is encountered, taken up, degraded in situ, or degraded at any rate. trans-Cinnamate is the same enzyme's other substrate, and Rhea gives the two reactions separate masters, but no marker in any namespace separates them: KEGG names the orthologue a 3-phenylpropionate/trans-cinnamate dioxygenase and NCBIfam NF042946 carries the same dual name. Curating cinnamate as a second GIFT would create two traits with identical evidence, so it is deliberately not curated and cinnamate is not claimed.cataboliccurated1The markers are orthology groups for the substrate-determining subunits; the shared ferredoxin and ferredoxin reductase components of the same system are deliberately not required, because they are interchangeable between systems and are annotated two to three times less often than the subunits they serve, so requiring them would report an annotation gap as a missing capability.
100hydroxyphenylpropanoate_hydroxylationmetabolic3-(3-Hydroxyphenyl)propanoate to 3-(2,3-dihydroxyphenyl)propanoateEncodes flavin-dependent hydroxylation of the meta-hydroxylated phenylpropanoid to the catecholic one, the second entry into the same ring-cleavage node. A positive call means the genome encodes one complete curated route. It does not mean the compound is encountered, taken up, degraded in situ, or degraded at any rate.cataboliccurated1Curated separately from the dioxygenase entry because the substrates differ; KEGG module M00545 ORs the two into one module, which gifter cannot do, since a route must connect the GIFT's own declared boundaries.
101dihydroxyphenylpropanoate_degradationmetabolic3-(2,3-Dihydroxyphenyl)propanoate to 2-oxopent-4-enoate and succinateEncodes extradiol cleavage of the catecholic phenylpropanoid and hydrolysis of the ring-opened product, releasing succinate and 2-oxopent-4-enoate. A positive call means the genome encodes one complete curated route. It does not mean the compound is encountered, taken up, degraded in situ, or degraded at any rate.cataboliccurated1Ends at 2-oxopent-4-enoate rather than at pyruvate and acetyl-CoA, so that the shared lower route is composed through the anchor instead of duplicated.
102glutamine_biosynthesismetabolicL-glutamate and ammonium to L-glutamineEncodes the ATP-dependent amidation of L-glutamate by glutamine synthetase. Glutamine is curated as its own capability rather than as part of ammonium assimilation because it is a required precursor elsewhere in the database -- pyrimidine, pyridoxal phosphate, tryptophan and histidine biosynthesis all consume its amide nitrogen -- and because a genome can carry glutamine synthetase without any glutamate synthase, in which case it amidates glutamate it cannot itself make.anaboliccurated1NULL
103alanine_biosynthesismetabolicPyruvate to L-alanineEncodes the formation of L-alanine from pyruvate, either by transamination from L-glutamate or by reductive amination with ammonium. KEGG has no module for alanine, and the textbook alanine transaminase orthology group K00814 is annotated in a single bacterial genome, so the trait is curated from the alanine-synthesising transaminases and alanine dehydrogenase instead. Only pyruvate is declared as a boundary: the two routes use different nitrogen donors, so declaring either would claim a requirement that half the routes do not have.anaboliccurated1NULL
104aspartate_biosynthesismetabolicOxaloacetate to L-aspartateEncodes the transamination that turns the citric acid cycle intermediate oxaloacetate into L-aspartate. One reaction, curated as a capability because it is the entry point of the entire aspartate family -- asparagine, the aspartate 4-semialdehyde trunk, lysine, threonine and methionine -- and because three curated GIFTs already declare L-aspartate as an input that nothing in the database produced.anaboliccurated1NULL
105asparagine_biosynthesismetabolicL-aspartate to L-asparagineEncodes the ATP-dependent amidation of L-aspartate, by the ammonia-dependent ligase AsnA or by the glutamine-hydrolysing synthase AsnB. Only aspartate is declared as a boundary: the two routes differ in nitrogen source, and unlike the methionine pair -- where sulfide and cysteine are genuinely different nutritional situations -- ammonium and the glutamine amide are interchangeable intracellular nitrogen, so the difference does not justify two capabilities.anaboliccurated1NULL
106dap_biosynthesismetabolicL-aspartate 4-semialdehyde to meso-diaminopimelateEncodes the diaminopimelate branch from the aspartate trunk to meso-2,6-diaminopimelate, by any of four alternative routes: succinylated, acetylated, dehydrogenase and aminotransferase. KEGG draws these as four separate modules, each repeating the aspartate kinase and semialdehyde dehydrogenase steps that gifter curates separately, and each scoring badly alone -- 51.4, 5.6, 6.8 and 17.2 per cent of bacterial genomes. As alternative routes of one capability they cover 75.3 per cent, which is what the route layer exists to express. The capability ends at meso-diaminopimelate rather than at lysine because that molecule is also the peptidoglycan cross-link residue.anaboliccurated1NULL
107lysine_biosynthesis_dapmetabolicmeso-diaminopimelate to L-lysineEncodes the decarboxylation that commits meso-diaminopimelate to L-lysine. Curated separately from the diaminopimelate branch because the two are separately informative: a genome can make the peptidoglycan precursor without making the amino acid, and LysA is present in 85.6 per cent of bacterial genomes while the branch that supplies it completes in 75.3 per cent.anaboliccurated1NULL
108oxoisovalerate_biosynthesismetabolicPyruvate to 3-methyl-2-oxobutanoateEncodes the acetohydroxyacid pathway from two pyruvates to 3-methyl-2-oxobutanoate, the branchpoint 2-oxo acid that supplies valine, leucine and pantothenate. Cut here rather than at valine because the same three enzymes also serve the isoleucine branch on a different substrate, so the 2-oxo acid, not the amino acid, is what the evidence identifies -- and because pantothenate biosynthesis already declared this molecule as an input that nothing produced.anaboliccurated1NULL
109valine_biosynthesismetabolic3-methyl-2-oxobutanoate to L-valineEncodes the branched-chain transamination that turns 3-methyl-2-oxobutanoate into L-valine. One reaction, curated as a capability because it is the step that establishes valine identity and because the branchpoint before it feeds pantothenate and leucine as well. The same aminotransferase serves leucine and isoleucine, so the marker fires for all three; what separates the three traits is the 2-oxo acid supply, and each of those is separately evidenced.anaboliccurated1NULL
110leucine_biosynthesismetabolic3-methyl-2-oxobutanoate to L-leucineEncodes the isopropylmalate chain extension that adds one carbon to 3-methyl-2-oxobutanoate, followed by transamination to L-leucine. Extended past the module boundary, which stops at 2-oxoisocaproate, because the amino acid is the capability a reader is asking about and the transamination is the same enzyme already curated for valine.anaboliccurated1NULL
111oxobutanoate_biosynthesis_citramalatemetabolicPyruvate to 2-oxobutanoateEncodes the citramalate route to 2-oxobutanoate, which reaches the isoleucine precursor from pyruvate without passing through threonine. Rare -- 3.3 per cent of bacterial genomes -- and curated because it is the only isoleucine route available to a genome that cannot make threonine, which is exactly the case a composition graph should be able to answer.anaboliccurated1NULL
112isoleucine_biosynthesismetabolic2-oxobutanoate to L-isoleucineEncodes the isoleucine branch of the acetohydroxyacid pathway, from 2-oxobutanoate to L-isoleucine. The four enzymes are the same ones that build valine from two pyruvates; the reactions are different because the substrate is. Cutting at 2-oxobutanoate is what makes the two amino acids separable, and it is also what connects isoleucine to its two suppliers: threonine deamination and the citramalate route.anaboliccurated1NULL
113phenylalanine_biosynthesismetabolicChorismate to L-phenylalanineEncodes the prephenate dehydratase branch from chorismate to L-phenylalanine. The final transamination is evidenced by a wider marker set than KEGG uses: requiring TyrB alone calls the trait in 2296 bacterial genomes where the discriminating aryl skeleton is present in 7796, and accepting the aspartate and branched-chain aminotransferases -- which do transaminate aromatic 2-oxo acids -- recovers 7733. The step is kept required because it is real chemistry, but the specificity of the claim rests on the skeleton, not on the transaminase.anaboliccurated1NULL
114tyrosine_biosynthesismetabolicChorismate to L-tyrosineEncodes the prephenate dehydrogenase branch from chorismate to L-tyrosine, with NAD- and NADP-dependent routes that are separately evidenced by different orthology groups. The final transamination carries the same widened marker set as phenylalanine biosynthesis, for the same measured reason.anaboliccurated1NULL
115tryptophan_biosynthesismetabolicChorismate and L-glutamine to L-tryptophanEncodes the five-step branch from chorismate to L-tryptophan. L-glutamine is declared as an input because the anthranilate synthase amidotransfer is the nitrogen source of the ring in every route, which is the same reading of an amidotransferase already applied to pyrimidine and pyridoxal phosphate biosynthesis; L-serine, which supplies the side chain, is not, because it is a co-substrate of the last step rather than the boundary the trait is about. The indole intermediate of tryptophan synthase is channelled between the two subunits and never released, so this GIFT does not connect to the indole anchor.anaboliccurated1NULL
116histidine_biosynthesismetabolicPRPP and L-glutamine to L-histidineEncodes the ten-step pathway from PRPP to L-histidine. The module boundary is kept unchanged because the pathway has no stable intermediate that another capability consumes, which is the test for a cut. L-glutamine is declared as an input for the imidazole glycerol-phosphate synthase amidotransfer; the AICAR released by the same reaction is not declared as an output, on the precedent of L-homocysteine, because it is an internal participant of purine core biosynthesis and an edge there would assert a composition nobody would read as biology.anaboliccurated1NULL
117proline_biosynthesismetabolicL-glutamate to L-prolineEncodes the phosphorylation, reduction, spontaneous cyclisation and second reduction that turn L-glutamate into L-proline. L-glutamate is declared as an input here, unlike in the transamination-dependent GIFTs of this layer, because its carbon skeleton becomes the product.anaboliccurated1NULL
118ornithine_biosynthesismetabolicL-glutamate to L-ornithineEncodes the acetylated branch from L-glutamate to L-ornithine, by either the linear route that hydrolyses the acetyl group off or the cyclic route that transfers it back onto glutamate. The cyclic ArgJ route is the dominant one outside the Enterobacteriaceae, and the two are separately evidenced. The LysW-carrier route of Thermus and the archaea is not curated: its distinguishing orthology group is annotated in no bacterial genome.anaboliccurated1NULL
119arginine_biosynthesismetabolicL-ornithine to L-arginineEncodes carbamoylation of L-ornithine to L-citrulline, condensation with L-aspartate and elimination of fumarate to give L-arginine. L-citrulline stays internal: the arginine deiminase pathway passes through the same molecule in the opposite direction, and declaring it would assert a composition edge between a biosynthetic and a catabolic capability that share one reversible enzyme rather than a metabolite boundary.anaboliccurated1NULL
120arginine_deiminase_pathwaymetabolicL-arginine to L-ornithine and ammoniumEncodes the arginine deiminase pathway: deimination of L-arginine to L-citrulline, phosphorolysis back to L-ornithine, and substrate-level phosphorylation of ADP from the carbamoyl phosphate released. The trait most users mean by arginine catabolism, and the principal acid-resistance and ATP-generating strategy of streptococci, lactobacilli and many oral and vaginal taxa. All three components are required: ornithine carbamoyltransferase alone is shared with arginine biosynthesis running the other way, so it is the deiminase and the carbamate kinase that identify the catabolic pathway. L-citrulline stays internal, which is why this GIFT and arginine biosynthesis share no boundary except the two amino acids themselves.cataboliccurated1NULL
121histidine_degradation_glutamatemetabolicL-histidine to L-glutamate and ammoniumEncodes the histidine utilisation pathway from L-histidine to L-glutamate: non-oxidative deamination, hydration, ring hydrolysis and release of the formyl group as formamide. Curated with the formamide-releasing hydrolase rather than the folate-dependent formiminotransferase, because the transferase route ends in the one-carbon pool, which gifter has no anchors for.cataboliccurated1NULL
122threonine_deaminationmetabolicL-threonine to 2-oxobutanoate and ammoniumEncodes the PLP-dependent deamination of L-threonine. The chemistry is catabolic wherever it runs, and the same enzyme serves the first step of isoleucine biosynthesis: curating it once, as catabolism, and letting isoleucine biosynthesis compose from the 2-oxobutanoate anchor is what keeps one reaction in one GIFT. The resulting threonine-to-isoleucine chain crosses modes, which is the case the composition rule anticipates.cataboliccurated1NULL
123serine_deaminationmetabolicL-serine to pyruvate and ammoniumEncodes the deamination of L-serine to pyruvate, the step that makes serine a fermentable substrate rather than only a biosynthetic product. Its product is the pyruvate anchor, so it connects the amino acid layer to the whole fermentation layer in one edge.cataboliccurated2K01752 is excluded because KEGG assigns it to complete single-chain proteins and to either isolated subunit of the split enzyme.
124glutamate_decarboxylation_gabametabolicL-glutamate to 4-aminobutanoateEncodes the PLP-dependent decarboxylation of L-glutamate to GABA. The reaction consumes a cytoplasmic proton, which is why it is the core of glutamate-dependent acid resistance; the product is also the most studied microbially produced neuroactive compound. gifter claims the encoded decarboxylation only: the antiporter that makes the system work as acid resistance is transport chemistry this layer does not curate, and no evidence layer here says whether GABA leaves the cell.cataboliccurated1NULL
125tryptophan_degradation_indolemetabolicL-tryptophan to indole, pyruvate and ammoniumEncodes tryptophanase, the beta-elimination that releases indole from L-tryptophan. One reaction, one orthology group, and the strongest host-signal claim in the amino acid layer: bacterial indole is an aryl hydrocarbon receptor ligand that modulates epithelial barrier function, and the reaction is what the classical clinical indole test detects. Curated as a capability on the same grounds as cytidylate biosynthesis: a single transformation that establishes a product identity nothing else in the database produces.cataboliccurated1NULL
126methionine_degradation_methanethiolmetabolicL-methionine to methanethiol and 2-oxobutanoateEncodes methionine gamma-lyase, which releases methanethiol, 2-oxobutanoate and ammonium from L-methionine. Methanethiol is a principal volatile sulfur compound of oral malodour and a documented colonocyte irritant. The enzyme is promiscuous towards homocysteine and cysteine; the GIFT is named for methionine and its marker is deliberately not accepted as evidence for any cysteine capability.cataboliccurated1NULL
127cysteine_degradation_sulfidemetabolicL-cysteine to hydrogen sulfide and pyruvateEncodes the dedicated cysteine desulfidases that release hydrogen sulfide, pyruvate and ammonium from L-cysteine. The trait is knowingly under-called: many PLP enzymes carry this activity as a side reaction, and accepting them would make every transsulfuration genome a sulfide producer, since cystathionine beta-lyase is already curated as evidence for cysteine biosynthesis. Only the dedicated desulfidase orthology groups are accepted, which is a claim about specificity rather than about prevalence. The product closes the sulfide anchor, which two biosynthesis GIFTs consumed and nothing produced.cataboliccurated1NULL
128glycine_reduction_sticklandmetabolicGlycine to acetyl phosphate and ammoniumEncodes the glycine reductase complex, the reductive half of Stickland fermentation: glycine is reduced and deaminated to acetyl phosphate, which phosphorylates ADP. The complete selenoprotein complex is required, which is what makes the trait specific -- 128 of 10151 bacterial genomes -- and it is diagnostic of proteolytic Clostridia including Clostridioides difficile. gifter states the encoded chemistry only: selenocysteine incorporation itself is a separate capability this layer does not evaluate.cataboliccurated1NULL
129proline_reduction_sticklandmetabolicL-proline to 5-aminopentanoateEncodes Stickland proline reduction: racemisation of L-proline to D-proline and reductive ring opening to 5-aminopentanoate by the selenoprotein proline reductase. The racemase is required because the reductase is specific for the D isomer, and the two together are what distinguishes the trait from proline oxidation. Rare and diagnostic, like glycine reduction, and it forms a cross-mode pair with proline biosynthesis.cataboliccurated1NULL
130mercury_detoxificationdefenseMercury detoxificationEncodes the machinery that detoxifies mercury by reducing Hg(II) to volatile elemental Hg(0), through the NADPH-dependent mercuric reductase MerA, with delivery of the metal to the reductase, mercury-responsive induction of the operon and organomercurial carbon-mercury lysis as accessory functions. A positive call means the genome encodes MerA-dependent reduction. It does not mean the organism survives mercury exposure: that depends on the dose, on which mercury species it meets, and on efflux and sequestration systems this GIFT does not describe.NULLcurated1Reduction is the only required function. A genome carrying merA alone detoxifies the Hg(II) that reaches its cytoplasm, which is the claim; requiring merT and merP would refuse such a genome on the strength of an operon architecture that varies, because merC and merE substitute for the pair in several lineages, and gifter has no evidence layer for how much metal gets in. Organomercurial lysis by MerB is curated as an accessory function and not as a second mechanism: broad-spectrum resistance is a genuinely different phenotype, and whether it deserves its own mechanism is recorded as an open question in inst/doc/proposal-aromatic-degradation.md. Mercury methylation by hgcAB is not this capability and is not curated: it makes mercury more toxic, not less.
131isocitrate_to_oxoglutaratemetabolicIsocitrate to 2-oxoglutarateEncodes oxidative decarboxylation of isocitrate to 2-oxoglutarate by either NADP- or NAD-dependent isocitrate dehydrogenase. A positive call establishes the oxidative fate of the isocitrate branchpoint; it does not mean the citric acid cycle closes.cataboliccurated1Separated from acetyl_coa_to_isocitrate so that the glyoxylate bypass can branch at a declared anchor without duplicating the upper segment. The two cofactor-specific reactions are alternative routes because their markers distinguish them.
132glyoxylate_bypassmetabolicIsocitrate and acetyl-CoA to succinate and malateEncodes the two-reaction glyoxylate bypass: isocitrate lyase cleaves isocitrate to succinate and glyoxylate, then malate synthase condenses the glyoxylate with acetyl-CoA to malate. A positive call means this carbon-conserving branch is encoded. It does not mean the glyoxylate cycle closes, carries flux, or supports growth on any substrate.cataboliccurated1Isocitrate is the branch boundary; glyoxylate is produced and consumed inside the complete route and remains internal. K01639 is refused because it is N-acetylneuraminate lyase, not malate synthase. K19282 is deferred because its malyl-CoA route requires two different Rhea reactions rather than the direct malate-synthase reaction curated here.
133nitrogen_fixationmetabolicDinitrogen to ammoniumEncodes reduction of dinitrogen to ammonium by a complete curated nitrogenase architecture, including the catalytic and electron-delivery components and the nitrogenase-specific cofactor-assembly proteins that cannot be replaced by housekeeping pathways. A positive call means the genome encodes nitrogen-fixation chemistry. It does not mean the system is expressed, protected from oxygen, supplied with reductant, or fixes nitrogen in situ.anaboliccurated1The molybdenum architecture requires NifHDK, NifEN and NifB; NifU, NifS, NifV and NifM are not required because their roles are not universally nitrogenase-specific or can be supplied by host pathways. A vanadium architecture requires VnfHDGK, VnfEN and NifB and is a separate route with its own Rhea master. NifH alone is explicitly insufficient. The Fe-only architecture is deferred because current KO groups do not separate AnfHDK from NifHDK while the minimum native assembly requirement remains context-dependent.
134assimilatory_sulfate_reductionmetabolicSulfate to hydrogen sulfideEncodes activation and assimilatory reduction of sulfate to hydrogen sulfide through either the direct APS or the PAPS branch and either NADPH- or ferredoxin-dependent sulfite reductase. A positive call means one complete assimilatory route is encoded. It does not mean sulfate is available, sulfur is incorporated into biomass, or dissimilatory sulfur respiration occurs.anaboliccurated1Four minimal routes materialise the APS/PAPS and NADPH/ferredoxin alternatives. The shared CysH KO K00390 is refused because KEGG assigns it both EC 1.8.4.8 and 1.8.4.10 and it cannot decide which branch is complete; the two branch reactions therefore use reaction-specific EC markers. Dissimilatory AprAB and DsrAB markers are not accepted. CysNC is represented at the correct system layer as a fusion that can satisfy APS kinase and, with CysD, sulfate adenylyltransferase.
135ectoine_biosynthesismetabolicAspartate semialdehyde to ectoineEncodes the EctB-EctA-EctC conversion of L-aspartate 4-semialdehyde to L-ectoine. A positive call means the three-step ectoine-forming chemistry is encoded. It does not mean ectoine is produced or accumulated, the organism tolerates osmotic stress, hydroxyectoine is formed, or ectoine is transported.anaboliccurated1Starts at the existing ASA branchpoint, so the aspartate kinase and semialdehyde dehydrogenase upstream of MetaCyc P101-PWY and KEGG M00033 are not duplicated. EctD, regulation and transport are excluded.
136heme_b_biosynthesismetabolicUroporphyrinogen III to heme bEncodes a complete protoporphyrin- or coproporphyrin-dependent route from uroporphyrinogen III to heme b. A positive call means heme-b-forming chemistry is encoded. It does not mean heme is available, incorporated into proteins, used for respiration, or made through the siroheme-dependent route.anaboliccurated1Seven minimal routes materialise HemF/HemN and HemY/HemG/HemJ combinations plus the coproporphyrin HemY-HemH-HemQ route. The siroheme route has a different input boundary and is deliberately not folded into this GIFT.
137dihydroxybenzoate_biosynthesismetabolicChorismate to 2,3-dihydroxybenzoateEncodes conversion of chorismate to 2,3-dihydroxybenzoate through isochorismate, the reusable catecholate branch that supplies enterobactin and related siderophores. A positive call does not identify the downstream siderophore, its secretion, iron uptake or any ecological effect.anaboliccurated1The isochorismate reaction and its existing systems are reused. EntB supplies the lyase step and is also the aryl carrier in the downstream enterobactin GIFT; those functions remain separate components.
138enterobactin_biosynthesismetabolic2,3-Dihydroxybenzoate and serine to enterobactinEncodes complete enterobactin assembly from 2,3-dihydroxybenzoate and L-serine by the EntB, EntD, EntE and EntF machinery. A positive call means the biosynthetic assembly line is encoded. It does not mean enterobactin is secreted, binds iron, is taken back up, supports virulence or changes iron acquisition in situ.anaboliccurated1The four proteins are jointly required components of one aggregate Rhea reaction system. The split at 2,3-dihydroxybenzoate lets the chorismate-derived head compose with other catecholate products without duplicating it.
139methylglyoxal_detoxificationdefenseGlutathione-dependent methylglyoxal detoxificationEncodes the two-enzyme glutathione-dependent conversion of methylglyoxal to D-lactate by glyoxalases I and II. A positive call means this complete detoxifying mechanism is encoded. It does not mean methylglyoxal is present, the enzymes are active, or the organism survives or resists methylglyoxal exposure.NULLcurated1The mechanism stops once the electrophile has been converted and glutathione regenerated. D-lactate oxidation is downstream metabolism; broad reductases, dehydrogenases and glyoxalase-III families are refused because their markers do not identify methylglyoxal at this specificity.
140superoxide_detoxificationdefenseComplete superoxide detoxificationEncodes removal of superoxide followed by removal of the hydrogen peroxide produced, using one accepted system for each required function. A positive call means a complete two-stage chemical-detoxification mechanism is encoded. It does not mean reactive oxygen species are present, the machinery is expressed, or the organism withstands oxidative stress.NULLcurated1SOD alone is incomplete because its product is hydrogen peroxide. Nickel SOD is refused without evidence for its required maturation protease, and superoxide reductase is deferred until its electron-delivery architecture is markable.
141choline_to_betainemetabolicCholine to glycine betaineEncodes complete oxidation of choline to glycine betaine through a BetA/BetB, GbsB/GbsA, choline-monooxygenase/BADH or choline-oxidase route. A positive call means the chemical conversion is encoded. It does not mean choline is transported or available, betaine accumulates, or the organism tolerates osmotic stress.anaboliccurated1The output reuses the existing BETAINE anchor and composes with betaine demethylation. K14085 is refused because its broad ALDH7A1 annotation cannot identify betaine aldehyde; K00130 is accepted because the orthology group is explicitly betaine-aldehyde dehydrogenase.
142siroheme_biosynthesismetabolicUroporphyrinogen III to sirohemeEncodes complete conversion of uroporphyrinogen III to siroheme by a multifunctional CysG enzyme or by complete methyltransferase, dehydrogenase and ferrochelatase alternatives. A positive call means siroheme-forming chemistry is encoded. It does not mean siroheme is made, incorporated into a reductase, used for sulfur or nitrogen metabolism, or converted to heme b.anaboliccurated1The route uses three Rhea masters because RHEA:32459 consolidates the two sequential methyl transfers that MetaCyc records separately. CysG can satisfy all three reactions; Met8 satisfies dehydrogenation and ferrochelation; SirC plus SirB supplies the split terminal pair. Broad CbiX-family markers are refused where they cannot distinguish iron from cobalt or nickel insertion, so archaeal siroheme synthesis is knowingly under-called.
143chitin_degradationmetabolicChitin to N-acetyl-D-glucosamineEncodes saccharification of chitin to free N-acetyl-D-glucosamine: endo-acting cleavage of the beta-1,4-GlcNAc backbone followed by exo-acting release of the monosaccharide. A positive call means the genome can liberate usable amino sugar from arthropod and fungal biomass.cataboliccurated1NULL
144mucin_sialic_acid_releasemetabolicMucin O-glycan to N-acetylneuraminateEncodes release of terminal N-acetylneuraminate from host mucin O-glycan. Sialic acid capping is the outermost layer of the glycan, so this is the activity that opens the chain to other foragers as well as the cell that carries it.cataboliccurated1Curated as a parallel monosaccharide-release capability from one polymer anchor: mucin has no polymer-to-oligomer cut, so the tier model does not apply and each exo-glycosidase is its own trait.
145mucin_fucose_releasemetabolicMucin O-glycan to L-fucoseEncodes release of terminal L-fucose from host mucin O-glycan. Fucosidase possession varies independently of the other mucin activities and tracks a distinct foraging strategy.cataboliccurated1Curated as a parallel monosaccharide-release capability from one polymer anchor: mucin has no polymer-to-oligomer cut, so the tier model does not apply and each exo-glycosidase is its own trait.
146mucin_galnac_releasemetabolicMucin O-glycan to N-acetyl-D-galactosamineEncodes release of the alpha-linked N-acetyl-D-galactosamine at the mucin O-glycan core, the linkage that attaches the glycan to the protein backbone.cataboliccurated1Curated as a parallel monosaccharide-release capability from one polymer anchor: mucin has no polymer-to-oligomer cut, so the tier model does not apply and each exo-glycosidase is its own trait.
147pectin_degradationmetabolicPectin to D-galacturonateEncodes hydrolytic saccharification of the pectin backbone to free D-galacturonate: endo-acting cleavage of the alpha-1,4-galacturonan chain followed by exo-acting release of the uronate, with de-esterification as accessory chemistry. A positive call means the genome can liberate usable uronate from the dominant soluble fibre of a plant-based diet.cataboliccurated1Curated on the hydrolytic chemistry only. The lyase chemistry is a separate capability, pectate_lyase_degradation, because beta-elimination and hydrolysis end at different metabolites and anchors are declared per GIFT.
148kdg_degradationmetabolic2-dehydro-3-deoxy-D-gluconate to pyruvate and D-glyceraldehyde 3-phosphateEncodes the lower Entner-Doudoroff segment: phosphorylation of 2-dehydro-3-deoxy-D-gluconate and aldol cleavage of the phosphorylated product into pyruvate and D-glyceraldehyde 3-phosphate. A positive call means the genome can finish any catabolic route that converges on the branchpoint, which the two hexuronate routes and the pectate lyase route all do.cataboliccurated1Cut out of galacturonate_degradation and glucuronate_degradation in release 2026.21.3, where the same two reactions were carried twice. KdgK and Eda are also the enzymes of the Entner-Doudoroff pathway proper and of gluconate and alginate catabolism, so the segment is carried by genomes that have no hexuronate head at all.
149pectate_lyase_degradationmetabolicPectin to 2-dehydro-3-deoxy-D-gluconate by beta-eliminationEncodes the lyase route through pectin: endo-acting beta-elimination of the galacturonan backbone, exo-acting release of unsaturated digalacturonate, and its conversion through 5-dehydro-4-deoxy-D-glucuronate and 3-deoxy-D-glycero-2,5-hexodiulosonate to the Entner-Doudoroff branchpoint. A positive call means the genome degrades pectin by the chemistry that predominates in gut Bacteroidetes, which the hydrolytic capability does not detect.cataboliccurated1The route runs past the polymer boundary to a monomeric anchor because beta-elimination yields unsaturated oligogalacturonides, which are not promoted to anchors. Oligogalacturonide lyase, the ketol isomerase and the 5-dehydrogenase have no other substrate in the database, so folding them in follows the granularity rule rather than excepting it. The exo-lyase step is required chemistry but its marker support is the thinnest in the route, which makes the call conservative.
150ectoine_degradationmetabolicL-ectoine to L-2,4-diaminobutanoateEncodes the committed, ectoine-specific part of ectoine catabolism: DoeA opens the ring and DoeB removes the acetyl group that EctA installed, leaving L-2,4-diaminobutanoate. A positive call means the organism encodes the capability to dismantle ectoine, not that ectoine is available, taken up, or used as a nutrient in the sampled environment. The boundary is the end of ectoine-specific chemistry; the transamination that follows is the same reaction ectoine_biosynthesis runs in the other direction, and is left outside.cataboliccurated1Cut at L-2,4-diaminobutanoate rather than at L-aspartate 4-semialdehyde or L-aspartate on purpose. Adding the DoeD step would mean attaching a second enzyme system to RHEA:11160, which ectoine_biosynthesis also uses, and K15785 was refused as an EctB alternative when that GIFT was curated. Evidence attaches to reactions rather than to routes, so admitting DoeD there would silently reverse that refusal.
151hydroxyectoine_biosynthesismetabolicL-ectoine to 5-hydroxyectoineEncodes hydroxylation of ectoine to 5-hydroxyectoine by the 2-oxoglutarate-dependent dioxygenase EctD. Curated separately from ectoine_biosynthesis because the product is a distinct compatible solute rather than a modified intermediate, and because only some ectoine producers encode the hydroxylase. A positive call names the encoded product and makes no osmotic- or thermotolerance claim.anaboliccurated1NULL
152lactate_formation_lactaldehydemetabolic(S)-lactaldehyde to (S)-lactateEncodes oxidation of (S)-lactaldehyde to (S)-lactate, the second fate of the lactaldehyde that fucose and rhamnose catabolism release. Curated separately from lactate_formation, which starts at pyruvate: the input boundaries differ, and a genome can encode one without the other. A positive call does not mean lactate is excreted.cataboliccurated1The lactaldehyde branchpoint now has two curated fates, reduction to propane-1,2-diol and oxidation to lactate, which is what makes it worth being an anchor.
153siroheme_to_heme_bmetabolicSiroheme to heme bEncodes a complete alternative (Ahb) route from siroheme to heme b, through 12,18-didecarboxysiroheme and Fe-coproporphyrin III. A positive call means the siroheme-dependent heme-b-forming chemistry is encoded. It does not mean heme is made, available, incorporated into proteins, or used for respiration, and it is not the protoporphyrin- or coproporphyrin-dependent route, which is curated separately as heme_b_biosynthesis.anaboliccurated1The first capability in gifter that depends on the NCBIFAM namespace. Its refusal in database 2026.20.3 named exactly this retrigger: AhbA and AhbB are jointly required and KEGG assigns both to K22225, so the heterodimer could not be evidenced. NF040708.3 and NF040707.3 separate them and K22225 is admitted nowhere. Two minimal routes differ only in the terminal step, AhbD or the peroxide-dependent HemQ that heme_b_biosynthesis already curates.
154lpt_lipopolysaccharide_export_apparatusstructuralLpt lipopolysaccharide export apparatusEncodes one complete curated Lpt machine capable of extracting lipopolysaccharide from the inner membrane, conducting it across the periplasm and inserting it into the outer leaflet of the outer membrane. A positive call means the canonical LptA--G apparatus is encoded; it does not mean lipopolysaccharide is synthesized, expressed or transported in a sampled condition, and it makes no permeability, viability or other phenotypic claim.NULLcurated1The canonical architecture requires LptB/C/F/G, LptA and LptD/E. MsbA, BAM, LptM and YedD are outside this claim. LptC-bypass suppressors depend on residue-level LptF evidence that the accepted markers cannot resolve. An LptE-independent architecture reported in Neisseria meningitidis is not generalized to all LptD proteins and remains an explicit under-call until discriminating evidence can encode that biological context.
155ribitol_phosphate_wall_teichoic_acidstructuralPoly(ribitol-phosphate) wall teichoic acidEncodes one complete curated architecture for building a poly(ribitol-phosphate) wall teichoic acid backbone, exporting it and attaching it to peptidoglycan. A positive call means either the Staphylococcus-type TarF/TarL design or the Bacillus subtilis W23-type TarK/TarL design is encoded; it does not mean the polymer is expressed, decorated, abundant or assembled in a sampled condition, and it makes no resistance, virulence or other phenotypic claim.NULLcurated1Both architectures require UDP-ManNAc supply, TagO/TagA/TagB linkage-unit construction, TagD-dependent CDP-glycerol supply, TarI/TarJ-dependent CDP-ribitol supply, TagG/TagH export and an LCP-family attachment enzyme. They differ only at the chemistry-specific priming and elongation function. The Staphylococcus architecture requires equivalog-grade NCBIfam TarF and TarL evidence; the W23 architecture requires the separate TarK and TarL orthologies. Both were admitted below the standing prevalence threshold by an explicit biological-importance decision. The 168-type glycerol-phosphate architecture remains excluded because no admitted marker distinguishes its TagF polymerase from the W23 non-WTA homologue.
156diglucosyl_diacylglycerol_anchored_lipoteichoic_acidstructuralDiglucosyldiacylglycerol-anchored poly(glycerol-phosphate) lipoteichoic acidEncodes a complete curated architecture for synthesizing the diglucosyldiacylglycerol anchor, translocating it across the cytoplasmic membrane and polymerizing a membrane-anchored poly(glycerol-phosphate) lipoteichoic acid chain. A positive call means those three encoded functions are supported; it does not mean the polymer is expressed, decorated, abundant or assembled in a sampled condition, and it makes no envelope-integrity, antibiotic-susceptibility, virulence or other phenotypic claim.NULLcurated1The name is deliberately narrower than lipoteichoic acid or type I lipoteichoic acid. The architecture requires equivalog-grade NCBIfam evidence for the processive YpfP/UgtP-family diglucosyldiacylglycerol synthase, the LtaA anchor flippase and LtaS. K03429 and K19005 are not admitted: the first is retained only as a prevalence proxy and the second spans related glycerophosphotransferase chemistry and cannot resolve primase requirements. Residual diacylglycerol-anchored material after ypfP loss, the Listeria LtaP/LtaS design, Bacillus paralogues, non-type-I LTA and D-alanylation or glycosylation are outside the claim.
157type_vi_secretion_apparatusstructuralType VI secretion apparatusEncodes one complete curated type VI secretion apparatus: the TssL/TssM membrane complex, the TssE/F/G/K baseplate, the VgrG spike, the Hcp inner tube, the TssB/TssC contractile sheath, the TssA assembly coordinator and the ClpV sheath-recycling ATPase. A positive call means that machinery is encoded. It does not mean the apparatus is expressed or fires, it does not identify any effector, immunity protein or target, and it makes no claim of interbacterial antagonism, virulence or any other phenotype.NULLcurated1The single curated architecture is the canonical proteobacterial-type apparatus (T6SS-i). The Francisella-type (T6SS-ii) and Bacteroidota-type (T6SS-iii) apparatuses use divergent components that the accepted markers do not reach, and are explicit under-calls rather than negatives. The TssJ lipoprotein is recorded as an accessory function because reference genomes with an experimentally active apparatus carry no TssJ marker in either namespace. PAAR tip proteins, effectors, immunity proteins, adaptors and regulators are outside the claim. Completeness is evaluated over the unordered marker set, so the call does not assert that the components lie in one locus.
158type_iii_secretion_injectisomestructuralType III secretion injectisomeEncodes one complete curated non-flagellar type III secretion apparatus: the SctR/S/T/U/V export apparatus, the SctN export ATPase, the SctD/SctJ inner-membrane rings, the SctC outer-membrane secretin, the SctQ sorting-platform protein, the SctI inner rod and either a needle filament or an Hrp pilus. A positive call means that machinery is encoded. It does not mean the injectisome is expressed or assembled, it does not identify any translocon, effector or host, and it makes no claim of virulence, symbiosis or any other phenotype.NULLcurated1The injectisome is a separate GIFT from flagellar_apparatus: every accepted marker is specific to the non-flagellar system, so flagellar export evidence cannot support this call and injectisome evidence cannot support the flagellum. The SctL stator is biologically required and is deliberately not a required component, because no accepted marker reaches the Inv-Mxi-Spa and Esc families and requiring it would report an absent machine in Shigella and enteropathogenic Escherichia coli. Translocon and needle-tip proteins, gatekeepers, the needle-length ruler, pilotins, chaperones and effectors are outside the claim. Chlamydial and rhizobial injectisomes and Hrp pili without an accepted pilin marker are explicit under-calls. Completeness is evaluated over the unordered marker set, so the call does not assert that the components lie in one locus.
159archaellumstructuralArchaellum machineryEncodes the machinery required to assemble an archaellum, the rotary type IV filament motility structure of archaea: the archaellin filament subunit, a class III signal peptidase that processes it, the FlaF/FlaG stator complex, the FlaI motor ATPase with its FlaH regulator, and the FlaJ membrane platform. A positive call means the genome encodes that machinery. It does not mean the organism swims, that archaella are expressed or assembled, that they rotate in either direction, or that the cell performs taxis.NULLcurated1Gene names follow the fla designations that KEGG uses; the arl designations (ArlB, ArlF, ArlG, ArlH, ArlI, ArlJ, ArlK) were proposed in PMID 29912330. The FlaI (K07332) and FlaJ (K07333) orthologies also collect the ATPases and platforms of archaeal type IV pili and the bindosome: in the 470-archaeon frame only 268 of 885 K07332 proteins in archaellum-encoding genomes pass the FlaI equivalog, so both KOs are accepted at putative confidence and the specificity of the call rests on archaellin, FlaF, FlaG and FlaH. No combination of FlaI, FlaJ and the peptidase fires the GIFT. The euryarchaeal FlaC/D/E switch complex and the crenarchaeal FlaX ring are lineage-restricted and are curated as accessory functions; see inst/doc/proposal-structural-gifts.md section 6.1.
160type_ii_secretion_systemstructuralType II secretion systemEncodes one complete curated type II secretion apparatus: the GspD outer-membrane secretin, the GspC/F/L/M inner-membrane platform, the GspE secretion ATPase, the GspG/H/I/J/K pseudopilus and the class III prepilin peptidase that processes its pseudopilins. A positive call means that machinery is encoded. It does not identify any secreted substrate, and it does not mean the apparatus is expressed, assembled or secreting, nor that the organism degrades any polymer, colonises a host or is virulent.NULLcurated1The prepilin peptidase is a shared component, not a discriminator: one enzyme processes both type IVa pilins and type II pseudopilins, and KEGG files most of them under PilD (K02654) rather than GspO (K02464). It is therefore accepted on this GIFT and on type_iva_pilus, and it contributes no specificity to either; 1,319 of the 1,536 complete genomes in the reference frame reach the role through PilD alone. The apparatus is nonetheless distinguishable from the pilus by its other four functions: 703 frame genomes complete this architecture without completing the type IVa pilus. GspC is required although its markers are the weakest in the inventory, missing in 335 of the 504 genomes that are one function short; those misses are spread over 108 genera rather than blinding whole clades, so they under-call individual genomes rather than excluding a lineage. The GspS pilotin, GspN, GspAB and secreted substrates are outside the claim.
161serine_chemoreceptionregulatorySerine chemoreceptionEncodes a Tsr-family L-serine-responsive chemoreceptor connected to the CheA-CheW, CheY and CheR-CheB chemotaxis circuit. A positive call means this signalling machinery is encoded. It does not mean the cell swims toward serine or senses no other ligand.NULLcurated1The receptor requires the Tsr-specific NCBIfam equivalog NF011615.0; the broad KO K05874 is deliberately not accepted for the ligand-specific reception function. The downstream functions are shared with the existing chemotaxis circuits. See inst/doc/proposal-regulatory-defense-expansion.md.
162beta_lactam_detoxificationdefenseBeta-lactam detoxificationEncodes a beta-lactamase that hydrolyses the beta-lactam ring of at least one beta-lactam antibiotic. A positive call means the catalytic machinery is encoded; it does not establish which drug is hydrolysed, expression, localisation, or resistance to treatment.NULLcurated1One required hydrolysis function has four alternative Ambler-class systems. The 66 accepted KOs are enzyme-specific EC 3.5.2.6 groups, not the broader metallo-beta-lactamase fold. RHEA:20401 records the class-level chemistry. See inst/doc/proposal-antimicrobial-detoxification.md and inst/doc/proposal-regulatory-defense-expansion.md.
163chloramphenicol_detoxificationdefenseChloramphenicol detoxificationEncodes a chloramphenicol O-acetyltransferase that converts chloramphenicol to chloramphenicol 3-acetate using acetyl-CoA. A positive call means the catalytic machinery is encoded. It does not mean the organism withstands chloramphenicol exposure.NULLcurated1Type A and type B chloramphenicol acetyltransferases are alternative systems of the same RHEA:18421 chemistry. The type B KO is accepted only while its EC assignment remains specific to chloramphenicol. See inst/doc/proposal-antimicrobial-detoxification.md.
anchor156 rows · 8 columns
anchor_pkanchor_idmoleculecompartmentnamechebi_iddescriptionchebi_name
1PRPPPRPPunspecified5-phospho-alpha-D-ribose 1-diphosphateCHEBI:58017Input boundary for de novo nucleotide core biosynthesis.5-O-phosphonato-alpha-D-ribofuranosyl diphosphate(5-)
2IMPIMPunspecifiedinosine 5'-monophosphate(2-)CHEBI:58053Purine core boundary connecting core and branch biosynthesis GIFTs.IMP(2-)
3AMPAMPunspecifiedadenosine 5'-monophosphate(2-)CHEBI:456215Output boundary of adenylate biosynthesis.adenosine 5'-monophosphate(2-)
4GMPGMPunspecifiedguanosine 5'-monophosphate(2-)CHEBI:58115Output boundary that establishes guanylate identity before shared nucleotide phosphorylation.guanosine 5'-monophosphate(2-)
5GLUTAMINEGLUTAMINEunspecifiedL-glutamineCHEBI:58359Nitrogen-donor input boundary for de novo pyrimidine core biosynthesis.L-glutamine zwitterion
6UMPUMPunspecifieduridine 5'-monophosphate(2-)CHEBI:57865Output boundary of de novo pyrimidine core biosynthesis.uridine 5'-monophosphate(2-)
7UTPUTPunspecifieduridine 5'-triphosphate(4-)CHEBI:46398Stable uridine nucleotide input immediately before cytidylate-specific amination.UTP(4-)
8CTPCTPunspecifiedcytidine 5'-triphosphate(4-)CHEBI:37563Output boundary that establishes cytidylate identity.CTP(4-)
9PG3PG3unspecified(2R)-3-phosphoglycerateCHEBI:58272Glycolytic intermediate; the junction where carbon leaves central metabolism for serine biosynthesis.3-phosphonato-D-glycerate(3-)
10SERINESERINEunspecifiedL-serineCHEBI:33384Stable amino acid product and the precursor of glycine and of both cysteine biosynthesis GIFTs.L-serine zwitterion
11GLYCINEGLYCINEunspecifiedglycineCHEBI:57305Output boundary of glycine biosynthesis.glycine zwitterion
12CYSTEINECYSTEINEunspecifiedL-cysteineCHEBI:35235Stable amino acid product; also the sulfur-donor input boundary of transsulfuration.L-cysteine zwitterion
13SULFIDESULFIDEunspecifiedhydrogen sulfideCHEBI:29919Assimilable inorganic sulfur input boundary shared by sulfide-dependent cysteine and methionine biosynthesis.hydrosulfide
14ASPARTATEASPARTATEunspecifiedL-aspartateCHEBI:29991Central amino acid input boundary of the aspartate family.L-aspartate(1-)
15ASAASAunspecifiedL-aspartate 4-semialdehydeCHEBI:537519Branchpoint separating the lysine and diaminopimelate branch from the threonine and methionine branch.L-aspartic acid 4-semialdehyde zwitterion
16HOMOSERINEHOMOSERINEunspecifiedL-homoserineCHEBI:57476Branchpoint that commits aspartate carbon to threonine or to methionine.L-homoserine zwitterion
17THREONINETHREONINEunspecifiedL-threonineCHEBI:57926Output boundary of threonine biosynthesis.L-threonine zwitterion
18METHIONINEMETHIONINEunspecifiedL-methionineCHEBI:57844Output boundary of methionine biosynthesis.L-methionine zwitterion
19HOMOCYSTEINEHOMOCYSTEINEunspecifiedL-homocysteineCHEBI:58199Input-only sulfur-donor boundary supplied by methionine salvage. Never declared as an output anchor; see the acyclicity note in database_changes.L-homocysteine zwitterion
20FUCOSEFUCOSEunspecifiedL-fucoseCHEBI:2181Deoxyhexose of host mucin O-glycans and plant cell walls.L-fucopyranose
21RHAMNOSERHAMNOSEunspecifiedL-rhamnopyranoseCHEBI:62346Deoxyhexose of pectic rhamnogalacturonan.L-rhamnopyranose
22GALACTOSEGALACTOSEunspecifiedbeta-D-galactoseCHEBI:27667Hexose released from lactose, galactans and host glycans.beta-D-galactose
23GLCNACGLCNACunspecifiedN-acetyl-D-glucosamineCHEBI:506227Amino sugar of chitin, peptidoglycan and host glycans. Deliberately compartment-unspecified: it is released outside the cell by chitinases and mucinases and recovered inside it by peptidoglycan recycling, and the two curated entries into glcnac_degradation start on opposite sides of the membrane.N-acetyl-D-glucosamine
24NEUACNEUACunspecifiedaceneuramateCHEBI:173083Open form of N-acetylneuraminate (sialic acid), the terminal residue of host mucin O-glycans released by sialidases.aceneuramate
25GLUCURONATEGLUCURONATEunspecifiedD-glucuronateCHEBI:58720Uronic acid of glucuronoxylan and host glycosaminoglycans.D-glucopyranuronate
26GALACTURONATEGALACTURONATEunspecifiedaldehydo-D-galacturonateCHEBI:12952Uronic acid backbone residue of pectin.aldehydo-D-galacturonate
27XYLULOSE_5PXYLULOSE_5PunspecifiedD-xylulose 5-phosphateCHEBI:57737Pentose phosphate pathway entry point for pentose catabolism.D-xylulose 5-phosphate(2-)
28FRUCTOSE_6PFRUCTOSE_6Punspecifiedbeta-D-fructose 6-phosphateCHEBI:57634Glycolytic entry point for amino sugar catabolism.beta-D-fructofuranose 6-phosphate(2-)
29GLUCOSE_1PGLUCOSE_1Punspecifiedalpha-D-glucose 1-phosphateCHEBI:58601First stable product of the Leloir pathway, before shared phosphoglucomutase chemistry.alpha-D-glucose 1-phosphate(2-)
30DHAPDHAPunspecifieddihydroxyacetone phosphateCHEBI:57642Glycolytic entry point for deoxyhexose catabolism.glycerone phosphate(2-)
31LACTALDEHYDELACTALDEHYDEunspecified(S)-lactaldehydeCHEBI:18041Co-product of deoxyhexose aldol cleavage.(S)-lactaldehyde
32PYRUVATEPYRUVATEunspecifiedpyruvateCHEBI:15361Central carbon entry point.pyruvate
33GAPGAPunspecifiedD-glyceraldehyde 3-phosphateCHEBI:59776Glycolytic entry point; distinct from the PG3 anchor of serine biosynthesis.D-glyceraldehyde 3-phosphate(2-)
34XYLOSE_EXXYLOSEextracellularD-xyloseCHEBI:53455Pentose released by xylan saccharification, outside the cell.D-xylopyranose
35XYLOSE_INXYLOSEcytoplasmicD-xyloseCHEBI:53455D-xylose in the cytoplasm, where isomerase-dependent catabolism begins.D-xylopyranose
36ARABINOSE_EXARABINOSEextracellularL-arabinoseCHEBI:17535Pentose released from arabinan and arabinoxylan side chains, outside the cell.L-arabinopyranose
37ARABINOSE_INARABINOSEcytoplasmicL-arabinoseCHEBI:17535L-arabinose in the cytoplasm, where catabolism begins.L-arabinopyranose
38ARABINOXYLANARABINOXYLANextracellulararabinoxylanNULLArabinose-decorated xylan of cereal and grass cell walls; the dominant hemicellulose of a plant-based diet. A substrate class rather than a single compound.NULL
39XYLANXYLANextracellularxylanCHEBI:37166Beta-1,4-linked xylose backbone remaining after side-chain removal. A substrate class rather than a single compound.xylan
40STARCHSTARCHextracellularstarchCHEBI:28017Alpha-glucan storage polysaccharide of plants, and the major digestible carbohydrate of most diets.starch
41GLUCOSEGLUCOSEunspecifiedD-glucoseCHEBI:4167Hexose released by alpha-glucosidase. Compartment unresolved: glucose is moved mainly by promiscuous carriers, so no uptake GIFT licenses a split.D-glucopyranose
42COLLAGENCOLLAGENextracellularcollagenNULLFibrillar triple-helical structural protein of animal extracellular matrix, and the most abundant protein of animal tissue. A substrate class rather than a single compound: it has no balanced-equation identity and Rhea represents it as the polymer [collagen].NULL
43COLLAGEN_PEPTIDESCOLLAGEN_PEPTIDESextracellularcollagen peptidesNULLHeterogeneous peptides released by cleavage of the collagen triple helix. Deliberately substrate-specific rather than a shared peptide pool, so that protein-degradation GIFTs do not connect through an undefined intermediate; see inst/doc/proposal-protein-degradation.md.NULL
44ACETYL_COAACETYL_COAcytoplasmicacetyl-CoACHEBI:57288Cytoplasmic acyl-CoA branchpoint where sugar, amino acid and fatty acid carbon converge. Declared as a boundary only for the GIFTs listed in gift_anchors; reactions elsewhere that consume acetyl-CoA internally do not gain an edge from it, because gifter derives composition from declared anchors and never from shared reaction participants.acetyl-CoA(4-)
45ACETATEACETATEunspecifiedacetateCHEBI:30089Two-carbon fermentation end product, and the CoA acceptor consumed by the butyryl-CoA:acetate CoA-transferase route. Compartment unresolved: no SCFA transport GIFT is evidenceable, so the extracellular claim that cross-feeding would need is deliberately not made.acetate
46BUTYRATEBUTYRATEunspecifiedbutanoateCHEBI:17968Four-carbon fermentation end product of the acetyl-CoA condensation route. Compartment unresolved, as for acetate.butyrate
47PROPIONATEPROPIONATEunspecifiedpropanoateCHEBI:17272Three-carbon fermentation end product reached by two curated routes with different inputs. Compartment unresolved, as for acetate.propionate
48PROPANEDIOLPROPANEDIOLunspecified(S)-propane-1,2-diolCHEBI:29002Reduced product of deoxyhexose aldol cleavage and the input of the propanediol route to propionate. Stereochemistry follows the (S)-lactaldehyde anchor it comes from; the dehydratase reaction RHEA:14569 is stereochemically unspecified in Rhea and is therefore stated at lower specificity than this boundary.(S)-propane-1,2-diol
49LACTATELACTATEunspecified(R)-lactateCHEBI:16004Input-only boundary of the acrylate route to propionate. Never declared as an output anchor: lactate formation is out of scope for this layer, so nothing in gifter produces it and the acyclicity argument is the one already recorded for L-homocysteine.(R)-lactate
50LACTATE_LLACTATE_Lunspecified(S)-lactateCHEBI:16651L-lactate, the enantiomer formed by the NAD-dependent L-lactate dehydrogenase of fermentative Bacillota and Actinomycetota. Declared as a separate anchor from the existing (R)-lactate rather than as a compartment variant of it, because the two are different molecules: the acrylate route to propanoate accepts only the (R) form, and the enzymes that form the two enantiomers are unrelated.(S)-lactate
51MALATEMALATEunspecified(S)-malateCHEBI:15589Central-carbon boundary produced by the glyoxylate bypass and consumed by malolactic fermentation. It remains internal to fumarate_oxaloacetate_interconversion, so that reaction participant creates no additional edge.(S)-malate(2-)
52CITRATECITRATEunspecifiedcitrateCHEBI:16947Input-only boundary of citrate fermentation. Declared unspecified rather than extracellular because no curated transport GIFT licenses a compartment split; the CitT carrier of the Enterobacteriaceae and the plasmid-borne CitP permease of the lactic acid bacteria are unrelated proteins and neither is curated.citrate(3-)
53ETHANOLETHANOLunspecifiedethanolCHEBI:16236Neutral fermentation end product of the bifunctional acetaldehyde/alcohol dehydrogenase route from acetyl-CoA.ethanol
54ACETOINACETOINunspecified(R)-acetoinCHEBI:15686Neutral fermentation end product of the acetolactate route from pyruvate, and the boundary the trait is named for. Butane-2,3-diol is one step further and is not curated: its dehydrogenase group K00004 is broad and is absent from several genomes that carry the acetolactate decarboxylase, so acetoin is where the evidence stops.(R)-acetoin
55GTPGTPunspecifiedGTPCHEBI:37565Purine nucleotide that supplies the pyrimidinedione ring of riboflavin and the pterin ring of folate. Input-only: guanylate biosynthesis is curated to GMP, and the phosphorylation between them is shared metabolism gifter does not curate.GTP(4-)
56RIBULOSE_5PRIBULOSE_5PunspecifiedD-ribulose 5-phosphateCHEBI:58121Pentose phosphate intermediate that supplies the four-carbon unit of the riboflavin xylene ring.D-ribulose 5-phosphate(2-)
57RIBOFLAVINRIBOFLAVINunspecifiedriboflavinCHEBI:57986Vitamin B2, and the boundary at which flavin identity is established. The kinase and adenylyltransferase that make FMN and FAD from it are shared housekeeping and are not curated.riboflavin(1-)
58CHORISMATECHORISMATEunspecifiedchorismateCHEBI:29748Aromatic branchpoint that leaves shikimate metabolism for 4-aminobenzoate and for menaquinone.chorismate(2-)
59PABAPABAunspecified4-aminobenzoateCHEBI:17836Vitamin-adjacent boundary metabolite: the aromatic half of folate, separately synthesised, separately auxotrophic, and separately salvaged.4-aminobenzoate
60THFTHFunspecified(6S)-5,6,7,8-tetrahydrofolateCHEBI:57453Vitamin B9 in the reduced form that carries one-carbon units. Output boundary of folate biosynthesis.(6S)-5,6,7,8-tetrahydrofolate(2-)
61AIRAIRunspecified5-amino-1-(5-phospho-beta-D-ribosyl)imidazoleCHEBI:137981Purine pathway intermediate that ThiC rearranges into the thiamine pyrimidine. Declared here as an input boundary only; it is never an output anchor, so it creates no edge from purine biosynthesis.5-amino-1-(5-phosphonato-beta-D-ribosyl)imidazol-3-ium
62DXPDXPunspecified1-deoxy-D-xylulose 5-phosphateCHEBI:57792Isoprenoid and thiamine precursor supplying the thiazole carbon skeleton and, in the DXP-dependent route, the pyridoxine ring.1-deoxy-D-xylulose 5-phosphate(2-)
63HMP_PPHMP_PPunspecified4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidineCHEBI:57841Activated thiamine pyrimidine moiety; the branchpoint where de novo synthesis and precursor salvage converge.4-amino-2-methyl-5-diphosphonatooxymethylpyrimidine(3-)
64THZ_PTHZ_Punspecified4-methyl-5-(2-phosphooxyethyl)-thiazoleCHEBI:58296Activated thiamine thiazole moiety; the second convergence point of de novo synthesis and salvage.4-methyl-5-(2-phosphonatooxyethyl)thiazole(2-)
65TMPTMPunspecifiedthiamine phosphateCHEBI:37575Vitamin B1 as the phosphate ester. The boundary stops here rather than at thiamine diphosphate because the ThiL kinase is unevenly annotated and its absence is an annotation gap rather than an auxotrophy.thiamine(1+) monophosphate(2-)
66HMPHMPunspecified4-amino-5-hydroxymethyl-2-methylpyrimidineCHEBI:16892Free thiamine pyrimidine, acquired from the environment and phosphorylated by salvage.4-amino-5-hydroxymethyl-2-methylpyrimidine
67HETHETunspecified5-(2-hydroxyethyl)-4-methylthiazoleCHEBI:17957Free thiamine thiazole, acquired from the environment and phosphorylated by salvage.5-(2-hydroxyethyl)-4-methylthiazole
68OXOISOVALERATEOXOISOVALERATEunspecified3-methyl-2-oxobutanoateCHEBI:11851Branched-chain 2-oxo acid shared with valine biosynthesis; the carbon skeleton of pantoate.3-methyl-2-oxobutanoate
69PANTOTHENATEPANTOTHENATEunspecified(R)-pantothenateCHEBI:29032Vitamin B5. The boundary stops here: the five steps that convert it to coenzyme A are shared housekeeping.(R)-pantothenate
70RIBOSE_5PRIBOSE_5PunspecifiedD-ribose 5-phosphateCHEBI:78679Pentose phosphate intermediate; the ring precursor of the DXP-independent route to pyridoxal 5-phosphate.D-ribose 5-phosphate
71E4PE4PunspecifiedD-erythrose 4-phosphateCHEBI:16897Pentose phosphate intermediate; the entry point of the DXP-dependent route to pyridoxal 5-phosphate.D-erythrose 4-phosphate(2-)
72PLPPLPunspecifiedpyridoxal 5'-phosphateCHEBI:597326Vitamin B6 in its catalytically active form, which is also the product of both biosynthetic routes, so no separate activation step exists to exclude.pyridoxal 5'-phosphate(2-)
73PIMELOYL_COAPIMELOYL_COAcytoplasmicpimeloyl-CoACHEBI:57360Cytoplasmic seven-carbon dicarboxylic thioester that supplies the biotin valeric acid side chain. The marker layer does not distinguish it from the acyl-carrier-protein thioester used by the BioC/BioH route, so the anchor names the CoA form and the claim covers both; both carriers are intracellular in the curated routes.pimeloyl-CoA(5-)
74BIOTINBIOTINunspecifiedbiotinCHEBI:57586Vitamin B7, the carboxyl carrier cofactor of acetyl-CoA and pyruvate carboxylases.biotinate
75QUINOLINATEQUINOLINATEunspecifiedquinolinateCHEBI:29959Committed pyridine precursor of NAD, and the point at which de novo synthesis is separated from salvage.quinolinate(2-)
76NAMNNAMNunspecifiednicotinate D-ribonucleotideCHEBI:57502Nicotinate mononucleotide: the junction where de novo quinolinate chemistry, nicotinate salvage and cobamide lower-ligand attachment all meet.nicotinate D-ribonucleotide(2-)
77NADNADunspecifiedNAD(+)CHEBI:57540Nicotinamide adenine dinucleotide, the product that makes a genome independent of exogenous niacin.NAD(1-)
78NICOTINATENICOTINATEunspecifiednicotinateCHEBI:32544Vitamin B3 as acquired from the environment; the input boundary of pyridine salvage.nicotinate
79UROGEN_IIIUROGEN_IIIunspecifieduroporphyrinogen IIICHEBI:57308Tetrapyrrole branchpoint. Heme, siroheme and the corrin ring all leave shared metabolism here, which is why the cobalamin claim starts at this molecule and not earlier.uroporphyrinogen III(8-)
80COBYRINATE_DIAMIDECOBYRINATE_DIAMIDEunspecifiedcob(II)yrinate a,c diamideCHEBI:58537Completed, cobalt-loaded corrin ring. Both the aerobic and the anaerobic ring routes converge here, and everything after it is shared by de novo synthesis and corrinoid salvage.cob(II)yrinic acid a,c diamide(4-)
81ADENOSYLCOBINAMIDE_PADENOSYLCOBINAMIDE_Punspecifiedadenosylcobinamide phosphateCHEBI:58502Adenosylated corrinoid carrying its aminopropanol arm, ready for lower-ligand attachment. This is the molecule a corrinoid salvager imports and remodels.adenosylcobinamide phosphate(1-)
82DMBDMBunspecified5,6-dimethylbenzimidazoleCHEBI:15890The lower ligand that makes a cobamide into vitamin B12. A genome that assembles the nucleotide loop without it makes a different cobamide, which is not the vitamin.5,6-dimethylbenzimidazole
83COBALAMINCOBALAMINunspecifiedadenosylcobalaminCHEBI:18408Vitamin B12 in its coenzyme form, complete with the dimethylbenzimidazole lower ligand.cobamamide
84MENAQUINONEMENAQUINONEunspecifiedmenaquinoneCHEBI:16374Vitamin K2. The terminal curated reaction is written on the quinol couple, as Rhea writes it; the anchor names the vitamin.menaquinone
85FMNH2FMNH2unspecifiedFMNH2CHEBI:57618Reduced flavin mononucleotide, consumed rather than recycled by BluB, which dismantles it to build the benzimidazole ring. Declared input-only: it is the one cofactor in this layer that a reaction destroys.FMNH2(2-)
86OXALOACETATEOXALOACETATEunspecifiedoxaloacetateCHEBI:16452Four-carbon junction connecting citric acid cycle chemistry, anaplerosis, gluconeogenesis and the aspartate family. Declared as both an input and an output of the cycle segments because the ring closes through it.oxaloacetate(2-)
87OXOGLUTARATEOXOGLUTARATEunspecified2-oxoglutarateCHEBI:16810The largest carbon-nitrogen junction in bacterial metabolism: the ammonium acceptor of glutamate synthesis and, through glutamate, the amino donor of most transaminations.2-oxoglutarate(2-)
88SUCCINATESUCCINATEunspecifiedsuccinateCHEBI:30031Boundary of citric acid cycle chemistry, of the Wood-Werkman route to propionate and of tetrapyrrole synthesis through succinyl-CoA. gifter makes no claim that a genome releases succinate; that trait is refused in inst/doc/proposal-organic-acid-formation.md section 6.4.succinate(2-)
89FUMARATEFUMARATEunspecifiedfumarateCHEBI:29806Oxidised partner of the succinate/fumarate couple. gifter models no electron acceptors, so this anchor supports no fumarate respiration claim, and it is deliberately not attached to the purine or pyrimidine GIFTs whose routes involve fumarate as a co-product.fumarate(2-)
90PEPPEPunspecifiedphosphoenolpyruvateCHEBI:58702Glycolytic intermediate and the C3 donor of the shikimate pathway, consumed twice: once by the DAHP synthase condensation with erythrose 4-phosphate and once by the EPSP synthase transfer. Declared as an input boundary only; nothing in gifter produces it yet.phosphonatoenolpyruvate
91SALICYLATESALICYLATEunspecifiedsalicylateCHEBI:307622-hydroxybenzoate. In bacteria it is a chorismate-derived siderophore building block, incorporated into pyochelin, yersiniabactin and mycobactin; in plants it is a defence hormone. The anchor names the free acid, which is where the curated chemistry stops: the salicyl-AMP ligase that commits it to a siderophore is a separate capability.salicylate
92TRYPTOPHANTRYPTOPHANunspecifiedL-tryptophanCHEBI:57912Aromatic amino acid and a branchpoint in its own right: the precursor of indole-3-acetate, of indole, of the kynurenines and of tryptophan-derived alkaloids, as well as a protein building block. Declared so that indole-3-acetate biosynthesis is not bundled with aromatic amino acid biosynthesis.L-tryptophan zwitterion
93INDOLE_3_ACETATEINDOLE_3_ACETATEunspecified(indol-3-yl)acetateCHEBI:30854The auxin. Bacterial production is a plant-interaction trait rather than a growth requirement, and the anchor is the free acid; conjugation to amino acids or sugars is not curated.indole-3-acetate
94AMMONIUMAMMONIUMunspecifiedammoniumCHEBI:28938Convergence point of every nitrogen-liberating capability and the entry point of assimilation. Declared under the nitrogen-anchor rule: ammonium is an anchor only where a reaction exists to liberate or assimilate it, never where it is a leaving group of chemistry aimed at something else. Three of the four curated reactions that mention it are therefore excluded; see database_changes.ammonium
95NITRATENITRATEunspecifiednitrateCHEBI:17632Environmental inorganic nitrogen source. Input-only, and deliberately compartment-unresolved: the specific NrtABCD importer covers 1582 genomes but the commoner NarK/NRT2 carrier is shared with nitrite and with respiratory contexts, so no transporter licenses a split. Supports no nitrate respiration claim; gifter models no electron acceptors.nitrate
96UREAUREAunspecifiedureaCHEBI:16199Host- and diet-derived nitrogen source, and independently the product of allantoin and creatinine degradation. The layer's clearest shared boundary. Compartment unresolved: three unrelated transport mechanisms carry it, two of them passive channels, and urea also arises intracellularly.urea
97URATEURATEunspecifiedurateCHEBI:17775Host purine end product and the entry point of ureide catabolism. This is the species RHEA:21368 itself uses, although ChEBI displays it under its systematic name.7,9-dihydro-1H-purine-2,6,8(3H)-trione
98ALLANTOINALLANTOINunspecified(S)-allantoinCHEBI:15678Branchpoint of purine nitrogen catabolism: released by urate degraders and consumed by the 774 genomes that degrade it while carrying no uricase of any kind. The clearest cross-feeding boundary in the database outside sugars.(S)-(+)-allantoin
99GLYOXYLATEGLYOXYLATEunspecifiedglyoxylateCHEBI:36655Carbon fate of allantoin degradation. It remains an output-only boundary: the glyoxylate bypass produces and consumes glyoxylate internally, so declaring an input edge would misstate the boundary of that complete route.glyoxylate
100SARCOSINESARCOSINEunspecifiedsarcosineCHEBI:57433Convergence point of betaine and creatinine catabolism, and the reason both are cut here. Its own demethylation is commoner than either upstream capability, so curating betaine-to-glycine and creatinine-to-glycine separately would duplicate the same reaction in two GIFTs.sarcosine zwitterion
101BETAINEBETAINEunspecifiedglycine betaineCHEBI:17750Diet- and host-derived osmolyte, and the product of carnitine catabolism through the betainyl-CoA route. Declared as both an input and an output boundary of different GIFTs, which is what makes carnitine reach glycine by composition.glycine betaine
102CARNITINECARNITINEunspecified(R)-carnitineCHEBI:16347Animal-tissue- and host-derived quaternary amine. Two curated capabilities consume it and they release different products, which is why they are separate GIFTs rather than two routes of one.(R)-carnitine
103CREATININECREATININEunspecifiedcreatinineCHEBI:16737Host muscle metabolite. Input-only.creatinine
104TRIMETHYLAMINETRIMETHYLAMINEunspecifiedtrimethylammoniumCHEBI:58389Released product that the producing organism does not use and that the host converts to trimethylamine N-oxide. Output-only. A positive call means the chemistry is encoded, not that trimethylamine is produced, released, or reaches a host.trimethylammonium
105METHYLAMINEMETHYLAMINEunspecifiedmethylammoniumCHEBI:59338Environmental and microbially derived methylated amine. Input-only.methylammonium
106TAURINE_EXTAURINEextracellulartaurineCHEBI:507393Host-derived aminosulfonate, released outside the cell by bile-salt hydrolases acting on taurine-conjugated bile acids. Split from the cytoplasmic form because TauABC is a specific and complete ABC importer, the same licence used for xylose and arabinose.taurine zwitterion
107TAURINE_INTAURINEcytoplasmictaurineCHEBI:507393Taurine in the cytoplasm, where both curated desulfonation capabilities begin.taurine zwitterion
108SULFITESULFITEunspecifiedsulfiteCHEBI:17359Product boundary of taurine desulfonation. Assimilatory sulfate reduction passes through sulfite internally on its way to sulfide; dissimilatory sulfite reduction remains outside this GIFT.sulfite
109GLUTAMATEGLUTAMATEunspecifiedL-glutamateCHEBI:29985The nitrogen a cell can actually build with, and the sink that keeps ammonium from being a terminal boundary. Declared for ammonium assimilation only; glutamate metabolism generally is not curated, and reactions elsewhere that consume it internally gain no edge from it.L-glutamate(1-)
110BENZOATEBENZOATEunspecifiedbenzoateCHEBI:16150Aromatic monocarboxylate. A plant secondary metabolite and a food preservative, and the compound most aerobic peripheral aromatic routes converge on before the ring is opened.benzoate
111CATECHOLCATECHOLunspecifiedcatecholCHEBI:18135The dihydroxylated ring that aerobic ring cleavage acts on. Several peripheral routes converge here, which is why it is a boundary rather than an internal intermediate.catechol
112OXOADIPATEOXOADIPATEunspecified3-oxoadipateCHEBI:15775Product of ortho ring cleavage and lactone hydrolysis. It is no longer aromatic, and it exists only because a ring was opened.3-oxoadipate(2-)
113OXOADIPYL_COAOXOADIPYL_COAcytoplasmic3-oxoadipyl-CoACHEBI:57348Cytoplasmic CoA thioester where the ortho-cleavage funnel and the aerobic phenylacetate route meet, one thiolysis short of central metabolism.3-oxoadipyl-CoA(5-)
114OXOPENTENOATEOXOPENTENOATEunspecified2-oxopent-4-enoateCHEBI:11641Product of meta ring cleavage and of extradiol cleavage of dihydroxyphenylpropanoate. Rhea writes the downstream hydratase on the enol tautomer, (2Z)-2-hydroxypenta-2,4-dienoate; the anchor is the molecule, not one tautomer.2-oxopent-4-enoate
115SUCCINYL_COASUCCINYL_COAcytoplasmicsuccinyl-CoACHEBI:57292Cytoplasmic central acyl-CoA metabolite. Introduced here as the exit of the aromatic funnel, and available to the citric acid cycle segments if they are ever cut at this node.succinyl-CoA(5-)
116PHENYLACETATEPHENYLACETATEunspecifiedphenylacetateCHEBI:18401Product of phenylalanine fermentation and a substrate for aerobic CoA-dependent ring degradation.phenylacetate
117PHENYLPROPANOATEPHENYLPROPANOATEunspecified3-phenylpropanoateCHEBI:51057Dietary phenylpropanoid, also produced by gut fermentation of plant polyphenols. trans-Cinnamate is the same enzyme's other substrate and is deliberately not a separate anchor; see the GIFT description.3-phenylpropionate
118HPPHPPunspecified3-(3-hydroxyphenyl)propanoateCHEBI:57277Meta-hydroxylated phenylpropanoid, the second entry into the same ring-cleavage node.3-(3-hydroxyphenyl)propanoate
119DHPPDHPPunspecified3-(2,3-dihydroxyphenyl)propanoateCHEBI:46951Catecholic phenylpropanoid where the two entry routes converge, and the substrate of extradiol cleavage.3-(2,3-dihydroxyphenyl)propanoate
120ANTHRANILATEANTHRANILATEunspecifiedanthranilateCHEBI:165672-Aminobenzoate. A tryptophan catabolite of both host and microbial kynurenine metabolism, and a peripheral entry into the catechol node.anthranilate
121PHENOLPHENOLunspecifiedphenolCHEBI:15882Product of microbial tyrosine fermentation and an industrial compound; hydroxylated to catechol in one step.phenol
122ALANINEALANINEunspecifiedL-alanineCHEBI:57972Stable amino acid product of pyruvate transamination or reductive amination.L-alanine zwitterion
123ASPARAGINEASPARAGINEunspecifiedL-asparagineCHEBI:58048Stable amino acid product; the amidated form of aspartate.L-asparagine zwitterion
124MESO_DAPMESO_DAPunspecifiedmeso-2,6-diaminopimelateCHEBI:57791Branchpoint where the four diaminopimelate routes converge. It is both the immediate lysine precursor and the peptidoglycan cross-link residue of most Gram-negative and many Gram-positive walls, which is why the layer cuts here rather than at lysine.meso-2,6-diaminopimelic acid dizwitterion
125LYSINELYSINEunspecifiedL-lysineCHEBI:32551Stable amino acid product of diaminopimelate decarboxylation.L-lysinium(1+)
126OXOBUTANOATEOXOBUTANOATEunspecified2-oxobutanoateCHEBI:16763Branchpoint 2-oxo acid that commits carbon to isoleucine. Reached by threonine deamination or by the citramalate route, and released again by methionine gamma-lyase, so it is the point where three otherwise unrelated capabilities meet.2-oxobutanoate
127VALINEVALINEunspecifiedL-valineCHEBI:57762Stable amino acid product of branched-chain transamination.L-valine zwitterion
128LEUCINELEUCINEunspecifiedL-leucineCHEBI:57427Stable amino acid product of the isopropylmalate chain extension.L-leucine zwitterion
129ISOLEUCINEISOLEUCINEunspecifiedL-isoleucineCHEBI:58045Stable amino acid product of the isoleucine branch of the acetohydroxyacid pathway.L-isoleucine zwitterion
130PHENYLALANINEPHENYLALANINEunspecifiedL-phenylalanineCHEBI:58095Stable aromatic amino acid product of the prephenate dehydratase branch.L-phenylalanine zwitterion
131TYROSINETYROSINEunspecifiedL-tyrosineCHEBI:58315Stable aromatic amino acid product of the prephenate dehydrogenase branch.L-tyrosine zwitterion
132HISTIDINEHISTIDINEunspecifiedL-histidineCHEBI:57595Stable amino acid product of the ten-step pathway from PRPP.L-histidine zwitterion
133PROLINEPROLINEunspecifiedL-prolineCHEBI:60039Stable amino acid product of glutamate cyclisation and reduction; also the substrate of Stickland proline reduction.L-proline zwitterion
134ORNITHINEORNITHINEunspecifiedL-ornithineCHEBI:46911Branchpoint of the glutamate family: the arginine precursor, the product of the arginine deiminase pathway, and the polyamine precursor. Declared with an unspecified compartment; the arginine/ornithine antiporter makes it a compartment-split candidate once transport is curated.L-ornithinium(1+)
135ARGININEARGININEunspecifiedL-arginineCHEBI:32682Stable amino acid product, and the substrate of the arginine deiminase pathway.L-argininium(1+)
136GABAGABAunspecified4-aminobutanoateCHEBI:59888Decarboxylation product of glutamate; a fermentable substrate for other community members and a neuroactive compound in the host gut.gamma-aminobutyric acid zwitterion
137INDOLEINDOLEunspecifiedindoleCHEBI:16881Released tryptophan catabolite. It is an aryl hydrocarbon receptor ligand and an interspecies signal, and it is the molecule the classical clinical indole test detects.1H-indole
138METHANETHIOLMETHANETHIOLunspecifiedmethanethiolCHEBI:16007Released volatile sulfur compound of methionine catabolism.methanethiol
139ACETYL_PHOSPHATEACETYL_PHOSPHATEunspecifiedacetyl phosphateCHEBI:22191Sole product of the Stickland glycine reduction and the phosphate donor of substrate-level ATP synthesis. Declared as a boundary because a metabolic GIFT must state one and glycine reductase has no other product; acetate interconversion continues to hold the same molecule internally, so the two do not connect until that GIFT is re-cut.acetyl phosphate(2-)
140AMINOPENTANOATEAMINOPENTANOATEunspecified5-aminopentanoateCHEBI:356010Released end product of Stickland proline reduction.5-aminopentanoic acid zwitterion
141ISOCITRATEISOCITRATEunspecifiedD-threo-isocitrateCHEBI:15562Central branchpoint exposed so the oxidative decarboxylation and glyoxylate bypass are separately composable without duplicating citrate synthase and aconitase.D-threo-isocitrate(3-)
142NITROGENNITROGENunspecifieddinitrogenCHEBI:17997Atmospheric dinitrogen at the boundary of nitrogen fixation. The unspecified compartment records no localisation or environmental availability claim.dinitrogen
143SULFATESULFATEunspecifiedsulfateCHEBI:16189Inorganic sulfur source at the boundary of assimilatory sulfate reduction. The unspecified compartment records no uptake claim.sulfate
144ECTOINEECTOINEunspecifiedL-ectoineCHEBI:58515Compatible-solute product of the EctABC route. Declaring it as an output does not claim accumulation, export or osmotic protection.ectoine zwitterion
145HEME_BHEME_Bunspecifiedheme bCHEBI:60344Iron porphyrin product at the end of the protoporphyrin and coproporphyrin route families. It is distinct from siroheme and downstream heme derivatives.ferroheme b(2-)
146DIHYDROXYBENZOATE_2_3DIHYDROXYBENZOATE_2_3unspecified2,3-dihydroxybenzoateCHEBI:36654Catecholate branchpoint between chorismate-derived head synthesis and enterobactin or other siderophore assembly.2,3-dihydroxybenzoate
147ENTEROBACTINENTEROBACTINunspecifiedenterobactinCHEBI:77805Cyclic catecholate siderophore product. The boundary does not assert secretion, metal binding in situ or uptake.enterobactin(1-)
148CHOLINECHOLINEunspecifiedcholineCHEBI:15354Quaternary ammonium precursor of glycine betaine. The unspecified compartment records no uptake or environmental-availability claim.choline
149SIROHEMESIROHEMEunspecifiedsirohemeCHEBI:60052Iron isobacteriochlorin cofactor and branchpoint product of siroheme biosynthesis. Declaring it does not imply cofactor incorporation, reductase activity, sulfur or nitrogen metabolism, or conversion through the alternative heme pathway.siroheme(8-)
150CHITINCHITINextracellularchitinCHEBI:17029Beta-1,4-linked N-acetyl-D-glucosamine polymer of arthropod and fungal cell walls, reaching the gut in dietary and microbial biomass.chitin
151MUCIN_O_GLYCANMUCIN_O_GLYCANextracellularmucin O-glycanNULLThe O-linked glycan of secreted host mucins, a heterogeneous branched structure with no single repeating unit and no chemical formula.NULL
152GALNACGALNACunspecifiedN-acetyl-D-galactosamineCHEBI:28037N-acetyl-D-galactosamine, the sugar alpha-linked to serine or threonine at the mucin O-glycan core.N-acetyl-D-galactosamine
153PECTINPECTINextracellularpectinCHEBI:17309Methyl-esterified alpha-1,4-D-galacturonan of the plant primary cell wall, the dominant soluble fibre of fruit and vegetable matter.pectin
154KDGKDGunspecified2-dehydro-3-deoxy-D-gluconateCHEBI:57990Entner-Doudoroff branchpoint. Galacturonate catabolism, glucuronate catabolism and the pectate lyase route all converge here, and the phosphorylation and aldol cleavage that follow are shared by all three.2-dehydro-3-deoxy-D-gluconate
155DABADABAunspecifiedL-2,4-diaminobutanoateCHEBI:58761End of ectoine-specific chemistry in the degradative direction, and the branchpoint ectoine biosynthesis passes through in the other. Declared as the output boundary of ectoine degradation; what consumes it is not yet curated, because the transamination that follows is the same reaction ectoine biosynthesis runs in reverse.L-2,4-diazaniumylbutyrate
156HYDROXYECTOINEHYDROXYECTOINEunspecified5-hydroxyectoineCHEBI:85413Product boundary of ectoine hydroxylation. A distinct compatible solute rather than a modified form of ectoine: it is retained and released under different conditions, and only some ectoine producers encode it.5-hydroxyectoine zwitterion
gift_anchor344 rows · 4 columns
gift_pkanchor_pkroleordinal
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22input1
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45input1
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gift_xref214 rows · 6 columns
gift_pknamespaceaccessionnamerelationnotes
1KEGG_MODULEM00048De novo purine biosynthesis, PRPP + glutamine => IMPequivalentSame boundaries; gifter materialises the eight alternative minimal routes that the module expresses compactly.
1KEGG_PATHWAYmap00230Purine metabolismsubset_ofNULL
2KEGG_MODULEM00049Adenine ribonucleotide biosynthesis, IMP => ADP,ATPsubset_ofgifter stops at AMP; the shared nucleotide phosphorylation that the module continues through is excluded.
2KEGG_PATHWAYmap00230Purine metabolismsubset_ofNULL
3KEGG_MODULEM00050Guanine ribonucleotide biosynthesis, IMP => GDP,GTPsubset_ofgifter stops at GMP; the shared nucleotide phosphorylation that the module continues through is excluded.
3KEGG_PATHWAYmap00230Purine metabolismsubset_ofNULL
4KEGG_MODULEM00051De novo pyrimidine biosynthesis, glutamine (+ PRPP) => UMPequivalentSame boundaries; the three dihydroorotate oxidation chemistries are separate routes rather than one step.
4KEGG_PATHWAYmap00240Pyrimidine metabolismsubset_ofNULL
5KEGG_MODULEM00052Pyrimidine ribonucleotide biosynthesis, UMP => UDP/UTP,CDP/CTPsubset_ofgifter curates only the CTP synthase reaction; shared UMP and UDP phosphorylation are excluded.
5KEGG_PATHWAYmap00240Pyrimidine metabolismsubset_ofNULL
6KEGG_MODULEM00020Serine biosynthesis, glycerate-3P => serineequivalentModule boundaries retained unchanged.
6KEGG_PATHWAYmap00260Glycine, serine and threonine metabolismsubset_ofNULL
6KEGG_PATHWAYmap01230Biosynthesis of amino acidssubset_ofNULL
7KEGG_PATHWAYmap00260Glycine, serine and threonine metabolismsubset_ofNo KEGG module covers serine to glycine.
7KEGG_PATHWAYmap01230Biosynthesis of amino acidssubset_ofNULL
8KEGG_MODULEM00018Threonine biosynthesis, aspartate => homoserine => threoninesubset_ofShared head of the module, cut out so it is curated once.
8KEGG_MODULEM00017Methionine biosynthesis, aspartate => homoserine => methioninesubset_ofShared head of the module, cut out so it is curated once.
8KEGG_MODULEM00016Lysine biosynthesis, succinyl-DAP pathway, aspartate => lysinesubset_ofThe semialdehyde anchor is where the lysine and diaminopimelate branch leaves the aspartate family.
8KEGG_PATHWAYmap00260Glycine, serine and threonine metabolismsubset_ofNULL
8KEGG_PATHWAYmap00300Lysine biosynthesissubset_ofNULL
9KEGG_MODULEM00018Threonine biosynthesis, aspartate => homoserine => threoninesubset_ofShared step of the module, cut out so it is curated once.
9KEGG_MODULEM00017Methionine biosynthesis, aspartate => homoserine => methioninesubset_ofShared step of the module, cut out so it is curated once.
9KEGG_PATHWAYmap00260Glycine, serine and threonine metabolismsubset_ofNULL
10KEGG_MODULEM00018Threonine biosynthesis, aspartate => homoserine => threoninesubset_ofTail of the module; the aspartate-to-homoserine head is composed from separate GIFTs.
10KEGG_PATHWAYmap00260Glycine, serine and threonine metabolismsubset_ofNULL
10KEGG_PATHWAYmap01230Biosynthesis of amino acidssubset_ofNULL
11KEGG_MODULEM00017Methionine biosynthesis, aspartate => homoserine => methioninesubset_ofTail of the module; the aspartate-to-homoserine head is composed from separate GIFTs.
11KEGG_PATHWAYmap00270Cysteine and methionine metabolismsubset_ofNULL
11KEGG_PATHWAYmap01230Biosynthesis of amino acidssubset_ofNULL
12KEGG_MODULEM00017Methionine biosynthesis, aspartate => homoserine => methionineoverlapsShares homoserine acylation and methionine synthase with the module, but the module contains no direct sulfhydrylation step.
12KEGG_PATHWAYmap00270Cysteine and methionine metabolismsubset_ofNULL
13KEGG_MODULEM00021Cysteine biosynthesis, serine => cysteineequivalentModule boundaries retained; the sulfide input is declared explicitly.
13KEGG_PATHWAYmap00270Cysteine and methionine metabolismsubset_ofNULL
13KEGG_PATHWAYmap00920Sulfur metabolismsubset_ofNULL
14KEGG_MODULEM00338Cysteine biosynthesis, homocysteine + serine => cysteinesuperset_ofThe module is one of the two curated routes; the other uses O-acetyl-L-serine.
14KEGG_MODULEM00609Cysteine biosynthesis, methionine => cysteineoverlapsOnly the two cysteine-forming steps of the module are curated; its four SAM-cycle steps are a different capability.
14KEGG_PATHWAYmap00270Cysteine and methionine metabolismsubset_ofNULL
19KEGG_MODULEM00632Galactose degradation, Leloir pathway, galactose => alpha-D-glucose-1PequivalentSame boundaries.
19KEGG_PATHWAYmap00052Galactose metabolismsubset_ofNULL
23KEGG_MODULEM00061Glucuronate degradation, glucuronate => pyruvate + glyceraldehyde-3Psubset_ofBoundaries diverged at the 2026.21.3 re-cut: the module runs to pyruvate and glyceraldehyde-3P, this GIFT stops at the branchpoint and kdg_degradation completes it.
23KEGG_PATHWAYmap00040Pentose and glucuronate interconversionssubset_ofNULL
22KEGG_PATHWAYmap00040Pentose and glucuronate interconversionssubset_ofNo KEGG module covers the galacturonate-specific head of this route.
15KEGG_PATHWAYmap00040Pentose and glucuronate interconversionssubset_ofNULL
16KEGG_PATHWAYmap00040Pentose and glucuronate interconversionssubset_ofNULL
17KEGG_PATHWAYmap00051Fructose and mannose metabolismsubset_ofNULL
18KEGG_PATHWAYmap00051Fructose and mannose metabolismsubset_ofNULL
20KEGG_PATHWAYmap00520Amino sugar and nucleotide sugar metabolismsubset_ofNULL
21KEGG_PATHWAYmap00520Amino sugar and nucleotide sugar metabolismsubset_ofNULL
24KEGG_PATHWAYmap02010ABC transportersrelatedBiologically adjacent context only. The KEGG map catalogues transporter architectures; it makes no claim about this substrate.
25KEGG_PATHWAYmap02010ABC transportersrelatedBiologically adjacent context only. The KEGG map catalogues transporter architectures; it makes no claim about this substrate.
28KEGG_PATHWAYmap00500Starch and sucrose metabolismsubset_ofNULL
26KEGG_PATHWAYmap00500Starch and sucrose metabolismrelatedAdjacent context only; the xylan capabilities are not part of this map.
27KEGG_PATHWAYmap00500Starch and sucrose metabolismrelatedAdjacent context only; the xylan capabilities are not part of this map.
30KEGG_PATHWAYmap02040Flagellar assemblysubset_ofThe KEGG map additionally contains the transcriptional regulators of flagellar gene expression (FlhDC, FliA, FlgM), which this structural GIFT deliberately excludes.
32KEGG_PATHWAYmap02030Bacterial chemotaxissubset_ofThe KEGG map additionally contains the flagellar motor the pathway steers, which is a separate structural GIFT, and receptor families whose signals this claim does not name.
33KEGG_PATHWAYmap02030Bacterial chemotaxissubset_ofOne receptor input of the KEGG map together with the shared downstream signalling functions.
34KEGG_PATHWAYmap02020Two-component systemsubset_ofOne of many two-component systems the KEGG map collects.
37KEGG_PATHWAYmap00620Pyruvate metabolismsubset_ofNULL
38KEGG_MODULEM00579Phosphate acetyltransferase-acetate kinase pathway, acetyl-CoA => acetateequivalentSame boundaries and same two reactions. gifter additionally records the direction per route and states that the markers do not evidence it.
38KEGG_PATHWAYmap00620Pyruvate metabolismsubset_ofNULL
39KEGG_PATHWAYmap00650Butanoate metabolismsubset_ofThe pathway map contains both terminal routes; gifter curates only the CoA-transferase one, so the relation is subset_of rather than overlaps.
40KEGG_PATHWAYmap00640Propanoate metabolismsubset_ofNULL
41KEGG_PATHWAYmap00640Propanoate metabolismsubset_ofNULL
42KEGG_PATHWAYmap00640Propanoate metabolismsubset_ofNULL
43KEGG_PATHWAYmap00620Pyruvate metabolismsubset_ofNULL
44KEGG_PATHWAYmap00620Pyruvate metabolismsubset_ofNULL
45KEGG_PATHWAYmap00620Pyruvate metabolismsubset_ofNULL
47KEGG_PATHWAYmap00620Pyruvate metabolismsubset_ofThe map draws both the AdhE route and the pyruvate decarboxylase route; gifter curates only the first.
48KEGG_PATHWAYmap00650Butanoate metabolismsubset_ofThe map continues to butane-2,3-diol, where gifter stops at acetoin.
49KEGG_MODULEM00125Riboflavin biosynthesis, plants and bacteria, GTP => riboflavin/FMN/FADoverlapsgifter stops at riboflavin and adds the lumazine synthase and riboflavin synthase steps that the module definition omits, so the boundaries overlap rather than match.
50KEGG_MODULEM00126Tetrahydrofolate biosynthesis, GTP => THFrelatedKEGG places 4-aminobenzoate synthesis outside the folate module; gifter curates it as its own capability.
51KEGG_MODULEM00126Tetrahydrofolate biosynthesis, GTP => THFsubset_ofgifter takes 4-aminobenzoate as an input anchor and curates its synthesis separately, so this GIFT covers less than the module.
51KEGG_MODULEM00840Tetrahydrofolate biosynthesis, mediated by ribA and trpF, GTP => THFrelatedAn alternative pterin route curated in 83 organisms; not curated here.
52KEGG_MODULEM00127Thiamine biosynthesis, prokaryotes, AIR (+ DXP/tyrosine) => TMP/TPPsubset_ofThe module spans both moieties and their condensation; this GIFT is the pyrimidine branch only.
53KEGG_MODULEM00127Thiamine biosynthesis, prokaryotes, AIR (+ DXP/tyrosine) => TMP/TPPsubset_ofThe thiazole branch of the module.
53KEGG_MODULEM00895Thiamine biosynthesis, prokaryotes, AIR (+ DXP/glycine) => TMP/TPPsubset_ofThe glycine-dependent variant is the ThiO route curated here.
54KEGG_MODULEM00127Thiamine biosynthesis, prokaryotes, AIR (+ DXP/tyrosine) => TMP/TPPsubset_ofThe condensation step of the module, without the TPP kinase.
55KEGG_MODULEM00899Thiamine salvage pathway, HMP/HET => TMPsuperset_ofgifter stops before the ThiE condensation, which is its own GIFT, and covers both precursor kinases.
56KEGG_MODULEM00119Pantothenate biosynthesis, valine/L-aspartate => pantothenatesuperset_ofgifter adds the aspartate decarboxylase and the pantothenate synthetase that the module definition omits, and drops the branched-chain aminotransferase, which belongs to valine metabolism.
57KEGG_MODULEM00916Pyridoxal phosphate biosynthesis, R5P + glyceraldehyde-3P + glutamine => pyridoxal-PequivalentSame boundaries and same two jointly required subunits.
58KEGG_MODULEM00124Pyridoxal phosphate biosynthesis, erythrose-4P => pyridoxal-PequivalentSame six steps and same boundaries.
59KEGG_MODULEM00123Biotin biosynthesis, pimeloyl-ACP/CoA => biotinequivalentSame boundaries and same four steps.
60KEGG_MODULEM00115NAD biosynthesis, aspartate => quinolinate => NADsubset_ofThe ring-forming half of the module.
61KEGG_MODULEM00115NAD biosynthesis, aspartate => quinolinate => NADsubset_ofOne step of the module.
62KEGG_MODULEM00115NAD biosynthesis, aspartate => quinolinate => NADsubset_ofThe trunk of the module, shared with salvage.
63KEGG_MODULEM00622Nicotinate degradation, nicotinate => fumaraterelatedA different fate for nicotinate; gifter curates its recovery into NAD rather than its catabolism.
64KEGG_MODULEM00924Cobalamin biosynthesis, anaerobic, uroporphyrinogen III => sirohydrochlorin => cobyrinate a,c-diamideequivalentSame boundaries; curated here as one of two routes of one capability.
64KEGG_MODULEM00925Cobalamin biosynthesis, aerobic, uroporphyrinogen III => precorrin 2 => cobyrinate a,c-diamideequivalentThe aerobic route of the same capability.
65KEGG_MODULEM00122Cobalamin biosynthesis, cobyrinate a,c-diamide => cobalaminsubset_ofgifter splits the module at adenosylcobinamide phosphate, because the ring and the nucleotide loop are separately present in genomes.
66KEGG_MODULEM00122Cobalamin biosynthesis, cobyrinate a,c-diamide => cobalaminsubset_ofThe lower-loop half of the module.
67KEGG_MODULEM00122Cobalamin biosynthesis, cobyrinate a,c-diamide => cobalaminrelatedKEGG places lower-ligand synthesis outside the cobalamin module.
68KEGG_MODULEM00116Menaquinone biosynthesis, chorismate (+ polyprenyl-PP) => menaquinoloverlapsSame boundaries, but gifter accepts EntC for the isochorismate synthase reaction and does not require MenH or the thioesterase.
68KEGG_MODULEM00930Menaquinone biosynthesis, futalosine pathwaysubset_ofgifter curates the futalosine route as one route of this capability and carries it through to the methylated quinone.
68KEGG_MODULEM00931Menaquinone biosynthesis, modified futalosine pathwayrelatedThe modified route differs only in the deaminase step, which is curated as not required here.
69KEGG_MODULEM00010Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutaratesubset_ofgifter cuts the module at the isocitrate branchpoint after citrate synthase and aconitase.
131KEGG_MODULEM00010Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutaratesubset_ofThe oxidative branch from the isocitrate cut to the module output.
70KEGG_MODULEM00011Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetatesubset_ofgifter cuts this module at succinate and fumarate, so each segment is part of it.
71KEGG_MODULEM00011Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetatesubset_ofgifter cuts this module at succinate and fumarate, so each segment is part of it.
72KEGG_MODULEM00011Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetatesubset_ofgifter cuts this module at succinate and fumarate, so each segment is part of it.
69KEGG_MODULEM00009Citrate cycle (TCA cycle, Krebs cycle)subset_ofUpper segment ending at the isocitrate branchpoint.
69KEGG_PATHWAYmap00020Citrate cycle (TCA cycle)subset_ofUpper segment ending at the isocitrate branchpoint.
131KEGG_MODULEM00009Citrate cycle (TCA cycle, Krebs cycle)subset_ofOxidative isocitrate branch.
131KEGG_PATHWAYmap00020Citrate cycle (TCA cycle)subset_ofOxidative isocitrate branch.
70KEGG_MODULEM00009Citrate cycle (TCA cycle, Krebs cycle)subset_ofNULL
70KEGG_PATHWAYmap00020Citrate cycle (TCA cycle)subset_ofNULL
71KEGG_MODULEM00009Citrate cycle (TCA cycle, Krebs cycle)subset_ofNULL
71KEGG_PATHWAYmap00020Citrate cycle (TCA cycle)subset_ofNULL
72KEGG_MODULEM00009Citrate cycle (TCA cycle, Krebs cycle)subset_ofNULL
72KEGG_PATHWAYmap00020Citrate cycle (TCA cycle)subset_ofNULL
73KEGG_MODULEM00022Shikimate pathway, phosphoenolpyruvate + erythrose-4P => chorismateoverlapsSame boundaries, reached independently. gifter does not require the shikimate dehydrogenase step, accepts YdiB for it, and excludes the eukaryotic pentafunctional AROM polypeptide K13830, which no prokaryotic genome in KEGG carries.
73KEGG_PATHWAYmap00400Phenylalanine, tyrosine and tryptophan biosynthesissubset_ofThe map continues from chorismate to the three aromatic amino acids; gifter stops at the branchpoint.
74KEGG_PATHWAYmap01053Biosynthesis of siderophore group nonribosomal peptidessubset_ofThe map covers assembly of the complete siderophores; gifter curates only the formation of the salicylate building block.
75KEGG_PATHWAYmap00380Tryptophan metabolismsubset_ofThe map carries every tryptophan fate including catabolism; gifter curates one biosynthetic branch of it.
76KEGG_PATHWAYmap00230Purine metabolismsubset_ofgifter curates only the urate-to-allantoin segment of the map.
77KEGG_PATHWAYmap00230Purine metabolismsubset_ofgifter curates only the allantoin-to-glyoxylate segment of the map.
78KEGG_PATHWAYmap00220Arginine biosynthesissubset_ofThe map carries urease; gifter curates the hydrolysis alone and takes urea as a boundary rather than as an arginine-cycle intermediate.
79KEGG_MODULEM00531Assimilatory nitrate reduction, nitrate => ammoniaequivalentSame boundaries; gifter materialises the four alternative minimal routes the module expresses as a definition.
79KEGG_PATHWAYmap00910Nitrogen metabolismsubset_ofThe map also carries respiration, denitrification and nitrification, none of which gifter models.
89KEGG_PATHWAYmap00910Nitrogen metabolismsubset_ofgifter curates only the ammonium-to-glutamate segment.
80KEGG_PATHWAYmap00260Glycine, serine and threonine metabolismsubset_ofNULL
81KEGG_PATHWAYmap00260Glycine, serine and threonine metabolismsubset_ofNULL
82KEGG_PATHWAYmap00330Arginine and proline metabolismsubset_ofNULL
85KEGG_PATHWAYmap00680Methane metabolismsubset_ofThe map treats methylamine as a methylotrophic carbon source; gifter's boundary is the nitrogen released alongside formaldehyde.
86KEGG_PATHWAYmap00430Taurine and hypotaurine metabolismsubset_ofNULL
87KEGG_PATHWAYmap00430Taurine and hypotaurine metabolismsubset_ofNULL
90KEGG_MODULEM00551Benzoate degradation, benzoate => catechol / methylbenzoate => methylcatecholsubset_ofThe module also claims the methylbenzoate branch. gifter curates only the benzoate boundary, because the same orthologues serve both substrates and two traits on one marker set would be indistinguishable.
90KEGG_PATHWAYmap00362Benzoate degradationsubset_ofNULL
91KEGG_MODULEM00637Anthranilate degradation, anthranilate => catecholequivalentSame single reaction and the same boundaries; gifter additionally records the two alternative oxygenase systems as alternatives rather than as one marker set.
92KEGG_MODULEM00548Benzene degradation, benzene => catecholoverlapsThe module names benzene as the substrate and attaches this marker set to benzene hydroxylation as well. gifter curates only the phenol reaction the enzyme performs, so the boundaries overlap rather than agree.
93KEGG_MODULEM00568Catechol ortho-cleavage, catechol => 3-oxoadipateequivalentSame four reactions and the same boundaries.
94KEGG_PATHWAYmap00362Benzoate degradationsubset_ofThe beta-ketoadipate exit is drawn in the pathway map but is outside the ortho-cleavage module, which stops at 3-oxoadipate.
95KEGG_PATHWAYmap00362Benzoate degradationsubset_ofNULL
96KEGG_MODULEM00569Catechol meta-cleavage, catechol => acetyl-CoA / 4-methylcatechol => propanoyl-CoAsubset_ofThe module runs to acetyl-CoA and also claims the 4-methylcatechol branch. gifter stops at 2-oxopent-4-enoate, curates the shared lower route as its own GIFT, and does not claim the methylated substrate.
97KEGG_MODULEM00569Catechol meta-cleavage, catechol => acetyl-CoA / 4-methylcatechol => propanoyl-CoAsubset_ofThe lower three reactions of the module, curated once because five KEGG modules duplicate them.
98KEGG_MODULEM00878Phenylacetate degradation, phenylacetate => acetyl-CoA/succinyl-CoAsubset_ofThe module runs through the terminal thiolysis, which gifter curates as the separate GIFT oxoadipyl_coa_thiolysis so that the ortho-cleavage funnel and this route share it.
98KEGG_PATHWAYmap00360Phenylalanine metabolismsubset_ofNULL
99KEGG_MODULEM00545Trans-cinnamate degradation, trans-cinnamate => acetyl-CoAsubset_ofThe module ORs two entry substrates and runs to acetyl-CoA. gifter curates the 3-phenylpropanoate entry only, as its own GIFT, and does not claim cinnamate.
100KEGG_MODULEM00545Trans-cinnamate degradation, trans-cinnamate => acetyl-CoAsubset_ofThe module's alternative first step, which acts on a different substrate and is therefore a separate GIFT here.
101KEGG_MODULEM00545Trans-cinnamate degradation, trans-cinnamate => acetyl-CoAsubset_ofThe module's ring-cleavage segment, cut at 2-oxopent-4-enoate so that the shared lower route is composed rather than duplicated.
102KEGG_PATHWAYmap00250Alanine, aspartate and glutamate metabolismoverlapsKEGG has no module for glutamine synthetase; the pathway map covers far more chemistry than this boundary.
103KEGG_PATHWAYmap00250Alanine, aspartate and glutamate metabolismoverlapsNo KEGG module exists for alanine biosynthesis.
104KEGG_PATHWAYmap00250Alanine, aspartate and glutamate metabolismoverlapsNo KEGG module exists for aspartate biosynthesis.
105KEGG_PATHWAYmap00250Alanine, aspartate and glutamate metabolismoverlapsNo KEGG module exists for asparagine biosynthesis.
106KEGG_MODULEM00016Lysine biosynthesis, succinyl-DAP pathway, aspartate => lysineoverlapsThe module runs from L-aspartate to L-lysine; this GIFT starts at the semialdehyde and stops at meso-diaminopimelate, and carries three further routes the module does not.
106KEGG_MODULEM00525Lysine biosynthesis, acetyl-DAP pathway, aspartate => lysineoverlapsSame boundary difference; curated here as the acetylated route.
106KEGG_MODULEM00526Lysine biosynthesis, DAP dehydrogenase pathway, aspartate => lysineoverlapsSame boundary difference; curated here as the dehydrogenase route.
106KEGG_MODULEM00527Lysine biosynthesis, DAP aminotransferase pathway, aspartate => lysineoverlapsSame boundary difference; curated here as the aminotransferase route.
107KEGG_MODULEM00016Lysine biosynthesis, succinyl-DAP pathway, aspartate => lysinesubset_ofThe final step of the module, curated as its own capability.
108KEGG_MODULEM00019Valine/isoleucine biosynthesis, pyruvate => valine / 2-oxobutanoate => isoleucinesubset_ofThe module fuses the valine and isoleucine branches and ends at both amino acids; this GIFT is the shared head of the valine branch only.
109KEGG_MODULEM00019Valine/isoleucine biosynthesis, pyruvate => valine / 2-oxobutanoate => isoleucinesubset_ofThe final step of the valine branch of the module.
110KEGG_MODULEM00432Leucine biosynthesis, 2-oxoisovalerate => 2-oxoisocaproatesuperset_ofSame start; this GIFT continues to L-leucine, which the module leaves out.
111KEGG_MODULEM00535Isoleucine biosynthesis, pyruvate => 2-oxobutanoateequivalentSame boundaries and same chemistry.
112KEGG_MODULEM00570Isoleucine biosynthesis, threonine => 2-oxobutanoate => isoleucinesubset_ofThe module includes threonine deamination, which gifter curates separately as catabolic chemistry.
113KEGG_MODULEM00024Phenylalanine biosynthesis, chorismate => phenylpyruvate => phenylalanineequivalentSame boundaries; the marker set of the final transamination is wider than the module.
114KEGG_MODULEM00025Tyrosine biosynthesis, chorismate => HPP => tyrosineequivalentSame boundaries; the marker set of the final transamination is wider than the module.
114KEGG_MODULEM00040Tyrosine biosynthesis, chorismate => arogenate => tyrosinerelatedThe arogenate route is not curated: its distinguishing orthology groups are annotated in no bacterial genome.
115KEGG_MODULEM00023Tryptophan biosynthesis, chorismate => tryptophanequivalentSame boundaries and same five steps.
116KEGG_MODULEM00026Histidine biosynthesis, PRPP => histidineequivalentSame boundaries and same chemistry.
117KEGG_MODULEM00015Proline biosynthesis, glutamate => prolineequivalentSame boundaries and same chemistry.
118KEGG_MODULEM00028Ornithine biosynthesis, glutamate => ornithineequivalentSame boundaries; both acetyl-recycling variants are curated as routes.
118KEGG_MODULEM00763Ornithine biosynthesis, mediated by LysW, glutamate => ornithinerelatedRefused for bacteria on evidence: K19412 is annotated in no bacterial genome.
119KEGG_MODULEM00844Arginine biosynthesis, ornithine => arginineequivalentSame boundaries and same chemistry.
120KEGG_PATHWAYmap00330Arginine and proline metabolismoverlapsKEGG has no module for the arginine deiminase pathway; the map covers much more chemistry.
121KEGG_MODULEM00045Histidine degradation, histidine => N-formiminoglutamate => glutamateequivalentSame boundaries; gifter curates the formamide-releasing final step and not the folate-dependent alternatives.
122KEGG_MODULEM00570Isoleucine biosynthesis, threonine => 2-oxobutanoate => isoleucinesubset_ofThe first step of the module, curated as its own capability because the chemistry is a deamination.
123KEGG_PATHWAYmap00260Glycine, serine and threonine metabolismoverlapsNo KEGG module covers serine deamination alone.
124KEGG_MODULEM00027GABA (gamma-Aminobutyrate) shuntsubset_ofThe first step of the shunt; the transaminase and semialdehyde dehydrogenase steps that follow are not curated here.
125KEGG_PATHWAYmap00380Tryptophan metabolismoverlapsKEGG has no module for tryptophanase.
126KEGG_PATHWAYmap00270Cysteine and methionine metabolismoverlapsKEGG has no module for methionine gamma-lyase.
127KEGG_PATHWAYmap00270Cysteine and methionine metabolismoverlapsKEGG has no module for cysteine desulfidation.
128KEGG_PATHWAYmap00260Glycine, serine and threonine metabolismoverlapsKEGG has no module for the glycine reductase complex.
129KEGG_PATHWAYmap00330Arginine and proline metabolismoverlapsKEGG has no module for the proline reductase complex.
132KEGG_MODULEM00012Glyoxylate cyclesubset_ofgifter curates the branch from isocitrate to succinate and malate; citrate synthase, aconitase and malate dehydrogenase remain separate composable GIFTs. The K19282 malyl-CoA alternative is deferred.
132KEGG_PATHWAYmap00630Glyoxylate and dicarboxylate metabolismsubset_ofThe two-reaction carbon-conserving branch only.
133KEGG_MODULEM00175Nitrogen fixation, nitrogen => ammoniaequivalentSame molecular boundaries. gifter requires the nitrogenase-specific NifB and EN cofactor assembly for the Mo route and separately materialises the V route.
133KEGG_PATHWAYmap00910Nitrogen metabolismsubset_ofThe nitrogen-fixation reaction only.
134KEGG_MODULEM00176Assimilatory sulfate reduction, sulfate => H2SequivalentSame molecular boundaries. gifter additionally materialises the direct APS branch and refuses K00390 where it cannot distinguish APS from PAPS reductase activity.
134KEGG_PATHWAYmap00920Sulfur metabolismsubset_ofThe assimilatory sulfate-to-sulfide route only; dissimilatory reduction is excluded.
135METACYCP101-PWYEctoine biosynthesissubset_ofThe GIFT starts at L-aspartate 4-semialdehyde and retains only the EctB-EctA-EctC tail; the record also contains aspartate kinase and aspartate-semialdehyde dehydrogenase.
135KEGG_MODULEM00033Ectoine biosynthesis, aspartate => ectoinesubset_ofThe module starts at aspartate; gifter starts at the existing ASA branchpoint.
136METACYCHEME-BIOSYNTHESIS-IIHeme b biosynthesis I (aerobic)equivalentSame UROGEN_III-to-heme-b boundaries; gifter materialises additional valid enzyme combinations as separate minimal routes.
136METACYCHEMESYN2-PWYHeme b biosynthesis II (oxygen-independent)equivalentSame UROGEN_III-to-heme-b boundaries; represented by the HemN-HemG and HemN-HemJ minimal routes.
136METACYCPWY-7766Heme b biosynthesis IV (Gram-positive bacteria)equivalentSame UROGEN_III-to-heme-b boundaries through coproporphyrin and coproheme.
136KEGG_MODULEM00121Heme biosynthesis, plants and bacteria, glutamate => hemesubset_ofThe module starts upstream of UROGEN_III; gifter retains its complete heme-b tail and materialises its independent enzyme alternatives.
136KEGG_MODULEM00926Heme biosynthesis, bacteria, glutamyl-tRNA => coproporphyrin III => hemesubset_ofThe module starts upstream of UROGEN_III; gifter retains the HemE-HemY-HemH-HemQ tail.
137METACYCENTBACSYN-PWYEnterobactin biosynthesissubset_ofThe GIFT is the chorismate-to-2,3-dihydroxybenzoate head only.
137KEGG_PATHWAYmap01053Biosynthesis of siderophore group nonribosomal peptidessubset_ofThe GIFT is the reusable catecholate-head segment only.
138METACYCENTBACSYN-PWYEnterobactin biosynthesissubset_ofThe GIFT starts at 2,3-dihydroxybenzoate plus serine and retains only enterobactin assembly.
138KEGG_PATHWAYmap01053Biosynthesis of siderophore group nonribosomal peptidessubset_ofThe GIFT is the EntB-EntD-EntE-EntF enterobactin assembly segment only.
139METACYCPWY-5386Methylglyoxal degradation Isubset_ofThe defense mechanism stops at D-lactate and regenerated glutathione; the pathway record continues with D-lactate oxidation.
140METACYCDETOX1-PWYSuperoxide radicals degradationequivalentSame chemical extent: superoxide dismutation followed by catalase removal of the peroxide product; gifter admits equivalent peroxide-removal systems.
140METACYCDETOX1-PWY-1Reactive oxygen species degradationsubset_ofThe GIFT covers the superoxide-to-peroxide-to-water branch, not the record's wider peroxide and glutathione reactions.
141METACYCBETSYN-PWYGlycine betaine biosynthesis I (Gram-negative bacteria)equivalentSame choline and glycine-betaine boundaries through the BetA-BetB architecture.
141METACYCPWY-3722Glycine betaine biosynthesis II (Gram-positive bacteria)equivalentSame choline and glycine-betaine boundaries through the GbsB-GbsA architecture.
141KEGG_MODULEM00555Betaine biosynthesis, choline => betaineequivalentSame boundaries; gifter materialises the genomically distinct first-enzyme and choline-oxidase alternatives and refuses broad ALDH7A1.
142METACYCPWY-5194Siroheme biosynthesisequivalentSame UROGEN_III-to-siroheme boundaries. MetaCyc records the two methyl transfers separately; gifter reuses the single overall Rhea master for that enzyme-catalysed conversion.
142KEGG_MODULEM00846Siroheme biosynthesis, glutamyl-tRNA => sirohemesubset_ofThe module begins upstream of UROGEN_III. gifter retains the three-reaction tail and excludes broad CbiX-family evidence that cannot establish iron insertion.
143KEGG_PATHWAYmap00520Amino sugar and nucleotide sugar metabolismsubset_ofNULL
144KEGG_PATHWAYmap00511Other glycan degradationsubset_ofNULL
145KEGG_PATHWAYmap00511Other glycan degradationsubset_ofNULL
146KEGG_PATHWAYmap00511Other glycan degradationsubset_ofNULL
147KEGG_PATHWAYmap00040Pentose and glucuronate interconversionssubset_ofNULL
148KEGG_PATHWAYmap00040Pentose and glucuronate interconversionssubset_ofNo KEGG module covers the shared lower segment on its own.
149KEGG_PATHWAYmap00040Pentose and glucuronate interconversionssubset_ofNULL
150KEGG_MODULEM00919Ectoine degradation, ectoine => aspartatesubset_ofThe module runs on through DoeD and DoeC to L-aspartate; gifter stops where ectoine-specific chemistry stops.
152KEGG_PATHWAYmap00620Pyruvate metabolismsubset_ofNULL
151KEGG_PATHWAYmap00260Glycine, serine and threonine metabolismsubset_ofKEGG places the ectoine chemistry in this map; the GIFT is one reaction of it.
153KEGG_MODULEM00847Heme biosynthesis, archaea, siroheme => hemeequivalentSame siroheme-to-heme-b boundaries, and the same two terminal alternatives: the module reads K22225 K22226 (K22227,K25033). gifter refuses K22225 and evidences the decarboxylase as an AhbA-AhbB heterodimer instead, so a genome KEGG calls complete on one K22225 gene is not complete here.
153METACYCPWY-7552Heme b biosynthesis from sirohemeequivalentSame siroheme-to-heme-b boundaries over the same three reactions. The identifier is carried from the MetaCyc reconnaissance in inst/doc/proposal-metacyc-expansion.md; MetaCyc pathway pages returned no content without a subscription.
155KEGG_PATHWAYmap00552Teichoic acid biosynthesissubset_ofThe KEGG map includes glycerol-phosphate WTA and decorations in addition to the two ribitol-phosphate architectures curated here; gifter additionally requires export and peptidoglycan attachment.
157KEGG_PATHWAYmap03070Bacterial secretion systemsubset_ofThe KEGG map covers every bacterial secretion system from Sec and Tat to type VI; this GIFT claims only the canonical type VI apparatus. KEGG retains no type VI secretion module, so no module cross-reference exists.
158KEGG_PATHWAYmap03070Bacterial secretion systemsubset_ofThe KEGG map covers every bacterial secretion system and additionally places the flagellar export apparatus beside the injectisome; this GIFT claims only the non-flagellar injectisome. KEGG retains no type III secretion module, so no module cross-reference exists.
160KEGG_PATHWAYmap03070Bacterial secretion systemsubset_ofThe KEGG map covers every bacterial secretion system and places the type IVa pilus machinery beside the type II apparatus they share a peptidase with; this GIFT claims only the Gsp apparatus. KEGG retains no type II secretion module.
161KEGG_PATHWAYmap02030Bacterial chemotaxissubset_ofThe Tsr-family serine input and shared downstream chemotaxis functions are a subset of the map, which also includes other receptors and the flagellar motor.
gift_route210 rows · 7 columns
route_pkgift_pkroute_idnamedescriptionstatusoxygen_requirement
11PCR_FOLATE_DIRECT_FOLATEFolate/direct/folate routeFolate-dependent GAR formylation, direct AIR carboxylation, and folate-dependent AICAR formylation.curatedindependent
21PCR_FOLATE_DIRECT_FORMATEFolate/direct/formate routeFolate-dependent GAR formylation, direct AIR carboxylation, and formate-dependent AICAR formylation.curatedindependent
31PCR_FOLATE_TWOSTEP_FOLATEFolate/two-step/folate routeFolate-dependent GAR formylation, two-step AIR carboxylation, and folate-dependent AICAR formylation.curatedindependent
41PCR_FOLATE_TWOSTEP_FORMATEFolate/two-step/formate routeFolate-dependent GAR formylation, two-step AIR carboxylation, and formate-dependent AICAR formylation.curatedindependent
51PCR_FORMATE_DIRECT_FOLATEFormate/direct/folate routeFormate-dependent GAR formylation, direct AIR carboxylation, and folate-dependent AICAR formylation.curatedindependent
61PCR_FORMATE_DIRECT_FORMATEFormate/direct/formate routeFormate-dependent GAR formylation, direct AIR carboxylation, and formate-dependent AICAR formylation.curatedindependent
71PCR_FORMATE_TWOSTEP_FOLATEFormate/two-step/folate routeFormate-dependent GAR formylation, two-step AIR carboxylation, and folate-dependent AICAR formylation.curatedindependent
81PCR_FORMATE_TWOSTEP_FORMATEFormate/two-step/formate routeFormate-dependent GAR formylation, two-step AIR carboxylation, and formate-dependent AICAR formylation.curatedindependent
92AMP_ADENYLOSUCCINATEAdenylosuccinate routeIMP to AMP through adenylosuccinate synthase and adenylosuccinate lyase.curatedindependent
103GMP_XMPXMP routeIMP to GMP through IMP dehydrogenase and glutamine-dependent GMP synthase.curatedindependent
114PYR_DHODH_FUMARATEFumarate-dependent DHODH routeDe novo UMP biosynthesis using fumarate-dependent dihydroorotate oxidation.curatedindependent
124PYR_DHODH_NADNAD-dependent DHODH routeDe novo UMP biosynthesis using NAD-dependent dihydroorotate oxidation.curatedindependent
134PYR_DHODH_QUINONEQuinone-dependent DHODH routeDe novo UMP biosynthesis using quinone-dependent dihydroorotate oxidation.curatedindependent
145CTP_GLUTAMINEGlutamine-dependent CTP synthase routeUTP to CTP through the complete glutamine-dependent CTP synthase reaction.curatedindependent
156SER_PHOSPHORYLATEDPhosphorylated serine route3-phosphoglycerate oxidation, transamination and dephosphorylation to L-serine.curatedindependent
167GLY_SHMTSerine hydroxymethyltransferase routeFolate-dependent removal of the serine hydroxymethyl group to give glycine.curatedindependent
178ASA_CANONICALAspartate kinase routeAspartate phosphorylation followed by NADPH-dependent reduction to the 4-semialdehyde.curatedindependent
189HSER_NADNAD-dependent homoserine dehydrogenase routeReduction of L-aspartate 4-semialdehyde to L-homoserine using NADH.curatedindependent
199HSER_NADPNADP-dependent homoserine dehydrogenase routeReduction of L-aspartate 4-semialdehyde to L-homoserine using NADPH.curatedindependent
2010THR_CANONICALHomoserine kinase routeHomoserine phosphorylation followed by threonine synthase.curatedindependent
2111MET_TS_SUCCINYL_B12Succinyl/transsulfuration/cobalamin routeO-succinylhomoserine transsulfuration with cobalamin-dependent methionine synthase.curatedindependent
2211MET_TS_SUCCINYL_FOLATESuccinyl/transsulfuration/cobalamin-independent routeO-succinylhomoserine transsulfuration with cobalamin-independent methionine synthase.curatedindependent
2311MET_TS_ACETYL_B12Acetyl/transsulfuration/cobalamin routeO-acetylhomoserine transsulfuration with cobalamin-dependent methionine synthase.curatedindependent
2411MET_TS_ACETYL_FOLATEAcetyl/transsulfuration/cobalamin-independent routeO-acetylhomoserine transsulfuration with cobalamin-independent methionine synthase.curatedindependent
2511MET_TS_PHOSPHO_B12Phospho/transsulfuration/cobalamin routePlant O-phosphohomoserine transsulfuration with cobalamin-dependent methionine synthase.curatedindependent
2611MET_TS_PHOSPHO_FOLATEPhospho/transsulfuration/cobalamin-independent routePlant O-phosphohomoserine transsulfuration with cobalamin-independent methionine synthase.curatedindependent
2712MET_SH_SUCCINYL_B12Succinyl/sulfhydrylation/cobalamin routeDirect sulfide incorporation into O-succinylhomoserine with cobalamin-dependent methionine synthase.curatedindependent
2812MET_SH_SUCCINYL_FOLATESuccinyl/sulfhydrylation/cobalamin-independent routeDirect sulfide incorporation into O-succinylhomoserine with cobalamin-independent methionine synthase.curatedindependent
2912MET_SH_ACETYL_B12Acetyl/sulfhydrylation/cobalamin routeDirect sulfide incorporation into O-acetylhomoserine with cobalamin-dependent methionine synthase.curatedindependent
3012MET_SH_ACETYL_FOLATEAcetyl/sulfhydrylation/cobalamin-independent routeDirect sulfide incorporation into O-acetylhomoserine with cobalamin-independent methionine synthase.curatedindependent
3113CYS_OAS_SULFIDEO-acetylserine sulfhydrylation routeSerine acetylation followed by sulfide incorporation.curatedindependent
3214CYS_RT_SERINESerine-dependent reverse transsulfuration routeCystathionine beta-synthase acting on L-serine, then cystathionine gamma-lyase.curatedindependent
3314CYS_RT_OASO-acetylserine-dependent reverse transsulfuration routeSerine acetylation, cystathionine beta-synthase acting on O-acetyl-L-serine, then cystathionine gamma-lyase.curatedindependent
3415XYL_ISOMERASEXylose isomerase routeIsomerisation to D-xylulose and phosphorylation to D-xylulose 5-phosphate.curatedindependent
3516ARA_ISOMERASEL-arabinose isomerase routeIsomerisation to L-ribulose, phosphorylation, and epimerisation to D-xylulose 5-phosphate.curatedindependent
3617FUC_ISOMERASEL-fucose isomerase routeIsomerisation to L-fuculose, phosphorylation, and aldol cleavage.curatedindependent
3718RHA_ISOMERASEL-rhamnose isomerase routeIsomerisation to L-rhamnulose, phosphorylation, and aldol cleavage.curatedindependent
3819GAL_LELOIRLeloir routeMutarotation, galactokinase, uridylyltransferase, and UDP-glucose regeneration.curatedindependent
3920GLCNAC_KINASEN-acetylglucosamine kinase routePhosphorylation by a cytoplasmic ATP-dependent kinase, deacetylation, and deamination to fructose 6-phosphate. This is the entry used by organisms that import N-acetylglucosamine unphosphorylated and by cell wall recycling, which recovers the sugar already inside the cell.curatedindependent
4021NEUAC_LYASEN-acetylneuraminate lyase routeLyase cleavage to N-acetylmannosamine, phosphorylation, epimerisation, deacetylation, and deamination.curatedindependent
4122GALUA_ISOMERASEGalacturonate isomerase routeIsomerisation to keto-D-tagaturonate, reduction to D-altronate and dehydration to the Entner-Doudoroff branchpoint.curatedindependent
4223GLCUA_ISOMERASEGlucuronate isomerase routeIsomerisation to keto-D-fructuronate, reduction to D-mannonate and dehydration to the Entner-Doudoroff branchpoint.curatedindependent
4324XYL_UPTAKE_ABCABC importer routeATP-driven translocation by a periplasmic-binding-protein-dependent importer.curatedindependent
4425ARA_UPTAKE_ABCABC importer routeATP-driven translocation by a periplasmic-binding-protein-dependent importer.curatedindependent
4526XYLAN_SACCHARIFICATIONEndo-xylanase and beta-xylosidase routeBackbone endohydrolysis then exo-acting release of D-xylose, with acetyl de-blocking as accessory chemistry.curatedindependent
4627AX_DEBRANCHArabinofuranosidase routeHydrolysis of alpha-L-arabinofuranosyl side chains.curatedindependent
4728STARCH_SACCHARIFICATIONAlpha-amylase and alpha-glucosidase routeBackbone endohydrolysis then exo-acting release of D-glucose, with alpha-1,6 debranching as accessory chemistry.curatedindependent
4829COLLAGEN_M9M9 microbial collagenase routeDirect cleavage of the collagen triple helix by a secreted family M9 collagenase.curatedindependent
4937PYR_ACOA_PDHPyruvate dehydrogenase complex routeNAD-dependent oxidative decarboxylation by the multienzyme dehydrogenase complex.curatedindependent
5037PYR_ACOA_PFORPyruvate:ferredoxin oxidoreductase routeFerredoxin-dependent oxidative decarboxylation; the oxygen-sensitive route of anaerobes.curatedanaerobic
5137PYR_ACOA_PFLPyruvate formate-lyase routeRadical-mediated non-oxidative cleavage releasing formate, requiring the activating enzyme to install the glycyl radical.curatedanaerobic
5238ACETATE_PTA_ACKAPhosphotransacetylase and acetate kinase routeTransfer of the acetyl group to phosphate and substrate-level phosphorylation of ADP, yielding acetate and ATP.curatedindependent
5339BUTYRATE_ACOA_TRANSFERASEAcetyl-CoA condensation with CoA-transferase releaseThiolytic condensation of two acetyl-CoA, reduction through 3-hydroxybutanoyl-CoA and crotonoyl-CoA to butanoyl-CoA, and CoA transfer onto acetate to release butanoate.curatedanaerobic
5440PROPANEDIOL_FUCOLactaldehyde reductase routeNADH-dependent reduction of (S)-lactaldehyde to (S)-propane-1,2-diol.curatedanaerobic
5541PROPIONATE_PDUPropanediol utilisation routeCoenzyme-B12-dependent dehydration to propanal, CoA-acylating oxidation to propanoyl-CoA, and substrate-level phosphorylation to propanoate.curatedanaerobic
5642PROPIONATE_ACRYLATEAcrylate routeCoA transfer from propanoyl-CoA onto lactate, dehydration to acryloyl-CoA, and reduction back to propanoyl-CoA, with propanoate released by the transfer step.curatedanaerobic
5743LACTATE_LDHNAD-dependent lactate dehydrogenase routeReduction of pyruvate by NADH to (S)-lactate, regenerating NAD+ for glycolysis.curatedindependent
5844LACTATE_RACEMASELactate racemase routeInterconversion of the two lactate enantiomers by the nickel-pincer racemase LarA. One traversal, not a mirrored pair: a flipped copy would complete on the same marker.curatedindependent
5945MALOLACTIC_MLEMalolactic enzyme routeDirect decarboxylation of (S)-malate to (S)-lactate, without a free pyruvate intermediate and without a separate decarboxylase.curatedindependent
6046CITRATE_LYASE_OADCitrate lyase and oxaloacetate decarboxylase routeCleavage of citrate to oxaloacetate and acetate by the holo-citrate lyase complex, followed by decarboxylation of oxaloacetate to pyruvate.curatedanaerobic
6147ETHANOL_ADHEBifunctional acetaldehyde/alcohol dehydrogenase routeReduction of acetyl-CoA to acetaldehyde and of acetaldehyde to ethanol, both steps carried by AdhE.curatedanaerobic
6248ACETOIN_ALS_BUDAAcetolactate synthase and decarboxylase routeCondensation of two pyruvate to (2S)-2-acetolactate and its decarboxylation to (R)-acetoin. The synthase step is curated but not required.curatedindependent
6349RIBOFLAVIN_GTPGTP and ribulose 5-phosphate routeThe canonical bacterial route. The 3.1.3.104 phosphatase step is curated as not required: the chemistry is universal but no orthology group covers it across bacteria, and requiring it would call 5261 genomes that carry every other step riboflavin-negative.curatedindependent
6450PABA_ADC4-amino-4-deoxychorismate routeAmination of chorismate and elimination of pyruvate. PabA, the glutamine amidotransferase subunit, is interchangeable with TrpG and is not required as evidence.curatedindependent
6551FOLATE_THFPterin and 4-aminobenzoate routeGTP cyclohydrolase I through dihydrofolate reductase.curatedindependent
6652HMP_THICThiC routePhosphomethylpyrimidine synthase followed by ThiD-mediated phosphorylation.curatedindependent
6753THZ_THIHTyrosine-dependent ThiH routeThiH cleaves L-tyrosine to 2-iminoacetate, which thiazole synthase condenses with DXP.curatedanaerobic
6853THZ_THIOGlycine-dependent ThiO routeThiO oxidises glycine to 2-iminoacetate, which thiazole synthase condenses with DXP.curatedaerobic
6954TMP_THIEThiamine phosphate synthase routeCondensation of the pyrimidine diphosphate and the thiazole phosphate.curatedindependent
7055SALVAGE_HMP_HETThiD and ThiM routeTwo successive ThiD phosphorylations of the pyrimidine and one ThiM phosphorylation of the thiazole.curatedindependent
7156PANTOTHENATE_PANBCDEPanB, PanE, PanD and PanC routeKetopantoate formation and reduction, beta-alanine formation, and ligation. The reduction accepts IlvC as well as PanE, which is a non-homologous replacement for that reaction rather than a widened marker.curatedindependent
7257PLP_R5PPdxS and PdxT routeOne reaction catalysed by a two-subunit complex.curatedindependent
7358PLP_DXPEpd, PdxB, SerC, PdxA and PdxJ routeThe transamination is curated in reverse relative to the Rhea master, which is written in the direction that consumes 4-phosphohydroxy-L-threonine.curatedindependent
7459BIOTIN_SAMS-adenosylmethionine-dependent transaminase routeThe BioA route used by Proteobacteria, in which the amino donor is S-adenosylmethionine.curatedindependent
7559BIOTIN_LYSLysine-dependent transaminase routeThe BioA route used by Bacillus and many Firmicutes, in which the amino donor is L-lysine.curatedindependent
7660QUIN_NADBL-aspartate oxidase routeNadB oxidises L-aspartate to iminosuccinate using molecular oxygen; the same enzyme uses fumarate anaerobically, which gifter does not curate.curatedaerobic
7760QUIN_NADXAspartate dehydrogenase routeNadX forms iminosuccinate with NAD as the acceptor, the route used by many anaerobes and archaea.curatedindependent
7861NAMN_NADCQuinolinate phosphoribosyltransferase routeA single reaction.curatedindependent
7962NAD_NH3Ammonia-dependent NAD synthetase routeNadE amidates deamido-NAD using ammonium.curatedindependent
8062NAD_GLNGlutamine-dependent NAD synthetase routeThe glutamine-hydrolysing synthetase, which is the only form in many organisms.curatedindependent
8163NAMN_PNCBNicotinate phosphoribosyltransferase routeA single ATP-dependent reaction.curatedindependent
8264CORRIN_ANAEROBICAnaerobic early-cobalt-insertion routeCobalt is inserted into sirohydrochlorin before ring contraction. The chelatase and the two reductase steps are curated in reverse relative to their Rhea masters, which are written in the cobalt-releasing and oxidising directions.curatedanaerobic
8364CORRIN_AEROBICAerobic late-cobalt-insertion routeThe ring is completed as the cobalt-free hydrogenobyrinate, amidated, and only then loaded with cobalt by the three-subunit CobNST chelatase. CobG makes the route strictly oxygen-dependent.curatedaerobic
8465COBINAMIDE_ARMAdenosylation and aminopropanol arm routeCobalt adenosylation, cobyric acid synthesis, and condensation with (R)-1-aminopropan-2-yl phosphate.curatedindependent
8566LOOP_DMBDimethylbenzimidazole loop routeGuanylyltransferase, phosphoribosyltransferase, ribazole phosphatase and ribazoletransferase.curatedindependent
8667DMB_BLUBBluB routeOne oxygen-dependent reaction that dismantles reduced FMN.curatedaerobic
8768MK_CLASSICClassical men routeIsochorismate through the naphthoate, then prenylation and methylation. The isochorismate synthase reaction accepts EntC as well as MenF: the two enzymes catalyse the same reaction, and route completeness supplies the pathway specificity.curatedindependent
8868MK_FUTALOSINEFutalosine routeThe chorismate-dehydratase route of Helicobacter, Campylobacter and Streptomyces, which shares only the terminal prenylation and methylation with the classical route. The deaminase step is not required, because the modified futalosine route omits it.curatedindependent
8969TCA1_CS_ACNCitrate synthase and aconitase routeCondensation to citrate and isomerisation to the isocitrate branchpoint.curatedindependent
9070TCA2_ODH_SCS2-oxoglutarate dehydrogenase complex routeIrreversible oxidative decarboxylation to succinyl-CoA by the multienzyme complex, then substrate-level phosphorylation to succinate.curatedindependent
9170TCA2_OFOR_SCSFerredoxin oxidoreductase routeFerredoxin-dependent oxidative decarboxylation to succinyl-CoA, then substrate-level phosphorylation. The same enzyme runs reductively in the reductive citric acid cycle.curatedanaerobic
9270TCA2_KGD_SSADH_NAD2-oxoglutarate decarboxylase bypass, NAD-dependentDecarboxylation to succinate semialdehyde followed by NAD-dependent oxidation to succinate. No succinyl-CoA intermediate and no substrate-level phosphorylation.curatedindependent
9370TCA2_KGD_SSADH_NADP2-oxoglutarate decarboxylase bypass, NADP-dependentAs the NAD bypass, with the NADP-dependent succinate-semialdehyde dehydrogenase.curatedindependent
9471TCA3_QUINONEQuinone-dependent succinate/fumarate coupleOne traversal of the couple, written from succinate to fumarate. The GIFT declares no direction; the route records the orientation relative to how Rhea writes the equation.curatedindependent
9572TCA4_FUMARASE_MDHFumarase and NAD-malate dehydrogenase routeHydration of fumarate to (S)-malate followed by NAD-dependent oxidation to oxaloacetate. Both steps are reversible.curatedindependent
9672TCA4_FUMARASE_MQOFumarase and malate:quinone oxidoreductase routeHydration of fumarate to (S)-malate followed by quinone-dependent oxidation to oxaloacetate. The second step is effectively unidirectional.curatedindependent
9773CHOR_SHIKIMATEShikimate pathwayThe seven-step sequence from phosphoenolpyruvate and erythrose 4-phosphate. The shikimate dehydrogenase step is curated as not required: K00014 is annotated in 5585 bacteria while every other step of the route is annotated in 8461 to 9149, and requiring it drops the route from 7644 to 5420 bacteria, removing 201 of 213 cyanobacteria and 1061 of 1642 Actinomycetota. Those organisms make aromatic amino acids and carry a shikimate dehydrogenase gene; KEGG simply does not assign it to a KO.curatedindependent
9874SAL_ISOCHORISMATEIsochorismate routeIsomerisation of chorismate to isochorismate followed by pyruvate elimination. The only known route from chorismate to salicylate, and the same two transformations whether a genome uses separate PchA and PchB proteins or a single bifunctional salicylate synthase.curatedindependent
9975IAA_IAMIndole-3-acetamide routeOxidative decarboxylation of tryptophan to indole-3-acetamide by IaaM, then hydrolysis to indole-3-acetate. Aerobic, because tryptophan 2-monooxygenase consumes molecular oxygen.curatedaerobic
10076URATE_URICASEUrate oxidase routeCofactor-independent urate oxidase, then hydrolysis of 5-hydroxyisourate and decarboxylation to (S)-allantoin.curatedaerobic
10176URATE_HPXOHpxO urate hydroxylase routeFlavin-dependent urate hydroxylase in place of urate oxidase, converging on the same hydrolysis and decarboxylation.curatedaerobic
10277ALLANTOIN_ALLANTOICASEAllantoicase routeAllantoinase then allantoicase, releasing one urea before the ureidoglycolate lyase releases the second.curatedindependent
10377ALLANTOIN_DEIMINASEAllantoate deiminase routeAllantoinase, then deamination of allantoate and hydrolysis of ureidoglycine, releasing two ammonium that the allantoicase route does not.curatedindependent
10478UREA_UREASEUrease routeNickel-dependent hydrolysis of urea to ammonium and hydrogencarbonate.curatedindependent
10579NITRATE_ASSIM_NAS_NADHNasAC with NAD(P)H nitrite reductaseAssimilatory nitrate reductase then a NAD(P)H-dependent nitrite reductase.curatedindependent
10679NITRATE_ASSIM_NAS_FDNasAC with ferredoxin nitrite reductaseAssimilatory nitrate reductase then ferredoxin-nitrite reductase.curatedindependent
10779NITRATE_ASSIM_NARB_NADHNarB with NAD(P)H nitrite reductaseFerredoxin-nitrate reductase then a NAD(P)H-dependent nitrite reductase.curatedindependent
10879NITRATE_ASSIM_NARB_FDNarB with ferredoxin nitrite reductaseThe fully ferredoxin-linked route, characteristic of cyanobacteria.curatedindependent
10980BETAINE_GBC_DGCMonooxygenase with ferredoxin dehydrogenaseGlycine betaine monooxygenase then the ferredoxin-dependent dimethylglycine dehydrogenase.curatedaerobic
11080BETAINE_GBC_DMGDHMonooxygenase with ETF dehydrogenaseGlycine betaine monooxygenase then the electron-transfer-flavoprotein dimethylglycine dehydrogenase.curatedaerobic
11180BETAINE_GBC_DMGOMonooxygenase with dimethylglycine oxidaseGlycine betaine monooxygenase then the oxygen-dependent dimethylglycine oxidase.curatedaerobic
11281SARCOSINE_OXIDASESarcosine oxidase routeOxygen-dependent oxidative demethylation, by either the heterotetrameric or the monomeric enzyme.curatedaerobic
11381SARCOSINE_DEHYDROGENASE_FDFerredoxin dehydrogenase routeFerredoxin-dependent demethylation by the same DgcAB pair that acts on dimethylglycine.curatedindependent
11482CREATININE_AMIDOHYDROLASECreatininase routeCyclic amide hydrolysis to creatine, then amidinohydrolysis to sarcosine and urea.curatedindependent
11583CARNITINE_CNTABCarnitine monooxygenase routeRieske oxygenase cleavage of carnitine, releasing free trimethylamine.curatedaerobic
11684CARNITINE_CDHCarnitine dehydrogenase routeOxidation to 3-dehydrocarnitine, retro-Claisen cleavage to betainyl-CoA, and thioester hydrolysis to glycine betaine.curatedindependent
11785METHYLAMINE_MADHMethylamine dehydrogenase routeOxidative deamination by the tryptophan-tryptophylquinone enzyme.curatedindependent
11886TAURINE_TAUDTaurine dioxygenase route2-oxoglutarate-dependent desulfonation, releasing sulfite and leaving the nitrogen on aminoacetaldehyde.curatedaerobic
11987TAURINE_TPA_XSCTransaminase routeTaurine-pyruvate transamination to sulfoacetaldehyde, then acetyltransferase cleavage. The nitrogen leaves as L-alanine.curatedindependent
12087TAURINE_TAUXY_XSCDehydrogenase routeTaurine dehydrogenase deamination to sulfoacetaldehyde, then acetyltransferase cleavage. The nitrogen leaves as ammonium.curatedindependent
12188TAURINE_UPTAKE_ABCABC importer routeATP-driven translocation by a periplasmic-binding-protein-dependent importer.curatedindependent
12289AMMONIUM_GS_GOGATGS-GOGAT route, NADPHGlutamine synthetase fixes ammonium onto glutamate, and NADPH-dependent glutamate synthase transfers the amide onto 2-oxoglutarate.curatedindependent
12389AMMONIUM_GS_GOGAT_FDGS-GOGAT route, ferredoxinAs the NADPH route, with the ferredoxin-dependent glutamate synthase.curatedindependent
12489AMMONIUM_GDH_NADPNADP-glutamate dehydrogenase routeDirect reductive amination of 2-oxoglutarate. Lower affinity for ammonium than GS-GOGAT and independent of it.curatedindependent
12589AMMONIUM_GDH_NADNAD-glutamate dehydrogenase routeDirect reductive amination of 2-oxoglutarate by the NAD-dependent enzyme.curatedindependent
12690BENZOATE_TO_CATECHOLBenzoate 1,2-dioxygenase routeRing dihydroxylation by the benABC oxygenase and decarboxylating dehydrogenation by benD.curatedaerobic
12791ANTHRANILATE_TO_CATECHOLAnthranilate 1,2-dioxygenase routeSingle-step oxidative deamination and decarboxylation to catechol.curatedaerobic
12892PHENOL_TO_CATECHOLMulticomponent phenol 2-monooxygenase routeSingle-step hydroxylation by the six-subunit phenol hydroxylase.curatedaerobic
12993CATECHOL_ORTHOIntradiol cleavage routeCatechol 1,2-dioxygenase, muconate cycloisomerase, muconolactone isomerase and enol-lactone hydrolysis.curatedaerobic
13094OXOADIPATE_COA_TRANSFERSuccinyl-CoA transferase routeCoA transfer from succinyl-CoA onto 3-oxoadipate by the pcaIJ transferase.curatedindependent
13195OXOADIPYL_COA_THIOLYSISBeta-ketothiolase routeThiolysis of 3-oxoadipyl-CoA to succinyl-CoA and acetyl-CoA.curatedindependent
13296CATECHOL_META_HYDROLYTICExtradiol cleavage, hydrolytic branchCatechol 2,3-dioxygenase followed by hydrolysis of the semialdehyde, releasing formate.curatedaerobic
13396CATECHOL_META_OXALOCROTONATEExtradiol cleavage, 4-oxalocrotonate branchCatechol 2,3-dioxygenase followed by oxidation of the semialdehyde, tautomerisation and decarboxylation.curatedaerobic
13497OXOPENTENOATE_LOWERHydratase-aldolase-dehydrogenase routeHydration to 4-hydroxy-2-oxopentanoate, retro-aldol cleavage to pyruvate and acetaldehyde, and acylating oxidation to acetyl-CoA.curatedindependent
13598PAA_COA_EPOXIDASEAerobic phenylacetyl-CoA epoxidase routeCoA ligation, ring epoxidation, oxepin isomerisation, hydrolytic ring opening and beta-oxidation to 3-oxoadipyl-CoA.curatedaerobic
13699PHENYLPROPANOATE_DIOXYGENASERing-hydroxylating dioxygenase routeDihydroxylation by the hcaEF oxygenase and dehydrogenation of the cis-diol by hcaB.curatedaerobic
137100HPP_MONOOXYGENASEFlavin monooxygenase routeSingle-step hydroxylation by mhpA.curatedaerobic
138101DHPP_EXTRADIOLExtradiol cleavage and hydrolysis routeRing cleavage by mhpB and hydrolysis by mhpC, releasing succinate.curatedaerobic
139102GLN_GSGlutamine synthetase routeSingle ATP-dependent amidation. The same reaction is the first step of the GS-GOGAT route of ammonium assimilation, where the glutamine formed is consumed internally by glutamate synthase rather than released.curatedindependent
140103ALA_TRANSAMINASEAlanine transaminase routeTransamination of pyruvate using L-glutamate, or L-valine in the case of transaminase C.curatedindependent
141103ALA_DEHYDROGENASEAlanine dehydrogenase routeReductive amination of pyruvate with ammonium. The enzyme is freely reversible and runs catabolically in several Firmicutes; gifter claims the encoded chemistry between the boundaries, not the direction of flux.curatedindependent
142104ASP_TRANSAMINASEAspartate aminotransferase routeReversible transamination from L-glutamate, run in the aspartate-forming direction.curatedindependent
143105ASN_AMMONIAAmmonia-dependent ligase routeAsnA amidates aspartate using free ammonium.curatedindependent
144105ASN_GLUTAMINEGlutamine-hydrolysing synthase routeAsnB amidates aspartate using the amide nitrogen of L-glutamine.curatedindependent
145106DAP_SUCCINYLSuccinylated routeSuccinyl protection of the tetrahydrodipicolinate amino group, transamination, desuccinylation and epimerisation. The dominant route in Proteobacteria.curatedindependent
146106DAP_ACETYLAcetylated routeThe same chemistry with acetyl rather than succinyl protection; found mainly in Bacillus.curatedindependent
147106DAP_DEHYDROGENASEDiaminopimelate dehydrogenase routeDirect reductive amination to meso-diaminopimelate, replacing four steps and needing no epimerase.curatedindependent
148106DAP_AMINOTRANSFERASELL-diaminopimelate aminotransferase routeSingle-step transamination to LL-diaminopimelate followed by epimerisation.curatedindependent
149107LYS_DECARBOXYLATIONDiaminopimelate decarboxylase routeSingle PLP-dependent decarboxylation.curatedindependent
150108OIV_CANONICALAcetohydroxyacid routeCondensation of two pyruvates, reductive isomerisation, and dehydration.curatedindependent
151109VAL_TRANSAMINATIONBranched-chain aminotransferase routeTransamination from L-glutamate, run in the valine-forming direction.curatedindependent
152110LEU_CANONICALIsopropylmalate routeAcetyl-CoA condensation, isomerisation through 2-isopropylmaleate, oxidative decarboxylation and transamination.curatedindependent
153111OBU_CITRAMALATECitramalate routeAcetyl-CoA condensation with pyruvate, isomerisation by the isopropylmalate isomerase acting on citramalate, and oxidative decarboxylation.curatedindependent
154112ILE_CANONICALAcetohydroxyacid routeCondensation with pyruvate, reductive isomerisation, dehydration and transamination.curatedindependent
155113PHE_CANONICALPrephenate dehydratase routeChorismate mutase, decarboxylative dehydration to phenylpyruvate, and transamination.curatedindependent
156114TYR_NADNAD-dependent prephenate dehydrogenase routeChorismate mutase, NAD-dependent oxidative decarboxylation, and transamination.curatedindependent
157114TYR_NADPNADP-dependent prephenate dehydrogenase routeThe same chemistry with the NADP-dependent dehydrogenase, a separate orthology group.curatedindependent
158115TRP_CANONICALAnthranilate routeAnthranilate synthesis, phosphoribosyl transfer, isomerisation, ring closure and the tryptophan synthase reaction.curatedindependent
159116HIS_CANONICALCanonical histidine routePhosphoribosyl transfer to ATP, pyrophosphohydrolysis, ring opening, isomerisation, glutamine-dependent cyclisation, dehydration, transamination, dephosphorylation and the two histidinol oxidations.curatedindependent
160117PRO_CANONICALGlutamate 5-kinase routeGlutamate phosphorylation and reduction to the 5-semialdehyde, which cyclises spontaneously, followed by reduction of the pyrroline to proline. The bifunctional P5C synthetase is an alternative system for the first two reactions.curatedindependent
161118ORN_DEACETYLASELinear acetylornithine deacetylase routeAcetylation, phosphorylation, reduction, transamination and hydrolytic deacetylation.curatedindependent
162118ORN_TRANSACETYLASECyclic ornithine acetyltransferase routeThe same chemistry, but the acetyl group is transferred from acetylornithine back onto glutamate rather than hydrolysed, which conserves it.curatedindependent
163119ARG_CANONICALCitrulline routeOrnithine carbamoyltransferase, argininosuccinate synthase and argininosuccinate lyase.curatedindependent
164120ADI_CANONICALArginine deiminase routeArginine deiminase, ornithine carbamoyltransferase run in the phosphorolytic direction, and carbamate kinase run in the ATP-forming direction.curatedindependent
165121HUT_FORMAMIDEFormimidoylglutamase routeHistidase, urocanate hydratase, imidazolonepropionase and formimidoylglutamase.curatedindependent
166122THR_DEAMINATIONThreonine ammonia-lyase routeSingle PLP-dependent deamination.curatedindependent
167123SER_DEAMINATIONL-serine ammonia-lyase routeSingle deamination supported by a complete single-chain iron-sulfur enzyme, both split iron-sulfur subunits, or a K17989-assigned PLP enzyme.curatedindependent
168124GAD_DECARBOXYLATIONGlutamate decarboxylase routeSingle PLP-dependent decarboxylation.curatedindependent
169125TNA_INDOLETryptophanase routeSingle PLP-dependent beta-elimination.curatedindependent
170126MGL_METHANETHIOLMethionine gamma-lyase routeSingle PLP-dependent gamma-elimination.curatedindependent
171127CYS_DESULFIDASECysteine desulfidase routeSingle beta-elimination by a dedicated L-cysteine desulfidase.curatedindependent
172128GRD_STICKLANDGlycine reductase routeSingle reductive deamination by the multi-subunit selenoprotein complex.curatedindependent
173129PRD_STICKLANDD-proline reductase routeProline racemisation followed by reductive ring opening.curatedindependent
174131TCA1_ICDH_NADPNADP-isocitrate dehydrogenase routeNADP-dependent oxidative decarboxylation to 2-oxoglutarate.curatedindependent
175131TCA1_ICDH_NADNAD-isocitrate dehydrogenase routeNAD-dependent oxidative decarboxylation to 2-oxoglutarate.curatedindependent
176132GLYOXYLATE_BYPASS_DIRECTDirect isocitrate-lyase and malate-synthase routeCleavage to succinate and glyoxylate followed by condensation of glyoxylate with acetyl-CoA to malate.curatedindependent
177133N_FIX_MOMolybdenum nitrogenase routeNifHDK catalysis with NifEN and NifB cofactor assembly.curatedanaerobic
178133N_FIX_VVanadium nitrogenase routeVnfHDGK catalysis with VnfEN and NifB cofactor assembly.curatedanaerobic
179134SULFATE_APS_NADPHAPS branch with NADPH sulfite reductaseSulfate activation to APS, direct APS reduction to sulfite, and NADPH-dependent reduction to sulfide.curatedindependent
180134SULFATE_APS_FDAPS branch with ferredoxin sulfite reductaseSulfate activation to APS, direct APS reduction to sulfite, and ferredoxin-dependent reduction to sulfide.curatedindependent
181134SULFATE_PAPS_NADPHPAPS branch with NADPH sulfite reductaseSulfate activation and APS phosphorylation, PAPS reduction to sulfite, and NADPH-dependent reduction to sulfide.curatedindependent
182134SULFATE_PAPS_FDPAPS branch with ferredoxin sulfite reductaseSulfate activation and APS phosphorylation, PAPS reduction to sulfite, and ferredoxin-dependent reduction to sulfide.curatedindependent
183135ECT_ABCEctABC routeEctB forms L-2,4-diaminobutanoate from ASA, EctA acetylates it, and EctC cyclises the acetylated intermediate to L-ectoine.curatedindependent
184136HEME_PROTO_HEMF_HEMYClassical HemF-HemY routeOxygen-dependent coproporphyrinogen and protoporphyrinogen oxidation followed by ferrochelation.curatedaerobic
185136HEME_PROTO_HEMF_HEMGClassical HemF-HemG routeOxygen-dependent HemF followed by menaquinone-dependent HemG and ferrochelation.curatedaerobic
186136HEME_PROTO_HEMF_HEMJClassical HemF-HemJ routeOxygen-dependent HemF followed by HemJ with an unresolved electron acceptor and ferrochelation.curatedaerobic
187136HEME_PROTO_HEMN_HEMYClassical HemN-HemY routeOxygen-independent HemN followed by oxygen-dependent HemY and ferrochelation.curatedaerobic
188136HEME_PROTO_HEMN_HEMGClassical HemN-HemG routeOxygen-independent radical-SAM HemN and menaquinone-dependent HemG followed by ferrochelation.curatedindependent
189136HEME_PROTO_HEMN_HEMJClassical HemN-HemJ routeOxygen-independent HemN and HemJ followed by ferrochelation; the HemJ electron acceptor remains abstract.curatedindependent
190136HEME_COPROCoproporphyrin-dependent HemY-HemH-HemQ routeHemY oxidises coproporphyrinogen, HemH inserts iron into coproporphyrin, and HemQ converts coproheme to heme b.curatedaerobic
191137DHB_CHORISMATEEntC-EntB-EntA catecholate head routeChorismate isomerisation, isochorismate hydrolysis and dehydrogenation form 2,3-dihydroxybenzoate.curatedindependent
192138ENTEROBACTIN_ENTBDEFEntB-EntD-EntE-EntF assembly routeThe activated aryl carrier, phosphopantetheinyl transferase, DHB ligase and serine-activating NRPS jointly assemble enterobactin.curatedindependent
193141BETAINE_BETABetA-BetB routeAcceptor-dependent choline dehydrogenase followed by NAD-dependent betaine-aldehyde dehydrogenase.curatedindependent
194141BETAINE_GBSGbsB-GbsA routeNAD-dependent choline dehydrogenase followed by NAD-dependent betaine-aldehyde dehydrogenase.curatedindependent
195141BETAINE_CMOCholine monooxygenase-BADH routeFerredoxin- and oxygen-dependent choline monooxygenase followed by NAD-dependent betaine-aldehyde dehydrogenase.curatedaerobic
196141BETAINE_CODACholine oxidase routeOne choline oxidase catalyses both oxygen-dependent oxidations from choline through betaine aldehyde to glycine betaine.curatedaerobic
197142SIROHEME_UROGENSiroheme route from uroporphyrinogen IIITwo SAM-dependent methyl transfers, precorrin-2 dehydrogenation and iron insertion form siroheme through multifunctional or split enzyme systems.curatedindependent
198143CHITIN_SACCHARIFICATIONEndochitinase and hexosaminidase routeBackbone endohydrolysis then exo-acting release of GlcNAc, with oxidative chain cleavage as accessory chemistry.curatedindependent
199144MUCIN_SIALIDASESialidase routeHydrolysis of the terminal alpha-linked sialic acid.curatedindependent
200145MUCIN_FUCOSIDASEAlpha-L-fucosidase routeHydrolysis of terminal alpha-L-fucosyl residues.curatedindependent
201146MUCIN_GALNACASEAlpha-N-acetylgalactosaminidase routeHydrolysis of the core alpha-linked N-acetyl-D-galactosamine.curatedindependent
202147PECTIN_SACCHARIFICATIONEndo- and exo-polygalacturonase routeBackbone endohydrolysis then exo-acting release of D-galacturonate, with methyl-ester removal as accessory chemistry.curatedindependent
203148KDG_EDLower Entner-Doudoroff routePhosphorylation of 2-dehydro-3-deoxy-D-gluconate and aldol cleavage of the product into pyruvate and D-glyceraldehyde 3-phosphate.curatedindependent
204149PECTATE_LYASEPectate lyase routeEndo- then exo-acting beta-elimination of the galacturonan backbone, followed by oligogalacturonide lyase, ketol isomerase and 5-dehydrogenase chemistry into the branchpoint. Direct entry on esterified pectin and de-esterification are accessory.curatedindependent
205150ECTOINE_DEG_DOEABDoeAB routeRing hydrolysis followed by deacetylation.curatedindependent
206151HYDROXYECTOINE_ECTDEctD routeSingle hydroxylation by the ectoine dioxygenase.curatedaerobic
207152LACTATE_FROM_LACTALDEHYDELactaldehyde dehydrogenase routeNAD-dependent oxidation of the aldehyde to the acid.curatedindependent
208153AHB_AHBDAhb route with AdoMet-dependent AhbD terminal stepAhbA-AhbB, AhbC and AhbD. The route described for Methanosarcina barkeri and the sulfate-reducing Deltaproteobacteria.curatedindependent
209153AHB_CHDCAhb route with peroxide-dependent HemQ terminal stepAhbA-AhbB and AhbC, closed by the hydrogen peroxide-dependent heme synthase that heme_b_biosynthesis already curates on its coproporphyrin route. KEGG M00847 admits this alternative for its terminal step.curatedaerobic
21020GLCNAC_PTSN-acetylglucosamine PTS routePhosphoenolpyruvate-dependent group translocation to N-acetylglucosamine 6-phosphate, then deacetylation and deamination to fructose 6-phosphate. The non-homologous alternative to the kinase route: the same boundaries, reached without a cytoplasmic kinase.curatedindependent
route_reaction633 rows · 5 columns
route_pkreaction_pkorientationstep_orderrequired
11reverse11
12forward21
13forward31
15forward41
16forward51
17reverse61
110forward71
111forward81
112forward91
114reverse101
21reverse11
22forward21
23forward31
25forward41
26forward51
27reverse61
210forward71
211forward81
213forward91
214reverse101
31reverse11
32forward21
33forward31
35forward41
36forward51
38forward61
39forward71
310forward81
311forward91
312forward101
314reverse111
41reverse11
42forward21
43forward31
45forward41
46forward51
48forward61
49forward71
410forward81
411forward91
413forward101
414reverse111
51reverse11
52forward21
54forward31
55forward41
56forward51
57reverse61
510forward71
511forward81
512forward91
514reverse101
61reverse11
62forward21
64forward31
65forward41
66forward51
67reverse61
610forward71
611forward81
613forward91
614reverse101
71reverse11
72forward21
74forward31
75forward41
76forward51
78forward61
79forward71
710forward81
711forward91
712forward101
714reverse111
81reverse11
82forward21
84forward31
85forward41
86forward51
88forward61
89forward71
810forward81
811forward91
813forward101
814reverse111
915forward11
916forward21
1017forward11
1018forward21
1119forward11
1120forward21
1121reverse31
1122forward41
1125reverse51
1126forward61
1219forward11
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1221reverse31
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3864reverse10
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56109reverse31
57110reverse11
58111forward11
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61115reverse11
61116reverse21
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70141forward11
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71144reverse21
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73150reverse31
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78162reverse11
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82169reverse31
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63119forward11
63120forward21
63121reverse31
63122forward40
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65134reverse71
66135forward11
66136forward21
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68138forward21
69140forward11
89213forward11
89214forward21
90217forward11
90219reverse21
91218forward11
91219reverse21
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94223forward11
95224reverse11
95225forward21
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197417reverse31
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reaction440 rows · 6 columns
reaction_pkreaction_idrhea_masternamedescriptionequation
1RHEA:14905RHEA:14905amidophosphoribosyltransferase reactionPRPP to 5-phosphoribosylamine; used in reverse relative to the Rhea master equation.5-phospho-beta-D-ribosylamine + L-glutamate + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + L-glutamine + H2O
2RHEA:17453RHEA:17453phosphoribosylamine--glycine ligase reactionFormation of phosphoribosylglycinamide.5-phospho-beta-D-ribosylamine + glycine + ATP = N(1)-(5-phospho-beta-D-ribosyl)glycinamide + ADP + phosphate + H(+)
3RHEA:15053RHEA:15053GAR transformylase reactionFolate-dependent formation of phosphoribosyl-N-formylglycinamide.N(1)-(5-phospho-beta-D-ribosyl)glycinamide + (6R)-10-formyltetrahydrofolate = N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide + (6S)-5,6,7,8-tetrahydrofolate + H(+)
4RHEA:24829RHEA:24829GAR formyltransferase 2 reactionFormate- and ATP-dependent alternative formation of phosphoribosyl-N-formylglycinamide.N(1)-(5-phospho-beta-D-ribosyl)glycinamide + formate + ATP = N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide + ADP + phosphate + H(+)
5RHEA:17129RHEA:17129FGAM synthase reactionFormation of phosphoribosylformylglycinamidine.N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide + L-glutamine + ATP + H2O = 2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine + L-glutamate + ADP + phosphate + H(+)
6RHEA:23032RHEA:23032AIR synthetase reactionCyclization to phosphoribosylaminoimidazole.2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + ADP + phosphate + H(+)
7RHEA:10792RHEA:10792AIR carboxylase reactionDirect AIR to CAIR conversion; used in reverse relative to the Rhea master equation.5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + H(+) = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + CO2
8RHEA:19317RHEA:19317N5-CAIR synthetase reactionATP-dependent formation of N5-carboxyaminoimidazole ribonucleotide.5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + hydrogencarbonate + ATP = 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole + ADP + phosphate + 2 H(+)
9RHEA:13193RHEA:13193N5-CAIR mutase reactionConversion of N5-carboxyaminoimidazole ribonucleotide to CAIR.5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole + H(+) = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
10RHEA:22628RHEA:22628SAICAR synthetase reactionFormation of succinylaminoimidazolecarboxamide ribotide.5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate + ATP = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + phosphate + 2 H(+)
11RHEA:23920RHEA:23920SAICAR lyase reactionFormation of AICAR and fumarate.(2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + fumarate
12RHEA:22192RHEA:22192AICAR transformylase reactionFolate-dependent formation of FAICAR.(6R)-10-formyltetrahydrofolate + 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide + (6S)-5,6,7,8-tetrahydrofolate
13RHEA:24836RHEA:24836FAICAR synthetase reactionFormate- and ATP-dependent alternative formation of FAICAR.5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + formate + ATP = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide + ADP + phosphate
14RHEA:18445RHEA:18445IMP cyclohydrolase reactionFAICAR to IMP ring closure; used in reverse relative to the Rhea master equation.IMP + H2O = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
15RHEA:15753RHEA:15753adenylosuccinate synthase reactionFormation of adenylosuccinate from IMP.IMP + L-aspartate + GTP = N(6)-(1,2-dicarboxyethyl)-AMP + GDP + phosphate + 2 H(+)
16RHEA:16853RHEA:16853adenylosuccinate lyase reactionFormation of AMP and fumarate from adenylosuccinate.N(6)-(1,2-dicarboxyethyl)-AMP = fumarate + AMP
17RHEA:11708RHEA:11708IMP dehydrogenase reactionNAD-dependent oxidation of IMP to XMP, committing the guanylate branch.IMP + NAD(+) + H2O = XMP + NADH + H(+)
18RHEA:11680RHEA:11680GMP synthase reactionGlutamine-dependent amination of XMP to GMP.XMP + L-glutamine + ATP + H2O = GMP + L-glutamate + AMP + diphosphate + 2 H(+)
19RHEA:18633RHEA:18633carbamoyl-phosphate synthase reactionGlutamine-dependent formation of carbamoyl phosphate.hydrogencarbonate + L-glutamine + 2 ATP + H2O = carbamoyl phosphate + L-glutamate + 2 ADP + phosphate + 2 H(+)
20RHEA:20013RHEA:20013aspartate carbamoyltransferase reactionFormation of N-carbamoyl-L-aspartate from carbamoyl phosphate and L-aspartate.carbamoyl phosphate + L-aspartate = N-carbamoyl-L-aspartate + phosphate + H(+)
21RHEA:24296RHEA:24296dihydroorotase reactionCyclization to (S)-dihydroorotate; used in reverse relative to the Rhea master equation.(S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate + H(+)
22RHEA:30059RHEA:30059fumarate-dependent dihydroorotate dehydrogenase reactionOxidation of (S)-dihydroorotate to orotate using fumarate.(S)-dihydroorotate + fumarate = orotate + succinate
23RHEA:30187RHEA:30187quinone-dependent dihydroorotate dehydrogenase reactionOxidation of (S)-dihydroorotate to orotate using a quinone.(S)-dihydroorotate + a quinone = orotate + a quinol
24RHEA:13513RHEA:13513NAD-dependent dihydroorotate dehydrogenase reactionOxidation of (S)-dihydroorotate to orotate using NAD(+).(S)-dihydroorotate + NAD(+) = orotate + NADH + H(+)
25RHEA:10380RHEA:10380orotate phosphoribosyltransferase reactionFormation of orotidine 5'-phosphate from orotate and PRPP; used in reverse relative to the Rhea master equation.orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate
26RHEA:11596RHEA:11596orotidine 5'-phosphate decarboxylase reactionFormation of UMP from orotidine 5'-phosphate.orotidine 5'-phosphate + H(+) = UMP + CO2
27RHEA:26426RHEA:26426CTP synthase reactionGlutamine-dependent amination of UTP to CTP.UTP + L-glutamine + ATP + H2O = CTP + L-glutamate + ADP + phosphate + 2 H(+)
28RHEA:12641RHEA:126413-phosphoglycerate dehydrogenase reactionNAD-dependent oxidation of 3-phosphoglycerate to 3-phosphooxypyruvate, the committing step of phosphorylated serine biosynthesis.(2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+)
29RHEA:14329RHEA:14329phosphoserine aminotransferase reactionGlutamate-dependent transamination forming O-phospho-L-serine; used in reverse relative to the Rhea master equation.O-phospho-L-serine + 2-oxoglutarate = 3-phosphooxypyruvate + L-glutamate
30RHEA:21208RHEA:21208phosphoserine phosphatase reactionHydrolysis of O-phospho-L-serine to L-serine.O-phospho-L-serine + H2O = L-serine + phosphate
31RHEA:15481RHEA:15481serine hydroxymethyltransferase reactionFolate-dependent interconversion of serine and glycine; used in reverse relative to the Rhea master equation to form glycine.(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine
32RHEA:23776RHEA:23776aspartate kinase reactionATP-dependent phosphorylation of L-aspartate, the committing step of the aspartate amino acid family.L-aspartate + ATP = 4-phospho-L-aspartate + ADP
33RHEA:24284RHEA:24284aspartate-semialdehyde dehydrogenase reactionNADPH-dependent reduction of 4-phospho-L-aspartate to the semialdehyde; used in reverse relative to the Rhea master equation.L-aspartate 4-semialdehyde + phosphate + NADP(+) = 4-phospho-L-aspartate + NADPH + H(+)
34RHEA:15757RHEA:15757homoserine dehydrogenase reaction (NAD)NAD-dependent reduction of L-aspartate 4-semialdehyde to L-homoserine; used in reverse relative to the Rhea master equation.L-homoserine + NAD(+) = L-aspartate 4-semialdehyde + NADH + H(+)
35RHEA:15761RHEA:15761homoserine dehydrogenase reaction (NADP)NADP-dependent reduction of L-aspartate 4-semialdehyde to L-homoserine; used in reverse relative to the Rhea master equation.L-homoserine + NADP(+) = L-aspartate 4-semialdehyde + NADPH + H(+)
36RHEA:13985RHEA:13985homoserine kinase reactionATP-dependent phosphorylation of L-homoserine to O-phospho-L-homoserine.L-homoserine + ATP = O-phospho-L-homoserine + ADP + H(+)
37RHEA:10840RHEA:10840threonine synthase reactionConversion of O-phospho-L-homoserine to L-threonine.O-phospho-L-homoserine + H2O = L-threonine + phosphate
38RHEA:22008RHEA:22008homoserine O-succinyltransferase reactionSuccinyl-CoA-dependent activation of L-homoserine.L-homoserine + succinyl-CoA = O-succinyl-L-homoserine + CoA
39RHEA:13701RHEA:13701homoserine O-acetyltransferase reactionAcetyl-CoA-dependent activation of L-homoserine.L-homoserine + acetyl-CoA = O-acetyl-L-homoserine + CoA
40RHEA:20397RHEA:20397cystathionine gamma-synthase reaction (O-succinylhomoserine)Cysteine-dependent formation of L,L-cystathionine from O-succinyl-L-homoserine.O-succinyl-L-homoserine + L-cysteine = L,L-cystathionine + succinate + H(+)
41RHEA:30931RHEA:30931cystathionine gamma-synthase reaction (O-acetylhomoserine)Cysteine-dependent formation of L,L-cystathionine from O-acetyl-L-homoserine.O-acetyl-L-homoserine + L-cysteine = L,L-cystathionine + acetate + H(+)
42RHEA:80891RHEA:80891plant cystathionine gamma-synthase reactionCysteine-dependent formation of L,L-cystathionine from O-phospho-L-homoserine.O-phospho-L-homoserine + L-cysteine = L,L-cystathionine + phosphate
43RHEA:13965RHEA:13965cystathionine beta-lyase reactionCleavage of L,L-cystathionine to L-homocysteine and pyruvate.L,L-cystathionine + H2O = L-homocysteine + pyruvate + NH4(+)
44RHEA:27826RHEA:27826O-succinylhomoserine sulfhydrylase reactionDirect incorporation of inorganic sulfide into O-succinyl-L-homoserine to give L-homocysteine.O-succinyl-L-homoserine + hydrogen sulfide = L-homocysteine + succinate
45RHEA:27822RHEA:27822O-acetylhomoserine sulfhydrylase reactionDirect incorporation of inorganic sulfide into O-acetyl-L-homoserine to give L-homocysteine.O-acetyl-L-homoserine + hydrogen sulfide = L-homocysteine + acetate
46RHEA:11172RHEA:11172cobalamin-dependent methionine synthase reactionMethyl transfer from 5-methyltetrahydrofolate to L-homocysteine.(6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine
47RHEA:21196RHEA:21196cobalamin-independent methionine synthase reactionMethyl transfer from 5-methyltetrahydropteroyltriglutamate to L-homocysteine.5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = tetrahydropteroyltri-L-glutamate + L-methionine
48RHEA:24560RHEA:24560serine O-acetyltransferase reactionAcetyl-CoA-dependent activation of L-serine to O-acetyl-L-serine.L-serine + acetyl-CoA = O-acetyl-L-serine + CoA
49RHEA:14829RHEA:14829cysteine synthase reactionIncorporation of inorganic sulfide into O-acetyl-L-serine to give L-cysteine.O-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate
50RHEA:10112RHEA:10112cystathionine beta-synthase reactionCondensation of L-serine with L-homocysteine to give L,L-cystathionine.L-homocysteine + L-serine = L,L-cystathionine + H2O
51RHEA:32743RHEA:32743cystathionine beta-synthase reaction (O-acetyl-L-serine)Condensation of O-acetyl-L-serine with L-homocysteine to give L,L-cystathionine.O-acetyl-L-serine + L-homocysteine = L,L-cystathionine + acetate + H(+)
52RHEA:14005RHEA:14005cystathionine gamma-lyase reactionCleavage of L,L-cystathionine to L-cysteine and 2-oxobutanoate.L,L-cystathionine + H2O = 2-oxobutanoate + L-cysteine + NH4(+)
53RHEA:22816RHEA:22816xylose isomerase reactionalpha-D-xylose = alpha-D-xylulofuranose.alpha-D-xylose = alpha-D-xylulofuranose
54RHEA:10964RHEA:10964xylulokinase reactionD-xylulose + ATP = D-xylulose 5-phosphate + ADP.D-xylulose + ATP = D-xylulose 5-phosphate + ADP + H(+)
55RHEA:14821RHEA:14821L-arabinose isomerase reactionbeta-L-arabinopyranose = L-ribulose.beta-L-arabinopyranose = L-ribulose
56RHEA:22072RHEA:22072L-ribulokinase reactionL-ribulose + ATP = L-ribulose 5-phosphate + ADP.L-ribulose + ATP = L-ribulose 5-phosphate + ADP + H(+)
57RHEA:22368RHEA:22368L-ribulose-5-phosphate 4-epimerase reactionL-ribulose 5-phosphate = D-xylulose 5-phosphate.L-ribulose 5-phosphate = D-xylulose 5-phosphate
58RHEA:17233RHEA:17233L-fucose isomerase reactionL-fucose = L-fuculose.L-fucose = L-fuculose
59RHEA:12376RHEA:12376L-fuculokinase reactionL-fuculose + ATP = L-fuculose 1-phosphate + ADP.L-fuculose + ATP = L-fuculose 1-phosphate + ADP + H(+)
60RHEA:12933RHEA:12933L-fuculose-1-phosphate aldolase reactionL-fuculose 1-phosphate = (S)-lactaldehyde + dihydroxyacetone phosphate.L-fuculose 1-phosphate = (S)-lactaldehyde + dihydroxyacetone phosphate
61RHEA:23160RHEA:23160L-rhamnose isomerase reactionL-rhamnopyranose = L-rhamnulose.L-rhamnopyranose = L-rhamnulose
62RHEA:20117RHEA:20117rhamnulokinase reactionL-rhamnulose + ATP = L-rhamnulose 1-phosphate + ADP.L-rhamnulose + ATP = L-rhamnulose 1-phosphate + ADP + H(+)
63RHEA:19689RHEA:19689rhamnulose-1-phosphate aldolase reactionL-rhamnulose 1-phosphate = (S)-lactaldehyde + dihydroxyacetone phosphate.L-rhamnulose 1-phosphate = (S)-lactaldehyde + dihydroxyacetone phosphate
64RHEA:28675RHEA:28675aldose 1-epimerase reaction on D-galactosealpha-D-galactose = beta-D-galactose; used in reverse for catabolism.alpha-D-galactose = beta-D-galactose
65RHEA:13553RHEA:13553galactokinase reactionalpha-D-galactose + ATP = alpha-D-galactose 1-phosphate + ADP.alpha-D-galactose + ATP = alpha-D-galactose 1-phosphate + ADP + H(+)
66RHEA:13989RHEA:13989galactose-1-phosphate uridylyltransferase reactionalpha-D-galactose 1-phosphate + UDP-alpha-D-glucose = alpha-D-glucose 1-phosphate + UDP-alpha-D-galactose.alpha-D-galactose 1-phosphate + UDP-alpha-D-glucose = alpha-D-glucose 1-phosphate + UDP-alpha-D-galactose
67RHEA:22168RHEA:22168UDP-glucose 4-epimerase reactionUDP-alpha-D-glucose = UDP-alpha-D-galactose; used in reverse to regenerate UDP-glucose.UDP-alpha-D-glucose = UDP-alpha-D-galactose
68RHEA:17417RHEA:17417N-acetylglucosamine kinase reactionN-acetyl-D-glucosamine + ATP = N-acetyl-D-glucosamine 6-phosphate + ADP.N-acetyl-D-glucosamine + ATP = N-acetyl-D-glucosamine 6-phosphate + ADP + H(+)
69RHEA:22936RHEA:22936N-acetylglucosamine-6-phosphate deacetylase reactionN-acetyl-D-glucosamine 6-phosphate + H2O = D-glucosamine 6-phosphate + acetate.N-acetyl-D-glucosamine 6-phosphate + H2O = D-glucosamine 6-phosphate + acetate
70RHEA:12172RHEA:12172glucosamine-6-phosphate deaminase reactionalpha-D-glucosamine 6-phosphate + H2O = beta-D-fructose 6-phosphate + ammonium.alpha-D-glucosamine 6-phosphate + H2O = beta-D-fructose 6-phosphate + NH4(+)
71RHEA:23296RHEA:23296N-acetylneuraminate lyase reactionaceneuramate = aldehydo-N-acetyl-D-mannosamine + pyruvate.aceneuramate = aldehydo-N-acetyl-D-mannosamine + pyruvate
72RHEA:25253RHEA:25253N-acetylmannosamine kinase reactionaldehydo-N-acetyl-D-mannosamine + ATP = aldehydo-N-acetyl-D-mannosamine 6-phosphate + ADP.aldehydo-N-acetyl-D-mannosamine + ATP = aldehydo-N-acetyl-D-mannosamine 6-phosphate + ADP + H(+)
73RHEA:25257RHEA:25257N-acetylmannosamine-6-phosphate 2-epimerase reactionN-acetyl-D-glucosamine 6-phosphate = aldehydo-N-acetyl-D-mannosamine 6-phosphate; used in reverse for catabolism.N-acetyl-D-glucosamine 6-phosphate = aldehydo-N-acetyl-D-mannosamine 6-phosphate
74RHEA:27702RHEA:27702glucuronate isomerase reaction on D-galacturonatealdehydo-D-galacturonate = keto-D-tagaturonate.aldehydo-D-galacturonate = keto-D-tagaturonate
75RHEA:17813RHEA:17813tagaturonate reductase reactionD-altronate + NAD+ = keto-D-tagaturonate + NADH; used in reverse for catabolism.D-altronate + NAD(+) = keto-D-tagaturonate + NADH + H(+)
76RHEA:15957RHEA:15957altronate dehydratase reactionD-altronate = 2-dehydro-3-deoxy-D-gluconate + H2O.D-altronate = 2-dehydro-3-deoxy-D-gluconate + H2O
77RHEA:14797RHEA:147972-dehydro-3-deoxygluconokinase reaction2-dehydro-3-deoxy-D-gluconate + ATP = 2-dehydro-3-deoxy-6-phospho-D-gluconate + ADP.2-dehydro-3-deoxy-D-gluconate + ATP = 2-dehydro-3-deoxy-6-phospho-D-gluconate + ADP + H(+)
78RHEA:17089RHEA:170892-dehydro-3-deoxy-phosphogluconate aldolase reaction2-dehydro-3-deoxy-6-phospho-D-gluconate = D-glyceraldehyde 3-phosphate + pyruvate.2-dehydro-3-deoxy-6-phospho-D-gluconate = D-glyceraldehyde 3-phosphate + pyruvate
79RHEA:13049RHEA:13049glucuronate isomerase reaction on D-glucuronateD-glucuronate = D-fructuronate.D-glucuronate = D-fructuronate
80RHEA:15729RHEA:15729fructuronate reductase reactionD-mannonate + NAD+ = keto-D-fructuronate + NADH; used in reverse for catabolism.D-mannonate + NAD(+) = keto-D-fructuronate + NADH + H(+)
81RHEA:20097RHEA:20097mannonate dehydratase reactionD-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O.D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O
82RHEA:29899RHEA:29899ABC-type D-xylose import reactionD-xylose(out) + ATP + H2O = D-xylose(in) + ADP + phosphate + H(+).D-xylose(out) + ATP + H2O = D-xylose(in) + ADP + phosphate + H(+)
83RHEA:30007RHEA:30007ABC-type L-arabinose import reactionL-arabinose(out) + ATP + H2O = L-arabinose(in) + ADP + phosphate + H(+).L-arabinose(out) + ATP + H2O = L-arabinose(in) + ADP + phosphate + H(+)
84RXN_ARABINOXYLAN_ARAF_RELEASENULLalpha-L-arabinofuranosidase reactionHydrolysis of terminal non-reducing alpha-L-arabinofuranosyl residues from arabinoxylan.NULL
85RXN_XYLAN_ENDO_1_4NULLendo-1,4-beta-xylanase reactionEndohydrolysis of (1->4)-beta-D-xylosidic linkages in xylan.NULL
86RXN_XYLOOLIGO_EXONULLxylan 1,4-beta-xylosidase reactionHydrolysis of (1->4)-beta-D-xylans to remove successive D-xylose residues from the non-reducing end.NULL
87RXN_STARCH_ENDO_1_4NULLalpha-amylase reactionEndohydrolysis of (1->4)-alpha-D-glucosidic linkages in starch.NULL
88RXN_STARCH_DEBRANCH_1_6NULLpullulanase reactionHydrolysis of (1->6)-alpha-D-glucosidic linkages in pullulan and amylopectin.NULL
89RXN_MALTOOLIGO_EXONULLalpha-glucosidase reactionHydrolysis of terminal non-reducing (1->4)-linked alpha-D-glucose residues, releasing alpha-D-glucose.NULL
90RXN_XYLAN_DEACETYLNULLacetylxylan esterase reactionHydrolysis of acetyl groups from the xylan backbone, exposing it to endo-acting xylanases.NULL
91RXN_COLLAGEN_HELIX_CLEAVAGENULLmicrobial collagenase reactionDigestion of native collagen in the triple-helical region at Gly bonds. Rhea covers collagen hydroxylation, glycosylation and crosslinking but contains no proteolytic cleavage of the helix, so this reaction carries no master and is identified by its EC cross-reference.NULL
92RHEA:28042RHEA:28042pyruvate dehydrogenase complex reactionpyruvate + NAD(+) + CoA = acetyl-CoA + CO2 + NADH.pyruvate + NAD(+) + CoA = acetyl-CoA + CO2 + NADH
93RHEA:12765RHEA:12765pyruvate:ferredoxin oxidoreductase reaction2 oxidized [2Fe-2S]-[ferredoxin] + pyruvate + CoA = 2 reduced [2Fe-2S]-[ferredoxin] + acetyl-CoA + CO2 + H(+). Oxygen-sensitive.2 oxidized [2Fe-2S]-[ferredoxin] + pyruvate + CoA = 2 reduced [2Fe-2S]-[ferredoxin] + acetyl-CoA + CO2 + H(+)
94RHEA:11844RHEA:11844pyruvate formate-lyase reactionformate + acetyl-CoA = pyruvate + CoA; used in reverse relative to the Rhea master equation.formate + acetyl-CoA = pyruvate + CoA
95RHEA:19521RHEA:19521phosphate acetyltransferase reactionacetyl-CoA + phosphate = acetyl phosphate + CoA.acetyl-CoA + phosphate = acetyl phosphate + CoA
96RHEA:11352RHEA:11352acetate kinase reactionacetate + ATP = acetyl phosphate + ADP; used in reverse for acetate formation.acetate + ATP = acetyl phosphate + ADP
97RHEA:21036RHEA:21036acetyl-CoA C-acetyltransferase reaction2 acetyl-CoA = acetoacetyl-CoA + CoA.2 acetyl-CoA = acetoacetyl-CoA + CoA
98RHEA:16197RHEA:161973-hydroxybutanoyl-CoA dehydrogenase reaction(3S)-3-hydroxybutanoyl-CoA + NADP(+) = acetoacetyl-CoA + NADPH + H(+); used in reverse. The NAD-dependent RHEA:30799 is the same enzyme's alternative cofactor mode, is annotated to the same orthologue, and is not treated as a genomically distinct route.(3S)-3-hydroxybutanoyl-CoA + NADP(+) = acetoacetyl-CoA + NADPH + H(+)
99RHEA:26558RHEA:265583-hydroxybutanoyl-CoA dehydratase reaction(3S)-3-hydroxybutanoyl-CoA = (2E)-butenoyl-CoA + H2O. The butanoyl-specific reaction is used rather than the generic short-chain master RHEA:52664, because a generic acyl chain length would not fix the product of the route.(3S)-3-hydroxybutanoyl-CoA = (2E)-butenoyl-CoA + H2O
100RHEA:24004RHEA:24004butanoyl-CoA dehydrogenase reactionbutanoyl-CoA + oxidized [electron-transfer flavoprotein] + H(+) = (2E)-butenoyl-CoA + reduced [electron-transfer flavoprotein]; used in reverse.butanoyl-CoA + oxidized [electron-transfer flavoprotein] + H(+) = (2E)-butenoyl-CoA + reduced [electron-transfer flavoprotein]
101RHEA:30071RHEA:30071butanoyl-CoA:acetate CoA-transferase reactionbutanoate + acetyl-CoA = butanoyl-CoA + acetate; used in reverse. The butanoate-specific reaction is used rather than the generic EC 2.8.3.8 master RHEA:13381, whose acyl-CoA is unspecified.butanoate + acetyl-CoA = butanoyl-CoA + acetate
102RHEA:15933RHEA:15933lactaldehyde reductase reaction(S)-propane-1,2-diol + NAD(+) = (S)-lactaldehyde + NADH + H(+); used in reverse.(S)-propane-1,2-diol + NAD(+) = (S)-lactaldehyde + NADH + H(+)
103RHEA:14569RHEA:14569propanediol dehydratase reactionpropane-1,2-diol = propanal + H2O. Adenosylcobalamin-dependent, and stereochemically unspecified in Rhea while the declared boundary is the (S) diol.propane-1,2-diol = propanal + H2O
104RHEA:36027RHEA:36027propionaldehyde dehydrogenase reactionpropanal + NAD(+) + CoA = propanoyl-CoA + NADH + H(+).propanal + NAD(+) + CoA = propanoyl-CoA + NADH + H(+)
105RHEA:28046RHEA:28046phosphate propanoyltransferase reactionpropanoyl-CoA + phosphate = propanoyl phosphate + CoA.propanoyl-CoA + phosphate = propanoyl phosphate + CoA
106RHEA:23148RHEA:23148propionate kinase reactionpropanoate + ATP = propanoyl phosphate + ADP; used in reverse for propionate formation.propanoate + ATP = propanoyl phosphate + ADP
107RXN_LACTATE_COA_TRANSFERNULLpropionate CoA-transferase reaction on lactate(R)-lactate + propanoyl-CoA = (R)-lactoyl-CoA + propanoate. Rhea's EC 2.8.3.1 master RHEA:23520 covers only the propanoate/acetyl-CoA transfer, so the lactate-accepting transfer of the acrylate pathway carries no master and is identified by KEGG R01449, which records it in the opposite direction, and by its EC cross-reference.NULL
108RHEA:34691RHEA:34691lactoyl-CoA dehydratase reaction(R)-lactoyl-CoA = acryloyl-CoA + H2O.(R)-lactoyl-CoA = acryloyl-CoA + H2O
109RHEA:34471RHEA:34471acryloyl-CoA reductase reactionpropanoyl-CoA + NAD(+) = acryloyl-CoA + NADH + H(+); used in reverse.propanoyl-CoA + NAD(+) = acryloyl-CoA + NADH + H(+)
110RHEA:23444RHEA:23444L-lactate dehydrogenase reaction(S)-lactate + NAD(+) = pyruvate + NADH + H(+); used in reverse for lactate formation.(S)-lactate + NAD(+) = pyruvate + NADH + H(+)
111RHEA:10960RHEA:10960lactate racemase reaction(S)-lactate = (R)-lactate.(S)-lactate = (R)-lactate
112RHEA:46276RHEA:46276malolactic enzyme reaction(S)-malate + H(+) = (S)-lactate + CO2. The decarboxylation makes the step irreversible, which is why malate may be a curated boundary while the reversible citric acid cycle reactions may not.(S)-malate + H(+) = (S)-lactate + CO2
113RHEA:10760RHEA:10760citrate lyase reactioncitrate = oxaloacetate + acetate. Rhea also splits the same chemistry into citryl-CoA half-reactions under EC 2.8.3.10 (RHEA:19405) and EC 4.1.3.34 (RHEA:20812); the EC 4.1.3.6 master is curated instead, so that one three-subunit enzyme is one curated step rather than two.citrate = oxaloacetate + acetate
114RHEA:15641RHEA:15641oxaloacetate decarboxylase reactionoxaloacetate + H(+) = pyruvate + CO2.oxaloacetate + H(+) = pyruvate + CO2
115RHEA:23288RHEA:23288acetaldehyde dehydrogenase (acetylating) reactionacetaldehyde + NAD(+) + CoA = acetyl-CoA + NADH + H(+); used in reverse for ethanol formation.acetaldehyde + NAD(+) + CoA = acetyl-CoA + NADH + H(+)
116RHEA:25290RHEA:25290alcohol dehydrogenase reaction on ethanolethanol + NAD(+) = acetaldehyde + NADH + H(+); used in reverse for ethanol formation. Curated at this specificity rather than at the generic primary-alcohol parent RHEA:10736, which would let the route claim a chain length its chemistry does not fix.ethanol + NAD(+) = acetaldehyde + NADH + H(+)
117RHEA:25249RHEA:25249acetolactate synthase reaction2 pyruvate + H(+) = (2S)-2-acetolactate + CO2.2 pyruvate + H(+) = (2S)-2-acetolactate + CO2
118RHEA:21580RHEA:21580acetolactate decarboxylase reaction(2S)-2-acetolactate + H(+) = (R)-acetoin + CO2.(2S)-2-acetolactate + H(+) = (R)-acetoin + CO2
119RHEA:23704RHEA:23704GTP cyclohydrolase II reactionGTP + 4 H2O = 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + formate + 2 phosphate + 3 H(+).GTP + 4 H2O = 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + formate + 2 phosphate + 3 H(+)
120RHEA:21868RHEA:21868diaminohydroxyphosphoribosylaminopyrimidine deaminase reaction2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + H2O + H(+) = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NH4(+).2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + H2O + H(+) = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NH4(+)
121RHEA:17845RHEA:178455-amino-6-(5-phosphoribosylamino)uracil reductase reaction5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP(+) = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH + H(+).5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP(+) = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH + H(+)
122RHEA:25197RHEA:251975-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase reaction5-amino-6-(5-phospho-D-ribitylamino)uracil + H2O = 5-amino-6-(D-ribitylamino)uracil + phosphate.5-amino-6-(5-phospho-D-ribitylamino)uracil + H2O = 5-amino-6-(D-ribitylamino)uracil + phosphate
123RHEA:18457RHEA:184573,4-dihydroxy-2-butanone 4-phosphate synthase reactionD-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate + formate + H(+).D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate + formate + H(+)
124RHEA:26152RHEA:261526,7-dimethyl-8-ribityllumazine synthase reaction(2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + phosphate + 2 H2O + H(+).(2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + phosphate + 2 H2O + H(+)
125RHEA:20772RHEA:20772riboflavin synthase reaction2 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) = 5-amino-6-(D-ribitylamino)uracil + riboflavin.2 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) = 5-amino-6-(D-ribitylamino)uracil + riboflavin
126RHEA:11672RHEA:116724-amino-4-deoxychorismate synthase reactionchorismate + L-glutamine = 4-amino-4-deoxychorismate + L-glutamate.chorismate + L-glutamine = 4-amino-4-deoxychorismate + L-glutamate
127RHEA:16201RHEA:162014-amino-4-deoxychorismate lyase reaction4-amino-4-deoxychorismate = 4-aminobenzoate + pyruvate + H(+).4-amino-4-deoxychorismate = 4-aminobenzoate + pyruvate + H(+)
128RHEA:17473RHEA:17473GTP cyclohydrolase I reactionGTP + H2O = 7,8-dihydroneopterin 3'-triphosphate + formate + H(+).GTP + H2O = 7,8-dihydroneopterin 3'-triphosphate + formate + H(+)
129RHEA:25302RHEA:25302dihydroneopterin triphosphate diphosphatase reaction7,8-dihydroneopterin 3'-triphosphate + H2O = 7,8-dihydroneopterin 3'-phosphate + diphosphate + H(+).7,8-dihydroneopterin 3'-triphosphate + H2O = 7,8-dihydroneopterin 3'-phosphate + diphosphate + H(+)
130RHEA:10540RHEA:10540dihydroneopterin aldolase reaction7,8-dihydroneopterin = 6-hydroxymethyl-7,8-dihydropterin + glycolaldehyde.7,8-dihydroneopterin = 6-hydroxymethyl-7,8-dihydropterin + glycolaldehyde
131RHEA:11412RHEA:114122-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase reaction6-hydroxymethyl-7,8-dihydropterin + ATP = (7,8-dihydropterin-6-yl)methyl diphosphate + AMP + H(+).6-hydroxymethyl-7,8-dihydropterin + ATP = (7,8-dihydropterin-6-yl)methyl diphosphate + AMP + H(+)
132RHEA:19949RHEA:19949dihydropteroate synthase reaction(7,8-dihydropterin-6-yl)methyl diphosphate + 4-aminobenzoate = 7,8-dihydropteroate + diphosphate.(7,8-dihydropterin-6-yl)methyl diphosphate + 4-aminobenzoate = 7,8-dihydropteroate + diphosphate
133RHEA:23584RHEA:23584dihydrofolate synthase reaction7,8-dihydropteroate + L-glutamate + ATP = 7,8-dihydrofolate + ADP + phosphate + H(+).7,8-dihydropteroate + L-glutamate + ATP = 7,8-dihydrofolate + ADP + phosphate + H(+)
134RHEA:15009RHEA:15009dihydrofolate reductase reaction(6S)-5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH + H(+).(6S)-5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH + H(+)
135RHEA:24840RHEA:24840phosphomethylpyrimidine synthase reaction5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + CO + 5'-deoxyadenosine + formate + L-methionine + 3 H(+).5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + CO + 5'-deoxyadenosine + formate + L-methionine + 3 H(+)
136RHEA:19893RHEA:19893phosphomethylpyrimidine kinase reaction4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + ATP = 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + ADP.4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + ATP = 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + ADP
137RHEA:26361RHEA:263612-iminoacetate synthase reactionL-tyrosine + S-adenosyl-L-methionine + NADPH = 2-iminoacetate + 4-methylphenol + 5'-deoxyadenosine + L-methionine + NADP(+).L-tyrosine + S-adenosyl-L-methionine + NADPH = 2-iminoacetate + 4-methylphenol + 5'-deoxyadenosine + L-methionine + NADP(+)
138RHEA:26297RHEA:26297thiazole synthase reaction[ThiS sulfur-carrier protein]-C-terminal-Gly-aminoethanethioate + 2-iminoacetate + 1-deoxy-D-xylulose 5-phosphate = [ThiS sulfur-carrier protein]-C-terminal Gly-Gly + 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + 2 H2O + H(+).[ThiS sulfur-carrier protein]-C-terminal-Gly-aminoethanethioate + 2-iminoacetate + 1-deoxy-D-xylulose 5-phosphate = [ThiS sulfur-carrier protein]-C-terminal Gly-Gly + 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + 2 H2O + H(+)
139RHEA:33343RHEA:33343glycine oxidase reactionglycine + O2 = 2-iminoacetate + H2O2.glycine + O2 = 2-iminoacetate + H2O2
140RHEA:22328RHEA:22328thiamine phosphate synthase reaction4-methyl-5-(2-phosphooxyethyl)-thiazole + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + H(+) = thiamine phosphate + diphosphate.4-methyl-5-(2-phosphooxyethyl)-thiazole + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + H(+) = thiamine phosphate + diphosphate
141RHEA:23096RHEA:23096hydroxymethylpyrimidine kinase reaction4-amino-5-hydroxymethyl-2-methylpyrimidine + ATP = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + ADP + H(+).4-amino-5-hydroxymethyl-2-methylpyrimidine + ATP = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + ADP + H(+)
142RHEA:24212RHEA:24212hydroxyethylthiazole kinase reaction5-(2-hydroxyethyl)-4-methylthiazole + ATP = 4-methyl-5-(2-phosphooxyethyl)-thiazole + ADP + H(+).5-(2-hydroxyethyl)-4-methylthiazole + ATP = 4-methyl-5-(2-phosphooxyethyl)-thiazole + ADP + H(+)
143RHEA:11824RHEA:118243-methyl-2-oxobutanoate hydroxymethyltransferase reaction(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + 3-methyl-2-oxobutanoate + H2O = 2-dehydropantoate + (6S)-5,6,7,8-tetrahydrofolate.(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + 3-methyl-2-oxobutanoate + H2O = 2-dehydropantoate + (6S)-5,6,7,8-tetrahydrofolate
144RHEA:16233RHEA:162332-dehydropantoate 2-reductase reaction(R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH + H(+).(R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH + H(+)
145RHEA:19497RHEA:19497aspartate 1-decarboxylase reactionL-aspartate + H(+) = beta-alanine + CO2.L-aspartate + H(+) = beta-alanine + CO2
146RHEA:10912RHEA:10912pantothenate synthetase reaction(R)-pantoate + beta-alanine + ATP = (R)-pantothenate + AMP + diphosphate + H(+).(R)-pantoate + beta-alanine + ATP = (R)-pantothenate + AMP + diphosphate + H(+)
147RHEA:31507RHEA:31507pyridoxal 5-phosphate synthase reactionaldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + phosphate + 3 H2O + H(+).aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + phosphate + 3 H2O + H(+)
148RHEA:12056RHEA:12056D-erythrose 4-phosphate dehydrogenase reactionD-erythrose 4-phosphate + NAD(+) + H2O = 4-phospho-D-erythronate + NADH + 2 H(+).D-erythrose 4-phosphate + NAD(+) + H2O = 4-phospho-D-erythronate + NADH + 2 H(+)
149RHEA:18829RHEA:18829erythronate-4-phosphate dehydrogenase reaction4-phospho-D-erythronate + NAD(+) = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + NADH + H(+).4-phospho-D-erythronate + NAD(+) = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + NADH + H(+)
150RHEA:16573RHEA:16573phosphohydroxythreonine transaminase reaction4-(phosphooxy)-L-threonine + 2-oxoglutarate = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate.4-(phosphooxy)-L-threonine + 2-oxoglutarate = (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate
151RHEA:32275RHEA:322754-hydroxythreonine-4-phosphate dehydrogenase reaction4-(phosphooxy)-L-threonine + NAD(+) = 3-amino-2-oxopropyl phosphate + CO2 + NADH.4-(phosphooxy)-L-threonine + NAD(+) = 3-amino-2-oxopropyl phosphate + CO2 + NADH
152RHEA:15265RHEA:15265pyridoxine 5-phosphate synthase reaction3-amino-2-oxopropyl phosphate + 1-deoxy-D-xylulose 5-phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O + H(+).3-amino-2-oxopropyl phosphate + 1-deoxy-D-xylulose 5-phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O + H(+)
153RHEA:15149RHEA:15149pyridoxine 5-phosphate oxidase reactionpyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2.pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2
154RHEA:20712RHEA:207128-amino-7-oxononanoate synthase reaction6-carboxyhexanoyl-CoA + L-alanine + H(+) = (8S)-8-amino-7-oxononanoate + CO2 + CoA.6-carboxyhexanoyl-CoA + L-alanine + H(+) = (8S)-8-amino-7-oxononanoate + CO2 + CoA
155RHEA:16861RHEA:16861adenosylmethionine-8-amino-7-oxononanoate transaminase reaction(8S)-8-amino-7-oxononanoate + S-adenosyl-L-methionine = S-adenosyl-4-methylsulfanyl-2-oxobutanoate + (7R,8S)-7,8-diammoniononanoate.(8S)-8-amino-7-oxononanoate + S-adenosyl-L-methionine = S-adenosyl-4-methylsulfanyl-2-oxobutanoate + (7R,8S)-7,8-diammoniononanoate
156RHEA:15805RHEA:15805dethiobiotin synthetase reaction(7R,8S)-7,8-diammoniononanoate + CO2 + ATP = (4R,5S)-dethiobiotin + ADP + phosphate + 3 H(+).(7R,8S)-7,8-diammoniononanoate + CO2 + ATP = (4R,5S)-dethiobiotin + ADP + phosphate + 3 H(+)
157RHEA:22060RHEA:22060biotin synthase reaction(4R,5S)-dethiobiotin + (sulfur carrier)-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = (sulfur carrier)-H + biotin + 2 5'-deoxyadenosine + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin].(4R,5S)-dethiobiotin + (sulfur carrier)-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = (sulfur carrier)-H + biotin + 2 5'-deoxyadenosine + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin]
158RHEA:26329RHEA:26329lysine-8-amino-7-oxononanoate transaminase reaction(8S)-8-amino-7-oxononanoate + L-lysine = (7R,8S)-7,8-diammoniononanoate + (S)-2-amino-6-oxohexanoate.(8S)-8-amino-7-oxononanoate + L-lysine = (7R,8S)-7,8-diammoniononanoate + (S)-2-amino-6-oxohexanoate
159RHEA:25876RHEA:25876L-aspartate oxidase reactionL-aspartate + O2 = iminosuccinate + H2O2.L-aspartate + O2 = iminosuccinate + H2O2
160RHEA:25888RHEA:25888quinolinate synthase reactioniminosuccinate + dihydroxyacetone phosphate = quinolinate + phosphate + 2 H2O + H(+).iminosuccinate + dihydroxyacetone phosphate = quinolinate + phosphate + 2 H2O + H(+)
161RHEA:42440RHEA:42440aspartate dehydrogenase reactionL-aspartate + NAD(+) = iminosuccinate + NADH + H(+).L-aspartate + NAD(+) = iminosuccinate + NADH + H(+)
162RHEA:12733RHEA:12733nicotinate-nucleotide pyrophosphorylase reactionnicotinate beta-D-ribonucleotide + CO2 + diphosphate = quinolinate + 5-phospho-alpha-D-ribose 1-diphosphate + 2 H(+).nicotinate beta-D-ribonucleotide + CO2 + diphosphate = quinolinate + 5-phospho-alpha-D-ribose 1-diphosphate + 2 H(+)
163RHEA:22860RHEA:22860nicotinate-nucleotide adenylyltransferase reactionnicotinate beta-D-ribonucleotide + ATP + H(+) = deamido-NAD(+) + diphosphate.nicotinate beta-D-ribonucleotide + ATP + H(+) = deamido-NAD(+) + diphosphate
164RHEA:21188RHEA:21188NAD synthetase (ammonia) reactiondeamido-NAD(+) + NH4(+) + ATP = AMP + diphosphate + NAD(+) + H(+).deamido-NAD(+) + NH4(+) + ATP = AMP + diphosphate + NAD(+) + H(+)
165RHEA:24384RHEA:24384NAD synthetase (glutamine-hydrolysing) reactiondeamido-NAD(+) + L-glutamine + ATP + H2O = L-glutamate + AMP + diphosphate + NAD(+) + H(+).deamido-NAD(+) + L-glutamine + ATP + H2O = L-glutamate + AMP + diphosphate + NAD(+) + H(+)
166RHEA:36163RHEA:36163nicotinate phosphoribosyltransferase reaction5-phospho-alpha-D-ribose 1-diphosphate + nicotinate + ATP + H2O = nicotinate beta-D-ribonucleotide + ADP + phosphate + diphosphate.5-phospho-alpha-D-ribose 1-diphosphate + nicotinate + ATP + H2O = nicotinate beta-D-ribonucleotide + ADP + phosphate + diphosphate
167RHEA:32459RHEA:32459uroporphyrinogen III C-methyltransferase reactionuroporphyrinogen III + 2 S-adenosyl-L-methionine = precorrin-2 + 2 S-adenosyl-L-homocysteine + H(+).uroporphyrinogen III + 2 S-adenosyl-L-methionine = precorrin-2 + 2 S-adenosyl-L-homocysteine + H(+)
168RHEA:15613RHEA:15613precorrin-2 dehydrogenase reactionprecorrin-2 + NAD(+) = sirohydrochlorin + NADH + 2 H(+).precorrin-2 + NAD(+) = sirohydrochlorin + NADH + 2 H(+)
169RHEA:15893RHEA:15893sirohydrochlorin cobaltochelatase reactionCo-sirohydrochlorin + 2 H(+) = sirohydrochlorin + Co(2+).Co-sirohydrochlorin + 2 H(+) = sirohydrochlorin + Co(2+)
170RHEA:17997RHEA:17997cobalt-factor II C20-methyltransferase reactionCo-precorrin-2 + S-adenosyl-L-methionine = Co-precorrin-3 + S-adenosyl-L-homocysteine + H(+).Co-precorrin-2 + S-adenosyl-L-methionine = Co-precorrin-3 + S-adenosyl-L-homocysteine + H(+)
171RHEA:36155RHEA:36155cobalt-factor III methyltransferase reactionCo(II)-factor III + AH2 + S-adenosyl-L-methionine = Co-precorrin-4 + A + S-adenosyl-L-homocysteine.Co(II)-factor III + AH2 + S-adenosyl-L-methionine = Co-precorrin-4 + A + S-adenosyl-L-homocysteine
172RHEA:26277RHEA:26277cobalt-precorrin-4 C11-methyltransferase reactionCo-precorrin-4 + S-adenosyl-L-methionine = Co-precorrin-5A + S-adenosyl-L-homocysteine + H(+).Co-precorrin-4 + S-adenosyl-L-methionine = Co-precorrin-5A + S-adenosyl-L-homocysteine + H(+)
173RHEA:26281RHEA:26281cobalt-precorrin-5A hydrolase reactionCo-precorrin-5A + H2O = Co-precorrin-5B + acetaldehyde + H(+).Co-precorrin-5A + H2O = Co-precorrin-5B + acetaldehyde + H(+)
174RHEA:26285RHEA:26285cobalt-precorrin-5B C1-methyltransferase reactionCo-precorrin-5B + S-adenosyl-L-methionine = Co-precorrin-6A + S-adenosyl-L-homocysteine.Co-precorrin-5B + S-adenosyl-L-methionine = Co-precorrin-6A + S-adenosyl-L-homocysteine
175RHEA:15625RHEA:15625cobalt-precorrin-6A reductase reactionCo-precorrin-6B + NAD(+) = Co-precorrin-6A + NADH + H(+).Co-precorrin-6B + NAD(+) = Co-precorrin-6A + NADH + H(+)
176RHEA:36067RHEA:36067cobalt-precorrin-6B C15-methyltransferase reactionCo-precorrin-6B + S-adenosyl-L-methionine = Co-precorrin-7 + S-adenosyl-L-homocysteine + CO2.Co-precorrin-6B + S-adenosyl-L-methionine = Co-precorrin-7 + S-adenosyl-L-homocysteine + CO2
177RHEA:34591RHEA:34591cobalt-precorrin-7 C5-methyltransferase reactionCo-precorrin-7 + S-adenosyl-L-methionine = Co-precorrin-8X + S-adenosyl-L-homocysteine + H(+).Co-precorrin-7 + S-adenosyl-L-methionine = Co-precorrin-8X + S-adenosyl-L-homocysteine + H(+)
178RHEA:16209RHEA:16209cobalt-precorrin-8 methylmutase reactionCo-precorrin-8X = cob(II)yrinate.Co-precorrin-8X = cob(II)yrinate
179RHEA:26289RHEA:26289cobyrinate a,c-diamide synthase reactioncob(II)yrinate + 2 L-glutamine + 2 ATP + 2 H2O = cob(II)yrinate a,c diamide + 2 L-glutamate + 2 ADP + 2 phosphate + 2 H(+).cob(II)yrinate + 2 L-glutamine + 2 ATP + 2 H2O = cob(II)yrinate a,c diamide + 2 L-glutamate + 2 ADP + 2 phosphate + 2 H(+)
180RHEA:16841RHEA:16841precorrin-2 C20-methyltransferase reactionprecorrin-2 + S-adenosyl-L-methionine = precorrin-3A + S-adenosyl-L-homocysteine + H(+).precorrin-2 + S-adenosyl-L-methionine = precorrin-3A + S-adenosyl-L-homocysteine + H(+)
181RHEA:17293RHEA:17293precorrin-3B synthase reactionprecorrin-3A + NADH + O2 + 2 H(+) = precorrin-3B + NAD(+) + H2O.precorrin-3A + NADH + O2 + 2 H(+) = precorrin-3B + NAD(+) + H2O
182RHEA:12761RHEA:12761precorrin-3B C17-methyltransferase reactionprecorrin-3B + S-adenosyl-L-methionine = precorrin-4 + S-adenosyl-L-homocysteine + 3 H(+).precorrin-3B + S-adenosyl-L-methionine = precorrin-4 + S-adenosyl-L-homocysteine + 3 H(+)
183RHEA:22012RHEA:22012precorrin-4 C11-methyltransferase reactionprecorrin-4 + S-adenosyl-L-methionine = precorrin-5 + S-adenosyl-L-homocysteine.precorrin-4 + S-adenosyl-L-methionine = precorrin-5 + S-adenosyl-L-homocysteine
184RHEA:18261RHEA:18261precorrin-6A synthase reactionprecorrin-5 + S-adenosyl-L-methionine + H2O = precorrin-6A + acetate + S-adenosyl-L-homocysteine + 2 H(+).precorrin-5 + S-adenosyl-L-methionine + H2O = precorrin-6A + acetate + S-adenosyl-L-homocysteine + 2 H(+)
185RHEA:23408RHEA:23408precorrin-6A reductase reactionprecorrin-6B + NADP(+) = precorrin-6A + NADPH + 2 H(+).precorrin-6B + NADP(+) = precorrin-6A + NADPH + 2 H(+)
186RHEA:17477RHEA:17477precorrin-6B C5,C15-methyltransferase reactionprecorrin-6B + 2 S-adenosyl-L-methionine = precorrin-8X + 2 S-adenosyl-L-homocysteine + CO2 + 3 H(+).precorrin-6B + 2 S-adenosyl-L-methionine = precorrin-8X + 2 S-adenosyl-L-homocysteine + CO2 + 3 H(+)
187RHEA:22512RHEA:22512precorrin-8X methylmutase reactionprecorrin-8X + 3 H(+) = hydrogenobyrinate.precorrin-8X + 3 H(+) = hydrogenobyrinate
188RHEA:12544RHEA:12544hydrogenobyrinate a,c-diamide synthase reactionhydrogenobyrinate + 2 L-glutamine + 2 ATP + 2 H2O = hydrogenobyrinate a,c-diamide + 2 L-glutamate + 2 ADP + 2 phosphate + 2 H(+).hydrogenobyrinate + 2 L-glutamine + 2 ATP + 2 H2O = hydrogenobyrinate a,c-diamide + 2 L-glutamate + 2 ADP + 2 phosphate + 2 H(+)
189RHEA:15341RHEA:15341cobaltochelatase CobNST reactionhydrogenobyrinate a,c-diamide + Co(2+) + ATP + H2O = cob(II)yrinate a,c diamide + ADP + phosphate + 5 H(+).hydrogenobyrinate a,c-diamide + Co(2+) + ATP + H2O = cob(II)yrinate a,c diamide + ADP + phosphate + 5 H(+)
190RHEA:11528RHEA:11528cob(I)yrinate a,c-diamide adenosyltransferase reaction2 cob(II)yrinate a,c diamide + reduced [electron-transfer flavoprotein] + 2 ATP = 2 adenosylcob(III)yrinate a,c-diamide + 2 triphosphate + oxidized [electron-transfer flavoprotein] + 3 H(+).2 cob(II)yrinate a,c diamide + reduced [electron-transfer flavoprotein] + 2 ATP = 2 adenosylcob(III)yrinate a,c-diamide + 2 triphosphate + oxidized [electron-transfer flavoprotein] + 3 H(+)
191RHEA:23256RHEA:23256adenosylcobyric acid synthase reactionadenosylcob(III)yrinate a,c-diamide + 4 L-glutamine + 4 ATP + 4 H2O = adenosylcob(III)yrate + 4 L-glutamate + 4 ADP + 4 phosphate + 4 H(+).adenosylcob(III)yrinate a,c-diamide + 4 L-glutamine + 4 ATP + 4 H2O = adenosylcob(III)yrate + 4 L-glutamate + 4 ADP + 4 phosphate + 4 H(+)
192RHEA:21896RHEA:21896adenosylcobinamide-phosphate synthase reaction(R)-1-aminopropan-2-yl phosphate + adenosylcob(III)yrate + ATP = adenosylcob(III)inamide phosphate + ADP + phosphate + H(+).(R)-1-aminopropan-2-yl phosphate + adenosylcob(III)yrate + ATP = adenosylcob(III)inamide phosphate + ADP + phosphate + H(+)
193RHEA:22712RHEA:22712adenosylcobinamide-phosphate guanylyltransferase reactionadenosylcob(III)inamide phosphate + GTP + H(+) = adenosylcob(III)inamide-GDP + diphosphate.adenosylcob(III)inamide phosphate + GTP + H(+) = adenosylcob(III)inamide-GDP + diphosphate
194RHEA:11196RHEA:11196nicotinate-nucleotide dimethylbenzimidazole phosphoribosyltransferase reaction5,6-dimethylbenzimidazole + nicotinate beta-D-ribonucleotide = alpha-ribazole 5'-phosphate + nicotinate + H(+).5,6-dimethylbenzimidazole + nicotinate beta-D-ribonucleotide = alpha-ribazole 5'-phosphate + nicotinate + H(+)
195RHEA:24456RHEA:24456alpha-ribazole phosphatase reactionalpha-ribazole 5'-phosphate + H2O = alpha-ribazole + phosphate.alpha-ribazole 5'-phosphate + H2O = alpha-ribazole + phosphate
196RHEA:16049RHEA:16049adenosylcobinamide-GDP ribazoletransferase reactionalpha-ribazole + adenosylcob(III)inamide-GDP = adenosylcob(III)alamin + GMP + H(+).alpha-ribazole + adenosylcob(III)inamide-GDP = adenosylcob(III)alamin + GMP + H(+)
197RHEA:27345RHEA:273455,6-dimethylbenzimidazole synthase reactionFMNH2 + O2 = dialurate + 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + H(+).FMNH2 + O2 = dialurate + 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + H(+)
198RHEA:18985RHEA:18985isochorismate synthase reactionchorismate = isochorismate.chorismate = isochorismate
199RHEA:25593RHEA:25593SEPHCHC synthase reactionisochorismate + 2-oxoglutarate + H(+) = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2.isochorismate + 2-oxoglutarate + H(+) = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2
200RHEA:25597RHEA:25597SHCHC synthase reaction5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate = (1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate + pyruvate.5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate = (1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate + pyruvate
201RHEA:10196RHEA:10196o-succinylbenzoate synthase reaction(1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H2O.(1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H2O
202RHEA:17009RHEA:17009o-succinylbenzoate-CoA ligase reaction2-succinylbenzoate + ATP + CoA = 2-succinylbenzoyl-CoA + AMP + diphosphate.2-succinylbenzoate + ATP + CoA = 2-succinylbenzoyl-CoA + AMP + diphosphate
203RHEA:26562RHEA:265621,4-dihydroxy-2-naphthoyl-CoA synthase reaction2-succinylbenzoyl-CoA + H(+) = 1,4-dihydroxy-2-naphthoyl-CoA + H2O.2-succinylbenzoyl-CoA + H(+) = 1,4-dihydroxy-2-naphthoyl-CoA + H2O
204RHEA:26309RHEA:263091,4-dihydroxy-2-naphthoyl-CoA hydrolase reaction1,4-dihydroxy-2-naphthoyl-CoA + H2O = 1,4-dihydroxy-2-naphthoate + CoA + H(+).1,4-dihydroxy-2-naphthoyl-CoA + H2O = 1,4-dihydroxy-2-naphthoate + CoA + H(+)
205RHEA:26478RHEA:264781,4-dihydroxy-2-naphthoate polyprenyltransferase reactionan all-trans-polyprenyl diphosphate + 1,4-dihydroxy-2-naphthoate + H(+) = a 2-demethylmenaquinol + CO2 + diphosphate.an all-trans-polyprenyl diphosphate + 1,4-dihydroxy-2-naphthoate + H(+) = a 2-demethylmenaquinol + CO2 + diphosphate
206RHEA:42640RHEA:42640demethylmenaquinol methyltransferase reactiona 2-demethylmenaquinol + S-adenosyl-L-methionine = a menaquinol + S-adenosyl-L-homocysteine + H(+).a 2-demethylmenaquinol + S-adenosyl-L-methionine = a menaquinol + S-adenosyl-L-homocysteine + H(+)
207RHEA:40051RHEA:40051chorismate dehydratase reactionchorismate = 3-[(1-carboxyvinyl)-oxy]benzoate + H2O.chorismate = 3-[(1-carboxyvinyl)-oxy]benzoate + H2O
208RHEA:33075RHEA:33075aminodeoxyfutalosine synthase reaction3-[(1-carboxyvinyl)-oxy]benzoate + S-adenosyl-L-methionine + H2O = 6-amino-6-deoxyfutalosine + hydrogencarbonate + L-methionine + H(+).3-[(1-carboxyvinyl)-oxy]benzoate + S-adenosyl-L-methionine + H2O = 6-amino-6-deoxyfutalosine + hydrogencarbonate + L-methionine + H(+)
209RHEA:40075RHEA:40075aminodeoxyfutalosine deaminase reaction6-amino-6-deoxyfutalosine + H2O + H(+) = futalosine + NH4(+).6-amino-6-deoxyfutalosine + H2O + H(+) = futalosine + NH4(+)
210RHEA:25904RHEA:25904futalosine hydrolase reactionfutalosine + H2O = dehypoxanthine futalosine + hypoxanthine.futalosine + H2O = dehypoxanthine futalosine + hypoxanthine
211RHEA:33083RHEA:33083cyclic dehypoxanthinyl futalosine synthase reactiondehypoxanthine futalosine + S-adenosyl-L-methionine = cyclic dehypoxanthinylfutalosinate + 5'-deoxyadenosine + L-methionine + H(+).dehypoxanthine futalosine + S-adenosyl-L-methionine = cyclic dehypoxanthinylfutalosinate + 5'-deoxyadenosine + L-methionine + H(+)
212RHEA:33087RHEA:330871,4-dihydroxy-6-naphthoate synthase reactioncyclic dehypoxanthinylfutalosinate = 1,4-dihydroxy-6-naphthoate + dihydroxyacetone.cyclic dehypoxanthinylfutalosinate = 1,4-dihydroxy-6-naphthoate + dihydroxyacetone
213RHEA:16845RHEA:16845citrate synthase reactionoxaloacetate + acetyl-CoA + H2O = citrate + CoA + H(+). Both the si- and the Re-citrate synthases catalyse this one reaction, which is why they are two enzyme systems and not two reactions.oxaloacetate + acetyl-CoA + H2O = citrate + CoA + H(+)
214RHEA:10336RHEA:10336aconitate hydratase reactioncitrate = D-threo-isocitrate. Rhea records the overall isomerisation, so cis-aconitate is not a separate curated step.citrate = D-threo-isocitrate
215RHEA:19629RHEA:19629isocitrate dehydrogenase reaction, NADP-dependentD-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH. The decarboxylation is irreversible, which is what licenses the direction of the GIFT that uses it.D-threo-isocitrate + NADP(+) = 2-oxoglutarate + CO2 + NADPH
216RHEA:23632RHEA:23632isocitrate dehydrogenase reaction, NAD-dependentD-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH.D-threo-isocitrate + NAD(+) = 2-oxoglutarate + CO2 + NADH
217RHEA:27786RHEA:277862-oxoglutarate dehydrogenase complex reaction2-oxoglutarate + NAD(+) + CoA = succinyl-CoA + CO2 + NADH. The overall reaction of the multienzyme complex, not the E1 half-reaction.2-oxoglutarate + NAD(+) + CoA = succinyl-CoA + CO2 + NADH
218RHEA:17297RHEA:172972-oxoglutarate:ferredoxin oxidoreductase reaction2 oxidized ferredoxin + 2-oxoglutarate + CoA = succinyl-CoA + 2 reduced ferredoxin + CO2 + H(+). Genuinely reversible; this is the reductive citric acid cycle enzyme.2 oxidized [2Fe-2S]-[ferredoxin] + 2-oxoglutarate + CoA = succinyl-CoA + 2 reduced [2Fe-2S]-[ferredoxin] + CO2 + H(+)
219RHEA:17661RHEA:17661succinyl-CoA synthetase reactionsuccinate + ATP + CoA = succinyl-CoA + ADP + phosphate. Rhea writes the succinyl-CoA-forming direction, so a route travelling towards succinate records this step as reverse.succinate + ATP + CoA = succinyl-CoA + ADP + phosphate
220RHEA:10524RHEA:105242-oxoglutarate decarboxylase reaction2-oxoglutarate + H(+) = succinate semialdehyde + CO2. The first step of the actinobacterial and cyanobacterial bypass of the dehydrogenase complex.2-oxoglutarate + H(+) = succinate semialdehyde + CO2
221RHEA:13217RHEA:13217succinate-semialdehyde dehydrogenase reaction, NAD-dependentsuccinate semialdehyde + NAD(+) + H2O = succinate + NADH + 2 H(+).succinate semialdehyde + NAD(+) + H2O = succinate + NADH + 2 H(+)
222RHEA:13213RHEA:13213succinate-semialdehyde dehydrogenase reaction, NADP-dependentsuccinate semialdehyde + NADP(+) + H2O = succinate + NADPH + 2 H(+). Curated separately from the NAD form because they are distinct Rhea masters with partly distinct markers.succinate semialdehyde + NADP(+) + H2O = succinate + NADPH + 2 H(+)
223RHEA:40523RHEA:40523succinate dehydrogenase and fumarate reductase reactiona quinone + succinate = fumarate + a quinol. The generic quinone form is curated deliberately: the ubiquinone, menaquinone and rhodoquinone reactions are separate Rhea masters and no genomic marker distinguishes which one an enzyme uses.a quinone + succinate = fumarate + a quinol
224RHEA:12460RHEA:12460fumarate hydratase reaction(S)-malate = fumarate + H2O. Rhea writes the fumarate-forming direction, so a route travelling from fumarate to malate records this step as reverse.(S)-malate = fumarate + H2O
225RHEA:21432RHEA:21432malate dehydrogenase reaction(S)-malate + NAD(+) = oxaloacetate + NADH + H(+). Near equilibrium and reversible in vivo.(S)-malate + NAD(+) = oxaloacetate + NADH + H(+)
226RHEA:46012RHEA:46012malate:quinone oxidoreductase reaction(S)-malate + a quinone = a quinol + oxaloacetate. Effectively unidirectional towards oxaloacetate, and the only step of the fumarate/oxaloacetate arm that is.(S)-malate + a quinone = a quinol + oxaloacetate
227RHEA:14717RHEA:147173-deoxy-7-phosphoheptulonate synthase reactionD-erythrose 4-phosphate + phosphoenolpyruvate + H2O = 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate + phosphate.D-erythrose 4-phosphate + phosphoenolpyruvate + H2O = 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate + phosphate
228RHEA:21968RHEA:219683-dehydroquinate synthase reaction7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate.7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate
229RHEA:21096RHEA:210963-dehydroquinate dehydratase reaction3-dehydroquinate = 3-dehydroshikimate + H2O.3-dehydroquinate = 3-dehydroshikimate + H2O
230RHEA:17737RHEA:17737shikimate dehydrogenase reactionshikimate + NADP(+) = 3-dehydroshikimate + NADPH + H(+); used in reverse relative to the Rhea master equation, because the biosynthetic direction reduces 3-dehydroshikimate.shikimate + NADP(+) = 3-dehydroshikimate + NADPH + H(+)
231RHEA:13121RHEA:13121shikimate kinase reactionshikimate + ATP = 3-phosphoshikimate + ADP + H(+).shikimate + ATP = 3-phosphoshikimate + ADP + H(+)
232RHEA:21256RHEA:212563-phosphoshikimate 1-carboxyvinyltransferase reaction3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3-phosphoshikimate + phosphate. The second of the two phosphoenolpyruvate inputs of the pathway.3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3-phosphoshikimate + phosphate
233RHEA:21020RHEA:21020chorismate synthase reaction5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate.5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate
234RHEA:27874RHEA:27874isochorismate pyruvate lyase reactionisochorismate = salicylate + pyruvate.isochorismate = salicylate + pyruvate
235RHEA:16165RHEA:16165tryptophan 2-monooxygenase reactionL-tryptophan + O2 = indole-3-acetamide + CO2 + H2O.L-tryptophan + O2 = indole-3-acetamide + CO2 + H2O
236RHEA:34371RHEA:34371indole-3-acetamide hydrolase reactionindole-3-acetamide + H2O = (indol-3-yl)acetate + NH4(+).indole-3-acetamide + H2O = (indol-3-yl)acetate + NH4(+)
237RHEA:21368RHEA:21368urate oxidase reactionurate + O2 + H2O = 5-hydroxyisourate + H2O2.urate + O2 + H2O = 5-hydroxyisourate + H2O2
238RHEA:27329RHEA:27329FAD-dependent urate hydroxylase reactionurate + NADH + O2 + H(+) = 5-hydroxyisourate + NAD(+) + H2O.urate + NADH + O2 + H(+) = 5-hydroxyisourate + NAD(+) + H2O
239RHEA:23736RHEA:237365-hydroxyisourate hydrolase reaction5-hydroxyisourate + H2O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate + H(+).5-hydroxyisourate + H2O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate + H(+)
240RHEA:26301RHEA:26301OHCU decarboxylase reaction5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate + H(+) = (S)-allantoin + CO2.5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate + H(+) = (S)-allantoin + CO2
241RHEA:17029RHEA:17029allantoinase reaction(S)-allantoin + H2O = allantoate + H(+).(S)-allantoin + H2O = allantoate + H(+)
242RHEA:11016RHEA:11016allantoicase reactionallantoate + H2O = (S)-ureidoglycolate + urea.allantoate + H2O = (S)-ureidoglycolate + urea
243RHEA:27485RHEA:27485allantoate deiminase reactionallantoate + H2O + 2 H(+) = (S)-2-ureidoglycine + NH4(+) + CO2.allantoate + H2O + 2 H(+) = (S)-2-ureidoglycine + NH4(+) + CO2
244RHEA:25241RHEA:25241(S)-ureidoglycine aminohydrolase reaction(S)-2-ureidoglycine + H2O = (S)-ureidoglycolate + NH4(+).(S)-2-ureidoglycine + H2O = (S)-ureidoglycolate + NH4(+)
245RHEA:11304RHEA:11304ureidoglycolate lyase reaction(S)-ureidoglycolate = urea + glyoxylate.(S)-ureidoglycolate = urea + glyoxylate
246RHEA:20557RHEA:20557urease reactionurea + 2 H2O + H(+) = hydrogencarbonate + 2 NH4(+).urea + 2 H2O + H(+) = hydrogencarbonate + 2 NH4(+)
247RHEA:21068RHEA:21068assimilatory nitrate reductase reactionnitrite + A + H2O = nitrate + AH2; used in reverse for assimilation. The acceptor is unspecified in the Rhea record because the assimilatory nitrate reductase EC was deleted; the marker is nonetheless specific to the assimilatory enzyme.nitrite + A + H2O = nitrate + AH2
248RHEA:21828RHEA:21828ferredoxin-nitrate reductase reactionnitrite + 2 oxidized [2Fe-2S]-[ferredoxin] + H2O = nitrate + 2 reduced [2Fe-2S]-[ferredoxin] + 2 H(+); used in reverse for assimilation.nitrite + 2 oxidized [2Fe-2S]-[ferredoxin] + H2O = nitrate + 2 reduced [2Fe-2S]-[ferredoxin] + 2 H(+)
249RHEA:18041RHEA:18041ferredoxin-nitrite reductase reaction6 oxidized [2Fe-2S]-[ferredoxin] + NH4(+) + 2 H2O = nitrite + 6 reduced [2Fe-2S]-[ferredoxin] + 8 H(+); used in reverse for assimilation.6 oxidized [2Fe-2S]-[ferredoxin] + NH4(+) + 2 H2O = nitrite + 6 reduced [2Fe-2S]-[ferredoxin] + 8 H(+)
250RHEA:24628RHEA:24628nitrite reductase (NADH) reactionNH4(+) + 3 NAD(+) + 2 H2O = nitrite + 3 NADH + 5 H(+); used in reverse for assimilation.NH4(+) + 3 NAD(+) + 2 H2O = nitrite + 3 NADH + 5 H(+)
251RHEA:45700RHEA:45700glycine betaine monooxygenase reactionglycine betaine + NADH + O2 + H(+) = N,N-dimethylglycine + formaldehyde + NAD(+) + H2O.glycine betaine + NADH + O2 + H(+) = N,N-dimethylglycine + formaldehyde + NAD(+) + H2O
252RHEA:74167RHEA:74167N,N-dimethylglycine dehydrogenase (ferredoxin) reactionoxidized 2[4Fe-4S]-[ferredoxin] + N,N-dimethylglycine + H2O = reduced 2[4Fe-4S]-[ferredoxin] + sarcosine + formaldehyde + 2 H(+).oxidized 2[4Fe-4S]-[ferredoxin] + N,N-dimethylglycine + H2O = reduced 2[4Fe-4S]-[ferredoxin] + sarcosine + formaldehyde + 2 H(+)
253RHEA:52856RHEA:52856N,N-dimethylglycine dehydrogenase (ETF) reaction(6S)-5,6,7,8-tetrahydrofolyl-(gamma-L-Glu)(n) + N,N-dimethylglycine + oxidized [electron-transfer flavoprotein] + H(+) = (6R)-5,10-methylenetetrahydrofolyl-(gamma-L-Glu)(n) + sarcosine + reduced [electron-transfer flavoprotein].(6S)-5,6,7,8-tetrahydrofolyl-(gamma-L-Glu)(n) + N,N-dimethylglycine + oxidized [electron-transfer flavoprotein] + H(+) = (6R)-5,10-methylenetetrahydrofolyl-(gamma-L-Glu)(n) + sarcosine + reduced [electron-transfer flavoprotein]
254RHEA:17077RHEA:17077dimethylglycine oxidase reactionN,N-dimethylglycine + O2 + H2O = sarcosine + formaldehyde + H2O2.N,N-dimethylglycine + O2 + H2O = sarcosine + formaldehyde + H2O2
255RHEA:13313RHEA:13313sarcosine oxidase reactionsarcosine + O2 + H2O = formaldehyde + glycine + H2O2.sarcosine + O2 + H2O = formaldehyde + glycine + H2O2
256RHEA:74155RHEA:74155sarcosine dehydrogenase (ferredoxin) reactionoxidized 2[4Fe-4S]-[ferredoxin] + sarcosine + H2O = reduced 2[4Fe-4S]-[ferredoxin] + formaldehyde + glycine + 2 H(+).oxidized 2[4Fe-4S]-[ferredoxin] + sarcosine + H2O = reduced 2[4Fe-4S]-[ferredoxin] + formaldehyde + glycine + 2 H(+)
257RHEA:14533RHEA:14533creatinine amidohydrolase reactioncreatinine + H2O = creatine.creatinine + H2O = creatine
258RHEA:22456RHEA:22456creatinase reactioncreatine + H2O = sarcosine + urea.creatine + H2O = sarcosine + urea
259RHEA:55396RHEA:55396carnitine monooxygenase reaction(R)-carnitine + NADH + O2 + H(+) = (3R)-3-hydroxy-4-oxobutanoate + trimethylamine + NAD(+) + H2O. Rhea also carries the NADPH form as RHEA:55368.(R)-carnitine + NADH + O2 + H(+) = (3R)-3-hydroxy-4-oxobutanoate + trimethylamine + NAD(+) + H2O
260RHEA:19265RHEA:19265carnitine 3-dehydrogenase reactioncarnitine + NAD(+) = 3-dehydrocarnitine + NADH + H(+).carnitine + NAD(+) = 3-dehydrocarnitine + NADH + H(+)
261RHEA:47044RHEA:470443-dehydrocarnitine:acetyl-CoA transferase reaction3-dehydrocarnitine + acetyl-CoA = N,N,N-trimethylglycyl-CoA + acetoacetate.3-dehydrocarnitine + acetyl-CoA = N,N,N-trimethylglycyl-CoA + acetoacetate
262RHEA:45716RHEA:45716betainyl-CoA thioesterase reactionN,N,N-trimethylglycyl-CoA + H2O = glycine betaine + CoA + H(+).N,N,N-trimethylglycyl-CoA + H2O = glycine betaine + CoA + H(+)
263RHEA:30207RHEA:30207methylamine dehydrogenase reaction2 oxidized [amicyanin] + methylamine + H2O = 2 reduced [amicyanin] + formaldehyde + NH4(+) + 2 H(+).2 oxidized [amicyanin] + methylamine + H2O = 2 reduced [amicyanin] + formaldehyde + NH4(+) + 2 H(+)
264RHEA:15909RHEA:15909taurine dioxygenase reactiontaurine + 2-oxoglutarate + O2 = aminoacetaldehyde + sulfite + succinate + CO2 + H(+).taurine + 2-oxoglutarate + O2 = aminoacetaldehyde + sulfite + succinate + CO2 + H(+)
265RHEA:10420RHEA:10420taurine-pyruvate aminotransferase reactiontaurine + pyruvate = sulfoacetaldehyde + L-alanine.taurine + pyruvate = sulfoacetaldehyde + L-alanine
266RHEA:18709RHEA:18709taurine dehydrogenase reactiontaurine + A + H2O = sulfoacetaldehyde + AH2 + NH4(+).taurine + A + H2O = sulfoacetaldehyde + AH2 + NH4(+)
267RHEA:24204RHEA:24204sulfoacetaldehyde acetyltransferase reactionacetyl phosphate + sulfite + H(+) = sulfoacetaldehyde + phosphate; used in reverse for taurine catabolism.acetyl phosphate + sulfite + H(+) = sulfoacetaldehyde + phosphate
268RHEA:14613RHEA:14613ABC-type taurine import reactiontaurine(out) + ATP + H2O = taurine(in) + ADP + phosphate + H(+).taurine(out) + ATP + H2O = taurine(in) + ADP + phosphate + H(+)
269RHEA:16169RHEA:16169glutamine synthetase reactionL-glutamate + NH4(+) + ATP = L-glutamine + ADP + phosphate + H(+).L-glutamate + NH4(+) + ATP = L-glutamine + ADP + phosphate + H(+)
270RHEA:15501RHEA:15501glutamate synthase (NADPH) reaction2 L-glutamate + NADP(+) = L-glutamine + 2-oxoglutarate + NADPH + H(+); used in reverse for assimilation.2 L-glutamate + NADP(+) = L-glutamine + 2-oxoglutarate + NADPH + H(+)
271RHEA:12128RHEA:12128glutamate synthase (ferredoxin) reaction2 oxidized [2Fe-2S]-[ferredoxin] + 2 L-glutamate = L-glutamine + 2 reduced [2Fe-2S]-[ferredoxin] + 2-oxoglutarate + 2 H(+); used in reverse for assimilation.2 oxidized [2Fe-2S]-[ferredoxin] + 2 L-glutamate = L-glutamine + 2 reduced [2Fe-2S]-[ferredoxin] + 2-oxoglutarate + 2 H(+)
272RHEA:11612RHEA:11612glutamate dehydrogenase (NADP+) reactionL-glutamate + NADP(+) + H2O = 2-oxoglutarate + NH4(+) + NADPH + H(+); used in reverse for assimilation.L-glutamate + NADP(+) + H2O = 2-oxoglutarate + NH4(+) + NADPH + H(+)
273RHEA:15133RHEA:15133glutamate dehydrogenase (NAD+) reactionL-glutamate + NAD(+) + H2O = 2-oxoglutarate + NH4(+) + NADH + H(+); used in reverse for assimilation.L-glutamate + NAD(+) + H2O = 2-oxoglutarate + NH4(+) + NADH + H(+)
274RHEA:12633RHEA:12633benzoate 1,2-dioxygenase reactionbenzoate + NADH + O2 + H(+) = (1R,6S)-1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate + NAD(+)benzoate + NADH + O2 + H(+) = (1R,6S)-1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate + NAD(+)
275RHEA:11560RHEA:11560dihydroxycyclohexadiene carboxylate dehydrogenase reaction(1R,6S)-1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate + NAD(+) = catechol + CO2 + NADH(1R,6S)-1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate + NAD(+) = catechol + CO2 + NADH
276RHEA:11072RHEA:11072anthranilate 1,2-dioxygenase reactionanthranilate + NADPH + O2 + 3 H(+) = catechol + NH4(+) + CO2 + NADP(+); Deaminating and decarboxylating; one step from anthranilate to catechol.anthranilate + NADPH + O2 + 3 H(+) = catechol + NH4(+) + CO2 + NADP(+)
277RHEA:57952RHEA:57952phenol 2-monooxygenase reactionphenol + NADH + O2 + H(+) = catechol + NAD(+) + H2Ophenol + NADH + O2 + H(+) = catechol + NAD(+) + H2O
278RHEA:23852RHEA:23852catechol 1,2-dioxygenase reactioncatechol + O2 = cis,cis-muconate + 2 H(+); Intradiol cleavage between the two hydroxyls.catechol + O2 = cis,cis-muconate + 2 H(+)
279RHEA:30031RHEA:30031muconate cycloisomerase reaction(S)-muconolactone = cis,cis-muconate + H(+); Rhea writes the ring-opening direction; degradation uses it in reverse.(S)-muconolactone = cis,cis-muconate + H(+)
280RHEA:12348RHEA:12348muconolactone isomerase reaction(S)-muconolactone = (4,5-dihydro-5-oxofuran-2-yl)-acetate(S)-muconolactone = (4,5-dihydro-5-oxofuran-2-yl)-acetate
281RHEA:10184RHEA:101843-oxoadipate enol-lactonase reaction(4,5-dihydro-5-oxofuran-2-yl)-acetate + H2O = 3-oxoadipate + H(+)(4,5-dihydro-5-oxofuran-2-yl)-acetate + H2O = 3-oxoadipate + H(+)
282RHEA:12048RHEA:120483-oxoadipate CoA-transferase reaction3-oxoadipate + succinyl-CoA = 3-oxoadipyl-CoA + succinate; Succinyl-CoA is the CoA donor and succinate the co-product; neither is a declared boundary of the GIFT that uses this step.3-oxoadipate + succinyl-CoA = 3-oxoadipyl-CoA + succinate
283RHEA:19481RHEA:194813-oxoadipyl-CoA thiolase reactionsuccinyl-CoA + acetyl-CoA = 3-oxoadipyl-CoA + CoA; Rhea writes the condensation direction; degradation uses it in reverse.succinyl-CoA + acetyl-CoA = 3-oxoadipyl-CoA + CoA
284RHEA:17337RHEA:17337catechol 2,3-dioxygenase reactioncatechol + O2 = (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + H(+); Extradiol cleavage adjacent to the hydroxyls.catechol + O2 = (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + H(+)
285RHEA:14549RHEA:145492-hydroxymuconate semialdehyde hydrolase reaction(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + H2O = 2-oxopent-4-enoate + formate + H(+)(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + H2O = 2-oxopent-4-enoate + formate + H(+)
286RHEA:34219RHEA:342192-hydroxymuconate semialdehyde dehydrogenase reaction(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + NAD(+) + H2O = (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H(+)(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + NAD(+) + H2O = (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H(+)
287RHEA:33431RHEA:334312-hydroxymuconate tautomerase reaction(2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (3E)-2-oxohex-3-enedioate(2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (3E)-2-oxohex-3-enedioate
288RHEA:24260RHEA:242604-oxalocrotonate decarboxylase reaction(3E)-2-oxohex-3-enedioate + H(+) = 2-oxopent-4-enoate + CO2(3E)-2-oxohex-3-enedioate + H(+) = 2-oxopent-4-enoate + CO2
289RHEA:22580RHEA:225802-oxopent-4-enoate hydratase reaction(S)-4-hydroxy-2-oxopentanoate = (2Z)-2-hydroxypenta-2,4-dienoate + H2O; Rhea writes the dehydration direction; degradation uses it in reverse. The substrate is the enol tautomer of 2-oxopent-4-enoate.(S)-4-hydroxy-2-oxopentanoate = (2Z)-2-hydroxypenta-2,4-dienoate + H2O
290RHEA:22624RHEA:226244-hydroxy-2-oxovalerate aldolase reaction(S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate(S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate
291RHEA:20956RHEA:20956phenylacetate-CoA ligase reaction2-phenylacetate + ATP + CoA = phenylacetyl-CoA + AMP + diphosphate2-phenylacetate + ATP + CoA = phenylacetyl-CoA + AMP + diphosphate
292RHEA:32171RHEA:32171phenylacetyl-CoA 1,2-epoxidase reactionphenylacetyl-CoA + NADPH + O2 + H(+) = 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA + NADP(+) + H2O; Ring activation without dihydroxylation, which is what distinguishes the CoA-dependent aerobic strategy.phenylacetyl-CoA + NADPH + O2 + H(+) = 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA + NADP(+) + H2O
293RHEA:31843RHEA:31843epoxyphenylacetyl-CoA isomerase reaction2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA = 2-oxepin-2(3H)-ylideneacetyl-CoA2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA = 2-oxepin-2(3H)-ylideneacetyl-CoA
294RHEA:31755RHEA:31755oxepin-CoA hydrolase reaction2-oxepin-2(3H)-ylideneacetyl-CoA + H2O = 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde; Hydrolytic ring opening; the same PaaZ protein carries the following dehydrogenase step.2-oxepin-2(3H)-ylideneacetyl-CoA + H2O = 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde
295RHEA:31747RHEA:317473-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase reaction3-oxo-5,6-dehydrosuberyl-CoA semialdehyde + NADP(+) + H2O = 3-oxo-5,6-didehydrosuberyl-CoA + NADPH + 2 H(+)3-oxo-5,6-dehydrosuberyl-CoA semialdehyde + NADP(+) + H2O = 3-oxo-5,6-didehydrosuberyl-CoA + NADPH + 2 H(+)
296RHEA:34799RHEA:347993-oxo-5,6-didehydrosuberyl-CoA thiolase reaction2,3-didehydroadipoyl-CoA + acetyl-CoA = 3-oxo-5,6-didehydrosuberyl-CoA + CoA; Rhea writes the condensation direction; degradation uses it in reverse. The same PaaJ thiolase catalyses the terminal thiolysis of the route as well.2,3-didehydroadipoyl-CoA + acetyl-CoA = 3-oxo-5,6-didehydrosuberyl-CoA + CoA
297RHEA:76647RHEA:766472,3-didehydroadipoyl-CoA hydratase reaction(3S)-3-hydroxyadipyl-CoA = (E)-2,3-didehydroadipoyl-CoA + H2O; Rhea writes the dehydration direction; degradation uses it in reverse.(3S)-3-hydroxyadipyl-CoA = (E)-2,3-didehydroadipoyl-CoA + H2O
298RHEA:34851RHEA:348513-hydroxyadipyl-CoA dehydrogenase reaction(3S)-3-hydroxyadipyl-CoA + NAD(+) = 3-oxoadipyl-CoA + NADH + H(+)(3S)-3-hydroxyadipyl-CoA + NAD(+) = 3-oxoadipyl-CoA + NADH + H(+)
299RHEA:20357RHEA:203573-phenylpropanoate dioxygenase reaction3-phenylpropanoate + NADH + O2 + H(+) = 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate + NAD(+); Rhea gives trans-cinnamate its own master, RHEA:25058, catalysed by the same enzyme. No marker separates the two substrates, so only this one is curated.3-phenylpropanoate + NADH + O2 + H(+) = 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate + NAD(+)
300RHEA:25062RHEA:25062dihydrodiol dehydrogenase reaction3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate + NAD(+) = 3-(2,3-dihydroxyphenyl)propanoate + NADH + H(+)3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate + NAD(+) = 3-(2,3-dihydroxyphenyl)propanoate + NADH + H(+)
301RHEA:24785RHEA:247853-(3-hydroxyphenyl)propanoate hydroxylase reaction3-(3-hydroxyphenyl)propanoate + NADH + O2 + H(+) = 3-(2,3-dihydroxyphenyl)propanoate + NAD(+) + H2O3-(3-hydroxyphenyl)propanoate + NADH + O2 + H(+) = 3-(2,3-dihydroxyphenyl)propanoate + NAD(+) + H2O
302RHEA:23840RHEA:238402,3-dihydroxyphenylpropanoate 1,2-dioxygenase reaction3-(2,3-dihydroxyphenyl)propanoate + O2 = (2Z,4E)-2-hydroxy-6-oxonona-2,4-dienedioate + H(+); Extradiol cleavage of the catecholic phenylpropanoid.3-(2,3-dihydroxyphenyl)propanoate + O2 = (2Z,4E)-2-hydroxy-6-oxonona-2,4-dienedioate + H(+)
303RHEA:34187RHEA:341872-hydroxy-6-oxononadienedioate hydrolase reaction(2Z,4E)-2-hydroxy-6-oxonona-2,4-dienedioate + H2O = (2Z)-2-hydroxypenta-2,4-dienoate + succinate + H(+); Releases succinate and the enol tautomer of 2-oxopent-4-enoate.(2Z,4E)-2-hydroxy-6-oxonona-2,4-dienedioate + H2O = (2Z)-2-hydroxypenta-2,4-dienoate + succinate + H(+)
304RHEA:10532RHEA:10532tryptophan synthase reactionReplacement of the glycerol phosphate moiety by L-serine, releasing L-tryptophan. The indole intermediate is channelled between the two subunits and is never free, which is why this GIFT does not connect to the indole anchor.(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + L-tryptophan + H2O
305RHEA:10676RHEA:106763-isopropylmalate dehydratase reaction, hydration halfHydration of 2-isopropylmaleate to (2R,3S)-3-isopropylmalate; the second half-reaction of the LeuCD isomerase.(2R,3S)-3-isopropylmalate = 2-isopropylmaleate + H2O
306RHEA:10932RHEA:10932argininosuccinate synthase reactionATP-dependent condensation of L-citrulline with L-aspartate.L-citrulline + L-aspartate + ATP = 2-(N(omega)-L-arginino)succinate + AMP + diphosphate + H(+)
307RHEA:11040RHEA:11040imidazoleglycerol-phosphate dehydratase reactionDehydration to imidazole acetol phosphate.D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O
308RHEA:11372RHEA:11372aspartate--ammonia ligase reactionATP-dependent amidation of L-aspartate with ammonium to L-asparagine.L-aspartate + NH4(+) + ATP = L-asparagine + AMP + diphosphate + H(+)
309RHEA:11768RHEA:11768anthranilate phosphoribosyltransferase reactionTransfer of the phosphoribosyl group of PRPP to anthranilate; run in the biosynthetic direction here.N-(5-phospho-beta-D-ribosyl)anthranilate + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + anthranilate
310RHEA:11960RHEA:11960N-succinyldiaminopimelate aminotransferase reactionTransamination of the succinylated oxo acid to N-succinyl-LL-diaminopimelate.N-succinyl-(2S,6S)-2,6-diaminopimelate + 2-oxoglutarate = (S)-2-succinylamino-6-oxoheptanedioate + L-glutamate
311RHEA:12228RHEA:12228asparagine synthase (glutamine-hydrolysing) reactionATP-dependent amidation of L-aspartate to L-asparagine using the amide nitrogen of L-glutamine.L-aspartate + L-glutamine + ATP + H2O = L-asparagine + L-glutamate + AMP + diphosphate + H(+)
312RHEA:13085RHEA:13085tetrahydrodipicolinate N-acetyltransferase reactionAcetylation of tetrahydrodipicolinate, opening the acetylated branch to diaminopimelate.(S)-2,3,4,5-tetrahydrodipicolinate + acetyl-CoA + H2O = L-2-acetamido-6-oxoheptanedioate + CoA
313RHEA:13493RHEA:13493ketol-acid reductoisomerase reaction (isoleucine branch)Isomerisation and NADPH-dependent reduction of (S)-2-ethyl-2-hydroxy-3-oxobutanoate to (2R,3R)-2,3-dihydroxy-3-methylpentanoate; run in the reductive direction for biosynthesis.(2R,3R)-2,3-dihydroxy-3-methylpentanoate + NADP(+) = (S)-2-ethyl-2-hydroxy-3-oxobutanoate + NADPH + H(+)
314RHEA:13561RHEA:13561diaminopimelate dehydrogenase reactionDirect reductive amination of the tetrahydrodipicolinate ring-opened oxo acid to meso-diaminopimelate, replacing four steps of the acylated routes with one.meso-2,6-diaminopimelate + NADP(+) + H2O = (S)-2-amino-6-oxoheptanedioate + NH4(+) + NADPH + H(+)
315RHEA:13869RHEA:13869prephenate dehydrogenase reaction (NAD)Oxidative decarboxylation of prephenate to 3-(4-hydroxyphenyl)pyruvate using NAD.prephenate + NAD(+) = 3-(4-hydroxyphenyl)pyruvate + CO2 + NADH
316RHEA:13897RHEA:13897chorismate mutase reactionClaisen rearrangement of chorismate to prephenate, the committed step of both phenylalanine and tyrosine biosynthesis.chorismate = prephenate
317RHEA:14109RHEA:14109pyrroline-5-carboxylate reductase reactionReduction of (S)-1-pyrroline-5-carboxylate to L-proline; run in the reductive direction for biosynthesis.L-proline + NADP(+) = (S)-1-pyrroline-5-carboxylate + NADPH + 2 H(+)
318RHEA:14465RHEA:14465histidinol-phosphate phosphatase reactionDephosphorylation of L-histidinol phosphate to L-histidinol.L-histidinol phosphate + H2O = L-histidinol + phosphate
319RHEA:14629RHEA:14629acetylglutamate kinase reactionPhosphorylation of N-acetyl-L-glutamate.N-acetyl-L-glutamate + ATP = N-acetyl-L-glutamyl 5-phosphate + ADP
320RHEA:14877RHEA:14877glutamate 5-kinase reactionPhosphorylation of L-glutamate, the committed step of proline biosynthesis.L-glutamate + ATP = L-glutamyl 5-phosphate + ADP
321RHEA:15093RHEA:15093aromatic aminotransferase reaction (tyrosine)Reversible transamination between L-tyrosine and 3-(4-hydroxyphenyl)pyruvate; run in the biosynthetic direction here.L-tyrosine + 2-oxoglutarate = 3-(4-hydroxyphenyl)pyruvate + L-glutamate
322RHEA:15101RHEA:15101diaminopimelate decarboxylase reactionDecarboxylation of meso-diaminopimelate to L-lysine, the step that commits the shared peptidoglycan precursor to the amino acid.meso-2,6-diaminopimelate + H(+) = L-lysine + CO2
323RHEA:15349RHEA:15349glutamate N-acetyltransferase reactionTransfer of the acetyl group from N-acetyl-L-ornithine to L-glutamate, releasing L-ornithine and regenerating N-acetyl-L-glutamate. The cyclic route conserves the acetyl group instead of hydrolysing it.N(2)-acetyl-L-ornithine + L-glutamate = N-acetyl-L-glutamate + L-ornithine
324RHEA:15393RHEA:15393diaminopimelate epimerase reactionEpimerisation of LL-diaminopimelate to the meso isomer, which is both the lysine precursor and the peptidoglycan cross-link residue.(2S,6S)-2,6-diaminopimelate = meso-2,6-diaminopimelate
325RHEA:15469RHEA:15469phosphoribosylformimino-AICAR-phosphate isomerase reactionAmadori rearrangement of the aminoimidazole carboxamide ribotide intermediate.1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide
326RHEA:15941RHEA:15941acetylornithine deacetylase reactionHydrolytic release of L-ornithine and acetate, the linear route ending of ornithine biosynthesis.N(2)-acetyl-L-ornithine + H2O = L-ornithine + acetate
327RHEA:16293RHEA:162933-isopropylmalate dehydratase reaction, dehydration halfDehydration of (2S)-2-isopropylmalate to 2-isopropylmaleate; the first half-reaction of the LeuCD isomerase.2-isopropylmaleate + H2O = (2S)-2-isopropylmalate
328RHEA:17325RHEA:17325tetrahydrodipicolinate N-succinyltransferase reactionSuccinylation of tetrahydrodipicolinate, opening the succinylated branch to diaminopimelate.(S)-2,3,4,5-tetrahydrodipicolinate + succinyl-CoA + H2O = (S)-2-succinylamino-6-oxoheptanedioate + CoA
329RHEA:18049RHEA:18049acetylornithine aminotransferase reactionTransamination to N-acetyl-L-ornithine; run in the biosynthetic direction here.N(2)-acetyl-L-ornithine + 2-oxoglutarate = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate
330RHEA:18321RHEA:18321branched-chain aminotransferase reaction (leucine)Reversible transamination between L-leucine and 4-methyl-2-oxopentanoate; run in the biosynthetic direction here.L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
331RHEA:18405RHEA:18405alanine dehydrogenase reactionReductive amination of pyruvate to L-alanine with ammonium; freely reversible and run catabolically in several Firmicutes.L-alanine + NAD(+) + H2O = pyruvate + NH4(+) + NADH + H(+)
332RHEA:18473RHEA:18473ATP phosphoribosyltransferase reactionCondensation of PRPP with ATP to phosphoribosyl-ATP; run in the biosynthetic direction here. The committed and feedback-regulated step of histidine biosynthesis.1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP
333RHEA:19045RHEA:19045citramalate synthase reactionCondensation of pyruvate with acetyl-CoA to (3R)-citramalate, the committed step of the threonine-independent isoleucine route.pyruvate + acetyl-CoA + H2O = (3R)-citramalate + CoA + H(+)
334RHEA:19453RHEA:19453alanine transaminase reactionReversible transamination between L-alanine and pyruvate; run in the pyruvate-to-alanine direction for biosynthesis.L-alanine + 2-oxoglutarate = pyruvate + L-glutamate
335RHEA:19513RHEA:19513ornithine carbamoyltransferase reactionCarbamoylation of L-ornithine to L-citrulline. Freely reversible: the biosynthetic direction builds citrulline, and the arginine deiminase pathway runs the same enzyme backwards to recover carbamoyl phosphate.carbamoyl phosphate + L-ornithine = L-citrulline + phosphate + H(+)
336RHEA:19541RHEA:19541glutamate-5-semialdehyde dehydrogenase reactionReduction of L-glutamyl 5-phosphate to the 5-semialdehyde, which cyclises spontaneously to 1-pyrroline-5-carboxylate; run in the reductive direction for biosynthesis.L-glutamate 5-semialdehyde + phosphate + NADP(+) = L-glutamyl 5-phosphate + NADPH + H(+)
337RHEA:20049RHEA:20049phosphoribosyl-AMP cyclohydrolase reactionRing opening of phosphoribosyl-AMP.1-(5-phospho-beta-D-ribosyl)-5'-AMP + H2O = 1-(5-phospho-beta-D-ribosyl)-5-[(5-phospho-beta-D-ribosylamino)methylideneamino]imidazole-4-carboxamide
338RHEA:20405RHEA:20405N-acetyldiaminopimelate deacetylase reactionHydrolytic removal of the acetyl group, releasing LL-diaminopimelate.N-acetyl-(2S,6S)-2,6-diaminopimelate + H2O = (2S,6S)-2,6-diaminopimelate + acetate
339RHEA:21524RHEA:215242-isopropylmalate synthase reactionCondensation of 3-methyl-2-oxobutanoate with acetyl-CoA, the committed step of leucine biosynthesis.3-methyl-2-oxobutanoate + acetyl-CoA + H2O = (2S)-2-isopropylmalate + CoA + H(+)
340RHEA:21540RHEA:21540phosphoribosylanthranilate isomerase reactionAmadori rearrangement of phosphoribosylanthranilate.N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate
341RHEA:21588RHEA:21588N-acetyl-gamma-glutamyl-phosphate reductase reactionReduction to N-acetyl-L-glutamate 5-semialdehyde; run in the reductive direction for biosynthesis.N-acetyl-L-glutamate 5-semialdehyde + phosphate + NADP(+) = N-acetyl-L-glutamyl 5-phosphate + NADPH + H(+)
342RHEA:21640RHEA:21640prephenate dehydrogenase reaction (NADP)Oxidative decarboxylation of prephenate to 3-(4-hydroxyphenyl)pyruvate using NADP.prephenate + NADP(+) = 3-(4-hydroxyphenyl)pyruvate + CO2 + NADPH
343RHEA:21648RHEA:21648prephenate dehydratase reactionDecarboxylative dehydration of prephenate to 3-phenylpyruvate.prephenate + H(+) = 3-phenylpyruvate + CO2 + H2O
344RHEA:21732RHEA:21732anthranilate synthase reactionAmination and aromatisation of chorismate to anthranilate using the amide nitrogen of L-glutamine. KEGG also lists an ammonia-dependent partial reaction for the same enzyme; as with the glutamine-dependent GMP synthase already curated, only the complete glutamine-dependent chemistry is used.chorismate + L-glutamine = anthranilate + pyruvate + L-glutamate + H(+)
345RHEA:21824RHEA:21824aspartate aminotransferase reactionReversible transamination between L-aspartate and oxaloacetate; run in the oxaloacetate-to-aspartate direction for biosynthesis.L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate
346RHEA:22068RHEA:22068ketol-acid reductoisomerase reaction (valine branch)Isomerisation and NADPH-dependent reduction of (2S)-2-acetolactate to (2R)-2,3-dihydroxy-3-methylbutanoate; run in the reductive direction for biosynthesis.(2R)-2,3-dihydroxy-3-methylbutanoate + NADP(+) = (2S)-2-acetolactate + NADPH + H(+)
347RHEA:22332RHEA:223322-methylmalate dehydratase reaction, dehydration halfDehydration of (3R)-citramalate to 2-methylmaleate, catalysed by the isopropylmalate isomerase acting on the citramalate substrate.(3R)-citramalate = 2-methylmaleate + H2O
348RHEA:22608RHEA:22608succinyl-diaminopimelate desuccinylase reactionHydrolytic removal of the succinyl group, releasing LL-diaminopimelate.N-succinyl-(2S,6S)-2,6-diaminopimelate + H2O = (2S,6S)-2,6-diaminopimelate + succinate
349RHEA:22828RHEA:22828phosphoribosyl-ATP pyrophosphohydrolase reactionHydrolysis of the pyrophosphate of phosphoribosyl-ATP.1-(5-phospho-beta-D-ribosyl)-ATP + H2O = 1-(5-phospho-beta-D-ribosyl)-5'-AMP + diphosphate + H(+)
350RHEA:23476RHEA:23476indole-3-glycerol-phosphate synthase reactionRing closure to (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate, which builds the indole ring.1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate + H(+) = (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O
351RHEA:23744RHEA:23744histidinol-phosphate aminotransferase reactionTransamination of imidazole acetol phosphate to L-histidinol phosphate; run in the biosynthetic direction here.L-histidinol phosphate + 2-oxoglutarate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate
352RHEA:23988RHEA:23988LL-diaminopimelate aminotransferase reactionSingle-step transamination of tetrahydrodipicolinate to LL-diaminopimelate, the plant and Chlamydia route.(2S,6S)-2,6-diaminopimelate + 2-oxoglutarate = (S)-2,3,4,5-tetrahydrodipicolinate + L-glutamate + H2O + H(+)
353RHEA:24020RHEA:24020argininosuccinate lyase reactionElimination of fumarate, releasing L-arginine.2-(N(omega)-L-arginino)succinate = fumarate + L-arginine
354RHEA:24292RHEA:24292amino-acid N-acetyltransferase reactionAcetylation of L-glutamate, which protects the amino group through the ornithine branch.L-glutamate + acetyl-CoA = N-acetyl-L-glutamate + CoA + H(+)
355RHEA:24793RHEA:24793imidazole glycerol-phosphate synthase reactionGlutamine-dependent cyclisation to imidazole glycerol phosphate, releasing AICAR into purine metabolism. AICAR is not declared as an anchor: it is an internal participant of the purine GIFT and declaring it would create an edge nobody would read as biology.5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamine = D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate + 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + L-glutamate + H(+)
356RHEA:24801RHEA:24801branched-chain aminotransferase reaction (isoleucine)Reversible transamination between L-isoleucine and (S)-3-methyl-2-oxopentanoate; run in the biosynthetic direction here.L-isoleucine + 2-oxoglutarate = (S)-3-methyl-2-oxopentanoate + L-glutamate
357RHEA:24809RHEA:24809dihydroxy-acid dehydratase reaction (valine branch)Dehydration of (2R)-2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate, the branchpoint 2-oxo acid shared with pantothenate biosynthesis.(2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O
358RHEA:24813RHEA:24813branched-chain aminotransferase reaction (valine)Reversible transamination between L-valine and 3-methyl-2-oxobutanoate; run in the biosynthetic direction here. The same enzyme catalyses the leucine and isoleucine transaminations, which is why the discriminating evidence for each amino acid is its 2-oxo acid supply rather than this step.L-valine + 2-oxoglutarate = 3-methyl-2-oxobutanoate + L-glutamate
359RHEA:25152RHEA:25152aromatic aminotransferase reaction (phenylalanine)Reversible transamination between L-phenylalanine and 3-phenylpyruvate; run in the biosynthetic direction here.L-phenylalanine + 2-oxoglutarate = 3-phenylpyruvate + L-glutamate
360RHEA:25315RHEA:25315N-acetyldiaminopimelate aminotransferase reactionTransamination of the acetylated oxo acid to N-acetyl-LL-diaminopimelate.N-acetyl-(2S,6S)-2,6-diaminopimelate + 2-oxoglutarate = L-2-acetamido-6-oxoheptanedioate + L-glutamate
361RHEA:27654RHEA:27654acetohydroxyacid synthase reaction (isoleucine branch)Condensation of 2-oxobutanoate with pyruvate to (S)-2-ethyl-2-hydroxy-3-oxobutanoate, the isoleucine-specific reaction of the same acetohydroxyacid synthase that condenses two pyruvates in the valine branch.2-oxobutanoate + pyruvate + H(+) = (S)-2-ethyl-2-hydroxy-3-oxobutanoate + CO2
362RHEA:27694RHEA:27694dihydroxy-acid dehydratase reaction (isoleucine branch)Dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate to (S)-3-methyl-2-oxopentanoate.(2R,3R)-2,3-dihydroxy-3-methylpentanoate = (S)-3-methyl-2-oxopentanoate + H2O
363RHEA:32271RHEA:322713-isopropylmalate dehydrogenase reactionOxidative decarboxylation of (2R,3S)-3-isopropylmalate to 4-methyl-2-oxopentanoate. Rhea states the overall reaction, so the spontaneous decarboxylation of the oxosuccinate intermediate is inside it.(2R,3S)-3-isopropylmalate + NAD(+) = 4-methyl-2-oxopentanoate + CO2 + NADH
364RHEA:32715RHEA:327153-methylmalate dehydrogenase reactionOxidative decarboxylation of (2R,3S)-3-methylmalate to 2-oxobutanoate, catalysed by the isopropylmalate dehydrogenase.(2R,3S)-3-methylmalate + NAD(+) = 2-oxobutanoate + CO2 + NADH
365RHEA:33799RHEA:33799histidinol dehydrogenase reaction, first oxidationNAD-dependent oxidation of L-histidinol to L-histidinal.L-histidinol + NAD(+) = L-histidinal + NADH + H(+)
366RHEA:33803RHEA:33803histidinol dehydrogenase reaction, second oxidationNAD-dependent oxidation of L-histidinal to L-histidine.L-histidinal + NAD(+) + H2O = L-histidine + NADH + 2 H(+)
367RHEA:34171RHEA:341714-hydroxy-tetrahydrodipicolinate synthase reactionCondensation of L-aspartate 4-semialdehyde with pyruvate, the committed step of the diaminopimelate pathway.L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O + H(+)
368RHEA:35331RHEA:353314-hydroxy-tetrahydrodipicolinate reductase reaction (NADPH)Reduction and dehydration of (2S,4S)-4-hydroxy-tetrahydrodipicolinate to tetrahydrodipicolinate. The NADH-linked variant RHEA:35323 is the same enzyme with the same orthology group, so it is not curated as a separate route: it would multiply the four diaminopimelate routes without adding any genomic discrimination.(S)-2,3,4,5-tetrahydrodipicolinate + NADP(+) + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NADPH + H(+)
369RHEA:42424RHEA:424242-methylmalate dehydratase reaction, hydration halfHydration of 2-methylmaleate to (2R,3S)-3-methylmalate.2-methylmaleate + H2O = (2R,3S)-3-methylmalate
370RHEA:10152RHEA:10152carbamate kinase reactionInterconversion of carbamoyl phosphate with ammonium and hydrogencarbonate; run in the phosphate-donating direction by the arginine deiminase pathway, where it is the substrate-level ATP-generating step.hydrogencarbonate + NH4(+) + ATP = carbamoyl phosphate + ADP + H2O + H(+)
371RHEA:10680RHEA:10680proline racemase reactionRacemisation of L-proline to D-proline, which is the substrate the proline reductase requires.L-proline = D-proline
372RHEA:12232RHEA:12232glycine reductase reactionReductive deamination of glycine to acetyl phosphate and ammonium by the selenoprotein glycine reductase complex; run in the glycine-consuming direction, which is the Stickland reductive half-reaction.acetyl phosphate + [thioredoxin]-disulfide + NH4(+) + H2O = [thioredoxin]-dithiol + glycine + phosphate + H(+)
373RHEA:12737RHEA:12737D-proline reductase reactionReductive ring opening of D-proline to 5-aminopentanoate by the selenoprotein proline reductase; run in the proline-consuming direction, which is the Stickland reductive half-reaction.[PrdC protein]-Se-L-selenocysteinyl-S-L-cysteine + 5-aminopentanoate = [PrdC protein]-L-selenocysteine/L-cysteine + D-proline
374RHEA:13101RHEA:13101urocanate hydratase reactionHydration of trans-urocanate to 4-imidazolone-5-propanoate; run in the hydration direction for catabolism.4-imidazolone-5-propanoate = trans-urocanate + H2O
375RHEA:17785RHEA:17785glutamate decarboxylase reactionPLP-dependent decarboxylation of L-glutamate to 4-aminobutanoate, consuming a cytoplasmic proton. The reaction is the core of the glutamate-dependent acid resistance system and the source of microbial GABA.L-glutamate + H(+) = 4-aminobutanoate + CO2
376RHEA:19169RHEA:19169serine ammonia-lyase reactionPLP- or iron-sulfur-dependent deamination of L-serine to pyruvate and ammonium, the step that makes serine a fermentable substrate rather than only a biosynthetic product.L-serine = pyruvate + NH4(+)
377RHEA:19553RHEA:19553tryptophanase reactionBeta-elimination of L-tryptophan to indole, pyruvate and ammonium. One PLP enzyme, one orthology group, and the basis of the classical clinical indole test.L-tryptophan + H2O = indole + pyruvate + NH4(+)
378RHEA:19597RHEA:19597arginine deiminase reactionHydrolytic deimination of L-arginine to L-citrulline and ammonium, the committed step of the arginine deiminase pathway.L-arginine + H2O = L-citrulline + NH4(+)
379RHEA:21232RHEA:21232histidine ammonia-lyase reactionNon-oxidative deamination of L-histidine to trans-urocanate, the committed step of histidine catabolism.L-histidine = trans-urocanate + NH4(+)
380RHEA:22108RHEA:22108threonine ammonia-lyase reactionPLP-dependent deamination of L-threonine to 2-oxobutanoate and ammonium. The chemistry is catabolic wherever it runs; the product is also the precursor isoleucine biosynthesis requires, which is why the two capabilities compose across modes rather than duplicating the reaction.L-threonine = 2-oxobutanoate + NH4(+)
381RHEA:22492RHEA:22492formimidoylglutamase reactionHydrolysis of N-formimidoyl-L-glutamate to formamide and L-glutamate, the route that releases the carbon skeleton without a folate-dependent transfer.N-formimidoyl-L-glutamate + H2O = formamide + L-glutamate
382RHEA:23660RHEA:23660imidazolonepropionase reactionRing hydrolysis to N-formimidoyl-L-glutamate.4-imidazolone-5-propanoate + H2O = N-formimidoyl-L-glutamate
383RHEA:23800RHEA:23800methionine gamma-lyase reactionGamma-elimination of L-methionine to methanethiol, 2-oxobutanoate and ammonium. The enzyme also accepts homocysteine and cysteine; the GIFT is named for methionine and this marker is deliberately not used as evidence for any cysteine trait.L-methionine + H2O = methanethiol + 2-oxobutanoate + NH4(+)
384RHEA:24931RHEA:24931cysteine desulfidase reactionBeta-elimination of L-cysteine to hydrogen sulfide, pyruvate and ammonium. Rhea files the same equation under the promiscuous cystathionine gamma-lyase, which is why only the dedicated desulfidase orthology groups are accepted as evidence here.L-cysteine + H2O = hydrogen sulfide + pyruvate + NH4(+) + H(+)
385RHEA:13245RHEA:13245isocitrate lyase reactionD-threo-isocitrate = glyoxylate + succinate.D-threo-isocitrate = glyoxylate + succinate
386RHEA:18181RHEA:18181malate synthase reactionGlyoxylate + acetyl-CoA + water = (S)-malate + CoA + proton.glyoxylate + acetyl-CoA + H2O = (S)-malate + CoA + H(+)
387RHEA:21448RHEA:21448molybdenum nitrogenase reactionDinitrogen + 8 reduced ferredoxin + 16 ATP + water is reduced to 2 ammonium with hydrogen, oxidised ferredoxin, ADP and phosphate. The electron carrier and energy coupling remain internal participants; the declared boundary is dinitrogen to ammonium.N2 + 8 reduced [2Fe-2S]-[ferredoxin] + 16 ATP + 16 H2O = H2 + 8 oxidized [2Fe-2S]-[ferredoxin] + 2 NH4(+) + 16 ADP + 16 phosphate + 6 H(+)
388RHEA:55540RHEA:55540vanadium nitrogenase reactionVanadium-dependent reduction of dinitrogen to ammonium with ferredoxin oxidation, ATP hydrolysis and greater hydrogen formation than the molybdenum reaction.N2 + 12 reduced [2Fe-2S]-[ferredoxin] + 40 ATP + 40 H2O = 3 H2 + 12 oxidized [2Fe-2S]-[ferredoxin] + 2 NH4(+) + 40 ADP + 40 phosphate + 26 H(+)
389RHEA:18133RHEA:18133sulfate adenylyltransferase reactionSulfate + ATP + proton = adenosine 5'-phosphosulfate + diphosphate.sulfate + ATP + H(+) = adenosine 5'-phosphosulfate + diphosphate
390RHEA:24152RHEA:24152adenylylsulfate kinase reactionAdenosine 5'-phosphosulfate + ATP = 3'-phosphoadenylyl sulfate + ADP + proton.adenosine 5'-phosphosulfate + ATP = 3'-phosphoadenylyl sulfate + ADP + H(+)
391RHEA:11724RHEA:11724PAPS reductase reactionRhea writes sulfite + oxidised thioredoxin + adenosine 3',5'-bisphosphate = PAPS + reduced thioredoxin; the assimilatory route traverses it in reverse.[thioredoxin]-disulfide + sulfite + adenosine 3',5'-bisphosphate + 2 H(+) = [thioredoxin]-dithiol + 3'-phosphoadenylyl sulfate
392RHEA:21976RHEA:21976APS reductase reactionRhea writes sulfite + oxidised thioredoxin + AMP = APS + reduced thioredoxin; the assimilatory route traverses it in reverse.[thioredoxin]-disulfide + sulfite + AMP + 2 H(+) = adenosine 5'-phosphosulfate + [thioredoxin]-dithiol
393RHEA:13801RHEA:13801NADPH sulfite reductase reactionRhea writes hydrogen sulfide oxidation to sulfite with NADP reduction; the assimilatory route traverses it in reverse.hydrogen sulfide + 3 NADP(+) + 3 H2O = sulfite + 3 NADPH + 4 H(+)
394RHEA:23132RHEA:23132ferredoxin sulfite reductase reactionRhea writes hydrogen sulfide oxidation to sulfite with ferredoxin reduction; the assimilatory route traverses it in reverse.hydrogen sulfide + 6 oxidized [2Fe-2S]-[ferredoxin] + 3 H2O = sulfite + 6 reduced [2Fe-2S]-[ferredoxin] + 7 H(+)
395RHEA:11160RHEA:11160diaminobutanoate aminotransferase reactionL-2,4-diaminobutanoate + 2-oxoglutarate = L-aspartate 4-semialdehyde + L-glutamate. Ectoine biosynthesis traverses the master in reverse.L-2,4-diaminobutanoate + 2-oxoglutarate = L-aspartate 4-semialdehyde + L-glutamate
396RHEA:16901RHEA:16901diaminobutanoate acetyltransferase reactionL-2,4-diaminobutanoate + acetyl-CoA = N-acetyl-L-2,4-diaminobutanoate + CoA + H(+).L-2,4-diaminobutanoate + acetyl-CoA = (2S)-4-acetamido-2-aminobutanoate + CoA + H(+)
397RHEA:17281RHEA:17281ectoine synthase reactionN-acetyl-L-2,4-diaminobutanoate = L-ectoine + water.(2S)-4-acetamido-2-aminobutanoate = L-ectoine + H2O
398RHEA:19865RHEA:19865uroporphyrinogen III decarboxylase reactionuroporphyrinogen III + 4 H(+) = coproporphyrinogen III + 4 carbon dioxide.uroporphyrinogen III + 4 H(+) = coproporphyrinogen III + 4 CO2
399RHEA:18257RHEA:18257oxygen-dependent coproporphyrinogen oxidase reactioncoproporphyrinogen III + oxygen + 2 H(+) = protoporphyrinogen IX + 2 carbon dioxide + 2 water.coproporphyrinogen III + O2 + 2 H(+) = protoporphyrinogen IX + 2 CO2 + 2 H2O
400RHEA:15425RHEA:15425oxygen-independent coproporphyrinogen oxidase reactioncoproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 5'-deoxyadenosine + 2 L-methionine + 2 carbon dioxide.coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 5'-deoxyadenosine + 2 L-methionine + 2 CO2
401RHEA:25576RHEA:25576oxygen-dependent protoporphyrinogen oxidase reactionprotoporphyrinogen IX + 3 oxygen = protoporphyrin IX + 3 hydrogen peroxide.protoporphyrinogen IX + 3 O2 = protoporphyrin IX + 3 H2O2
402RHEA:27409RHEA:27409menaquinone-dependent protoporphyrinogen oxidase reactionprotoporphyrinogen IX + 3 menaquinone = protoporphyrin IX + 3 menaquinol.protoporphyrinogen IX + 3 a menaquinone = protoporphyrin IX + 3 a menaquinol
403RHEA:62000RHEA:62000HemJ protoporphyrinogen oxidase reactionprotoporphyrinogen IX + 3 A = protoporphyrin IX + 3 AH2. Rhea leaves the electron acceptor abstract; the HemJ marker identifies the enzyme.protoporphyrinogen IX + 3 A = protoporphyrin IX + 3 AH2
404RHEA:22584RHEA:22584protoporphyrin ferrochelatase reactionheme b + 2 H(+) = protoporphyrin IX + Fe(2+). Heme biosynthesis traverses the master in reverse.heme b + 2 H(+) = protoporphyrin IX + Fe(2+)
405RHEA:43436RHEA:43436coproporphyrinogen III oxidase reactioncoproporphyrinogen III + 3 oxygen = coproporphyrin III + 3 hydrogen peroxide.coproporphyrinogen III + 3 O2 = coproporphyrin III + 3 H2O2
406RHEA:49572RHEA:49572coproporphyrin ferrochelatase reactionFe-coproporphyrin III + 2 H(+) = coproporphyrin III + Fe(2+). Heme biosynthesis traverses the master in reverse.Fe-coproporphyrin III + 2 H(+) = coproporphyrin III + Fe(2+)
407RHEA:56516RHEA:56516hydrogen peroxide-dependent heme synthase reactionFe-coproporphyrin III + 2 hydrogen peroxide + 2 H(+) = heme b + 2 carbon dioxide + 4 water.Fe-coproporphyrin III + 2 H2O2 + 2 H(+) = heme b + 2 CO2 + 4 H2O
408RHEA:11112RHEA:11112isochorismate lyase reactionisochorismate + water = 2,3-dihydro-2,3-dihydroxybenzoate + pyruvate.isochorismate + H2O = (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate
409RHEA:23824RHEA:238242,3-dihydro-2,3-dihydroxybenzoate dehydrogenase reaction2,3-dihydro-2,3-dihydroxybenzoate + NAD(+) = 2,3-dihydroxybenzoate + NADH + H(+).(2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + NAD(+) = 2,3-dihydroxybenzoate + NADH + H(+)
410RHEA:30571RHEA:30571enterobactin synthetase aggregate reaction3 2,3-dihydroxybenzoate + 3 L-serine + 6 ATP = enterobactin + 6 AMP + 6 diphosphate + 4 H(+). The complete enzyme system includes carrier activation and both NRPS substrates.3 2,3-dihydroxybenzoate + 3 L-serine + 6 ATP = enterobactin + 6 AMP + 6 diphosphate + 4 H(+)
411RHEA:17433RHEA:17433acceptor-dependent choline dehydrogenase reactioncholine + A = betaine aldehyde + AH2.choline + A = betaine aldehyde + AH2
412RHEA:33051RHEA:33051NAD-dependent choline dehydrogenase reactioncholine + NAD(+) = betaine aldehyde + NADH + H(+).choline + NAD(+) = betaine aldehyde + NADH + H(+)
413RHEA:17769RHEA:17769choline monooxygenase reactioncholine + reduced ferredoxin + oxygen + protons = betaine aldehyde hydrate + oxidized ferredoxin + water.choline + 2 reduced [2Fe-2S]-[ferredoxin] + O2 + 2 H(+) = betaine aldehyde hydrate + 2 oxidized [2Fe-2S]-[ferredoxin] + H2O
414RHEA:13505RHEA:13505choline oxidase first reactioncholine + oxygen = betaine aldehyde + hydrogen peroxide.choline + O2 = betaine aldehyde + H2O2
415RHEA:20369RHEA:20369choline oxidase second reactionbetaine aldehyde + oxygen + water = glycine betaine + hydrogen peroxide + H(+).betaine aldehyde + O2 + H2O = glycine betaine + H2O2 + H(+)
416RHEA:15305RHEA:15305betaine-aldehyde dehydrogenase reactionbetaine aldehyde + NAD(+) + water = glycine betaine + NADH + 2 H(+). The NADP reaction is not materialised because the same accepted KO serves both and adds no genomic discrimination.betaine aldehyde + NAD(+) + H2O = glycine betaine + NADH + 2 H(+)
417RHEA:24360RHEA:24360sirohydrochlorin ferrochelatase reactionsiroheme + 2 H(+) = sirohydrochlorin + Fe(2+).siroheme + 2 H(+) = sirohydrochlorin + Fe(2+)
418RXN_CHITIN_ENDONULLendochitinase reactionRandom endohydrolysis of (1->4)-beta-linkages of N-acetyl-D-glucosamine in chitin, releasing chito-oligosaccharides.NULL
419RXN_CHITOBIOSE_EXONULLbeta-N-acetylhexosaminidase reactionHydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues from chito-oligosaccharides, releasing free GlcNAc.NULL
420RXN_CHITIN_LPMONULLlytic chitin monooxygenase reactionOxidative cleavage of crystalline chitin chains, generating new chain ends for the endo-acting chitinase.NULL
421RXN_MUCIN_NEUAC_RELEASENULLmucin sialidase reactionHydrolysis of terminal alpha-linked N-acetylneuraminate from mucin O-glycan, exposing the underlying chain.NULL
422RXN_MUCIN_FUCOSE_RELEASENULLmucin alpha-L-fucosidase reactionHydrolysis of terminal alpha-L-fucosyl residues from mucin O-glycan, releasing free L-fucose.NULL
423RXN_MUCIN_GALNAC_RELEASENULLmucin alpha-N-acetylgalactosaminidase reactionHydrolysis of the terminal alpha-linked N-acetyl-D-galactosamine of the mucin O-glycan core.NULL
424RXN_PECTIN_ENDO_PGNULLendo-polygalacturonase reactionRandom endohydrolysis of (1->4)-alpha-D-galactosiduronic linkages in pectate, releasing oligogalacturonides.NULL
425RXN_OLIGOGALACTURONIDE_EXONULLexo-polygalacturonase reactionHydrolysis of oligogalacturonides from the non-reducing end, releasing successive D-galacturonate residues.NULL
426RXN_PECTIN_DEMETHYLNULLpectinesterase reactionHydrolysis of the methyl esters of the galacturonan backbone, exposing it to the depolymerising enzymes.NULL
427RXN_PECTATE_ENDO_PLNULLpectate lyase reactionEliminative cleavage of (1->4)-alpha-D-galacturonan to give oligosaccharides carrying 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends.NULL
428RHEA:57104RHEA:57104pectate disaccharide-lyase reaction[(1->4)-alpha-D-galacturonosyl](n) = 4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate + [(1->4)-alpha-D-galacturonosyl](n-2).[(1->4)-alpha-D-galacturonosyl](n) = 4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate + [(1->4)-alpha-D-galacturonosyl](n-2)
429RHEA:20269RHEA:20269oligogalacturonide lyase reaction4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate = 2 5-dehydro-4-deoxy-D-glucuronate.4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate = 2 5-dehydro-4-deoxy-D-glucuronate
430RHEA:23896RHEA:238964-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase reaction5-dehydro-4-deoxy-D-glucuronate = 3-deoxy-D-glycero-2,5-hexodiulosonate.5-dehydro-4-deoxy-D-glucuronate = 3-deoxy-D-glycero-2,5-hexodiulosonate
431RHEA:24232RHEA:242322-dehydro-3-deoxy-D-gluconate 5-dehydrogenase reaction2-dehydro-3-deoxy-D-gluconate + NAD+ = 3-deoxy-D-glycero-2,5-hexodiulosonate + NADH + H(+); used in reverse for catabolism.2-dehydro-3-deoxy-D-gluconate + NAD(+) = 3-deoxy-D-glycero-2,5-hexodiulosonate + NADH + H(+)
432RXN_PECTIN_LYASENULLpectin lyase reactionEliminative cleavage of (1->4)-alpha-D-galacturonan methyl ester, acting on the esterified backbone without prior de-esterification.NULL
433RHEA:52304RHEA:52304ectoine hydrolase reactionL-ectoine + H2O = (2S)-2-acetamido-4-aminobutanoate. DoeA opens the ectoine ring, the committed step of ectoine catabolism.L-ectoine + H2O = (2S)-2-acetamido-4-aminobutanoate
434RHEA:40951RHEA:40951N2-acetyl-L-2,4-diaminobutanoate deacetylase reaction(2S)-2-acetamido-4-aminobutanoate + H2O = L-2,4-diaminobutanoate + acetate. DoeB removes the acetyl group EctA installed during biosynthesis.(2S)-2-acetamido-4-aminobutanoate + H2O = L-2,4-diaminobutanoate + acetate
435RHEA:45740RHEA:45740ectoine hydroxylase reactionL-ectoine + 2-oxoglutarate + O2 = 5-hydroxyectoine + succinate + CO2. A 2-oxoglutarate-dependent dioxygenase; the co-substrate and its succinate product are internal chemistry and are not anchors, as for the taurine dioxygenase.L-ectoine + 2-oxoglutarate + O2 = 5-hydroxyectoine + succinate + CO2
436RHEA:14277RHEA:14277lactaldehyde dehydrogenase reaction(S)-lactaldehyde + NAD(+) + H2O = (S)-lactate + NADH + 2 H(+). The oxidative fate of lactaldehyde, alternative to its reduction to propane-1,2-diol.(S)-lactaldehyde + NAD(+) + H2O = (S)-lactate + NADH + 2 H(+)
437RHEA:19093RHEA:19093siroheme decarboxylase reactionsiroheme + 2 H(+) = 12,18-didecarboxysiroheme + 2 carbon dioxide.siroheme + 2 H(+) = 12,18-didecarboxysiroheme + 2 CO2
438RHEA:37431RHEA:37431Fe-coproporphyrin III synthase reaction12,18-didecarboxysiroheme + 2 reduced acceptor + 2 S-adenosyl-L-methionine = Fe-coproporphyrin III + 2 5'-deoxyadenosine + 2 L-methionine + 2 acetate + 2 acceptor + 2 H(+).12,18-didecarboxysiroheme + 2 AH2 + 2 S-adenosyl-L-methionine = Fe-coproporphyrin III + 2 5'-deoxyadenosine + 2 L-methionine + 2 acetate + 2 A + 2 H(+)
439RHEA:56520RHEA:56520AdoMet-dependent heme synthase reactionFe-coproporphyrin III + 2 S-adenosyl-L-methionine = heme b + 2 5'-deoxyadenosine + 2 L-methionine + 2 carbon dioxide.Fe-coproporphyrin III + 2 S-adenosyl-L-methionine = heme b + 2 5'-deoxyadenosine + 2 L-methionine + 2 CO2
440RHEA:49240RHEA:49240N-acetylglucosamine phosphotransferase system translocation reactionN(pros)-phospho-L-histidyl-[protein] + N-acetyl-D-glucosamine(out) = N-acetyl-D-glucosamine 6-phosphate(in) + L-histidyl-[protein]. Phosphoenolpyruvate-dependent group translocation: the sugar crosses the membrane and is phosphorylated in one step, so a cell using it never needs a cytoplasmic N-acetylglucosamine kinase.N(pros)-phospho-L-histidyl-[protein] + N-acetyl-D-glucosamine(out) = N-acetyl-D-glucosamine 6-phosphate(in) + L-histidyl-[protein]
reaction_xref764 rows · 4 columns
reaction_pknamespaceaccessionnotes
1KEGG_REACTIONR01072NULL
1EC2.4.2.14NULL
2KEGG_REACTIONR04144NULL
2EC6.3.4.13NULL
3KEGG_REACTIONR04325NULL
3EC2.1.2.2NULL
4KEGG_REACTIONR06974NULL
4EC6.3.1.21NULL
5KEGG_REACTIONR04463NULL
5EC6.3.5.3NULL
6KEGG_REACTIONR04208NULL
6EC6.3.3.1NULL
7KEGG_REACTIONR04209NULL
7EC4.1.1.21NULL
8KEGG_REACTIONR07404NULL
8EC6.3.4.18NULL
9KEGG_REACTIONR07405NULL
9EC5.4.99.18NULL
10KEGG_REACTIONR04591NULL
10EC6.3.2.6NULL
11KEGG_REACTIONR04559NULL
11EC4.3.2.2NULL
12KEGG_REACTIONR04560NULL
12EC2.1.2.3NULL
13KEGG_REACTIONR06975NULL
13EC6.3.4.23NULL
14KEGG_REACTIONR01127NULL
14EC3.5.4.10NULL
15KEGG_REACTIONR01135NULL
15EC6.3.4.4NULL
16KEGG_REACTIONR01083NULL
16EC4.3.2.2NULL
17KEGG_REACTIONR01130NULL
17EC1.1.1.205NULL
18KEGG_REACTIONR01231NULL
18EC6.3.5.2NULL
19KEGG_REACTIONR00575NULL
19EC6.3.5.5NULL
20KEGG_REACTIONR01397NULL
20EC2.1.3.2NULL
21KEGG_REACTIONR01993NULL
21EC3.5.2.3NULL
22KEGG_REACTIONR01867NULL
22EC1.3.98.1NULL
23KEGG_REACTIONR01868NULL
23EC1.3.5.2NULL
24KEGG_REACTIONR01869NULL
24EC1.3.1.14NULL
25KEGG_REACTIONR01870NULL
25EC2.4.2.10NULL
26KEGG_REACTIONR00965NULL
26EC4.1.1.23NULL
27KEGG_REACTIONR00573NULL
27EC6.3.4.2NULL
28KEGG_REACTIONR01513NULL
28EC1.1.1.95NULL
29KEGG_REACTIONR04173NULL
29EC2.6.1.52NULL
30KEGG_REACTIONR00582NULL
30EC3.1.3.3NULL
31KEGG_REACTIONR00945NULL
31EC2.1.2.1NULL
32KEGG_REACTIONR00480NULL
32EC2.7.2.4NULL
33KEGG_REACTIONR02291NULL
33EC1.2.1.11NULL
34KEGG_REACTIONR01773NULL
34EC1.1.1.3NULL
35KEGG_REACTIONR01775NULL
35EC1.1.1.3NULL
36KEGG_REACTIONR01771NULL
36EC2.7.1.39NULL
37KEGG_REACTIONR01466NULL
37EC4.2.3.1NULL
38KEGG_REACTIONR01777NULL
38EC2.3.1.46NULL
39KEGG_REACTIONR01776NULL
39EC2.3.1.31NULL
40KEGG_REACTIONR03260NULL
40EC2.5.1.48NULL
41KEGG_REACTIONR03217NULL
42KEGG_REACTIONR13363NULL
42EC2.5.1.160NULL
43KEGG_REACTIONR01286NULL
44KEGG_REACTIONR01288NULL
45KEGG_REACTIONR01287NULL
45EC2.5.1.49NULL
46KEGG_REACTIONR00946NULL
46EC2.1.1.13NULL
47KEGG_REACTIONR04405NULL
47EC2.1.1.14NULL
48KEGG_REACTIONR00586NULL
48EC2.3.1.30NULL
49KEGG_REACTIONR00897NULL
49EC2.5.1.47NULL
50KEGG_REACTIONR01290NULL
50EC4.2.1.22NULL
51KEGG_REACTIONR10305NULL
51EC2.5.1.134NULL
52KEGG_REACTIONR01001NULL
52EC4.4.1.1NULL
53EC5.3.1.5NULL
54EC2.7.1.17NULL
55EC5.3.1.4NULL
56EC2.7.1.16NULL
57EC5.1.3.4NULL
58EC5.3.1.25NULL
59EC2.7.1.51NULL
60EC4.1.2.17NULL
61EC5.3.1.14NULL
62EC2.7.1.5NULL
63EC4.1.2.19NULL
64EC5.1.3.3NULL
65EC2.7.1.6NULL
66EC2.7.7.12NULL
67EC5.1.3.2NULL
68EC2.7.1.59NULL
69EC3.5.1.25NULL
70EC3.5.99.6NULL
71EC4.1.3.3NULL
72EC2.7.1.60NULL
73EC5.1.3.9NULL
74EC5.3.1.12NULL
75EC1.1.1.58NULL
76EC4.2.1.7NULL
77EC2.7.1.45NULL
78EC4.1.2.14NULL
79EC5.3.1.12NULL
80EC1.1.1.57NULL
81EC4.2.1.8NULL
82EC7.5.2.10NULL
83EC7.5.2.12NULL
84EC3.2.1.55NULL
85EC3.2.1.8NULL
86EC3.2.1.37NULL
87EC3.2.1.1NULL
88EC3.2.1.41NULL
89EC3.2.1.20NULL
90EC3.1.1.72NULL
91EC3.4.24.3NULL
92KEGG_REACTIONR00209NULL
92EC1.2.1.104NULL
93KEGG_REACTIONR01196NULL
93EC1.2.7.1NULL
94KEGG_REACTIONR00212NULL
94EC2.3.1.54NULL
95KEGG_REACTIONR00230NULL
95EC2.3.1.8NULL
96KEGG_REACTIONR00315NULL
96EC2.7.2.1NULL
97KEGG_REACTIONR00238NULL
97EC2.3.1.9NULL
98KEGG_REACTIONR01976NULL
98EC1.1.1.157NULL
99KEGG_REACTIONR03026NULL
99EC4.2.1.150Rhea maps this master to EC 4.2.1.116 only. KEGG assigns EC 4.2.1.150 to the accepted orthologue K01715.
100KEGG_REACTIONR01175NULL
100EC1.3.8.1NULL
101KEGG_REACTIONR01179NULL
102KEGG_REACTIONR02257Rhea maps this master to R02258, the (S)-specific form. R02257 is the same oxidoreduction written without the diol's stereochemistry, and it is the reaction KEGG links to the accepted orthologue K00048.
102EC1.1.1.77NULL
103KEGG_REACTIONR02376NULL
103EC4.2.1.28NULL
104KEGG_REACTIONR09097NULL
104EC1.2.1.87NULL
105KEGG_REACTIONR00921NULL
105EC2.3.1.222NULL
106KEGG_REACTIONR01353NULL
106EC2.7.2.15NULL
107KEGG_REACTIONR01449NULL
107EC2.8.3.1NULL
108KEGG_REACTIONR02963NULL
108EC4.2.1.54NULL
109KEGG_REACTIONR10161NULL
109EC1.3.1.95NULL
110KEGG_REACTIONR00703NULL
110EC1.1.1.27NULL
111KEGG_REACTIONR01450NULL
111EC5.1.2.1NULL
112KEGG_REACTIONR11074NULL
112EC4.1.1.101NULL
113KEGG_REACTIONR00362NULL
113EC4.1.3.6NULL
114KEGG_REACTIONR00217NULL
114EC4.1.1.112NULL
115KEGG_REACTIONR00228NULL
115EC1.2.1.10NULL
116KEGG_REACTIONR00754NULL
116EC1.1.1.1NULL
117KEGG_REACTIONR00226NULL
117EC2.2.1.6NULL
118KEGG_REACTIONR02948NULL
118EC4.1.1.5NULL
119KEGG_REACTIONR00425NULL
119EC3.5.4.25NULL
120KEGG_REACTIONR03459NULL
120EC3.5.4.26NULL
121KEGG_REACTIONR03458NULL
121EC1.1.1.193NULL
122KEGG_REACTIONR07280NULL
122EC3.1.3.104NULL
123KEGG_REACTIONR07281NULL
123EC4.1.99.12NULL
124KEGG_REACTIONR04457NULL
124EC2.5.1.78NULL
125KEGG_REACTIONR00066NULL
125EC2.5.1.9NULL
126KEGG_REACTIONR01716NULL
126EC2.6.1.85NULL
127KEGG_REACTIONR05553NULL
127EC4.1.3.38NULL
128KEGG_REACTIONR00424NULL
128EC3.5.4.16NULL
129KEGG_REACTIONR04638NULL
129EC3.6.1.67NULL
130KEGG_REACTIONR03504NULL
130EC4.1.2.25NULL
131KEGG_REACTIONR03503NULL
131EC2.7.6.3NULL
132KEGG_REACTIONR03067NULL
132EC2.5.1.15NULL
133KEGG_REACTIONR02237NULL
133EC6.3.2.12NULL
134KEGG_REACTIONR00939NULL
134EC1.5.1.3NULL
135KEGG_REACTIONR03472NULL
135EC4.1.99.17NULL
136KEGG_REACTIONR04509NULL
136EC2.7.4.7NULL
137KEGG_REACTIONR10246NULL
137EC4.1.99.19NULL
138KEGG_REACTIONR10247NULL
138EC2.8.1.10NULL
139EC1.4.3.19Rhea records no EC number for this master. KEGG assigns this one to the accepted orthologue K03153.
140KEGG_REACTIONR03223NULL
140EC2.5.1.3NULL
141KEGG_REACTIONR03471NULL
141EC2.7.1.49NULL
142KEGG_REACTIONR04448NULL
142EC2.7.1.50NULL
143KEGG_REACTIONR01226NULL
143EC2.1.2.11NULL
144KEGG_REACTIONR02472NULL
144EC1.1.1.169NULL
145KEGG_REACTIONR00489NULL
145EC4.1.1.11NULL
146KEGG_REACTIONR02473NULL
146EC6.3.2.1NULL
147KEGG_REACTIONR10089NULL
147EC4.3.3.6NULL
148KEGG_REACTIONR01825NULL
148EC1.2.1.72NULL
149KEGG_REACTIONR04210NULL
149EC1.1.1.290NULL
150KEGG_REACTIONR05085NULL
150EC2.6.1.52NULL
151KEGG_REACTIONR05837NULL
151EC1.1.1.262NULL
152KEGG_REACTIONR05838NULL
152EC2.6.99.2NULL
153KEGG_REACTIONR00278NULL
153EC1.4.3.5NULL
154KEGG_REACTIONR03210NULL
154EC2.3.1.47NULL
155KEGG_REACTIONR03231NULL
155EC2.6.1.62NULL
156KEGG_REACTIONR03182NULL
156EC6.3.3.3NULL
157KEGG_REACTIONR01078NULL
157EC2.8.1.6NULL
158KEGG_REACTIONR10699NULL
158EC2.6.1.105NULL
159KEGG_REACTIONR00481NULL
159EC1.4.3.16NULL
160KEGG_REACTIONR04292NULL
160EC2.5.1.72NULL
161KEGG_REACTIONR07410NULL
161EC1.4.1.29NULL
162KEGG_REACTIONR03348NULL
162EC2.4.2.19NULL
163KEGG_REACTIONR03005NULL
163EC2.7.7.18NULL
164KEGG_REACTIONR00189NULL
164EC6.3.1.5NULL
165KEGG_REACTIONR00257NULL
165EC6.3.5.1NULL
166KEGG_REACTIONR01724NULL
166EC6.3.4.21NULL
167KEGG_REACTIONR03194NULL
167EC2.1.1.107NULL
168KEGG_REACTIONR03947NULL
168EC1.3.1.76NULL
169KEGG_REACTIONR05807NULL
169EC4.99.1.3NULL
170KEGG_REACTIONR05808NULL
170EC2.1.1.151NULL
171KEGG_REACTIONR11580Rhea records no KEGG reaction for this master. KEGG assigns this one to the accepted orthologues K05934, K13541 and K21479.
171EC2.1.1.272NULL
172KEGG_REACTIONR05810NULL
172EC2.1.1.271NULL
173KEGG_REACTIONR07772NULL
173EC3.7.1.12NULL
174KEGG_REACTIONR07773NULL
174EC2.1.1.195NULL
175KEGG_REACTIONR05812NULL
175EC1.3.1.106NULL
176KEGG_REACTIONR07774Rhea records no KEGG reaction for this master. KEGG assigns this one to the accepted orthologues K00595 and K02191.
176EC2.1.1.196NULL
177KEGG_REACTIONR07775NULL
177EC2.1.1.289NULL
178KEGG_REACTIONR05814NULL
178EC5.4.99.60NULL
179KEGG_REACTIONR05815NULL
179EC6.3.5.11NULL
180KEGG_REACTIONR03948NULL
180EC2.1.1.130NULL
181KEGG_REACTIONR05217NULL
181EC1.14.13.83NULL
182KEGG_REACTIONR05180NULL
182EC2.1.1.131NULL
183KEGG_REACTIONR05181NULL
183EC2.1.1.133NULL
184KEGG_REACTIONR05219NULL
184EC2.1.1.152NULL
185KEGG_REACTIONR05150NULL
185EC1.3.1.54NULL
186KEGG_REACTIONR05149NULL
186EC2.1.1.132NULL
187KEGG_REACTIONR05177NULL
187EC5.4.99.61NULL
188KEGG_REACTIONR05224NULL
188EC6.3.5.9NULL
189KEGG_REACTIONR05227NULL
189EC6.6.1.2NULL
190KEGG_REACTIONR12184Rhea maps this master to R05220, written on cob(I)yrinate. R12184 is written on cob(II)yrinate as the Rhea equation is, and KEGG links it to the accepted orthologues K00798 and K19221.
190EC2.5.1.17NULL
191KEGG_REACTIONR05225NULL
191EC6.3.5.10NULL
192KEGG_REACTIONR06529NULL
192EC6.3.1.10NULL
193KEGG_REACTIONR05222NULL
193EC2.7.7.62NULL
194KEGG_REACTIONR04148NULL
194EC2.4.2.21NULL
195KEGG_REACTIONR04594NULL
195EC3.1.3.73NULL
196KEGG_REACTIONR05223NULL
196EC2.7.8.26NULL
197EC1.13.11.79NULL
198KEGG_REACTIONR01717NULL
198EC5.4.4.2NULL
199KEGG_REACTIONR08165NULL
199EC2.2.1.9NULL
200KEGG_REACTIONR08166NULL
200EC4.2.99.20NULL
201KEGG_REACTIONR04031NULL
201EC4.2.1.113NULL
202KEGG_REACTIONR04030NULL
202EC6.2.1.26NULL
203KEGG_REACTIONR07263NULL
203EC4.1.3.36NULL
204KEGG_REACTIONR07262NULL
204EC3.1.2.28NULL
205KEGG_REACTIONR10757Rhea maps this master to R05617, which KEGG no longer lists. R10757 states the same prenyl transfer and is the reaction KEGG links to the accepted orthologue K02548.
205EC2.5.1.74NULL
206KEGG_REACTIONR09736NULL
206EC2.1.1.163NULL
207KEGG_REACTIONR10666NULL
207EC4.2.1.151NULL
208KEGG_REACTIONR10667NULL
208EC2.5.1.120NULL
209KEGG_REACTIONR10695NULL
209EC3.5.4.40NULL
210KEGG_REACTIONR08587Rhea records no KEGG reaction for this master. KEGG assigns this one to the accepted orthologue K11783.
210EC3.2.2.26NULL
211KEGG_REACTIONR08588Rhea records no KEGG reaction for this master. KEGG assigns this one to the accepted orthologue K11784.
211EC1.21.98.1NULL
212KEGG_REACTIONR08589Rhea records no KEGG reaction for this master. KEGG assigns this one to the accepted orthologue K11785.
212EC4.1.99.29NULL
213KEGG_REACTIONR00351NULL
214KEGG_REACTIONR01324NULL
215KEGG_REACTIONR00267NULL
216KEGG_REACTIONR00709NULL
217KEGG_REACTIONR08549NULL
218KEGG_REACTIONR01197NULL
219KEGG_REACTIONR00405NULL
220KEGG_REACTIONR00272NULL
221KEGG_REACTIONR00713NULL
222KEGG_REACTIONR00714NULL
223KEGG_REACTIONR02164NULL
224KEGG_REACTIONR01082NULL
225KEGG_REACTIONR00342NULL
226KEGG_REACTIONR00361NULL
213EC2.3.3.1NULL
214EC4.2.1.3NULL
215EC1.1.1.42NULL
216EC1.1.1.41NULL
217EC1.2.1.105NULL
218EC1.2.7.3NULL
219EC6.2.1.5NULL
220EC4.1.1.71NULL
221EC1.2.1.24NULL
222EC1.2.1.16NULL
223EC1.3.5.1NULL
224EC4.2.1.2NULL
225EC1.1.1.37NULL
226EC1.1.5.4NULL
227KEGG_REACTIONR01826NULL
227EC2.5.1.54NULL
228KEGG_REACTIONR03083NULL
228EC4.2.3.4NULL
229KEGG_REACTIONR03084NULL
229EC4.2.1.10NULL
230KEGG_REACTIONR02413NULL
230EC1.1.1.25NULL
230EC1.1.1.282NULL
231KEGG_REACTIONR02412NULL
231EC2.7.1.71NULL
232KEGG_REACTIONR03460NULL
232EC2.5.1.19NULL
233KEGG_REACTIONR01714NULL
233EC4.2.3.5NULL
234KEGG_REACTIONR06602NULL
234EC4.2.99.21NULL
235KEGG_REACTIONR00679NULL
235EC1.13.12.3NULL
236KEGG_REACTIONR03096NULL
236EC3.5.1.4NULL
237EC1.7.3.3NULL
238EC1.14.13.113NULL
239EC3.5.2.17NULL
240EC4.1.1.97NULL
241EC3.5.2.5NULL
242EC3.5.3.4NULL
243EC3.5.3.9NULL
244EC3.5.3.26NULL
245EC4.3.2.3NULL
246EC3.5.1.5NULL
248EC1.7.7.2NULL
249EC1.7.7.1NULL
250EC1.7.1.15NULL
251EC1.14.13.251NULL
252EC1.5.7.3NULL
253EC1.5.8.4NULL
254EC1.5.3.10NULL
255EC1.5.3.1NULL
256EC1.5.7.3NULL
257EC3.5.2.10NULL
258EC3.5.3.3NULL
259EC1.14.13.239NULL
260EC1.1.1.108NULL
261EC2.3.1.317NULL
262EC3.1.2.33NULL
263EC1.4.9.1NULL
264EC1.14.11.17NULL
265EC2.6.1.77NULL
267EC2.3.3.15NULL
268EC7.6.2.7NULL
269EC6.3.1.2NULL
270EC1.4.1.13NULL
271EC1.4.7.1NULL
272EC1.4.1.4NULL
273EC1.4.1.2NULL
274EC1.14.12.10NULL
274KEGG_REACTIONR05621NULL
275EC1.3.1.25NULL
275KEGG_REACTIONR00813NULL
276EC1.14.12.1NULL
276KEGG_REACTIONR00825NULL
277EC1.14.13.244NULL
277KEGG_REACTIONR10043NULL
278EC1.13.11.1NULL
278KEGG_REACTIONR00817NULL
279EC5.5.1.1NULL
279KEGG_REACTIONR06989NULL
280EC5.3.3.4NULL
280KEGG_REACTIONR06990NULL
281EC3.1.1.24NULL
281KEGG_REACTIONR02991NULL
282EC2.8.3.6NULL
282KEGG_REACTIONR02990NULL
283EC2.3.1.174NULL
283KEGG_REACTIONR00829NULL
284EC1.13.11.2NULL
284KEGG_REACTIONR00816NULL
285EC3.7.1.9NULL
285KEGG_REACTIONR02604NULL
286EC1.2.1.85NULL
286KEGG_REACTIONR02762NULL
287EC5.3.2.6NULL
288EC4.1.1.77NULL
288KEGG_REACTIONR02602NULL
289EC4.2.1.80NULL
289KEGG_REACTIONR02601NULL
290EC4.1.3.39NULL
290KEGG_REACTIONR00750NULL
291EC6.2.1.30NULL
291KEGG_REACTIONR02539NULL
292EC1.14.13.149NULL
293EC5.3.3.18NULL
294EC3.3.2.12NULL
295EC1.2.1.91NULL
296EC2.3.1.223NULL
296KEGG_REACTIONR09839NULL
297EC4.2.1.17NULL
297KEGG_REACTIONR06942NULL
298KEGG_REACTIONR06941NULL
299EC1.14.12.19NULL
299KEGG_REACTIONR06782NULL
300EC1.3.1.87NULL
300KEGG_REACTIONR06784NULL
301EC1.14.13.127NULL
301KEGG_REACTIONR06786NULL
302EC1.13.11.16NULL
302KEGG_REACTIONR04376NULL
303EC3.7.1.14NULL
303KEGG_REACTIONR02603NULL
304KEGG_REACTIONR02722NULL
304EC4.2.1.20NULL
305KEGG_REACTIONR04001NULL
305EC4.2.1.33Rhea records no EC number for this master. KEGG assigns this one to the accepted orthologues K01702, K01703 and K01704.
306KEGG_REACTIONR01954NULL
306EC6.3.4.5NULL
307KEGG_REACTIONR03457NULL
307EC4.2.1.19NULL
308KEGG_REACTIONR00483NULL
308EC6.3.1.1NULL
309KEGG_REACTIONR01073NULL
309EC2.4.2.18NULL
310KEGG_REACTIONR04475NULL
310EC2.6.1.17NULL
311KEGG_REACTIONR00578NULL
311EC6.3.5.4NULL
312KEGG_REACTIONR04364NULL
312EC2.3.1.89NULL
313KEGG_REACTIONR05069Rhea records no KEGG reaction for this master. R05069 is the isomerisation half of the reductoisomerase reaction, and KEGG links it to the accepted orthologue K00053.
313EC1.1.1.86NULL
314KEGG_REACTIONR02755NULL
314EC1.4.1.16NULL
315KEGG_REACTIONR01728NULL
315EC1.3.1.12NULL
316KEGG_REACTIONR01715NULL
316EC5.4.99.5NULL
317KEGG_REACTIONR01251NULL
317EC1.5.1.2NULL
318KEGG_REACTIONR03013NULL
318EC3.1.3.15NULL
319KEGG_REACTIONR02649NULL
319EC2.7.2.8NULL
320KEGG_REACTIONR00239NULL
320EC2.7.2.11NULL
321KEGG_REACTIONR00734NULL
321EC2.6.1.57NULL
322KEGG_REACTIONR00451NULL
322EC4.1.1.20NULL
323KEGG_REACTIONR02282NULL
323EC2.3.1.35NULL
324KEGG_REACTIONR02735NULL
324EC5.1.1.7NULL
325KEGG_REACTIONR04640NULL
325EC5.3.1.16NULL
326KEGG_REACTIONR00669NULL
326EC3.5.1.16NULL
327KEGG_REACTIONR03968NULL
327EC4.2.1.33Rhea records no EC number for this master. KEGG assigns this one to the accepted orthologues K01702, K01703 and K01704.
328KEGG_REACTIONR04365NULL
328EC2.3.1.117NULL
329KEGG_REACTIONR02283NULL
329EC2.6.1.11NULL
330KEGG_REACTIONR01090NULL
330EC2.6.1.42NULL
331KEGG_REACTIONR00396NULL
331EC1.4.1.1NULL
332KEGG_REACTIONR01071NULL
332EC2.4.2.17NULL
333KEGG_REACTIONR07399NULL
333EC2.3.3.21NULL
334KEGG_REACTIONR00258NULL
334EC2.6.1.2NULL
335KEGG_REACTIONR01398NULL
335EC2.1.3.3NULL
336KEGG_REACTIONR03313NULL
336EC1.2.1.41NULL
337KEGG_REACTIONR04037NULL
337EC3.5.4.19NULL
338KEGG_REACTIONR02733NULL
338EC3.5.1.47NULL
339KEGG_REACTIONR01213NULL
339EC2.3.3.13NULL
340KEGG_REACTIONR03509NULL
340EC5.3.1.24NULL
341KEGG_REACTIONR03443NULL
341EC1.2.1.38NULL
342KEGG_REACTIONR01730NULL
342EC1.3.1.13NULL
343KEGG_REACTIONR01373NULL
343EC4.2.1.51NULL
344KEGG_REACTIONR00986NULL
344EC4.1.3.27NULL
345KEGG_REACTIONR00355NULL
345EC2.6.1.1NULL
346KEGG_REACTIONR04439NULL
346EC1.1.1.86NULL
347KEGG_REACTIONR03896NULL
347EC4.2.1.35NULL
348KEGG_REACTIONR02734NULL
348EC3.5.1.18NULL
349KEGG_REACTIONR04035NULL
349EC3.6.1.31NULL
350KEGG_REACTIONR03508NULL
350EC4.1.1.48NULL
351KEGG_REACTIONR03243NULL
351EC2.6.1.9NULL
352KEGG_REACTIONR07613NULL
352EC2.6.1.83NULL
353KEGG_REACTIONR01086NULL
353EC4.3.2.1NULL
354KEGG_REACTIONR00259NULL
354EC2.3.1.1NULL
355KEGG_REACTIONR04558NULL
355EC4.3.2.10NULL
356KEGG_REACTIONR02199NULL
356EC2.6.1.42NULL
357KEGG_REACTIONR04441NULL
357EC4.2.1.9NULL
358KEGG_REACTIONR01214NULL
358EC2.6.1.42NULL
359KEGG_REACTIONR00694NULL
359EC2.6.1.57NULL
360KEGG_REACTIONR04467NULL
361KEGG_REACTIONR08648NULL
361EC2.2.1.6NULL
362KEGG_REACTIONR05070NULL
362EC4.2.1.9NULL
363KEGG_REACTIONR10052NULL
363EC1.1.1.85NULL
364KEGG_REACTIONR00994NULL
364EC1.1.1.85Rhea maps this master to the preliminary EC 1.1.1.n5 only. KEGG assigns EC 1.1.1.85 to the accepted orthologue K00052.
365KEGG_REACTIONR03012NULL
365EC1.1.1.23Rhea records no EC number for this master. KEGG assigns this one to the accepted orthologues K00013 and K14152.
366KEGG_REACTIONR01163NULL
366EC1.1.1.23Rhea records no EC number for this master. KEGG assigns this one to the accepted orthologues K00013 and K14152.
367KEGG_REACTIONR10147NULL
367EC4.3.3.7NULL
368KEGG_REACTIONR04199NULL
368EC1.17.1.8NULL
369KEGG_REACTIONR03898NULL
369EC4.2.1.35NULL
370KEGG_REACTIONR00150NULL
370EC2.7.2.2NULL
371KEGG_REACTIONR01255NULL
371EC5.1.1.4NULL
372KEGG_REACTIONR07226NULL
372EC1.21.4.2NULL
373KEGG_REACTIONR02825NULL
373EC1.21.4.1NULL
374KEGG_REACTIONR02914NULL
374EC4.2.1.49NULL
375KEGG_REACTIONR00261NULL
375EC4.1.1.15NULL
376KEGG_REACTIONR00220NULL
376EC4.3.1.17NULL
377KEGG_REACTIONR00673NULL
377EC4.1.99.1NULL
378KEGG_REACTIONR00552NULL
378EC3.5.3.6NULL
379KEGG_REACTIONR01168NULL
379EC4.3.1.3NULL
380KEGG_REACTIONR00996NULL
380EC4.3.1.19NULL
381KEGG_REACTIONR02285NULL
381EC3.5.3.8NULL
382KEGG_REACTIONR02288NULL
382EC3.5.2.7NULL
383KEGG_REACTIONR00654NULL
383EC4.4.1.11NULL
384KEGG_REACTIONR00782NULL
384EC4.4.1.28NULL
385KEGG_REACTIONR00479NULL
385EC4.1.3.1NULL
386KEGG_REACTIONR00472NULL
386EC2.3.3.9NULL
387KEGG_REACTIONR05185NULL
387EC1.18.6.1NULL
388KEGG_REACTIONR12084NULL
388EC1.18.6.2NULL
389KEGG_REACTIONR00529NULL
389EC2.7.7.4NULL
390KEGG_REACTIONR00509NULL
390EC2.7.1.25NULL
391KEGG_REACTIONR02021NULL
391EC1.8.4.8NULL
392KEGG_REACTIONR07176NULL
392EC1.8.4.10NULL
393KEGG_REACTIONR00858NULL
393EC1.8.1.2NULL
394KEGG_REACTIONR00859NULL
394EC1.8.7.1NULL
395KEGG_REACTIONR06977NULL
395EC2.6.1.76NULL
396KEGG_REACTIONR06978NULL
396EC2.3.1.178NULL
397KEGG_REACTIONR06979NULL
397EC4.2.1.108NULL
398KEGG_REACTIONR03197NULL
398EC4.1.1.37NULL
399KEGG_REACTIONR03220NULL
399EC1.3.3.3NULL
400KEGG_REACTIONR06895NULL
400EC1.3.98.3NULL
401KEGG_REACTIONR03222NULL
401EC1.3.3.4NULL
402EC1.3.5.3NULL
403KEGG_REACTIONR12605NULL
404KEGG_REACTIONR00310NULL
404EC4.98.1.1NULL
405KEGG_REACTIONR04178NULL
405EC1.3.3.15NULL
406KEGG_REACTIONR11329NULL
406EC4.99.1.9NULL
407KEGG_REACTIONR11522NULL
407EC1.3.98.5NULL
408KEGG_REACTIONR03037NULL
408EC3.3.2.1NULL
409KEGG_REACTIONR01505NULL
409EC1.3.1.28NULL
410KEGG_REACTIONR07644NULL
410EC6.3.2.14NULL
411KEGG_REACTIONR01025NULL
411EC1.1.99.1NULL
412KEGG_REACTIONR08557NULL
413KEGG_REACTIONR07409NULL
413EC1.14.15.7NULL
414KEGG_REACTIONR01022NULL
415KEGG_REACTIONR08211NULL
416KEGG_REACTIONR02565NULL
416EC1.2.1.8NULL
417KEGG_REACTIONR02864NULL
417EC4.99.1.4NULL
418EC3.2.1.14NULL
419EC3.2.1.52NULL
420EC1.14.99.53NULL
421EC3.2.1.18NULL
422EC3.2.1.51NULL
423EC3.2.1.49NULL
424EC3.2.1.15NULL
425EC3.2.1.67NULL
426EC3.1.1.11NULL
427EC4.2.2.2NULL
428EC4.2.2.9NULL
429EC4.2.2.6NULL
430EC5.3.1.17NULL
431EC1.1.1.127NULL
432EC4.2.2.10NULL
433EC3.5.4.44NULL
434EC3.5.1.125NULL
435EC1.14.11.55NULL
436EC1.2.1.22NULL
437KEGG_REACTIONR12000NULL
437EC4.1.1.111NULL
438KEGG_REACTIONR12001Rhea records no KEGG reaction for this master. KEGG assigns this one to the accepted orthologue K22226.
439KEGG_REACTIONR12002Rhea records no KEGG reaction for this master. KEGG assigns this one to the accepted orthologue K22227.
439EC1.3.98.6NULL
440EC2.7.1.193NULL
enzyme_system505 rows · 5 columns
system_pkreaction_pksystem_idnamedescription
11SYS_14905_PURFamidophosphoribosyltransferaseSingle catalytic protein system.
22SYS_17453_MONOMERphosphoribosylamine--glycine ligaseSingle-protein catalytic system with alternative orthology markers.
33SYS_15053_FOLATEGAR transformylaseSingle-protein folate-dependent catalytic system with alternative orthology markers.
44SYS_24829_FORMATEGAR formyltransferase 2Single-protein formate-dependent catalytic system.
55SYS_17129_LARGElarge-type FGAM synthaseSingle-protein FGAM synthase architecture.
65SYS_17129_TRIMERsmall-type FGAM synthase trimeric systemThree required protein components.
75SYS_17129_DIMERsmall-type FGAM synthase two-component systemTwo required protein components.
86SYS_23032_AIR_SYNTHASEAIR synthetaseSingle-protein catalytic system with alternative orthology markers.
97SYS_10792_DIRECTdirect AIR carboxylaseSingle-protein direct carboxylation system.
108SYS_19317_N5CAIR_SYNTHASEN5-CAIR synthetaseFirst enzyme of the two-reaction AIR carboxylation route.
119SYS_13193_N5CAIR_MUTASEN5-CAIR mutaseSecond enzyme of the two-reaction AIR carboxylation route.
1210SYS_22628_SAICARSAICAR synthetaseSingle-protein catalytic system with alternative orthology markers.
1311SYS_23920_LYASESAICAR lyaseSingle-protein catalytic system.
1412SYS_22192_FOLATEAICAR transformylaseSingle-protein folate-dependent catalytic system.
1513SYS_24836_FORMATEFAICAR synthetaseSingle-protein formate-dependent catalytic system.
1614SYS_18445_CYCLASEIMP cyclohydrolaseSingle-protein catalytic system with alternative orthology markers.
1715SYS_15753_ADSSadenylosuccinate synthaseSingle-protein catalytic system.
1816SYS_16853_ADSLadenylosuccinate lyaseSingle-protein catalytic system.
1917SYS_11708_IMPDHIMP dehydrogenaseSingle-protein catalytic system.
2018SYS_11680_GMP_SYNTHASEGMP synthaseSingle-protein glutamine-hydrolyzing catalytic system.
2119SYS_18633_MONOMERmonomeric carbamoyl-phosphate synthaseSingle-protein catalytic system including multifunctional architectures.
2219SYS_18633_HETERODIMERheterodimeric carbamoyl-phosphate synthaseTwo required protein subunits.
2320SYS_20013_MONOMERmonomeric aspartate carbamoyltransferaseSingle-protein catalytic system including multifunctional architectures.
2420SYS_20013_CATALYTICaspartate carbamoyltransferase catalytic subunitSingle-protein catalytic system; the PyrI regulatory subunit is allosteric and is not required evidence.
2521SYS_24296_DIHYDROOROTASEdihydroorotaseSingle-protein catalytic system including the multifunctional CAD architecture.
2622SYS_30059_FUMARATEfumarate-dependent dihydroorotate dehydrogenaseSingle-protein catalytic system.
2723SYS_30187_QUINONEquinone-dependent dihydroorotate dehydrogenaseSingle-protein catalytic system.
2824SYS_13513_NADNAD-dependent dihydroorotate dehydrogenaseTwo required protein subunits of the class 1B holoenzyme.
2925SYS_10380_OPRTorotate phosphoribosyltransferaseSingle-protein catalytic system including bifunctional UMP synthase.
3026SYS_11596_OMP_DECARBOXYLASEorotidine 5'-phosphate decarboxylaseSingle-protein catalytic system including bifunctional UMP synthase.
3127SYS_26426_CTP_SYNTHASECTP synthaseSingle-protein glutamine-hydrolyzing catalytic system.
3228SYS_12641_SERA3-phosphoglycerate dehydrogenaseSingle-protein catalytic system.
3329SYS_14329_SERCphosphoserine aminotransferaseSingle-protein catalytic system.
3430SYS_21208_PSPphosphoserine phosphataseSingle-protein catalytic system with alternative orthology markers.
3531SYS_15481_SHMTserine hydroxymethyltransferaseSingle-protein catalytic system.
3632SYS_23776_AKaspartate kinaseSingle-protein catalytic system including bifunctional architectures.
3733SYS_24284_ASDaspartate-semialdehyde dehydrogenaseSingle-protein catalytic system.
3834SYS_15757_HOM_NADNAD-dependent homoserine dehydrogenaseSingle-protein catalytic system including bifunctional aspartokinase architectures.
3935SYS_15761_HOM_NADPNADP-dependent homoserine dehydrogenaseSingle-protein catalytic system including bifunctional aspartokinase architectures.
4036SYS_13985_HSKhomoserine kinaseSingle-protein catalytic system with alternative orthology markers.
4137SYS_10840_THRCthreonine synthaseSingle-protein catalytic system.
4238SYS_22008_ACYLTRANSFERASEhomoserine O-succinyltransferaseSingle-protein catalytic system; MetA and MetX orthologues are both accepted because KEGG assigns both acyl chemistries to both.
4339SYS_13701_ACYLTRANSFERASEhomoserine O-acetyltransferaseSingle-protein catalytic system; MetA and MetX orthologues are both accepted because KEGG assigns both acyl chemistries to both.
4440SYS_20397_METBcystathionine gamma-synthaseSingle-protein catalytic system acting on O-succinyl-L-homoserine.
4541SYS_30931_METBcystathionine gamma-synthaseSingle-protein catalytic system acting on O-acetyl-L-homoserine.
4642SYS_80891_CGS1plant cystathionine gamma-synthaseSingle-protein catalytic system acting on O-phospho-L-homoserine.
4743SYS_13965_CBLcystathionine beta-lyaseSingle-protein catalytic system with alternative orthology markers.
4844SYS_27826_METZO-succinylhomoserine sulfhydrylaseSingle-protein catalytic system restricted to the dedicated sulfhydrylase orthologue.
4945SYS_27822_METYO-acetylhomoserine sulfhydrylaseSingle-protein catalytic system with alternative orthology markers.
5046SYS_11172_METHcobalamin-dependent methionine synthaseSingle-protein catalytic system; the cobalamin cofactor is not a separate evidence component.
5147SYS_21196_METEcobalamin-independent methionine synthaseSingle-protein catalytic system.
5248SYS_24560_CYSEserine O-acetyltransferaseSingle-protein catalytic system.
5349SYS_14829_OASScysteine synthaseSingle-protein catalytic system with alternative orthology markers.
5450SYS_10112_CBScystathionine beta-synthaseSingle-protein catalytic system acting on L-serine.
5551SYS_32743_MCCAcystathionine beta-synthase (O-acetyl-L-serine)Single-protein catalytic system acting on O-acetyl-L-serine.
5652SYS_14005_CGLcystathionine gamma-lyaseSingle-protein catalytic system with alternative orthology markers.
5753SYS_22816_XYLAxylose isomeraseSingle-protein catalytic system.
5854SYS_10964_XYLBxylulokinaseSingle-protein catalytic system.
5955SYS_14821_ARAAL-arabinose isomeraseSingle-protein catalytic system.
6056SYS_22072_ARABL-ribulokinaseSingle-protein catalytic system.
6157SYS_22368_ARADL-ribulose-5-phosphate 4-epimeraseSingle-protein catalytic system.
6258SYS_17233_FUCIL-fucose isomeraseSingle-protein catalytic system.
6359SYS_12376_FUCKL-fuculokinaseSingle-protein catalytic system.
6460SYS_12933_FUCAL-fuculose-1-phosphate aldolaseSingle-protein catalytic system.
6561SYS_23160_RHAAL-rhamnose isomeraseSingle-protein catalytic system.
6662SYS_20117_RHABrhamnulokinaseSingle-protein catalytic system.
6763SYS_19689_RHADrhamnulose-1-phosphate aldolaseSingle-protein catalytic system.
6864SYS_28675_GALMaldose 1-epimeraseSingle-protein catalytic system.
6965SYS_13553_GALKgalactokinaseSingle-protein catalytic system.
7066SYS_13989_GALTgalactose-1-phosphate uridylyltransferaseSingle-protein catalytic system.
7167SYS_22168_GALEUDP-glucose 4-epimeraseSingle-protein catalytic system.
7268SYS_17417_NAGKN-acetylglucosamine kinaseSingle-protein catalytic system.
7369SYS_22936_NAGAN-acetylglucosamine-6-phosphate deacetylaseSingle-protein catalytic system.
7470SYS_12172_NAGBglucosamine-6-phosphate deaminaseSingle-protein catalytic system.
7571SYS_23296_NANAN-acetylneuraminate lyaseSingle-protein catalytic system.
7672SYS_25253_NANKN-acetylmannosamine kinaseSingle-protein catalytic system.
7773SYS_25257_NANEN-acetylmannosamine-6-phosphate 2-epimeraseSingle-protein catalytic system.
7874SYS_27702_UXACglucuronate isomeraseSingle-protein catalytic system.
7975SYS_17813_UXABtagaturonate reductaseSingle-protein catalytic system.
8077SYS_14797_KDGK2-dehydro-3-deoxygluconokinaseSingle-protein catalytic system.
8178SYS_17089_EDA2-dehydro-3-deoxy-phosphogluconate aldolaseSingle-protein catalytic system.
8279SYS_13049_UXACglucuronate isomeraseSingle-protein catalytic system.
8380SYS_15729_UXUBfructuronate reductaseSingle-protein catalytic system.
8481SYS_20097_UXUAmannonate dehydrataseSingle-protein catalytic system.
8576SYS_15957_MONOMERaltronate hydrolaseSingle-protein catalytic system.
8676SYS_15957_HETERODIMERtwo-subunit altronate dehydrataseTwo jointly required protein subunits.
8782SYS_29899_XYLFGHXylFGH ABC importerThree jointly required subunits.
8882SYS_29899_XACGHIXacGHI dual-specificity ABC importerThree jointly required subunits; characterised on both pentoses.
8983SYS_30007_ARAFGHAraFGH ABC importerThree jointly required subunits.
9083SYS_30007_XACGHIXacGHI dual-specificity ABC importerThree jointly required subunits; characterised on both pentoses.
9184SYS_ARAFalpha-L-arabinofuranosidaseSingle-protein catalytic system; CAZy families and orthologues are alternative evidence for the same role.
9285SYS_XYLANASEendo-1,4-beta-xylanaseSingle-protein catalytic system; CAZy families and orthologues are alternative evidence for the same role.
9386SYS_XYLOSIDASExylan 1,4-beta-xylosidaseSingle-protein catalytic system; CAZy families and orthologues are alternative evidence for the same role.
9487SYS_AMYLASEalpha-amylaseSingle-protein catalytic system; CAZy families and orthologues are alternative evidence for the same role.
9588SYS_PULLULANASEpullulanaseSingle-protein catalytic system; CAZy families and orthologues are alternative evidence for the same role.
9689SYS_GLUCOSIDASEalpha-glucosidaseSingle-protein catalytic system; CAZy families and orthologues are alternative evidence for the same role.
9790SYS_DEACETYLacetylxylan esteraseSingle-protein catalytic system; CAZy families and orthologues are alternative evidence for the same role.
9891SYS_COLLAGENASE_M9microbial collagenaseSingle-protein catalytic system; the orthologue and the Pfam domain are alternative evidence for the same protein, not alternative enzymes.
9992SYS_28042_PDH_E1ABalpha/beta-E1 pyruvate dehydrogenase complexFour jointly required components; the E1 decarboxylase is a separate alpha and beta subunit pair.
10092SYS_28042_PDH_E1fused-E1 pyruvate dehydrogenase complexThree jointly required components; the E1 decarboxylase is a single polypeptide, as in Escherichia coli AceE.
10193SYS_12765_POR_FOUR_SUBUNITfour-subunit pyruvate:ferredoxin oxidoreductaseFour jointly required subunits of the archaeal and clostridial PorABCD architecture.
10293SYS_12765_NIFJfused pyruvate:ferredoxin/flavodoxin oxidoreductaseSingle fused polypeptide carrying all four domains.
10394SYS_11844_PFLpyruvate formate-lyase with its activating enzymeTwo jointly required proteins: the lyase is inactive until the activating enzyme installs its glycyl radical.
10495SYS_19521_PTAphosphate acetyltransferaseSingle-protein catalytic system with alternative orthology markers.
10596SYS_11352_ACKAacetate kinaseSingle catalytic protein system.
10697SYS_21036_THIOLASEacetyl-CoA C-acetyltransferaseSingle catalytic protein system.
10798SYS_16197_HBD3-hydroxybutanoyl-CoA dehydrogenaseSingle catalytic protein system.
10899SYS_26558_CROTONASE3-hydroxybutanoyl-CoA dehydrataseSingle catalytic protein system.
109100SYS_24004_BCDbutanoyl-CoA dehydrogenaseSingle catalytic protein system. The electron-transfer flavoprotein partner is not a required component: K03521 and K03522 are the generic fixA and fixB orthologues shared with nitrogen fixation, present in 7729 KEGG organisms, so requiring them would cost recall without adding specificity.
110101SYS_30071_BUTbutyryl-CoA:acetate CoA-transferaseSingle catalytic protein system evidenced by a substrate-specific sequence family rather than an orthology group.
111102SYS_15933_FUCOlactaldehyde reductaseSingle catalytic protein system.
112103SYS_14569_PDUCDEcoenzyme-B12-dependent propanediol dehydrataseThree jointly required subunits of the PduCDE holoenzyme.
113104SYS_36027_PDUPCoA-acylating propionaldehyde dehydrogenaseSingle catalytic protein system.
114105SYS_28046_PDULphosphate propanoyltransferaseSingle catalytic protein system.
115106SYS_23148_PROPIONATE_KINASEpropionate kinaseSingle-protein catalytic system with alternative orthology markers.
116107SYS_LACTATE_COAT_PCTpropionate CoA-transferaseSingle catalytic protein system.
117108SYS_34691_LCDlactoyl-CoA dehydrataseTwo jointly required subunits. The LcdC activator has no orthology group and is not required evidence.
118109SYS_34471_ACRCacryloyl-CoA reductaseSingle catalytic protein system.
119110SYS_23444_LDHNAD-dependent L-lactate dehydrogenaseSingle catalytic protein system. Only the NAD-dependent enzyme is accepted; the quinone- and cytochrome-dependent L-lactate dehydrogenases are separate orthology groups and evidence the consuming direction, which is what makes this trait's direction evidenced rather than asserted.
120111SYS_10960_LARlactate racemaseSingle catalytic protein system. The LarBCE maturation proteins that install the nickel-pincer cofactor are not required evidence: they are a maturation pathway rather than part of the racemase, and requiring them would make the trait a cofactor claim.
121112SYS_46276_MLEmalolactic enzymeSingle catalytic protein system.
122113SYS_10760_CITLYASEcitrate lyase holoenzymeThree subunits and the ligase that activates them. Apo-citrate lyase carries an unacetylated acyl-carrier subunit and is inactive, so the ligase is required rather than accessory; 912 of the 960 genomes with the three subunits carry it, so requiring it costs almost nothing.
123114SYS_15641_OAD_NAsodium-extruding oxaloacetate decarboxylaseMembrane-bound decarboxylase of the Enterobacteriaceae and the lactic acid bacteria. Only the alpha subunit is required: KEGG assigns the beta subunit group K01572 in a single organism, so requiring it would refuse the trait everywhere.
124114SYS_15641_OAD_SOLUBLEsoluble oxaloacetate decarboxylaseAlternative single-protein system, accepted as an OR alternative to the sodium-extruding complex.
125115SYS_23288_ADHEbifunctional acetaldehyde dehydrogenaseSingle catalytic protein system. The same protein carries the alcohol dehydrogenase activity of the next step, so the route rests on one marker across two reactions.
126116SYS_25290_ADHEbifunctional alcohol dehydrogenaseSingle catalytic protein system, the second activity of the same protein.
127117SYS_25249_ALSacetolactate synthaseSingle catalytic protein system for a step the route does not require. Its orthology group is the anabolic branched-chain amino acid synthase, so it is curated for the chemistry and excluded from the evidence.
128118SYS_21580_BUDAacetolactate decarboxylaseSingle catalytic protein system, and the step the trait rests on. The enzyme exists only for this pathway.
129119SYS_23704_RIBAGTP cyclohydrolase IISingle catalytic protein system.
130119SYS_23704_RIBABbifunctional RibABSingle catalytic protein system.
131120SYS_21868_RIBDpyrimidine deaminase RibDSingle catalytic protein system.
132120SYS_21868_RIBGbifunctional deaminase-reductase RibGSingle catalytic protein system.
133121SYS_17845_RIBD2pyrimidine reductase RibDSingle catalytic protein system.
134121SYS_17845_RIBG2bifunctional deaminase-reductase RibGSingle catalytic protein system.
135122SYS_25197_PHOSPHATASE5-amino-6-(5-phospho-D-ribitylamino)uracil phosphataseSingle catalytic protein system.
136123SYS_18457_RIBB3,4-dihydroxy-2-butanone 4-phosphate synthaseSingle catalytic protein system.
137123SYS_18457_RIBAB2bifunctional RibABSingle catalytic protein system.
138124SYS_26152_RIBH6,7-dimethyl-8-ribityllumazine synthaseSingle catalytic protein system.
139125SYS_20772_RIBEriboflavin synthaseSingle catalytic protein system.
140126SYS_11672_PABB4-amino-4-deoxychorismate synthaseSingle catalytic protein system.
141126SYS_11672_PABBCbifunctional PabBCSingle catalytic protein system.
142127SYS_16201_PABC4-amino-4-deoxychorismate lyaseSingle catalytic protein system.
143127SYS_16201_PABBC2bifunctional PabBCSingle catalytic protein system.
144128SYS_17473_FOLEGTP cyclohydrolase ISingle catalytic protein system.
145129SYS_25302_NUDBdihydroneopterin triphosphate diphosphataseSingle catalytic protein system.
146130SYS_10540_FOLBdihydroneopterin aldolaseSingle catalytic protein system.
147131SYS_11412_FOLK6-hydroxymethyl-7,8-dihydropterin pyrophosphokinaseSingle catalytic protein system.
148132SYS_19949_FOLPdihydropteroate synthaseSingle catalytic protein system.
149133SYS_23584_FOLCdihydrofolate synthaseSingle catalytic protein system.
150134SYS_15009_FOLAdihydrofolate reductaseSingle catalytic protein system.
151135SYS_24840_THICphosphomethylpyrimidine synthase ThiCSingle catalytic protein system.
152136SYS_19893_THIDphosphomethylpyrimidine kinase ThiDSingle catalytic protein system.
153137SYS_26361_THIH2-iminoacetate synthase ThiHSingle catalytic protein system.
154138SYS_26297_THIGthiazole synthase ThiGSingle catalytic protein system.
155139SYS_33343_THIOglycine oxidase ThiOSingle catalytic protein system.
156140SYS_22328_THIEthiamine phosphate synthase ThiESingle catalytic protein system.
157141SYS_23096_THID_HMPhydroxymethylpyrimidine kinase ThiDSingle catalytic protein system.
158142SYS_24212_THIMhydroxyethylthiazole kinase ThiMSingle catalytic protein system.
159143SYS_11824_PANB3-methyl-2-oxobutanoate hydroxymethyltransferase PanBSingle catalytic protein system.
160144SYS_16233_PANE2-dehydropantoate 2-reductase PanESingle catalytic protein system.
161144SYS_16233_ILVCketol-acid reductoisomerase IlvCSingle catalytic protein system.
162145SYS_19497_PANDaspartate 1-decarboxylase PanDSingle catalytic protein system.
163146SYS_10912_PANCpantothenate synthetase PanCSingle catalytic protein system.
164147SYS_31507_PDXSTpyridoxal 5-phosphate synthase complexTwo jointly required subunits: the synthase and its glutaminase partner.
165148SYS_12056_EPDD-erythrose 4-phosphate dehydrogenase EpdSingle catalytic protein system.
166149SYS_18829_PDXBerythronate-4-phosphate dehydrogenase PdxBSingle catalytic protein system.
167150SYS_16573_SERCphosphoserine aminotransferase SerCSingle catalytic protein system.
168151SYS_32275_PDXA4-hydroxythreonine-4-phosphate dehydrogenase PdxASingle catalytic protein system.
169152SYS_15265_PDXJpyridoxine 5-phosphate synthase PdxJSingle catalytic protein system.
170153SYS_15149_PDXHpyridoxine 5-phosphate oxidase PdxHSingle catalytic protein system.
171154SYS_20712_BIOF8-amino-7-oxononanoate synthase BioFSingle catalytic protein system.
172155SYS_16861_BIOAadenosylmethionine-dependent DAPA transaminase BioASingle catalytic protein system.
173156SYS_15805_BIODdethiobiotin synthetase BioDSingle catalytic protein system.
174157SYS_22060_BIOBbiotin synthase BioBSingle catalytic protein system.
175158SYS_26329_BIOA_LYSlysine-dependent DAPA transaminase BioASingle catalytic protein system.
176159SYS_25876_NADBL-aspartate oxidase NadBSingle catalytic protein system.
177160SYS_25888_NADAquinolinate synthase NadASingle catalytic protein system.
178161SYS_42440_NADXaspartate dehydrogenase NadXSingle catalytic protein system.
179162SYS_12733_NADCnicotinate-nucleotide pyrophosphorylase NadCSingle catalytic protein system.
180163SYS_22860_NADDnicotinate-nucleotide adenylyltransferase NadDSingle catalytic protein system.
181164SYS_21188_NADENAD synthetase NadESingle catalytic protein system.
182165SYS_24384_NADE_GLNglutamine-hydrolysing NAD synthetaseSingle catalytic protein system.
183166SYS_36163_PNCBnicotinate phosphoribosyltransferase PncBSingle catalytic protein system.
184167SYS_32459_COBAuroporphyrin-III C-methyltransferase CobASingle catalytic protein system.
185167SYS_32459_CYSGmultifunctional siroheme synthase CysGSingle catalytic protein system.
186168SYS_15613_SIRCprecorrin-2 dehydrogenase SirCSingle catalytic protein system.
187168SYS_15613_CYSG2multifunctional siroheme synthase CysGSingle catalytic protein system.
188169SYS_15893_CBIKsirohydrochlorin cobaltochelataseSingle catalytic protein system.
189170SYS_17997_CBILcobalt-factor II C20-methyltransferase CbiLSingle catalytic protein system.
190171SYS_36155_CBIHcobalt-factor III methyltransferase CbiHSingle catalytic protein system.
191172SYS_26277_CBIFcobalt-precorrin-4 C11-methyltransferase CbiFSingle catalytic protein system.
192173SYS_26281_CBIGcobalt-precorrin-5A hydrolase CbiGSingle catalytic protein system.
193174SYS_26285_CBIDcobalt-precorrin-5B C1-methyltransferase CbiDSingle catalytic protein system.
194175SYS_15625_CBIJcobalt-precorrin-6A reductase CbiJSingle catalytic protein system.
195176SYS_36067_CBITcobalt-precorrin-6B C15-methyltransferase CbiTSingle catalytic protein system.
196177SYS_34591_CBIEcobalt-precorrin-7 C5-methyltransferase CbiESingle catalytic protein system.
197178SYS_16209_CBICcobalt-precorrin-8 methylmutase CbiCSingle catalytic protein system.
198179SYS_26289_CBIAcobyrinate a,c-diamide synthase CbiASingle catalytic protein system.
199180SYS_16841_COBIprecorrin-2 C20-methyltransferase CobISingle catalytic protein system.
200181SYS_17293_COBGprecorrin-3B synthase CobGSingle catalytic protein system.
201182SYS_12761_COBJprecorrin-3B C17-methyltransferase CobJSingle catalytic protein system.
202183SYS_22012_COBMprecorrin-4 C11-methyltransferase CobMSingle catalytic protein system.
203184SYS_18261_COBFprecorrin-6A synthase CobFSingle catalytic protein system.
204185SYS_23408_COBKprecorrin-6A reductase CobKSingle catalytic protein system.
205186SYS_17477_COBLprecorrin-6B C5,C15-methyltransferase CobLSingle catalytic protein system.
206187SYS_22512_COBHprecorrin-8X methylmutase CobHSingle catalytic protein system.
207188SYS_12544_COBBhydrogenobyrinate a,c-diamide synthase CobBSingle catalytic protein system.
208189SYS_15341_COBNSTcobaltochelatase CobNSTThree jointly required subunits; late cobalt insertion is what distinguishes the aerobic route.
209190SYS_11528_COBA_ADOcob(I)yrinate a,c-diamide adenosyltransferaseSingle catalytic protein system.
210191SYS_23256_CBIPadenosylcobyric acid synthase CbiPSingle catalytic protein system.
211192SYS_21896_CBIBadenosylcobinamide-phosphate synthaseSingle catalytic protein system.
212193SYS_22712_COBUadenosylcobinamide-phosphate guanylyltransferase CobUSingle catalytic protein system.
213194SYS_11196_COBTnicotinate-nucleotide dimethylbenzimidazole phosphoribosyltransferase CobTSingle catalytic protein system.
214195SYS_24456_COBC_Palpha-ribazole phosphatase CobCSingle catalytic protein system.
215196SYS_16049_COBS_TRANSFERASEadenosylcobinamide-GDP ribazoletransferase CobSSingle catalytic protein system.
216197SYS_27345_BLUB5,6-dimethylbenzimidazole synthase BluBSingle catalytic protein system.
217198SYS_18985_MENFmenaquinone-specific isochorismate synthase MenFSingle catalytic protein system.
218198SYS_18985_ENTCisochorismate synthase EntCSingle catalytic protein system.
219199SYS_25593_MENDSEPHCHC synthase MenDSingle catalytic protein system.
220200SYS_25597_MENHSHCHC synthase MenHSingle catalytic protein system.
221201SYS_10196_MENCo-succinylbenzoate synthase MenCSingle catalytic protein system.
222202SYS_17009_MENEo-succinylbenzoate-CoA ligase MenESingle catalytic protein system.
223203SYS_26562_MENB1,4-dihydroxy-2-naphthoyl-CoA synthase MenBSingle catalytic protein system.
224204SYS_26309_MENI1,4-dihydroxy-2-naphthoyl-CoA hydrolase MenISingle catalytic protein system.
225205SYS_26478_MENA1,4-dihydroxy-2-naphthoate polyprenyltransferase MenASingle catalytic protein system.
226206SYS_42640_MENGdemethylmenaquinol methyltransferase MenGSingle catalytic protein system.
227207SYS_40051_MQNAchorismate dehydratase MqnASingle catalytic protein system.
228208SYS_33075_MQNEaminodeoxyfutalosine synthase MqnESingle catalytic protein system.
229209SYS_40075_MQNXaminodeoxyfutalosine deaminase MqnXSingle catalytic protein system.
230210SYS_25904_MQNBfutalosine hydrolase MqnBSingle catalytic protein system.
231211SYS_33083_MQNCcyclic dehypoxanthinyl futalosine synthase MqnCSingle catalytic protein system.
232212SYS_33087_MQND1,4-dihydroxy-6-naphthoate synthase MqnDSingle catalytic protein system.
233213SYS_16845_CS_SIsi-citrate synthaseSingle catalytic protein, EC 2.3.3.1, the canonical gltA group.
234213SYS_16845_CS_RERe-citrate synthaseSingle catalytic protein, EC 2.3.3.3. Same reaction, unrelated protein: a non-homologous replacement.
235213SYS_16845_CS_METHYLCITRATE_GROUPcitrate synthase of the 2-methylcitrate synthase orthology groupThe group KEGG names prpC. It is accepted because it carries genuine citrate synthases, including Staphylococcus aureus citZ and Bacteroides thetaiotaomicron BT_2070, and because KEGG lists it as a citrate synthase alternative in modules M00009 and M00010. It also carries true 2-methylcitrate synthases, so the evidence is recorded as ambiguous.
236214SYS_10336_ACONITASEaconitate hydrataseSingle catalytic protein with three alternative orthology groups. K01682 and K27802 are bifunctional with 2-methylisocitrate dehydratase and still catalyse this reaction.
237215SYS_19629_ICDH_NADPNADP-dependent isocitrate dehydrogenaseSingle catalytic protein.
238216SYS_23632_ICDH_NADNAD-dependent isocitrate dehydrogenaseSingle catalytic protein.
239217SYS_27786_ODH_COMPLEX2-oxoglutarate dehydrogenase multienzyme complexThree jointly required components. The E3 dihydrolipoyl dehydrogenase is shared with pyruvate dehydrogenase, which is why it is required together with the 2-oxoglutarate-specific E1 and E2 rather than alone.
240218SYS_17297_KOR2-oxoglutarate:ferredoxin oxidoreductaseTwo jointly required catalytic subunits. Four-subunit forms exist and their gamma and delta subunits are not required, because requiring them would call the two-subunit enzymes negative.
241219SYS_17661_SUCCDsuccinyl-CoA synthetase, sucCD typeTwo jointly required subunits.
242219SYS_17661_LSCsuccinyl-CoA synthetase, LSC typeTwo jointly required subunits. KEGG records both the ADP- and the GDP-forming EC numbers for this group, which is why the two nucleotide specificities are not curated as separate reactions.
243220SYS_10524_KGD2-oxoglutarate decarboxylaseSingle multifunctional catalytic protein.
244221SYS_13217_SSADH_NADNAD-dependent succinate-semialdehyde dehydrogenaseSingle catalytic protein with alternative orthology groups.
245222SYS_13213_SSADH_NADPNADP-dependent succinate-semialdehyde dehydrogenaseSingle catalytic protein with alternative orthology groups.
246223SYS_40523_SDH_FRD_SHAREDsuccinate dehydrogenase and fumarate reductase, shared orthology groupTwo jointly required catalytic subunits. KEGG names these groups sdhA, frdA and sdhB, frdB because outside the Enterobacteriaceae the two enzymes are not separated. The membrane anchor subunits are not required: they are poorly conserved and requiring them would call 402 further genomes negative.
247223SYS_40523_SDH_MITOCHONDRIALsuccinate dehydrogenase, mitochondrial typeTwo jointly required catalytic subunits of the eukaryotic and alphaproteobacterial-type complex.
248223SYS_40523_FRD_DEDICATEDfumarate reductase, dedicated groupTwo jointly required catalytic subunits. This group exists as a separate orthology group almost only in the Enterobacteriaceae, where it is a paralogue of the succinate dehydrogenase the same genomes also carry.
249224SYS_12460_FUMCfumarate hydratase class IISingle catalytic protein.
250224SYS_12460_FUMA_SINGLEfumarate hydratase class I, single chainSingle catalytic protein.
251224SYS_12460_FUMABfumarate hydratase class I, two subunitsTwo jointly required subunits of the split class I enzyme.
252225SYS_21432_MDHNAD-dependent malate dehydrogenaseSingle catalytic protein with alternative orthology groups for the bacterial and the eukaryotic enzymes.
253226SYS_46012_MQOmalate:quinone oxidoreductaseSingle catalytic protein.
254227SYS_14717_CLASSIclass I DAHP synthaseSingle catalytic protein system. The AroF/AroG/AroH family of allosterically regulated enzymes.
255227SYS_14717_CLASSIIclass II DAHP synthaseSingle catalytic protein system. A structurally unrelated family found in Mycobacterium, Streptomyces and many archaea; a non-homologous replacement for class I rather than a variant of it.
256227SYS_14717_DAHPCMbifunctional DAHP synthase/chorismate mutaseSingle catalytic protein system carrying both the first step of the pathway and the first step of the phenylalanine and tyrosine branch.
257228SYS_21968_AROB3-dehydroquinate synthase AroBSingle catalytic protein system.
258228SYS_21968_AROKBbifunctional AroKBSingle catalytic protein system carrying both the dehydroquinate synthase and the shikimate kinase activity.
259229SYS_21096_TYPEItype I 3-dehydroquinate dehydrataseSingle catalytic protein system. A Schiff-base enzyme, mechanistically and structurally unrelated to type II.
260229SYS_21096_TYPEIItype II 3-dehydroquinate dehydrataseSingle catalytic protein system. A dodecameric enzyme with an anti elimination mechanism; a non-homologous replacement for type I.
261229SYS_21096_ARODEbifunctional AroDESingle catalytic protein system carrying both the dehydratase and the shikimate dehydrogenase activity.
262230SYS_17737_AROEshikimate dehydrogenase AroESingle catalytic protein system.
263230SYS_17737_ARODEbifunctional AroDESingle catalytic protein system carrying both the dehydroquinate dehydratase and the shikimate dehydrogenase activity.
264230SYS_17737_YDIBquinate/shikimate dehydrogenase YdiBSingle catalytic protein system. An AroE paralogue that accepts both quinate and shikimate, and that Rhea records against this master reaction alongside AroE.
265231SYS_13121_AROKLshikimate kinase AroK or AroLSingle catalytic protein system.
266231SYS_13121_AROKBbifunctional AroKBSingle catalytic protein system carrying both the shikimate kinase and the dehydroquinate synthase activity.
267232SYS_21256_AROAEPSP synthase AroASingle catalytic protein system.
268232SYS_21256_FUSIONbifunctional prephenate dehydrogenase/EPSP synthaseSingle catalytic protein system carrying the carboxyvinyl transfer fused to a branch-pathway dehydrogenase.
269233SYS_21020_AROCchorismate synthase AroCSingle catalytic protein system.
270198SYS_18985_PCHAsalicylate biosynthesis isochorismate synthase PchASingle catalytic protein system.
271198SYS_18985_MBTIsalicylate synthase MbtISingle catalytic protein system. Bifunctional: it isomerises chorismate and eliminates pyruvate in one active site, and releases free isochorismate slowly enough to have been characterised as an isochorismate synthase in its own right.
272234SYS_27874_PCHBisochorismate pyruvate lyase PchBSingle catalytic protein system.
273234SYS_27874_MBTIsalicylate synthase MbtISingle catalytic protein system carrying the second half of the salicylate synthase reaction.
274235SYS_16165_IAAMtryptophan 2-monooxygenase IaaMSingle catalytic protein system.
275236SYS_34371_IAAHindole-3-acetamide hydrolase IaaHSingle catalytic protein system.
276236SYS_34371_AMIDASEamidase signature family hydrolaseSingle catalytic protein system. The broad amidase group, accepted here only because the preceding monooxygenase carries the pathway claim.
277237SYS_21368_URICASEurate oxidaseSingle-protein catalytic system.
278238SYS_27329_HPXOHpxO urate hydroxylaseSingle-protein catalytic system; a flavin-dependent alternative to the cofactor-independent urate oxidase.
279239SYS_23736_HIUH5-hydroxyisourate hydrolaseSingle-protein catalytic system; the transthyretin-like protein.
280240SYS_26301_OHCUDCOHCU decarboxylaseSingle-protein catalytic system. The step also proceeds spontaneously to racemic allantoin, which is why the routes curate it with required = 0.
281241SYS_17029_ALLBallantoinaseSingle-protein catalytic system.
282242SYS_11016_ALCallantoicaseSingle-protein catalytic system.
283243SYS_27485_ALLCallantoate deiminaseSingle-protein catalytic system.
284244SYS_25241_YLBAureidoglycine aminohydrolaseSingle-protein catalytic system.
285245SYS_11304_ALLAureidoglycolate lyaseSingle-protein catalytic system.
286246SYS_20557_UREABCurease catalytic coreThree jointly required subunits. The nickel maturation proteins UreD, UreE, UreF and UreG are deliberately excluded: they perform metallocentre assembly rather than catalysis, and requiring all four costs 984 genomes.
287247SYS_21068_NASACNasA/NasC assimilatory nitrate reductaseSingle catalytic subunit. The NasB diaphorase subunit is not required: it is annotated in 439 bacteria against 2796 for the catalytic subunit.
288248SYS_21828_NARBNarB ferredoxin-nitrate reductaseSingle-protein catalytic system.
289249SYS_18041_NIRANirA ferredoxin-nitrite reductaseSingle-protein catalytic system.
290250SYS_24628_NIRBDNirBD nitrite reductaseTwo jointly required subunits.
291250SYS_24628_NASDENasDE nitrite reductaseTwo jointly required subunits of the nitrate-assimilation operon.
292251SYS_45700_GBCABGbcAB glycine betaine monooxygenaseTwo jointly required subunits: the Rieske oxygenase and its reductase.
293252SYS_74167_DGCABDgcAB dimethylglycine dehydrogenaseTwo jointly required subunits. The same protein pair also carries the sarcosine reaction RHEA:74155, so it is a multifunctional system represented at both reactions.
294253SYS_52856_DMGDHdimethylglycine dehydrogenaseSingle-protein catalytic system.
295254SYS_17077_DMGOdimethylglycine oxidaseSingle-protein catalytic system.
296255SYS_13313_SOXABGDheterotetrameric sarcosine oxidaseFour jointly required subunits.
297255SYS_13313_SOXMONOmonomeric sarcosine oxidaseSingle-protein alternative to the heterotetramer.
298256SYS_74155_DGCABDgcAB sarcosine dehydrogenaseTwo jointly required subunits; the same multifunctional pair that carries RHEA:74167.
299257SYS_14533_CRNAcreatininaseSingle-protein catalytic system.
300258SYS_22456_CREAcreatinaseSingle-protein catalytic system.
301259SYS_55396_CNTABCntAB carnitine monooxygenaseTwo jointly required subunits: the Rieske oxygenase and its reductase.
302260SYS_19265_CDHAcarnitine 3-dehydrogenaseSingle-protein catalytic system; K27497 is a bifunctional protein that also carries the thioesterase step.
303261SYS_47044_CDHCCdhC 3-dehydrocarnitine transferaseSingle-protein catalytic system. Despite the enzyme name, the product is the betainyl thioester and no free trimethylamine is released.
304262SYS_45716_BCTbetainyl-CoA thioesteraseSingle-protein catalytic system. Its only orthology group is bifunctional with carnitine 3-dehydrogenase, so the step is curated with required = 0.
305263SYS_30207_MAUABMauAB methylamine dehydrogenaseTwo jointly required subunits of the tryptophan-tryptophylquinone enzyme.
306264SYS_15909_TAUDTauD taurine dioxygenaseSingle-protein catalytic system.
307265SYS_10420_TPATpa taurine-pyruvate aminotransferaseSingle-protein catalytic system.
308266SYS_18709_TAUXYTauXY taurine dehydrogenaseTwo jointly required subunits.
309267SYS_24204_XSCXsc sulfoacetaldehyde acetyltransferaseSingle-protein catalytic system.
310268SYS_14613_TAUABCTauABC ABC importerThree jointly required subunits.
311269SYS_16169_GLNAglutamine synthetaseSingle-protein catalytic system.
312270SYS_15501_GLTBDGltBD glutamate synthaseTwo jointly required chains.
313271SYS_12128_GLTSGltS ferredoxin-dependent glutamate synthaseSingle-protein catalytic system.
314272SYS_11612_GDHANADP-dependent glutamate dehydrogenaseSingle-protein catalytic system.
315273SYS_15133_GDHNAD-dependent glutamate dehydrogenaseSingle-protein catalytic system.
316274SYS_12633_BENABbenzoate 1,2-dioxygenase oxygenase componentTwo-subunit oxygenase. The shared ferredoxin and ferredoxin reductase components of this system are deliberately not curated: they are interchangeable between Rieske systems and are annotated two to three times less often than the substrate-determining subunits, so requiring them would turn an annotation gap into a missing capability.
317275SYS_11560_BENDdihydroxycyclohexadiene carboxylate dehydrogenaseSingle-protein catalytic system.
318276SYS_11072_ANTABanthranilate 1,2-dioxygenase, antAB systemTwo-subunit oxygenase of the ant type. The shared ferredoxin and ferredoxin reductase components of this system are deliberately not curated: they are interchangeable between Rieske systems and are annotated two to three times less often than the substrate-determining subunits, so requiring them would turn an annotation gap into a missing capability.
319276SYS_11072_ANDAanthranilate 1,2-dioxygenase, andAcAd systemAlternative two-subunit oxygenase annotated to a different orthology group. The shared ferredoxin and ferredoxin reductase components of this system are deliberately not curated: they are interchangeable between Rieske systems and are annotated two to three times less often than the substrate-determining subunits, so requiring them would turn an annotation gap into a missing capability.
320277SYS_57952_DMPmulticomponent phenol 2-monooxygenaseSix jointly required subunits. Unlike the Rieske systems in this layer these components are the enzyme itself, not interchangeable electron carriers, so all six are required.
321278SYS_23852_CATAcatechol 1,2-dioxygenaseSingle-protein catalytic system.
322279SYS_30031_CATBmuconate cycloisomeraseSingle-protein catalytic system.
323280SYS_12348_CATCmuconolactone isomeraseSingle-protein catalytic system.
324281SYS_10184_PCAD3-oxoadipate enol-lactonaseSingle-protein catalytic system.
325281SYS_10184_PCALfused enol-lactonase/decarboxylase PcaLAlternative single-protein system in which the hydrolase is fused to a 4-carboxymuconolactone decarboxylase.
326282SYS_12048_PCAIJ3-oxoadipate CoA-transferaseTwo jointly required subunits of the heterotetrameric transferase.
327283SYS_19481_PCAF3-oxoadipyl-CoA thiolaseSingle-protein catalytic system.
328284SYS_17337_XYLEcatechol 2,3-dioxygenaseSingle-protein catalytic system with two accepted markers in different namespaces.
329285SYS_14549_XYLF2-hydroxymuconate semialdehyde hydrolaseSingle-protein catalytic system.
330286SYS_34219_XYLG2-hydroxymuconate semialdehyde dehydrogenaseSingle-protein catalytic system.
331287SYS_33431_XYLH2-hydroxymuconate tautomeraseSingle-protein catalytic system.
332288SYS_24260_XYLI4-oxalocrotonate decarboxylaseSingle-protein catalytic system.
333289SYS_22580_MHPD2-oxopent-4-enoate hydratase, mhp typeSingle-protein catalytic system.
334289SYS_22580_XYLJ2-oxopent-4-enoate hydratase, bph/xyl typeAlternative single-protein system annotated to a separate orthology group.
335290SYS_22624_MHPE4-hydroxy-2-oxovalerate aldolase, mhp typeSingle-protein catalytic system.
336290SYS_22624_XYLK4-hydroxy-2-oxovalerate aldolase, bph/xyl typeAlternative single-protein system annotated to a separate orthology group.
337115SYS_23288_MHPFacylating acetaldehyde dehydrogenase, mhp typeAlternative system for a reaction already curated for ethanol formation. MhpF is the standalone counterpart of the AdhE aldehyde domain and carries no alcohol dehydrogenase activity.
338115SYS_23288_XYLQacylating acetaldehyde dehydrogenase, bph/xyl typeAlternative system annotated to a separate orthology group.
339291SYS_20956_PAAKphenylacetate-CoA ligaseSingle-protein catalytic system with two accepted markers in different namespaces.
340292SYS_32171_PAAABCDEring-1,2-phenylacetyl-CoA epoxidaseFive jointly required subunits of the epoxidase complex.
341293SYS_31843_PAAGepoxyphenylacetyl-CoA isomeraseSingle-protein catalytic system.
342294SYS_31755_PAAZoxepin-CoA hydrolaseSingle-protein catalytic system; the same bifunctional PaaZ protein carries the next step.
343295SYS_31747_PAAZ3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenaseSingle-protein catalytic system; the same bifunctional PaaZ protein carries the preceding step.
344296SYS_34799_PAAJ3-oxo-5,6-didehydrosuberyl-CoA thiolaseSingle-protein catalytic system.
345297SYS_76647_PAAF2,3-didehydroadipoyl-CoA hydrataseSingle-protein catalytic system using a chain-generic beta-oxidation orthologue.
346298SYS_34851_PAAH3-hydroxyadipyl-CoA dehydrogenaseSingle-protein catalytic system using a chain-generic beta-oxidation orthologue.
347299SYS_20357_HCAEF3-phenylpropanoate dioxygenase oxygenase componentTwo-subunit Rieske oxygenase. The shared ferredoxin and ferredoxin reductase components of this system are deliberately not curated: they are interchangeable between Rieske systems and are annotated two to three times less often than the substrate-determining subunits, so requiring them would turn an annotation gap into a missing capability.
348300SYS_25062_HCABcis-dihydrodiol dehydrogenaseSingle-protein catalytic system.
349301SYS_24785_MHPA3-(3-hydroxyphenyl)propanoate hydroxylaseSingle-protein flavin monooxygenase system.
350302SYS_23840_MHPB2,3-dihydroxyphenylpropanoate 1,2-dioxygenaseSingle-protein catalytic system.
351303SYS_34187_MHPC2-hydroxy-6-oxononadienedioate hydrolaseSingle-protein catalytic system.
352304SYS_10532_TRPABtryptophan synthase complexAlpha and beta subunits are jointly required.
353304SYS_10532_TRPAB_FUSEDtryptophan synthase, fusedSingle polypeptide carrying both chains.
354305SYS_10676_LEUCD3-isopropylmalate dehydratase complexLarge and small subunits are jointly required.
355305SYS_10676_LEUC_SINGLE3-isopropylmalate dehydratase, single-chainSingle-chain isopropylmalate isomerase.
356306SYS_10932_ARGGargininosuccinate synthaseSingle catalytic protein.
357307SYS_11040_HISB_DEHYDRATASEimidazoleglycerol-phosphate dehydrataseSingle catalytic protein.
358307SYS_11040_HISB_BIFUNCTIONALbifunctional imidazoleglycerol-phosphate dehydratase/histidinol-phosphataseThe Enterobacterial HisB carries both activities on one chain.
359308SYS_11372_ASNAaspartate--ammonia ligaseSingle catalytic protein.
360309SYS_11768_TRPDanthranilate phosphoribosyltransferaseSingle catalytic protein.
361310SYS_11960_DAPCN-succinyldiaminopimelate aminotransferaseSingle catalytic protein; alternative orthologs are OR.
362311SYS_12228_ASNBasparagine synthase (glutamine-hydrolysing)Single catalytic protein.
363312SYS_13085_DAPHtetrahydrodipicolinate N-acetyltransferaseSingle catalytic protein.
364313SYS_13493_ILVCketol-acid reductoisomeraseSingle catalytic protein.
365314SYS_13561_DDHdiaminopimelate dehydrogenaseSingle catalytic protein.
366315SYS_13869_PDHprephenate dehydrogenaseSingle catalytic protein; TyrA is bifunctional with the mutase.
367316SYS_13897_CMchorismate mutaseSingle catalytic protein; the bifunctional P-protein and T-protein forms are alternatives.
368317SYS_14109_PROCpyrroline-5-carboxylate reductaseSingle catalytic protein.
369318SYS_14465_HISNhistidinol-phosphate phosphataseSingle catalytic protein; three non-homologous phosphatase families are known.
370318SYS_14465_HISB_BIFUNCTIONALbifunctional imidazoleglycerol-phosphate dehydratase/histidinol-phosphataseThe Enterobacterial HisB carries both activities on one chain.
371319SYS_14629_ARGBacetylglutamate kinaseSingle catalytic protein; several bifunctional forms exist.
372320SYS_14877_PROBglutamate 5-kinaseSingle catalytic protein.
373320SYS_14877_P5CSdelta-1-pyrroline-5-carboxylate synthetaseBifunctional kinase and dehydrogenase on one chain.
374321SYS_15093_AROATaromatic aminotransferaseSingle catalytic protein; alternative orthologs are OR.
375322SYS_15101_LYSAdiaminopimelate decarboxylaseSingle catalytic protein.
376323SYS_15349_ARGJglutamate N-acetyltransferaseSingle catalytic protein.
377324SYS_15393_DAPFdiaminopimelate epimeraseSingle catalytic protein.
378325SYS_15469_HISAphosphoribosylformimino-AICAR-phosphate isomeraseSingle catalytic protein.
379326SYS_15941_ARGEacetylornithine deacetylaseSingle catalytic protein.
380327SYS_16293_LEUCD3-isopropylmalate dehydratase complexLarge and small subunits are jointly required.
381327SYS_16293_LEUC_SINGLE3-isopropylmalate dehydratase, single-chainSingle-chain isopropylmalate isomerase.
382328SYS_17325_DAPDtetrahydrodipicolinate N-succinyltransferaseSingle catalytic protein.
383329SYS_18049_ARGDacetylornithine aminotransferaseSingle catalytic protein.
384330SYS_18321_ILVEbranched-chain aminotransferaseSingle catalytic protein.
385331SYS_18405_ALDalanine dehydrogenaseSingle catalytic protein.
386332SYS_18473_HISGATP phosphoribosyltransferaseCatalytic subunit. The HisZ regulatory subunit found in some Firmicutes is not required.
387333SYS_19045_CIMAcitramalate synthaseSingle catalytic protein.
388334SYS_19453_ALAAalanine-synthesising transaminaseSingle catalytic protein; alternative orthologs are OR.
389334SYS_19453_AVTAvaline-pyruvate transaminaseTransaminase C, which forms alanine using L-valine as the amino donor.
390335SYS_19513_ARGFornithine carbamoyltransferaseSingle catalytic protein.
391336SYS_19541_PROAglutamate-5-semialdehyde dehydrogenaseSingle catalytic protein.
392336SYS_19541_P5CSdelta-1-pyrroline-5-carboxylate synthetaseBifunctional kinase and dehydrogenase on one chain.
393337SYS_20049_HISIphosphoribosyl-AMP cyclohydrolaseSingle catalytic protein; several bifunctional forms exist.
394338SYS_20405_DAPLN-acetyldiaminopimelate deacetylaseSingle catalytic protein.
395339SYS_21524_LEUA2-isopropylmalate synthaseSingle catalytic protein.
396340SYS_21540_TRPFphosphoribosylanthranilate isomeraseSingle catalytic protein.
397341SYS_21588_ARGCN-acetyl-gamma-glutamyl-phosphate reductaseSingle catalytic protein.
398342SYS_21640_PDHNprephenate dehydrogenase (NADP+)Single catalytic protein.
399343SYS_21648_PDTprephenate dehydrataseSingle catalytic protein; PheA is bifunctional with the mutase.
400344SYS_21732_TRPEGanthranilate synthase complexComponent I and the glutamine amidotransferase component II are jointly required.
401344SYS_21732_TRPEG_FUSEDanthranilate synthase, fusedSingle polypeptide carrying both anthranilate synthase functions.
402345SYS_21824_ASPATaspartate aminotransferaseSingle catalytic protein; alternative orthologs are OR.
403346SYS_22068_ILVCketol-acid reductoisomeraseSingle catalytic protein.
404347SYS_22332_LEUCD3-isopropylmalate/2-methylmalate dehydratase complexLarge and small subunits are jointly required.
405348SYS_22608_DAPEsuccinyl-diaminopimelate desuccinylaseSingle catalytic protein.
406349SYS_22828_HISEphosphoribosyl-ATP pyrophosphohydrolaseSingle catalytic protein; several bifunctional forms exist.
407350SYS_23476_TRPCindole-3-glycerol-phosphate synthaseSingle catalytic protein.
408351SYS_23744_HISChistidinol-phosphate aminotransferaseSingle catalytic protein.
409352SYS_23988_DAPLTLL-diaminopimelate aminotransferaseSingle catalytic protein.
410353SYS_24020_ARGHargininosuccinate lyaseSingle catalytic protein.
411354SYS_24292_ARGAamino-acid N-acetyltransferaseSingle catalytic protein; several bifunctional forms exist.
412355SYS_24793_HISFHimidazole glycerol-phosphate synthase complexThe cyclase and the glutamine amidotransferase subunits are jointly required.
413355SYS_24793_HISF_FUSEDimidazole glycerol-phosphate synthase, fusedSingle polypeptide carrying both functions.
414356SYS_24801_ILVEbranched-chain aminotransferaseSingle catalytic protein.
415357SYS_24809_ILVDdihydroxy-acid dehydrataseSingle catalytic protein.
416358SYS_24813_ILVEbranched-chain aminotransferaseSingle catalytic protein.
417359SYS_25152_AROATaromatic aminotransferaseSingle catalytic protein; alternative orthologs are OR.
418360SYS_25315_DAPXN-acetyldiaminopimelate aminotransferaseSingle catalytic protein.
419361SYS_27654_ILVBNacetohydroxyacid synthaseCatalytic large subunit. The IlvN/IlvH small subunit is regulatory and is not required, on the precedent already recorded for the PyrI regulatory subunit of aspartate carbamoyltransferase.
420362SYS_27694_ILVDdihydroxy-acid dehydrataseSingle catalytic protein.
421363SYS_32271_LEUB3-isopropylmalate dehydrogenaseSingle catalytic protein.
422364SYS_32715_LEUB3-isopropylmalate dehydrogenaseSingle catalytic protein.
423365SYS_33799_HISDhistidinol dehydrogenaseSingle catalytic protein carrying out both oxidations.
424366SYS_33803_HISDhistidinol dehydrogenaseSingle catalytic protein carrying out both oxidations.
425367SYS_34171_DAPA4-hydroxy-tetrahydrodipicolinate synthaseSingle catalytic protein.
426368SYS_35331_DAPB4-hydroxy-tetrahydrodipicolinate reductaseSingle catalytic protein.
427369SYS_42424_LEUCD3-isopropylmalate/2-methylmalate dehydratase complexLarge and small subunits are jointly required.
428370SYS_10152_ARCCcarbamate kinaseSingle catalytic protein.
429371SYS_10680_PRDFproline racemaseSingle catalytic protein.
430372SYS_12232_GRDglycine reductase complexSelenoprotein A, the substrate-specific protein B subunits and both protein C subunits are jointly required.
431373SYS_12737_PRDD-proline reductase complexPrdA and the selenocysteine-containing PrdB are jointly required. The PrdD and PrdE stabilising proteins are not required, on the precedent recorded for the PyrI regulatory subunit.
432374SYS_13101_HUTUurocanate hydrataseSingle catalytic protein.
433375SYS_17785_GADglutamate decarboxylaseSingle catalytic protein.
434376SYS_19169_SDAAsingle-chain iron-sulfur L-serine ammonia-lyaseOne complete catalytic protein; the split alpha and beta chains are a separate system.
435376SYS_19169_SDA_SPLITsplit iron-sulfur L-serine ammonia-lyaseBoth SdaAA alpha and SdaAB beta are required.
436376SYS_19169_SDSPLP-dependent serine/threonine ammonia-lyaseOne complete K17989-assigned catalytic protein.
437377SYS_19553_TNAAtryptophanaseSingle catalytic protein.
438378SYS_19597_ARCAarginine deiminaseSingle catalytic protein.
439379SYS_21232_HUTHhistidine ammonia-lyaseSingle catalytic protein.
440380SYS_22108_ILVAthreonine ammonia-lyaseSingle catalytic protein; the biosynthetic IlvA and the catabolic TdcB belong to the same orthology group.
441381SYS_22492_HUTGformimidoylglutamaseSingle catalytic protein.
442382SYS_23660_HUTIimidazolonepropionaseSingle catalytic protein.
443383SYS_23800_MGLmethionine gamma-lyaseSingle catalytic protein.
444384SYS_24931_CDSL-cysteine desulfidaseSingle catalytic protein. The promiscuous PLP enzymes that also carry this activity -- cystathionine beta-lyase, cystathionine gamma-lyase, MalY -- are deliberately excluded: accepting them would make every transsulfuration genome a sulfide producer, and MetC is already curated as evidence for cysteine biosynthesis.
445385SYS_13245_ICLisocitrate lyaseSingle catalytic protein.
446386SYS_18181_MALSmalate synthaseSingle direct malate-synthase protein; the two-step malyl-CoA implementation is not folded into this reaction.
447387SYS_21448_NIFmolybdenum nitrogenase with cofactor assemblyNifHDK catalysis and electron delivery plus the NifEN scaffold and NifB precursor synthesis. Every component is required.
448388SYS_55543_VNFvanadium nitrogenase with cofactor assemblyVnfHDGK catalysis and electron delivery plus the VnfEN scaffold and shared NifB precursor synthesis. Every component is required.
449389SYS_18136_MET3monomeric sulfate adenylyltransferaseSingle catalytic Met3/Sat protein.
450389SYS_18136_CYSDNheterodimeric CysDN sulfate adenylyltransferaseBoth CysN and CysD are required.
451389SYS_18136_CYSD_CYSNCCysD with bifunctional CysNC sulfate adenylyltransferaseCysNC supplies the CysN sulfurylase subunit and CysD supplies its required partner.
452390SYS_24152_CYSCAPS kinase CysCSingle catalytic protein.
453390SYS_24152_CYSNCAPS kinase domain of CysNCThe bifunctional fusion supplies the complete kinase activity.
454391SYS_11724_CYSH_PAPSPAPS reductaseReaction-specific activity marker used because the CysH KO also spans APS reductase.
455392SYS_21976_CYSH_APSAPS reductaseReaction-specific activity marker used because the CysH KO also spans PAPS reductase.
456393SYS_13804_CYSJINADPH sulfite reductase CysJIBoth the flavoprotein and siroheme subunits are required.
457394SYS_23132_SIRferredoxin sulfite reductaseSingle catalytic siroheme protein.
458395SYS_11160_ECTBEctB diaminobutanoate aminotransferaseSingle catalytic protein.
459396SYS_16901_ECTAEctA diaminobutanoate acetyltransferaseSingle catalytic protein.
460397SYS_17281_ECTCEctC ectoine synthaseSingle catalytic protein.
461398SYS_19865_HEMEHemE uroporphyrinogen decarboxylaseSingle catalytic protein shared by every curated heme-b route.
462399SYS_18257_HEMFHemF oxygen-dependent coproporphyrinogen oxidaseSingle catalytic protein.
463400SYS_15425_HEMNHemN oxygen-independent coproporphyrinogen oxidaseSingle radical-SAM catalytic protein.
464401SYS_25576_HEMYHemY protoporphyrinogen oxidaseSingle catalytic protein; the same KO also supplies the copro-specific reaction in its own system.
465402SYS_27409_HEMGHemG menaquinone-dependent protoporphyrinogen oxidaseSingle catalytic protein.
466403SYS_62000_HEMJHemJ protoporphyrinogen oxidaseSingle catalytic protein; the electron acceptor remains abstract in Rhea.
467404SYS_22584_HEMHHemH protoporphyrin ferrochelataseSingle catalytic protein; the same KO also supplies coproferrochelatase in its own system.
468405SYS_43436_HEMYHemY coproporphyrinogen oxidaseSingle catalytic protein using the copro-specific activity of HemY.
469406SYS_49572_HEMHHemH coproporphyrin ferrochelataseSingle catalytic protein using the copro-specific activity of HemH.
470407SYS_56516_HEMQHemQ hydrogen peroxide-dependent heme synthaseSingle catalytic protein.
471408SYS_11112_ENTBEntB isochorismate lyaseSingle bifunctional protein; this system uses its lyase domain.
472409SYS_23824_ENTAEntA dihydroxybenzoate dehydrogenaseSingle catalytic protein.
473410SYS_30571_ENTBDEFEnterobactin synthetase machineryEntB, EntD, EntE and EntF are jointly required for carrier activation, substrate loading, condensation and cyclisation.
474411SYS_17433_BETABetA choline dehydrogenaseSingle catalytic protein.
475412SYS_33051_GBSBGbsB choline dehydrogenaseSingle catalytic protein of the Gram-positive GbsAB architecture.
476413SYS_17769_CMOcholine monooxygenaseSingle catalytic protein.
477414SYS_13505_CODAcholine oxidase, first oxidationSingle catalytic protein; the same marker is required again for the second reaction.
478415SYS_20369_CODAcholine oxidase, second oxidationSingle catalytic protein; the same marker supplies the first reaction too.
479416SYS_15305_BADHbetaine-aldehyde dehydrogenaseSingle catalytic protein accepted only on the substrate-specific KO.
480417SYS_24360_CYSGmultifunctional siroheme synthase CysG ferrochelataseSingle catalytic protein system; the same CysG marker also supplies the preceding methylation and dehydrogenation reactions.
481417SYS_24360_MET8bifunctional precorrin-2 dehydrogenase and sirohydrochlorin ferrochelatase Met8Single catalytic protein system; the same Met8 marker also supplies the preceding dehydrogenation reaction.
482417SYS_24360_SIRBsirohydrochlorin ferrochelatase SirBSingle catalytic protein system.
483418SYS_CHITINASEendochitinaseSingle catalytic protein system; alternative markers are OR.
484419SYS_CHITOBIASEbeta-N-acetylhexosaminidaseSingle catalytic protein system; alternative markers are OR.
485420SYS_CHITIN_LPMOlytic polysaccharide monooxygenaseSingle catalytic protein system; alternative markers are OR.
486421SYS_SIALIDASEsialidaseSingle catalytic protein system; alternative markers are OR.
487422SYS_FUCOSIDASEalpha-L-fucosidaseSingle catalytic protein system; alternative markers are OR.
488423SYS_GALNACASEalpha-N-acetylgalactosaminidaseSingle catalytic protein system; alternative markers are OR.
489424SYS_ENDO_PGendo-polygalacturonaseSingle catalytic protein system; alternative markers are OR.
490425SYS_EXO_PGexo-polygalacturonaseSingle catalytic protein system; alternative markers are OR.
491426SYS_PECTINESTERASEpectinesteraseSingle catalytic protein system; alternative markers are OR.
492427SYS_ENDO_PLendo-pectate lyaseSingle catalytic protein system; alternative markers are OR.
493428SYS_57104_PELWXpectate disaccharide-lyaseSingle-protein catalytic system.
494429SYS_20269_OGLoligogalacturonide lyaseSingle-protein catalytic system.
495430SYS_23896_KDUI4-deoxy-L-threo-5-hexosulose-uronate ketol-isomeraseSingle-protein catalytic system.
496431SYS_24232_KDUD2-dehydro-3-deoxy-D-gluconate 5-dehydrogenaseSingle-protein catalytic system.
497432SYS_PECTIN_LYASEpectin lyaseSingle catalytic protein system; alternative markers are OR.
498433SYS_52304_DOEADoeA ectoine hydrolaseSingle catalytic protein.
499434SYS_40951_DOEBDoeB N2-acetyldiaminobutanoate deacetylaseSingle catalytic protein.
500435SYS_45740_ECTDEctD ectoine hydroxylaseSingle catalytic protein.
501436SYS_14277_ALDHlactaldehyde dehydrogenaseSingle catalytic protein.
502437SYS_19093_AHBABAhbA-AhbB siroheme decarboxylaseHeterodimer of two distinct subunits, both required.
503438SYS_37431_AHBCAhbC Fe-coproporphyrin III synthaseSingle catalytic radical SAM protein.
504439SYS_56520_AHBDAhbD AdoMet-dependent heme synthaseSingle catalytic radical SAM protein.
505440SYS_49240_NAGENagE N-acetylglucosamine-specific enzyme IIOne substrate-specific enzyme II. The phospho-histidyl carrier this reaction consumes is regenerated by the general PTS enzyme I and HPr, which stand to it as ATP regeneration stands to the kinase reaction of the other route; gifter curates no cofactor regeneration and does not curate them here.
enzyme_component607 rows · 5 columns
component_pksystem_pkcomponent_idnamedescription
11COMP_14905_CATALYTICamidophosphoribosyltransferase proteinRequired catalytic protein.
22COMP_17453_CATALYTICGAR synthetase proteinRequired catalytic protein; alternative markers are OR.
33COMP_15053_CATALYTICGAR transformylase proteinRequired catalytic protein; alternative markers are OR.
44COMP_24829_CATALYTICGAR formyltransferase 2 proteinRequired catalytic protein.
55COMP_17129_LARGElarge FGAM synthase proteinRequired single-protein architecture.
66COMP_17129_TRI_AFGAM synthase trimer component ARequired component one of three.
76COMP_17129_TRI_BFGAM synthase trimer component BRequired component two of three.
86COMP_17129_TRI_CFGAM synthase trimer component CRequired component three of three.
97COMP_17129_DI_AFGAM synthase two-component protein ARequired component one of two.
107COMP_17129_DI_BFGAM synthase two-component protein BRequired component two of two.
118COMP_23032_CATALYTICAIR synthetase proteinRequired catalytic protein; alternative markers are OR.
129COMP_10792_CATALYTICdirect AIR carboxylase proteinRequired catalytic protein; alternative markers are OR.
1310COMP_19317_CATALYTICN5-CAIR synthetase proteinRequired catalytic protein.
1411COMP_13193_CATALYTICN5-CAIR mutase proteinRequired catalytic protein.
1512COMP_22628_CATALYTICSAICAR synthetase proteinRequired catalytic protein; alternative markers are OR.
1613COMP_23920_CATALYTICSAICAR lyase proteinRequired catalytic protein.
1714COMP_22192_CATALYTICAICAR transformylase proteinRequired catalytic protein; alternative markers are OR.
1815COMP_24836_CATALYTICFAICAR synthetase proteinRequired catalytic protein.
1916COMP_18445_CATALYTICIMP cyclohydrolase proteinRequired catalytic protein; alternative markers are OR.
2017COMP_15753_CATALYTICadenylosuccinate synthase proteinRequired catalytic protein.
2118COMP_16853_CATALYTICadenylosuccinate lyase proteinRequired catalytic protein.
2219COMP_11708_CATALYTICIMP dehydrogenase proteinRequired catalytic protein.
2320COMP_11680_CATALYTICGMP synthase proteinRequired catalytic protein.
2421COMP_18633_MONOMERcarbamoyl-phosphate synthase proteinRequired catalytic protein; alternative markers are OR.
2522COMP_18633_LARGEcarbamoyl-phosphate synthase large subunitRequired catalytic large subunit.
2622COMP_18633_SMALLcarbamoyl-phosphate synthase small subunitRequired glutamine-hydrolyzing small subunit.
2723COMP_20013_MONOMERaspartate carbamoyltransferase proteinRequired catalytic protein; alternative markers are OR.
2824COMP_20013_CATALYTICaspartate carbamoyltransferase catalytic subunitRequired catalytic subunit; catalytically competent without the PyrI regulatory subunit.
2925COMP_24296_CATALYTICdihydroorotase proteinRequired catalytic protein; alternative markers are OR.
3026COMP_30059_CATALYTICfumarate-dependent dihydroorotate dehydrogenase proteinRequired catalytic protein.
3127COMP_30187_CATALYTICquinone-dependent dihydroorotate dehydrogenase proteinRequired catalytic protein.
3228COMP_13513_CATALYTICNAD-dependent dihydroorotate dehydrogenase catalytic subunitRequired PyrDb catalytic subunit.
3328COMP_13513_ELECTRONNAD-dependent dihydroorotate dehydrogenase electron transfer subunitRequired PyrK electron transfer subunit; NAD+ reduction depends on it.
3429COMP_10380_CATALYTICorotate phosphoribosyltransferase proteinRequired catalytic protein; alternative markers are OR.
3530COMP_11596_CATALYTICorotidine 5'-phosphate decarboxylase proteinRequired catalytic protein; alternative markers are OR.
3631COMP_26426_CATALYTICCTP synthase proteinRequired catalytic protein.
3732COMP_12641_CATALYTIC3-phosphoglycerate dehydrogenase proteinRequired catalytic protein.
3833COMP_14329_CATALYTICphosphoserine aminotransferase proteinRequired catalytic protein.
3934COMP_21208_CATALYTICphosphoserine phosphatase proteinRequired catalytic protein; alternative markers are OR.
4035COMP_15481_CATALYTICserine hydroxymethyltransferase proteinRequired catalytic protein.
4136COMP_23776_CATALYTICaspartate kinase proteinRequired catalytic protein; alternative markers are OR.
4237COMP_24284_CATALYTICaspartate-semialdehyde dehydrogenase proteinRequired catalytic protein.
4338COMP_15757_CATALYTICNAD-dependent homoserine dehydrogenase proteinRequired catalytic protein; alternative markers are OR.
4439COMP_15761_CATALYTICNADP-dependent homoserine dehydrogenase proteinRequired catalytic protein; alternative markers are OR.
4540COMP_13985_CATALYTIChomoserine kinase proteinRequired catalytic protein; alternative markers are OR.
4641COMP_10840_CATALYTICthreonine synthase proteinRequired catalytic protein.
4742COMP_22008_CATALYTIChomoserine acyltransferase proteinRequired catalytic protein; alternative markers are OR.
4843COMP_13701_CATALYTIChomoserine acyltransferase proteinRequired catalytic protein; alternative markers are OR.
4944COMP_20397_CATALYTICcystathionine gamma-synthase proteinRequired catalytic protein.
5045COMP_30931_CATALYTICcystathionine gamma-synthase proteinRequired catalytic protein.
5146COMP_80891_CATALYTICplant cystathionine gamma-synthase proteinRequired catalytic protein.
5247COMP_13965_CATALYTICcystathionine beta-lyase proteinRequired catalytic protein; alternative markers are OR.
5348COMP_27826_CATALYTICO-succinylhomoserine sulfhydrylase proteinRequired catalytic protein; alternative markers are OR.
5449COMP_27822_CATALYTICO-acetylhomoserine sulfhydrylase proteinRequired catalytic protein; alternative markers are OR.
5550COMP_11172_CATALYTICcobalamin-dependent methionine synthase proteinRequired catalytic protein; alternative markers are OR.
5651COMP_21196_CATALYTICcobalamin-independent methionine synthase proteinRequired catalytic protein.
5752COMP_24560_CATALYTICserine O-acetyltransferase proteinRequired catalytic protein; alternative markers are OR.
5853COMP_14829_CATALYTICcysteine synthase proteinRequired catalytic protein; alternative markers are OR.
5954COMP_10112_CATALYTICcystathionine beta-synthase proteinRequired catalytic protein; alternative markers are OR.
6055COMP_32743_CATALYTICcystathionine beta-synthase proteinRequired catalytic protein.
6156COMP_14005_CATALYTICcystathionine gamma-lyase proteinRequired catalytic protein; alternative markers are OR.
6257COMP_22816_CATALYTICxylose isomerase proteinRequired catalytic protein; alternative markers are OR.
6358COMP_10964_CATALYTICxylulokinase proteinRequired catalytic protein; alternative markers are OR.
6459COMP_14821_CATALYTICL-arabinose isomerase proteinRequired catalytic protein; alternative markers are OR.
6560COMP_22072_CATALYTICL-ribulokinase proteinRequired catalytic protein; alternative markers are OR.
6661COMP_22368_CATALYTICL-ribulose-5-phosphate 4-epimerase proteinRequired catalytic protein; alternative markers are OR.
6762COMP_17233_CATALYTICL-fucose isomerase proteinRequired catalytic protein; alternative markers are OR.
6863COMP_12376_CATALYTICL-fuculokinase proteinRequired catalytic protein; alternative markers are OR.
6964COMP_12933_CATALYTICL-fuculose-1-phosphate aldolase proteinRequired catalytic protein; alternative markers are OR.
7065COMP_23160_CATALYTICL-rhamnose isomerase proteinRequired catalytic protein; alternative markers are OR.
7166COMP_20117_CATALYTICrhamnulokinase proteinRequired catalytic protein; alternative markers are OR.
7267COMP_19689_CATALYTICrhamnulose-1-phosphate aldolase proteinRequired catalytic protein; alternative markers are OR.
7368COMP_28675_CATALYTICaldose 1-epimerase proteinRequired catalytic protein; alternative markers are OR.
7469COMP_13553_CATALYTICgalactokinase proteinRequired catalytic protein; alternative markers are OR.
7570COMP_13989_CATALYTICgalactose-1-phosphate uridylyltransferase proteinRequired catalytic protein; alternative markers are OR.
7671COMP_22168_CATALYTICUDP-glucose 4-epimerase proteinRequired catalytic protein; alternative markers are OR.
7772COMP_17417_CATALYTICN-acetylglucosamine kinase proteinRequired catalytic protein; alternative markers are OR.
7873COMP_22936_CATALYTICN-acetylglucosamine-6-phosphate deacetylase proteinRequired catalytic protein; alternative markers are OR.
7974COMP_12172_CATALYTICglucosamine-6-phosphate deaminase proteinRequired catalytic protein; alternative markers are OR.
8075COMP_23296_CATALYTICN-acetylneuraminate lyase proteinRequired catalytic protein; alternative markers are OR.
8176COMP_25253_CATALYTICN-acetylmannosamine kinase proteinRequired catalytic protein; alternative markers are OR.
8277COMP_25257_CATALYTICN-acetylmannosamine-6-phosphate 2-epimerase proteinRequired catalytic protein; alternative markers are OR.
8378COMP_27702_CATALYTICglucuronate isomerase proteinRequired catalytic protein; alternative markers are OR.
8479COMP_17813_CATALYTICtagaturonate reductase proteinRequired catalytic protein; alternative markers are OR.
8580COMP_14797_CATALYTIC2-dehydro-3-deoxygluconokinase proteinRequired catalytic protein; alternative markers are OR.
8681COMP_17089_CATALYTIC2-dehydro-3-deoxy-phosphogluconate aldolase proteinRequired catalytic protein; alternative markers are OR.
8782COMP_13049_CATALYTICglucuronate isomerase proteinRequired catalytic protein; alternative markers are OR.
8883COMP_15729_CATALYTICfructuronate reductase proteinRequired catalytic protein; alternative markers are OR.
8984COMP_20097_CATALYTICmannonate dehydratase proteinRequired catalytic protein; alternative markers are OR.
9085COMP_15957_CATALYTICaltronate hydrolase proteinRequired catalytic protein.
9186COMP_15957_SMALLaltronate dehydratase small subunitRequired subunit one of two.
9286COMP_15957_LARGEaltronate dehydratase large subunitRequired subunit two of two.
9387COMP_29899_SBPsubstrate-binding proteinRequired subunit of the importer.
9487COMP_29899_PERMEASEpermeaseRequired subunit of the importer.
9587COMP_29899_ATPASEATP-binding proteinRequired subunit of the importer.
9688COMP_29899_XAC_SBPsubstrate-binding proteinRequired subunit of the importer.
9788COMP_29899_XAC_PERM1permease one of twoRequired subunit of the importer.
9888COMP_29899_XAC_PERM2permease two of twoRequired subunit of the importer.
9989COMP_30007_SBPsubstrate-binding proteinRequired subunit of the importer.
10089COMP_30007_PERMEASEpermeaseRequired subunit of the importer.
10189COMP_30007_ATPASEATP-binding proteinRequired subunit of the importer.
10290COMP_30007_XAC_SBPsubstrate-binding proteinRequired subunit of the importer.
10390COMP_30007_XAC_PERM1permease one of twoRequired subunit of the importer.
10490COMP_30007_XAC_PERM2permease two of twoRequired subunit of the importer.
10591COMP_ARAFalpha-L-arabinofuranosidase proteinRequired catalytic protein; alternative markers are OR.
10692COMP_XYLANASEendo-1,4-beta-xylanase proteinRequired catalytic protein; alternative markers are OR.
10793COMP_XYLOSIDASExylan 1,4-beta-xylosidase proteinRequired catalytic protein; alternative markers are OR.
10894COMP_AMYLASEalpha-amylase proteinRequired catalytic protein; alternative markers are OR.
10995COMP_PULLULANASEpullulanase proteinRequired catalytic protein; alternative markers are OR.
11096COMP_GLUCOSIDASEalpha-glucosidase proteinRequired catalytic protein; alternative markers are OR.
11197COMP_DEACETYLacetylxylan esterase proteinRequired catalytic protein; alternative markers are OR.
11298COMP_COLLAGENASE_M9collagenase catalytic proteinRequired catalytic protein; alternative markers are OR.
11399COMP_28042_AB_E1_ALPHAE1 component alpha subunitRequired subunit of the complex.
11499COMP_28042_AB_E1_BETAE1 component beta subunitRequired subunit of the complex.
11599COMP_28042_AB_E2E2 dihydrolipoyllysine acetyltransferaseRequired subunit of the complex.
11699COMP_28042_AB_E3E3 dihydrolipoyl dehydrogenaseRequired subunit of the complex.
117100COMP_28042_E1_FUSEDfused E1 componentRequired subunit of the complex.
118100COMP_28042_E1_E2E2 dihydrolipoyllysine acetyltransferaseRequired subunit of the complex.
119100COMP_28042_E1_E3E3 dihydrolipoyl dehydrogenaseRequired subunit of the complex.
120101COMP_12765_POR_ALPHAPorA alpha subunitRequired subunit.
121101COMP_12765_POR_BETAPorB beta subunitRequired subunit.
122101COMP_12765_POR_GAMMAPorC gamma subunitRequired subunit.
123101COMP_12765_POR_DELTAPorD delta subunitRequired subunit.
124102COMP_12765_NIFJ_CATALYTICfused oxidoreductase proteinRequired catalytic protein.
125103COMP_11844_LYASEformate C-acetyltransferase proteinRequired catalytic protein.
126103COMP_11844_ACTIVASEpyruvate formate-lyase activating enzymeRequired radical S-adenosylmethionine activating protein; the lyase has no activity without it.
127104COMP_19521_CATALYTICphosphate acetyltransferase proteinRequired catalytic protein; alternative markers are OR.
128105COMP_11352_CATALYTICacetate kinase proteinRequired catalytic protein.
129106COMP_21036_CATALYTICacetyl-CoA C-acetyltransferase proteinRequired catalytic protein.
130107COMP_16197_CATALYTIC3-hydroxybutanoyl-CoA dehydrogenase proteinRequired catalytic protein.
131108COMP_26558_CATALYTIC3-hydroxybutanoyl-CoA dehydratase proteinRequired catalytic protein.
132109COMP_24004_CATALYTICbutanoyl-CoA dehydrogenase proteinRequired catalytic protein.
133110COMP_30071_CATALYTICbutyryl-CoA:acetate CoA-transferase proteinRequired catalytic protein. The claim rests on this component alone being substrate-specific, which is why no orthology marker is accepted for it.
134111COMP_15933_CATALYTIClactaldehyde reductase proteinRequired catalytic protein.
135112COMP_14569_PDUCpropanediol dehydratase large subunitRequired subunit of the holoenzyme.
136112COMP_14569_PDUDpropanediol dehydratase medium subunitRequired subunit of the holoenzyme.
137112COMP_14569_PDUEpropanediol dehydratase small subunitRequired subunit of the holoenzyme.
138113COMP_36027_CATALYTICpropionaldehyde dehydrogenase proteinRequired catalytic protein.
139114COMP_28046_CATALYTICphosphate propanoyltransferase proteinRequired catalytic protein.
140115COMP_23148_CATALYTICpropionate kinase proteinRequired catalytic protein; alternative markers are OR.
141116COMP_LACTATE_COAT_CATALYTICpropionate CoA-transferase proteinRequired catalytic protein.
142117COMP_34691_LCDAlactoyl-CoA dehydratase alpha subunitRequired subunit.
143117COMP_34691_LCDBlactoyl-CoA dehydratase beta subunitRequired subunit.
144118COMP_34471_CATALYTICacryloyl-CoA reductase proteinRequired catalytic protein.
145119COMP_23444_CATALYTICL-lactate dehydrogenase proteinRequired catalytic protein.
146120COMP_10960_LARAlactate racemase proteinRequired catalytic protein.
147121COMP_46276_CATALYTICmalolactic enzyme proteinRequired catalytic protein.
148122COMP_10760_CITFcitrate lyase alpha subunitRequired subunit; carries the citrate CoA-transferase half of the reaction.
149122COMP_10760_CITEcitrate lyase beta subunitRequired subunit; carries the citryl-CoA lyase half of the reaction.
150122COMP_10760_CITDcitrate lyase acyl-carrier subunitRequired subunit.
151122COMP_10760_CITCcitrate lyase ligaseRequired activating enzyme; without it the acyl-carrier subunit is unacetylated and the complex is inactive.
152123COMP_15641_OADAoxaloacetate decarboxylase alpha subunitRequired subunit; the carboxyltransferase that carries the catalytic activity.
153124COMP_15641_SOLUBLEsoluble oxaloacetate decarboxylase proteinRequired catalytic protein.
154125COMP_23288_CATALYTICbifunctional acetaldehyde/alcohol dehydrogenase proteinRequired catalytic protein.
155126COMP_25290_CATALYTICbifunctional acetaldehyde/alcohol dehydrogenase proteinRequired catalytic protein; the same protein as the preceding step.
156127COMP_25249_CATALYTICacetolactate synthase large subunitRequired catalytic protein of a step the route does not require.
157128COMP_21580_CATALYTICacetolactate decarboxylase proteinRequired catalytic protein.
158129COMP_23704_CATALYTICGTP cyclohydrolase IIRequired catalytic protein.
159130COMP_23704_RIBABbifunctional RibABRequired catalytic protein.
160131COMP_21868_CATALYTICpyrimidine deaminase RibDRequired catalytic protein.
161132COMP_21868_RIBGbifunctional deaminase-reductase RibGRequired catalytic protein.
162133COMP_17845_CATALYTICpyrimidine reductase RibDRequired catalytic protein.
163134COMP_17845_RIBG2bifunctional deaminase-reductase RibGRequired catalytic protein.
164135COMP_25197_CATALYTIC5-amino-6-(5-phospho-D-ribitylamino)uracil phosphataseRequired catalytic protein.
165136COMP_18457_CATALYTIC3,4-dihydroxy-2-butanone 4-phosphate synthaseRequired catalytic protein.
166137COMP_18457_RIBAB2bifunctional RibABRequired catalytic protein.
167138COMP_26152_CATALYTIC6,7-dimethyl-8-ribityllumazine synthaseRequired catalytic protein.
168139COMP_20772_CATALYTICriboflavin synthaseRequired catalytic protein.
169140COMP_11672_CATALYTIC4-amino-4-deoxychorismate synthaseRequired catalytic protein.
170141COMP_11672_PABBCbifunctional PabBCRequired catalytic protein.
171142COMP_16201_CATALYTIC4-amino-4-deoxychorismate lyaseRequired catalytic protein.
172143COMP_16201_PABBC2bifunctional PabBCRequired catalytic protein.
173144COMP_17473_CATALYTICGTP cyclohydrolase IRequired catalytic protein.
174145COMP_25302_CATALYTICdihydroneopterin triphosphate diphosphataseRequired catalytic protein.
175146COMP_10540_CATALYTICdihydroneopterin aldolaseRequired catalytic protein.
176147COMP_11412_CATALYTIC6-hydroxymethyl-7,8-dihydropterin pyrophosphokinaseRequired catalytic protein.
177148COMP_19949_CATALYTICdihydropteroate synthaseRequired catalytic protein.
178149COMP_23584_CATALYTICdihydrofolate synthaseRequired catalytic protein.
179150COMP_15009_CATALYTICdihydrofolate reductaseRequired catalytic protein.
180151COMP_24840_CATALYTICphosphomethylpyrimidine synthase ThiCRequired catalytic protein.
181152COMP_19893_CATALYTICphosphomethylpyrimidine kinase ThiDRequired catalytic protein.
182153COMP_26361_CATALYTIC2-iminoacetate synthase ThiHRequired catalytic protein.
183154COMP_26297_CATALYTICthiazole synthase ThiGRequired catalytic protein.
184155COMP_33343_CATALYTICglycine oxidase ThiORequired catalytic protein.
185156COMP_22328_CATALYTICthiamine phosphate synthase ThiERequired catalytic protein.
186157COMP_23096_CATALYTIChydroxymethylpyrimidine kinase ThiDRequired catalytic protein.
187158COMP_24212_CATALYTIChydroxyethylthiazole kinase ThiMRequired catalytic protein.
188159COMP_11824_CATALYTIC3-methyl-2-oxobutanoate hydroxymethyltransferase PanBRequired catalytic protein.
189160COMP_16233_CATALYTIC2-dehydropantoate 2-reductase PanERequired catalytic protein.
190161COMP_16233_ILVCketol-acid reductoisomerase IlvCRequired catalytic protein.
191162COMP_19497_CATALYTICaspartate 1-decarboxylase PanDRequired catalytic protein.
192163COMP_10912_CATALYTICpantothenate synthetase PanCRequired catalytic protein.
193164COMP_31507_PDXSPLP synthase subunit PdxSRequired subunit of the complex.
194164COMP_31507_PDXTPLP synthase glutaminase subunit PdxTRequired subunit of the complex.
195165COMP_12056_CATALYTICD-erythrose 4-phosphate dehydrogenase EpdRequired catalytic protein.
196166COMP_18829_CATALYTICerythronate-4-phosphate dehydrogenase PdxBRequired catalytic protein.
197167COMP_16573_CATALYTICphosphoserine aminotransferase SerCRequired catalytic protein.
198168COMP_32275_CATALYTIC4-hydroxythreonine-4-phosphate dehydrogenase PdxARequired catalytic protein.
199169COMP_15265_CATALYTICpyridoxine 5-phosphate synthase PdxJRequired catalytic protein.
200170COMP_15149_CATALYTICpyridoxine 5-phosphate oxidase PdxHRequired catalytic protein.
201171COMP_20712_CATALYTIC8-amino-7-oxononanoate synthase BioFRequired catalytic protein.
202172COMP_16861_CATALYTICadenosylmethionine-dependent DAPA transaminase BioARequired catalytic protein.
203173COMP_15805_CATALYTICdethiobiotin synthetase BioDRequired catalytic protein.
204174COMP_22060_CATALYTICbiotin synthase BioBRequired catalytic protein.
205175COMP_26329_CATALYTIClysine-dependent DAPA transaminase BioARequired catalytic protein.
206176COMP_25876_CATALYTICL-aspartate oxidase NadBRequired catalytic protein.
207177COMP_25888_CATALYTICquinolinate synthase NadARequired catalytic protein.
208178COMP_42440_CATALYTICaspartate dehydrogenase NadXRequired catalytic protein.
209179COMP_12733_CATALYTICnicotinate-nucleotide pyrophosphorylase NadCRequired catalytic protein.
210180COMP_22860_CATALYTICnicotinate-nucleotide adenylyltransferase NadDRequired catalytic protein.
211181COMP_21188_CATALYTICNAD synthetase NadERequired catalytic protein.
212182COMP_24384_CATALYTICglutamine-hydrolysing NAD synthetaseRequired catalytic protein.
213183COMP_36163_CATALYTICnicotinate phosphoribosyltransferase PncBRequired catalytic protein.
214184COMP_32459_CATALYTICuroporphyrin-III C-methyltransferase CobARequired catalytic protein.
215185COMP_32459_CYSGmultifunctional siroheme synthase CysGRequired catalytic protein.
216186COMP_15613_CATALYTICprecorrin-2 dehydrogenase SirCRequired catalytic protein.
217187COMP_15613_CYSG2multifunctional siroheme synthase CysGRequired catalytic protein.
218188COMP_15893_CATALYTICsirohydrochlorin cobaltochelataseRequired catalytic protein.
219189COMP_17997_CATALYTICcobalt-factor II C20-methyltransferase CbiLRequired catalytic protein.
220190COMP_36155_CATALYTICcobalt-factor III methyltransferase CbiHRequired catalytic protein.
221191COMP_26277_CATALYTICcobalt-precorrin-4 C11-methyltransferase CbiFRequired catalytic protein.
222192COMP_26281_CATALYTICcobalt-precorrin-5A hydrolase CbiGRequired catalytic protein.
223193COMP_26285_CATALYTICcobalt-precorrin-5B C1-methyltransferase CbiDRequired catalytic protein.
224194COMP_15625_CATALYTICcobalt-precorrin-6A reductase CbiJRequired catalytic protein.
225195COMP_36067_CATALYTICcobalt-precorrin-6B C15-methyltransferase CbiTRequired catalytic protein.
226196COMP_34591_CATALYTICcobalt-precorrin-7 C5-methyltransferase CbiERequired catalytic protein.
227197COMP_16209_CATALYTICcobalt-precorrin-8 methylmutase CbiCRequired catalytic protein.
228198COMP_26289_CATALYTICcobyrinate a,c-diamide synthase CbiARequired catalytic protein.
229199COMP_16841_CATALYTICprecorrin-2 C20-methyltransferase CobIRequired catalytic protein.
230200COMP_17293_CATALYTICprecorrin-3B synthase CobGRequired catalytic protein.
231201COMP_12761_CATALYTICprecorrin-3B C17-methyltransferase CobJRequired catalytic protein.
232202COMP_22012_CATALYTICprecorrin-4 C11-methyltransferase CobMRequired catalytic protein.
233203COMP_18261_CATALYTICprecorrin-6A synthase CobFRequired catalytic protein.
234204COMP_23408_CATALYTICprecorrin-6A reductase CobKRequired catalytic protein.
235205COMP_17477_CATALYTICprecorrin-6B C5,C15-methyltransferase CobLRequired catalytic protein.
236206COMP_22512_CATALYTICprecorrin-8X methylmutase CobHRequired catalytic protein.
237207COMP_12544_CATALYTIChydrogenobyrinate a,c-diamide synthase CobBRequired catalytic protein.
238208COMP_15341_COBNcobaltochelatase subunit CobNRequired subunit of the complex.
239208COMP_15341_COBS_SUBcobaltochelatase subunit CobSRequired subunit of the complex.
240208COMP_15341_COBT_SUBcobaltochelatase subunit CobTRequired subunit of the complex.
241209COMP_11528_CATALYTICcob(I)yrinate a,c-diamide adenosyltransferaseRequired catalytic protein.
242210COMP_23256_CATALYTICadenosylcobyric acid synthase CbiPRequired catalytic protein.
243211COMP_21896_CATALYTICadenosylcobinamide-phosphate synthaseRequired catalytic protein.
244212COMP_22712_CATALYTICadenosylcobinamide-phosphate guanylyltransferase CobURequired catalytic protein.
245213COMP_11196_CATALYTICnicotinate-nucleotide dimethylbenzimidazole phosphoribosyltransferase CobTRequired catalytic protein.
246214COMP_24456_CATALYTICalpha-ribazole phosphatase CobCRequired catalytic protein.
247215COMP_16049_CATALYTICadenosylcobinamide-GDP ribazoletransferase CobSRequired catalytic protein.
248216COMP_27345_CATALYTIC5,6-dimethylbenzimidazole synthase BluBRequired catalytic protein.
249217COMP_18985_CATALYTICmenaquinone-specific isochorismate synthase MenFRequired catalytic protein.
250218COMP_18985_ENTCisochorismate synthase EntCRequired catalytic protein.
251219COMP_25593_CATALYTICSEPHCHC synthase MenDRequired catalytic protein.
252220COMP_25597_CATALYTICSHCHC synthase MenHRequired catalytic protein.
253221COMP_10196_CATALYTICo-succinylbenzoate synthase MenCRequired catalytic protein.
254222COMP_17009_CATALYTICo-succinylbenzoate-CoA ligase MenERequired catalytic protein.
255223COMP_26562_CATALYTIC1,4-dihydroxy-2-naphthoyl-CoA synthase MenBRequired catalytic protein.
256224COMP_26309_CATALYTIC1,4-dihydroxy-2-naphthoyl-CoA hydrolase MenIRequired catalytic protein.
257225COMP_26478_CATALYTIC1,4-dihydroxy-2-naphthoate polyprenyltransferase MenARequired catalytic protein.
258226COMP_42640_CATALYTICdemethylmenaquinol methyltransferase MenGRequired catalytic protein.
259227COMP_40051_CATALYTICchorismate dehydratase MqnARequired catalytic protein.
260228COMP_33075_CATALYTICaminodeoxyfutalosine synthase MqnERequired catalytic protein.
261229COMP_40075_CATALYTICaminodeoxyfutalosine deaminase MqnXRequired catalytic protein.
262230COMP_25904_CATALYTICfutalosine hydrolase MqnBRequired catalytic protein.
263231COMP_33083_CATALYTICcyclic dehypoxanthinyl futalosine synthase MqnCRequired catalytic protein.
264232COMP_33087_CATALYTIC1,4-dihydroxy-6-naphthoate synthase MqnDRequired catalytic protein.
265233COMP_16845_CS_SIcitrate synthaseCatalytic protein.
266234COMP_16845_CS_RERe-citrate synthaseCatalytic protein.
267235COMP_16845_CS_METHYLCITRATE_GROUPcitrate synthase, 2-methylcitrate synthase groupCatalytic protein.
268236COMP_10336_CATALYTICaconitate hydrataseCatalytic protein.
269237COMP_19629_CATALYTICisocitrate dehydrogenaseCatalytic protein.
270238COMP_23632_CATALYTICisocitrate dehydrogenaseCatalytic protein.
271239COMP_27786_E1E1, 2-oxoglutarate dehydrogenaseDecarboxylating component.
272239COMP_27786_E2E2, dihydrolipoyllysine succinyltransferaseAcyltransferase component.
273239COMP_27786_E3E3, dihydrolipoyl dehydrogenaseFlavoprotein component, shared with other 2-oxo acid dehydrogenase complexes.
274240COMP_17297_ALPHAoxidoreductase alpha subunitCatalytic subunit.
275240COMP_17297_BETAoxidoreductase beta subunitCatalytic subunit.
276241COMP_17661_ALPHAsuccinyl-CoA synthetase alpha subunitCatalytic subunit.
277241COMP_17661_BETAsuccinyl-CoA synthetase beta subunitCatalytic subunit.
278242COMP_17661_LSC_ALPHAsuccinyl-CoA ligase alpha subunitCatalytic subunit.
279242COMP_17661_LSC_BETAsuccinyl-CoA ligase beta subunitCatalytic subunit.
280243COMP_10524_CATALYTIC2-oxoglutarate decarboxylaseCatalytic protein.
281244COMP_13217_CATALYTICsuccinate-semialdehyde dehydrogenaseCatalytic protein.
282245COMP_13213_CATALYTICsuccinate-semialdehyde dehydrogenaseCatalytic protein.
283246COMP_40523_FLAVOPROTEINflavoprotein subunitCatalytic subunit.
284246COMP_40523_IRON_SULFURiron-sulfur subunitCatalytic subunit.
285247COMP_40523_SDHASDHA flavoprotein subunitCatalytic subunit.
286247COMP_40523_SDHBSDHB iron-sulfur subunitCatalytic subunit.
287248COMP_40523_FRDAFrdA flavoprotein subunitCatalytic subunit.
288248COMP_40523_FRDBFrdB iron-sulfur subunitCatalytic subunit.
289249COMP_12460_FUMCfumarase class IICatalytic protein.
290250COMP_12460_FUMAfumarase class ICatalytic protein.
291251COMP_12460_FUMA_ALPHAfumarase class I alpha subunitCatalytic subunit.
292251COMP_12460_FUMB_BETAfumarase class I beta subunitCatalytic subunit.
293252COMP_21432_CATALYTICmalate dehydrogenaseCatalytic protein.
294253COMP_46012_CATALYTICmalate:quinone oxidoreductaseCatalytic protein.
295254COMP_14717_CLASSIclass I DAHP synthaseRequired catalytic protein.
296255COMP_14717_CLASSIIclass II DAHP synthaseRequired catalytic protein.
297256COMP_14717_DAHPCMbifunctional DAHP synthase/chorismate mutaseRequired catalytic protein.
298257COMP_21968_CATALYTIC3-dehydroquinate synthaseRequired catalytic protein.
299258COMP_21968_AROKBbifunctional AroKBRequired catalytic protein.
300259COMP_21096_TYPEItype I 3-dehydroquinate dehydrataseRequired catalytic protein.
301260COMP_21096_TYPEIItype II 3-dehydroquinate dehydrataseRequired catalytic protein.
302261COMP_21096_ARODEbifunctional AroDERequired catalytic protein.
303262COMP_17737_AROEshikimate dehydrogenase AroERequired catalytic protein.
304263COMP_17737_ARODEbifunctional AroDERequired catalytic protein.
305264COMP_17737_YDIBquinate/shikimate dehydrogenase YdiBRequired catalytic protein.
306265COMP_13121_CATALYTICshikimate kinaseRequired catalytic protein.
307266COMP_13121_AROKBbifunctional AroKBRequired catalytic protein.
308267COMP_21256_CATALYTICEPSP synthaseRequired catalytic protein.
309268COMP_21256_FUSIONbifunctional prephenate dehydrogenase/EPSP synthaseRequired catalytic protein.
310269COMP_21020_CATALYTICchorismate synthaseRequired catalytic protein.
311270COMP_18985_PCHAisochorismate synthase PchARequired catalytic protein.
312271COMP_18985_MBTIsalicylate synthase MbtIRequired catalytic protein.
313272COMP_27874_CATALYTICisochorismate pyruvate lyase PchBRequired catalytic protein.
314273COMP_27874_MBTIsalicylate synthase MbtIRequired catalytic protein.
315274COMP_16165_CATALYTICtryptophan 2-monooxygenaseRequired catalytic protein.
316275COMP_34371_CATALYTICindole-3-acetamide hydrolaseRequired catalytic protein.
317276COMP_34371_AMIDASEamidase signature family hydrolaseRequired catalytic protein.
318277COMP_21368_URICASEurate oxidase proteinRequired catalytic protein.
319278COMP_27329_HPXOurate hydroxylase proteinRequired catalytic protein.
320279COMP_23736_HIUHhydroxyisourate hydrolase proteinRequired catalytic protein.
321280COMP_26301_OHCUDCOHCU decarboxylase proteinRequired catalytic protein.
322281COMP_17029_ALLBallantoinase proteinRequired catalytic protein.
323282COMP_11016_ALCallantoicase proteinRequired catalytic protein.
324283COMP_27485_ALLCallantoate deiminase proteinRequired catalytic protein.
325284COMP_25241_YLBAureidoglycine aminohydrolase proteinRequired catalytic protein.
326285COMP_11304_ALLAureidoglycolate lyase proteinRequired catalytic protein.
327286COMP_20557_ALPHAurease subunit alphaRequired subunit.
328286COMP_20557_BETAurease subunit betaRequired subunit.
329286COMP_20557_GAMMAurease subunit gammaRequired subunit.
330287COMP_21068_CATALYTICassimilatory nitrate reductase catalytic subunitRequired catalytic protein.
331288COMP_21828_NARBferredoxin-nitrate reductase proteinRequired catalytic protein.
332289COMP_18041_NIRAferredoxin-nitrite reductase proteinRequired catalytic protein.
333290COMP_24628_NIRBnitrite reductase large subunitRequired subunit.
334290COMP_24628_NIRDnitrite reductase small subunitRequired subunit.
335291COMP_24628_NASDassimilatory nitrite reductase large subunitRequired subunit.
336291COMP_24628_NASEassimilatory nitrite reductase small subunitRequired subunit.
337292COMP_45700_GBCAglycine betaine monooxygenase subunit ARequired subunit.
338292COMP_45700_GBCBglycine betaine monooxygenase subunit BRequired subunit.
339293COMP_74167_DGCAdimethylglycine dehydrogenase catalytic subunitRequired subunit.
340293COMP_74167_DGCBdimethylglycine dehydrogenase ferredoxin subunitRequired subunit.
341294COMP_52856_DMGDHdimethylglycine dehydrogenase proteinRequired catalytic protein.
342295COMP_17077_DMGOdimethylglycine oxidase proteinRequired catalytic protein.
343296COMP_13313_SOXAsarcosine oxidase subunit alphaRequired subunit.
344296COMP_13313_SOXBsarcosine oxidase subunit betaRequired subunit.
345296COMP_13313_SOXGsarcosine oxidase subunit gammaRequired subunit.
346296COMP_13313_SOXDsarcosine oxidase subunit deltaRequired subunit.
347297COMP_13313_MONOmonomeric sarcosine oxidase proteinRequired catalytic protein.
348298COMP_74155_DGCAsarcosine dehydrogenase catalytic subunitRequired subunit.
349298COMP_74155_DGCBsarcosine dehydrogenase ferredoxin subunitRequired subunit.
350299COMP_14533_CRNAcreatininase proteinRequired catalytic protein.
351300COMP_22456_CREAcreatinase proteinRequired catalytic protein.
352301COMP_55396_CNTAcarnitine monooxygenase oxygenase subunitRequired subunit.
353301COMP_55396_CNTBcarnitine monooxygenase reductase subunitRequired subunit.
354302COMP_19265_CDHAcarnitine 3-dehydrogenase proteinRequired catalytic protein.
355303COMP_47044_CDHC3-dehydrocarnitine transferase proteinRequired catalytic protein.
356304COMP_45716_BCTbetainyl-CoA thioesterase proteinRequired catalytic protein.
357305COMP_30207_MAUAmethylamine dehydrogenase light chainRequired subunit.
358305COMP_30207_MAUBmethylamine dehydrogenase heavy chainRequired subunit.
359306COMP_15909_TAUDtaurine dioxygenase proteinRequired catalytic protein.
360307COMP_10420_TPAtaurine-pyruvate aminotransferase proteinRequired catalytic protein.
361308COMP_18709_TAUXtaurine dehydrogenase small subunitRequired subunit.
362308COMP_18709_TAUYtaurine dehydrogenase large subunitRequired subunit.
363309COMP_24204_XSCsulfoacetaldehyde acetyltransferase proteinRequired catalytic protein.
364310COMP_14613_SBPtaurine substrate-binding proteinRequired subunit.
365310COMP_14613_ATPASEtaurine transport ATP-binding proteinRequired subunit.
366310COMP_14613_PERMEASEtaurine transport permeaseRequired subunit.
367311COMP_16169_GLNAglutamine synthetase proteinRequired catalytic protein.
368312COMP_15501_GLTBglutamate synthase large chainRequired subunit.
369312COMP_15501_GLTDglutamate synthase small chainRequired subunit.
370313COMP_12128_GLTSferredoxin-glutamate synthase proteinRequired catalytic protein.
371314COMP_11612_GDHANADP-glutamate dehydrogenase proteinRequired catalytic protein.
372315COMP_15133_GDHNAD-glutamate dehydrogenase proteinRequired catalytic protein.
373316COMP_12633_ALPHAbenzoate 1,2-dioxygenase alpha subunitRequired catalytic subunit; it carries the active site and determines the substrate.
374316COMP_12633_BETAbenzoate 1,2-dioxygenase beta subunitRequired structural subunit of the oxygenase.
375317COMP_11560_CATALYTICbenD dehydrogenase proteinRequired catalytic protein.
376318COMP_11072_ANTAanthranilate 1,2-dioxygenase large subunitRequired catalytic subunit.
377318COMP_11072_ANTBanthranilate 1,2-dioxygenase small subunitRequired structural subunit.
378319COMP_11072_ANDACanthranilate 1,2-dioxygenase large subunit, and typeRequired catalytic subunit.
379319COMP_11072_ANDADanthranilate 1,2-dioxygenase small subunit, and typeRequired structural subunit.
380320COMP_57952_P0phenol hydroxylase P0 componentRequired assembly component.
381320COMP_57952_P1phenol hydroxylase P1 componentRequired component.
382320COMP_57952_P2phenol hydroxylase P2 componentRequired component.
383320COMP_57952_P3phenol hydroxylase P3 componentRequired catalytic component.
384320COMP_57952_P4phenol hydroxylase P4 componentRequired component.
385320COMP_57952_P5phenol hydroxylase P5 componentRequired reductase component of the enzyme.
386321COMP_23852_CATALYTICcatechol 1,2-dioxygenase proteinRequired catalytic protein.
387322COMP_30031_CATALYTICmuconate cycloisomerase proteinRequired catalytic protein.
388323COMP_12348_CATALYTICmuconolactone isomerase proteinRequired catalytic protein.
389324COMP_10184_PCADenol-lactonase proteinRequired catalytic protein.
390325COMP_10184_PCALPcaL bifunctional proteinRequired catalytic protein.
391326COMP_12048_ALPHACoA-transferase alpha subunitRequired subunit.
392326COMP_12048_BETACoA-transferase beta subunitRequired subunit.
393327COMP_19481_CATALYTICbeta-ketoadipyl-CoA thiolase proteinRequired catalytic protein.
394328COMP_17337_CATALYTICcatechol 2,3-dioxygenase proteinRequired catalytic protein.
395329COMP_14549_CATALYTICsemialdehyde hydrolase proteinRequired catalytic protein.
396330COMP_34219_CATALYTICsemialdehyde dehydrogenase proteinRequired catalytic protein.
397331COMP_33431_CATALYTICtautomerase proteinRequired catalytic protein.
398332COMP_24260_CATALYTICdecarboxylase proteinRequired catalytic protein.
399333COMP_22580_MHPDhydratase protein, mhp typeRequired catalytic protein.
400334COMP_22580_XYLJhydratase protein, bph/xyl typeRequired catalytic protein.
401335COMP_22624_MHPEaldolase protein, mhp typeRequired catalytic protein.
402336COMP_22624_XYLKaldolase protein, bph/xyl typeRequired catalytic protein.
403337COMP_23288_MHPFacetaldehyde dehydrogenase protein, mhp typeRequired catalytic protein.
404338COMP_23288_XYLQacetaldehyde dehydrogenase protein, bph/xyl typeRequired catalytic protein.
405339COMP_20956_CATALYTICphenylacetate-CoA ligase proteinRequired catalytic protein; the committed step and the substrate-determining one.
406340COMP_32171_PAAAepoxidase subunit PaaARequired catalytic subunit.
407340COMP_32171_PAABepoxidase subunit PaaBRequired subunit.
408340COMP_32171_PAACepoxidase subunit PaaCRequired subunit.
409340COMP_32171_PAADepoxidase subunit PaaDRequired subunit.
410340COMP_32171_PAAEepoxidase reductase subunit PaaERequired subunit. Unlike the interchangeable Rieske reductases refused elsewhere in this layer, PaaE is a dedicated subunit of this complex.
411341COMP_31843_CATALYTICPaaG isomerase proteinRequired catalytic protein.
412342COMP_31755_CATALYTICPaaZ hydrolase domain proteinRequired catalytic protein.
413343COMP_31747_CATALYTICPaaZ dehydrogenase domain proteinRequired catalytic protein.
414344COMP_34799_CATALYTICPaaJ thiolase proteinRequired catalytic protein.
415345COMP_76647_CATALYTICPaaF hydratase proteinRequired catalytic protein. The specificity of the trait rests on the ligase and the epoxidase, not on this step.
416346COMP_34851_CATALYTICPaaH dehydrogenase proteinRequired catalytic protein.
417347COMP_20357_ALPHA3-phenylpropanoate dioxygenase alpha subunitRequired catalytic subunit.
418347COMP_20357_BETA3-phenylpropanoate dioxygenase beta subunitRequired structural subunit.
419348COMP_25062_CATALYTICHcaB dehydrogenase proteinRequired catalytic protein.
420349COMP_24785_CATALYTICMhpA hydroxylase proteinRequired catalytic protein.
421350COMP_23840_CATALYTICMhpB dioxygenase proteinRequired catalytic protein.
422351COMP_34187_CATALYTICMhpC hydrolase proteinRequired catalytic protein.
423352COMP_10532_TRPAB_ALPHAtryptophan synthase alpha chainRequired subunit.
424352COMP_10532_TRPAB_BETAtryptophan synthase beta chainRequired subunit.
425353COMP_10532_TRPAB_FUSED_CATALYTICfused tryptophan synthase proteinRequired catalytic protein.
426354COMP_10676_LEUCD_LARGE3-isopropylmalate dehydratase large subunitRequired subunit.
427354COMP_10676_LEUCD_SMALL3-isopropylmalate dehydratase small subunitRequired subunit.
428355COMP_10676_LEUC_SINGLE_CATALYTIC3-isopropylmalate dehydratase proteinRequired catalytic protein.
429356COMP_10932_CATALYTICargininosuccinate synthase proteinRequired catalytic protein.
430357COMP_11040_HISB_DEHYDRATASE_CATALYTICimidazoleglycerol-phosphate dehydratase proteinRequired catalytic protein.
431358COMP_11040_HISB_BIFUNCTIONAL_CATALYTICbifunctional HisB proteinRequired catalytic protein.
432359COMP_11372_CATALYTICaspartate--ammonia ligase proteinRequired catalytic protein.
433360COMP_11768_CATALYTICanthranilate phosphoribosyltransferase proteinRequired catalytic protein.
434361COMP_11960_CATALYTICsuccinyldiaminopimelate transaminase proteinRequired catalytic protein.
435362COMP_12228_CATALYTICasparagine synthase proteinRequired catalytic protein.
436363COMP_13085_CATALYTICN-acetyltransferase proteinRequired catalytic protein.
437364COMP_13493_CATALYTICketol-acid reductoisomerase proteinRequired catalytic protein.
438365COMP_13561_CATALYTICdiaminopimelate dehydrogenase proteinRequired catalytic protein.
439366COMP_13869_CATALYTICprephenate dehydrogenase proteinRequired catalytic protein.
440367COMP_13897_CATALYTICchorismate mutase proteinRequired catalytic protein.
441368COMP_14109_CATALYTICpyrroline-5-carboxylate reductase proteinRequired catalytic protein.
442369COMP_14465_HISN_CATALYTIChistidinol-phosphate phosphatase proteinRequired catalytic protein.
443370COMP_14465_HISB_BIFUNCTIONAL_CATALYTICbifunctional HisB proteinRequired catalytic protein.
444371COMP_14629_CATALYTICacetylglutamate kinase proteinRequired catalytic protein.
445372COMP_14877_PROB_CATALYTICglutamate 5-kinase proteinRequired catalytic protein.
446373COMP_14877_P5CS_CATALYTICP5C synthetase proteinRequired catalytic protein.
447374COMP_15093_CATALYTICaromatic aminotransferase proteinRequired catalytic protein. The marker set is deliberately wider than the KEGG module, which accepts only TyrB and the fungal Aro8: the aspartate and branched-chain aminotransferases transaminate aromatic 2-oxo acids as well, and requiring TyrB alone calls the trait in a third of the genomes that carry the aryl skeleton.
448375COMP_15101_CATALYTICdiaminopimelate decarboxylase proteinRequired catalytic protein.
449376COMP_15349_CATALYTICornithine acetyltransferase proteinRequired catalytic protein.
450377COMP_15393_CATALYTICdiaminopimelate epimerase proteinRequired catalytic protein.
451378COMP_15469_CATALYTICProFAR isomerase proteinRequired catalytic protein.
452379COMP_15941_CATALYTICacetylornithine deacetylase proteinRequired catalytic protein.
453380COMP_16293_LEUCD_LARGE3-isopropylmalate dehydratase large subunitRequired subunit.
454380COMP_16293_LEUCD_SMALL3-isopropylmalate dehydratase small subunitRequired subunit.
455381COMP_16293_LEUC_SINGLE_CATALYTIC3-isopropylmalate dehydratase proteinRequired catalytic protein.
456382COMP_17325_CATALYTICN-succinyltransferase proteinRequired catalytic protein.
457383COMP_18049_CATALYTICacetylornithine aminotransferase proteinRequired catalytic protein.
458384COMP_18321_CATALYTICbranched-chain amino acid aminotransferase proteinRequired catalytic protein.
459385COMP_18405_CATALYTICalanine dehydrogenase proteinRequired catalytic protein.
460386COMP_18473_CATALYTICATP phosphoribosyltransferase proteinRequired catalytic protein.
461387COMP_19045_CATALYTICcitramalate synthase proteinRequired catalytic protein.
462388COMP_19453_ALAA_CATALYTICalanine-synthesising transaminase proteinRequired catalytic protein.
463389COMP_19453_AVTA_CATALYTICvaline-pyruvate transaminase proteinRequired catalytic protein.
464390COMP_19513_CATALYTICornithine carbamoyltransferase proteinRequired catalytic protein.
465391COMP_19541_PROA_CATALYTICglutamate-5-semialdehyde dehydrogenase proteinRequired catalytic protein.
466392COMP_19541_P5CS_CATALYTICP5C synthetase proteinRequired catalytic protein.
467393COMP_20049_CATALYTICphosphoribosyl-AMP cyclohydrolase proteinRequired catalytic protein.
468394COMP_20405_CATALYTICdeacetylase proteinRequired catalytic protein.
469395COMP_21524_CATALYTIC2-isopropylmalate synthase proteinRequired catalytic protein.
470396COMP_21540_CATALYTICphosphoribosylanthranilate isomerase proteinRequired catalytic protein.
471397COMP_21588_CATALYTICacetylglutamyl-phosphate reductase proteinRequired catalytic protein.
472398COMP_21640_CATALYTICprephenate dehydrogenase (NADP+) proteinRequired catalytic protein.
473399COMP_21648_CATALYTICprephenate dehydratase proteinRequired catalytic protein.
474400COMP_21732_TRPEG_COMP1anthranilate synthase component IRequired subunit.
475400COMP_21732_TRPEG_COMP2anthranilate synthase component IIRequired glutamine amidotransferase subunit.
476401COMP_21732_TRPEG_FUSED_CATALYTICfused anthranilate synthase proteinRequired catalytic protein.
477402COMP_21824_CATALYTICaspartate aminotransferase proteinRequired catalytic protein.
478403COMP_22068_CATALYTICketol-acid reductoisomerase proteinRequired catalytic protein.
479404COMP_22332_LARGEdehydratase large subunitRequired subunit.
480404COMP_22332_SMALLdehydratase small subunitRequired subunit.
481405COMP_22608_CATALYTICdesuccinylase proteinRequired catalytic protein.
482406COMP_22828_CATALYTICphosphoribosyl-ATP pyrophosphohydrolase proteinRequired catalytic protein.
483407COMP_23476_CATALYTICindole-3-glycerol-phosphate synthase proteinRequired catalytic protein.
484408COMP_23744_CATALYTIChistidinol-phosphate aminotransferase proteinRequired catalytic protein.
485409COMP_23988_CATALYTICLL-diaminopimelate aminotransferase proteinRequired catalytic protein.
486410COMP_24020_CATALYTICargininosuccinate lyase proteinRequired catalytic protein.
487411COMP_24292_CATALYTICN-acetylglutamate synthase proteinRequired catalytic protein.
488412COMP_24793_HISFH_CYCLASEimidazole glycerol-phosphate synthase cyclase subunitRequired subunit.
489412COMP_24793_HISFH_AMIDOTRANSFERASEimidazole glycerol-phosphate synthase amidotransferase subunitRequired glutamine amidotransferase subunit.
490413COMP_24793_HISF_FUSED_CATALYTICfused imidazole glycerol-phosphate synthase proteinRequired catalytic protein.
491414COMP_24801_CATALYTICbranched-chain amino acid aminotransferase proteinRequired catalytic protein.
492415COMP_24809_CATALYTICdihydroxy-acid dehydratase proteinRequired catalytic protein.
493416COMP_24813_CATALYTICbranched-chain amino acid aminotransferase proteinRequired catalytic protein.
494417COMP_25152_CATALYTICaromatic aminotransferase proteinRequired catalytic protein. The marker set is deliberately wider than the KEGG module, which accepts only TyrB and the fungal Aro8: the aspartate and branched-chain aminotransferases transaminate aromatic 2-oxo acids as well, and requiring TyrB alone calls the trait in a third of the genomes that carry the aryl skeleton.
495418COMP_25315_CATALYTICacetyldiaminopimelate transaminase proteinRequired catalytic protein.
496419COMP_27654_CATALYTICacetohydroxyacid synthase large subunitRequired catalytic subunit.
497420COMP_27694_CATALYTICdihydroxy-acid dehydratase proteinRequired catalytic protein.
498421COMP_32271_CATALYTIC3-isopropylmalate dehydrogenase proteinRequired catalytic protein.
499422COMP_32715_CATALYTIC3-isopropylmalate dehydrogenase proteinRequired catalytic protein.
500423COMP_33799_CATALYTIChistidinol dehydrogenase proteinRequired catalytic protein.
501424COMP_33803_CATALYTIChistidinol dehydrogenase proteinRequired catalytic protein.
502425COMP_34171_CATALYTICdihydrodipicolinate synthase proteinRequired catalytic protein.
503426COMP_35331_CATALYTICdihydrodipicolinate reductase proteinRequired catalytic protein.
504427COMP_42424_LARGEdehydratase large subunitRequired subunit.
505427COMP_42424_SMALLdehydratase small subunitRequired subunit.
506428COMP_10152_CATALYTICcarbamate kinase proteinRequired catalytic protein.
507429COMP_10680_CATALYTICproline racemase proteinRequired catalytic protein.
508430COMP_12232_SELAglycine reductase selenoprotein ARequired subunit.
509430COMP_12232_B_ALPHABETAglycine reductase protein B, alpha and beta subunitRequired substrate-specific subunit.
510430COMP_12232_B_GAMMAglycine reductase protein B, gamma subunitRequired substrate-specific subunit.
511430COMP_12232_C_ALPHAglycine reductase protein C, alpha subunitRequired subunit.
512430COMP_12232_C_BETAglycine reductase protein C, beta subunitRequired subunit.
513431COMP_12737_PRDAD-proline reductase PrdARequired subunit.
514431COMP_12737_PRDBD-proline reductase PrdBRequired selenocysteine-containing subunit.
515432COMP_13101_CATALYTICurocanate hydratase proteinRequired catalytic protein.
516433COMP_17785_CATALYTICglutamate decarboxylase proteinRequired catalytic protein.
517434COMP_19169_CATALYTICsingle-chain L-serine dehydrataseRequired complete catalytic protein.
518435COMP_19169_SDA_ALPHASdaAA alpha subunitRequired split-enzyme alpha chain.
519435COMP_19169_SDA_BETASdaAB beta subunitRequired split-enzyme beta chain.
520436COMP_19169_SDSPLP-dependent serine/threonine ammonia-lyaseRequired catalytic protein.
521437COMP_19553_CATALYTICtryptophanase proteinRequired catalytic protein.
522438COMP_19597_CATALYTICarginine deiminase proteinRequired catalytic protein.
523439COMP_21232_CATALYTIChistidine ammonia-lyase proteinRequired catalytic protein.
524440COMP_22108_CATALYTICthreonine ammonia-lyase proteinRequired catalytic protein.
525441COMP_22492_CATALYTICformimidoylglutamase proteinRequired catalytic protein.
526442COMP_23660_CATALYTICimidazolonepropionase proteinRequired catalytic protein.
527443COMP_23800_CATALYTICmethionine gamma-lyase proteinRequired catalytic protein.
528444COMP_24931_CATALYTICL-cysteine desulfidase proteinRequired catalytic protein.
529445COMP_13245_CATALYTICisocitrate lyaseRequired catalytic protein.
530446COMP_18181_CATALYTICmalate synthaseRequired catalytic protein.
531447COMP_21448_NIFHNifH nitrogenase iron proteinRequired ATP-dependent electron-delivery component.
532447COMP_21448_NIFDNifD molybdenum-iron alpha chainRequired catalytic component.
533447COMP_21448_NIFKNifK molybdenum-iron beta chainRequired catalytic component.
534447COMP_21448_NIFBNifB cofactor precursor synthaseRequired nitrogenase-specific cofactor assembly enzyme.
535447COMP_21448_NIFENifE cofactor scaffold componentRequired nitrogenase-specific cofactor assembly component.
536447COMP_21448_NIFNNifN cofactor scaffold componentRequired nitrogenase-specific cofactor assembly component.
537448COMP_55543_VNFHVnfH vanadium nitrogenase iron proteinRequired ATP-dependent electron-delivery component.
538448COMP_55543_VNFDVnfD vanadium nitrogenase alpha chainRequired catalytic component.
539448COMP_55543_VNFKVnfK vanadium nitrogenase beta chainRequired catalytic component.
540448COMP_55543_VNFGVnfG vanadium nitrogenase delta subunitRequired catalytic component specific to the alternative nitrogenase architecture.
541448COMP_55543_NIFBNifB cofactor precursor synthaseRequired shared nitrogenase cofactor assembly enzyme.
542448COMP_55543_VNFEVnfE cofactor scaffold componentRequired vanadium-cofactor assembly component.
543448COMP_55543_VNFNVnfN cofactor scaffold componentRequired vanadium-cofactor assembly component.
544449COMP_18136_MET3sulfate adenylyltransferaseRequired catalytic protein.
545450COMP_18136_CYSNCysN sulfurylase subunitRequired catalytic subunit.
546450COMP_18136_CYSDCysD sulfurylase subunitRequired catalytic subunit.
547451COMP_18136_CYSNCCysNC sulfurylase-kinase fusionRequired sulfurylase subunit supplied by the fusion.
548451COMP_18136_CYSD_FUSCysD sulfurylase subunitRequired partner of the sulfurylase domain in CysNC.
549452COMP_24152_CYSCAPS kinaseRequired catalytic protein.
550453COMP_24152_CYSNCCysNC sulfurylase-kinase fusionRequired kinase domain supplied by the fusion.
551454COMP_11724_CYSHPAPS reductaseRequired catalytic activity.
552455COMP_21976_CYSHAPS reductaseRequired catalytic activity.
553456COMP_13804_CYSJCysJ sulfite-reductase flavoproteinRequired electron-transfer subunit.
554456COMP_13804_CYSICysI sulfite-reductase hemoproteinRequired catalytic subunit.
555457COMP_23132_SIRferredoxin sulfite reductaseRequired catalytic protein.
556458COMP_11160_ECTBEctBRequired catalytic protein.
557459COMP_16901_ECTAEctARequired catalytic protein.
558460COMP_17281_ECTCEctCRequired catalytic protein.
559461COMP_19865_HEMEHemERequired catalytic protein.
560462COMP_18257_HEMFHemFRequired catalytic protein.
561463COMP_15425_HEMNHemNRequired catalytic protein.
562464COMP_25576_HEMYHemY protoporphyrinogen oxidaseRequired catalytic protein.
563465COMP_27409_HEMGHemGRequired catalytic protein.
564466COMP_62000_HEMJHemJRequired catalytic protein.
565467COMP_22584_HEMHHemH protoporphyrin ferrochelataseRequired catalytic protein.
566468COMP_43436_HEMYHemY coproporphyrinogen oxidaseRequired catalytic protein.
567469COMP_49572_HEMHHemH coproporphyrin ferrochelataseRequired catalytic protein.
568470COMP_56516_HEMQHemQRequired catalytic protein.
569471COMP_11112_ENTBEntB isochorismate lyaseRequired catalytic protein; its aryl-carrier domain is separately required downstream.
570472COMP_23824_ENTAEntARequired catalytic protein.
571473COMP_30571_ENTBEntB aryl carrierRequired phosphopantetheinylated carrier component.
572473COMP_30571_ENTDEntD phosphopantetheinyl transferaseRequired to activate the EntB and EntF carrier domains.
573473COMP_30571_ENTEEntE dihydroxybenzoate ligaseRequired to load 2,3-dihydroxybenzoate onto holo-EntB.
574473COMP_30571_ENTFEntF nonribosomal peptide synthetaseRequired for serine activation, condensation and trilactone cyclisation.
575474COMP_17433_BETABetARequired catalytic protein.
576475COMP_33051_GBSBGbsBRequired catalytic protein.
577476COMP_17769_CMOcholine monooxygenaseRequired catalytic protein.
578477COMP_13505_CODAcholine oxidaseRequired catalytic protein.
579478COMP_20369_CODAcholine oxidaseRequired catalytic protein.
580479COMP_15305_BADHbetaine-aldehyde dehydrogenaseRequired catalytic protein.
581480COMP_24360_CYSGmultifunctional siroheme synthase CysGRequired catalytic protein.
582481COMP_24360_MET8precorrin-2 dehydrogenase and sirohydrochlorin ferrochelatase Met8Required catalytic protein.
583482COMP_24360_SIRBsirohydrochlorin ferrochelatase SirBRequired catalytic protein.
584483COMP_CHITINASEendochitinase proteinRequired catalytic protein.
585484COMP_CHITOBIASEbeta-N-acetylhexosaminidase proteinRequired catalytic protein.
586485COMP_CHITIN_LPMOlytic polysaccharide monooxygenase proteinRequired catalytic protein.
587486COMP_SIALIDASEsialidase proteinRequired catalytic protein.
588487COMP_FUCOSIDASEalpha-L-fucosidase proteinRequired catalytic protein.
589488COMP_GALNACASEalpha-N-acetylgalactosaminidase proteinRequired catalytic protein.
590489COMP_ENDO_PGendo-polygalacturonase proteinRequired catalytic protein.
591490COMP_EXO_PGexo-polygalacturonase proteinRequired catalytic protein.
592491COMP_PECTINESTERASEpectinesterase proteinRequired catalytic protein.
593492COMP_ENDO_PLendo-pectate lyase proteinRequired catalytic protein; alternative markers are OR.
594493COMP_57104_CATALYTICpectate disaccharide-lyase proteinRequired catalytic protein; alternative markers are OR.
595494COMP_20269_CATALYTIColigogalacturonide lyase proteinRequired catalytic protein; alternative markers are OR.
596495COMP_23896_CATALYTICketol-isomerase proteinRequired catalytic protein; alternative markers are OR.
597496COMP_24232_CATALYTIC2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase proteinRequired catalytic protein; alternative markers are OR.
598497COMP_PECTIN_LYASEpectin lyase proteinRequired catalytic protein; alternative markers are OR.
599498COMP_52304_DOEAectoine hydrolaseRequired catalytic protein.
600499COMP_40951_DOEBN2-acetyl-L-2,4-diaminobutanoate deacetylaseRequired catalytic protein.
601500COMP_45740_ECTDectoine hydroxylaseRequired catalytic protein.
602501COMP_14277_ALDHlactaldehyde dehydrogenaseRequired catalytic protein.
603502COMP_19093_AHBAAhbARequired siroheme decarboxylase alpha subunit.
604502COMP_19093_AHBBAhbBRequired siroheme decarboxylase beta subunit.
605503COMP_37431_AHBCAhbCRequired catalytic protein.
606504COMP_56520_AHBDAhbDRequired catalytic protein.
607505COMP_49240_EIIN-acetylglucosamine-specific enzyme II proteinRequired protein; alternative markers are OR. The enzyme II occurs as one fused EIICBA or EIICB polypeptide and as separate EIIB and EIIC chains; the fused forms and the substrate-specific EIIB are what the admitted namespaces resolve.
gift_architecture11 rows · 6 columns
architecture_pkgift_pkarchitecture_idnamedescriptionstatus
130ARCH_FLAGELLUM_DIDERMdiderm flagellar apparatusThe flagellum of a Gram-negative style envelope, in which the rod passes through P- and L-ring bushings.curated
230ARCH_FLAGELLUM_MONODERMmonoderm flagellar apparatusThe flagellum of a single-membrane envelope, which is built without L and P rings. It is a distinct architecture rather than the diderm architecture with an optional part, because the bushings are absent by construction and not merely unannotated.curated
331ARCH_T4AP_COREtype IVa pilus machineryThe conserved type IVa pilus machine: prepilin processing, a major pilin, an extension ATPase, the inner membrane platform, the alignment subcomplex and the outer membrane secretin, with retraction as an accessory function.curated
4154ARCH_LPT_CANONICALcanonical LptA--G apparatusThe seven-component trans-envelope Lpt machine, represented as an inner-membrane extractor, a periplasmic bridge and an outer-membrane translocon.curated
5155ARCH_RIBITOL_WTA_STAPHYLOCOCCUSStaphylococcus-type poly(ribitol-phosphate) WTAComplete ribitol-phosphate WTA construction using the Staphylococcus TarF glycerol-phosphate primase and bifunctional TarL ribitol-phosphate primase/polymerase, together with the shared linkage, donor, export and attachment functions.curated
6155ARCH_RIBITOL_WTA_W23W23-type poly(ribitol-phosphate) WTAComplete ribitol-phosphate WTA construction using the Bacillus subtilis W23 TarK ribitol-phosphate primase and TarL elongating polymerase, together with the shared linkage, donor, export and attachment functions.curated
7156ARCH_LTA_GLC2DAGdiglucosyldiacylglycerol-anchored poly(glycerol-phosphate) LTAThe three-function architecture in which YpfP/UgtP-family synthesis supplies the diglucosyldiacylglycerol anchor, LtaA presents it at the outer leaflet of the cytoplasmic membrane and LtaS polymerizes the glycerol-phosphate chain.curated
8157ARCH_T6SS_Icanonical type VI secretion apparatus (T6SS-i)The proteobacterial-type contractile apparatus: an envelope-spanning membrane complex, a baseplate, a VgrG spike, an Hcp tube wrapped by a TssB/TssC sheath, the TssA coordinator and the ClpV recycling ATPase, with the TssJ lipoprotein as an accessory function.curated
9158ARCH_T3SS_INJECTISOMEnon-flagellar type III secretion injectisomeThe injectisome basal body, export apparatus and sorting platform with an inner rod and an extracellular filament, which is either a needle or an Hrp pilus.curated
10159ARCH_ARCHAELLUM_COREarchaellum core machineryThe archaellum inventory shared by the euryarchaeal and crenarchaeal deletion series: archaellin, its class III signal peptidase, the FlaF/FlaG stator, the FlaH/FlaI motor and the FlaJ platform. The euryarchaeal FlaC/D/E switch complex and the crenarchaeal FlaX ring are accessory, because each is restricted to part of the archaellated lineages and the frame cannot measure FlaX.curated
11160ARCH_T2SS_CANONICALcanonical Gsp type II secretion apparatusThe four subassemblies of the general secretion pathway -- outer-membrane secretin, inner-membrane platform, cytoplasmic ATPase and pseudopilus -- together with the class III peptidase that matures the pseudopilins.curated
architecture_function73 rows · 4 columns
architecture_pkfunction_pkordinalrequired
1111
1221
1331
1441
11051
1561
1671
1781
1891
19101
2111
2221
2331
2441
2551
2661
2771
2881
2991
31111
31221
31331
31441
31551
31661
31770
41811
41921
42031
52111
52221
52331
52441
52551
52761
52871
62111
62221
62331
62441
62651
62761
62871
72911
73021
73131
83211
83320
83431
83541
83651
83761
83871
83981
94011
94121
94231
94341
94451
94561
94671
104711
104821
104931
105041
105151
105260
105370
115411
115521
115631
115741
115851
structural_function58 rows · 4 columns
function_pkfunction_idnamedescription
1SF_FLAGELLAR_EXPORT_GATEflagellar type III export gateMembrane-embedded export gate that translocates the axial subunits of the flagellum (rod, hook and filament) across the cytoplasmic membrane. Without it no axial structure can be built.
2SF_FLAGELLAR_EXPORT_ATPASEflagellar export ATPase complexCytoplasmic ATPase complex that delivers export substrates to the gate. FliJ is deliberately not required: it is a small, poorly conserved escort whose orthology assignment is unreliable, and requiring it would report absent machinery in genomes that build flagella.
3SF_FLAGELLAR_MS_RINGflagellar MS ringThe membrane and supramembrane ring that nucleates basal body assembly and houses the export apparatus.
4SF_FLAGELLAR_RODflagellar basal body rodThe drive shaft that transmits torque from the motor across the cell envelope to the hook, together with the rod-MS ring junction protein.
5SF_FLAGELLAR_C_RINGflagellar C ring and switch complexThe cytoplasmic ring that couples the stator to the rotor and switches rotational sense. FliY, which replaces FliN in some Firmicutes, is not accepted as evidence because its KEGG orthologue K02424 is assigned to an L-cystine transport binding protein and is therefore not specific to the flagellar switch.
6SF_FLAGELLAR_HOOKflagellar hookThe curved universal joint that transmits torque from the rod to the filament. FlgD is excluded because it is a transient assembly scaffold rather than a part of the finished structure.
7SF_FLAGELLAR_HOOK_FILAMENT_JUNCTIONflagellar hook-filament junctionThe hook-associated proteins that adapt the hook to the filament; without them flagellin polymerises without being retained.
8SF_FLAGELLAR_FILAMENTflagellar filamentThe helical propeller: polymerised flagellin together with the distal cap that permits its ordered polymerisation.
9SF_FLAGELLAR_STATORflagellar stator torque generatorThe membrane-anchored ion-conducting stator units that generate torque against the C ring. The curated claim is deliberately silent about the coupling ion; see the description of SYS_SF_FLAGELLAR_STATOR_MOTAB.
10SF_FLAGELLAR_OUTER_RINGflagellar L and P ringsThe outer membrane and peptidoglycan bushings through which the rod passes in a diderm envelope. Monoderms build a flagellum without them, which is why they belong to a separate architecture rather than being an optional part of one.
11SF_T4AP_PREPILIN_PEPTIDASEtype IV prepilin peptidaseCleaves and N-methylates the type IV prepilin leader, without which no pilin can be polymerised.
12SF_T4AP_MAJOR_PILINtype IVa major pilinThe subunit polymerised into the pilus fibre.
13SF_T4AP_ASSEMBLY_ATPASEtype IVa pilus assembly ATPaseThe cytoplasmic motor ATPase that powers pilus extension.
14SF_T4AP_PLATFORMtype IVa pilus inner membrane platformThe polytopic inner membrane protein that transfers pilin subunits from the membrane into the growing fibre.
15SF_T4AP_ALIGNMENT_COMPLEXtype IVa pilus alignment subcomplexThe envelope-spanning subcomplex that aligns the inner membrane platform with the outer membrane secretin.
16SF_T4AP_SECRETINtype IVa pilus secretinThe outer membrane channel through which the pilus fibre emerges.
17SF_T4AP_RETRACTION_ATPASEtype IVa pilus retraction ATPaseThe ATPase that depolymerises the fibre. It is accessory to assembling a pilus and is therefore not required by the architecture; a genome without it is expected to build a pilus it cannot retract.
18SF_LPT_INNER_MEMBRANE_EXTRACTIONLpt inner-membrane extractionThe LptB2FGC complex extracts lipopolysaccharide from the inner membrane and passes it into the trans-envelope bridge.
19SF_LPT_PERIPLASMIC_BRIDGELpt periplasmic bridgeLptA extends the periplasm-spanning hydrophobic groove that conducts lipopolysaccharide between the inner- and outer-membrane complexes.
20SF_LPT_OUTER_MEMBRANE_TRANSLOCONLpt outer-membrane transloconThe LptDE complex receives lipopolysaccharide from the bridge and inserts it into the outer leaflet of the outer membrane.
21SF_WTA_UDP_MANNAC_SUPPLYUDP-ManNAc donor supplyProvides UDP-N-acetylmannosamine for the conserved wall-teichoic-acid linkage unit through a non-hydrolysing UDP-GlcNAc 2-epimerase.
22SF_WTA_LINKAGE_UNITwall-teichoic-acid linkage-unit constructionTagO initiates the undecaprenyl-linked unit, TagA adds N-acetylmannosamine and TagB primes it with glycerol phosphate; all three roles are jointly required.
23SF_WTA_CDP_GLYCEROL_SUPPLYCDP-glycerol donor supplyTagD produces the CDP-glycerol used for the conserved glycerol-phosphate linkage step in ribitol-phosphate WTA assembly.
24SF_WTA_CDP_RIBITOL_SUPPLYCDP-ribitol donor supplyTarJ produces ribitol 5-phosphate and TarI activates it as CDP-ribitol for ribitol-phosphate backbone construction.
25SF_RIBITOL_WTA_STAPH_POLYMERIZATIONStaphylococcus-type ribitol-WTA priming and polymerizationThe Staphylococcus design uses TarF to add the glycerol-phosphate adaptor and bifunctional TarL to prime and extend the ribitol-phosphate chain.
26SF_RIBITOL_WTA_W23_POLYMERIZATIONW23-type ribitol-WTA priming and polymerizationThe Bacillus subtilis W23 design uses TarK to prime the ribitol-phosphate chain and TarL to extend it; the two roles are jointly required.
27SF_WTA_EXPORTwall-teichoic-acid exportThe TagG/TagH ABC transporter exports the completed wall teichoic acid precursor across the cytoplasmic membrane.
28SF_WTA_PEPTIDOGLYCAN_ATTACHMENTwall-teichoic-acid attachment to peptidoglycanAn LCP-family ligase transfers the exported wall teichoic acid from its lipid carrier to peptidoglycan.
29SF_LTA_GLC2DAG_ANCHOR_SYNTHESISdiglucosyldiacylglycerol anchor synthesisA processive glycosyltransferase forms the diglucosyldiacylglycerol membrane anchor that distinguishes this LTA boundary from residual diacylglycerol-anchored material.
30SF_LTA_GLC2DAG_TRANSLOCATIONdiglucosyldiacylglycerol anchor translocationLtaA flips the glycolipid anchor across the cytoplasmic membrane so that extracellular polymerization can proceed from it.
31SF_LTA_POLYGLYCEROL_PHOSPHATE_POLYMERIZATIONlipoteichoic-acid poly(glycerol-phosphate) polymerizationLtaS transfers glycerol phosphate from phosphatidylglycerol to construct the membrane-anchored poly(glycerol-phosphate) LTA chain.
32SF_T6SS_MEMBRANE_COMPLEXType VI membrane complexThe envelope-spanning complex that anchors the baseplate and forms the channel through which the tube and spike are propelled.
33SF_T6SS_MEMBRANE_LIPOPROTEINType VI outer-membrane lipoproteinThe TssJ lipoprotein that completes the membrane complex in many proteobacteria. It is accessory to the curated architecture: Agrobacterium and Acinetobacter reference genomes, whose apparatus is experimentally active, carry no TssJ marker in either namespace, so requiring it would report an absent machine in genomes that build one.
34SF_T6SS_BASEPLATEType VI baseplateThe assembly platform that docks on the membrane complex and from which the tube and sheath polymerise.
35SF_T6SS_SPIKEType VI spikeThe VgrG trimer that caps the tube and is expelled with it. PAAR tip proteins are not required: no admitted marker is specific to them.
36SF_T6SS_INNER_TUBEType VI inner tubeThe stack of Hcp hexamers that is propelled out of the cell.
37SF_T6SS_SHEATHType VI contractile sheathThe TssB/TssC sheath whose contraction propels the tube.
38SF_T6SS_ASSEMBLY_COORDINATIONType VI assembly coordinationTssA primes and coordinates the polymerisation of the tube and the sheath from the baseplate.
39SF_T6SS_SHEATH_RECYCLINGType VI sheath recyclingThe ClpV ATPase that disassembles the contracted sheath. It is required rather than accessory because ClpV-mediated remodelling of the sheath is experimentally crucial for type VI secretion.
40SF_T3SS_EXPORT_APPARATUSInjectisome export apparatusThe inner-membrane export gate through which substrates enter the secretion channel.
41SF_T3SS_EXPORT_ATPASEInjectisome export ATPaseThe cytoplasmic ATPase that prepares substrates for export. The SctL stator that tethers it is deliberately not required: its orthology assignment does not reach the Inv-Mxi-Spa and Esc families in either namespace, and requiring it would report an absent machine in genomes that build an injectisome.
42SF_T3SS_INNER_MEMBRANE_RINGSInjectisome inner-membrane ringsThe two concentric rings that house the export apparatus in the inner membrane.
43SF_T3SS_SECRETINInjectisome outer-membrane secretinThe outer-membrane ring through which the filament emerges. The flagellum has no homologue of it.
44SF_T3SS_SORTING_PLATFORMInjectisome sorting platformThe cytoplasmic platform protein that orders substrates for secretion. SctK is not required because its orthology assignment is unreliable.
45SF_T3SS_INNER_RODInjectisome inner rodThe short rod that connects the export apparatus to the extracellular filament inside the basal body.
46SF_T3SS_EXTRACELLULAR_FILAMENTInjectisome extracellular filamentThe hollow filament that carries substrates away from the cell surface: a needle in animal-associated systems or an Hrp pilus in plant-associated ones.
47SF_ARCHAELLUM_FILAMENTarchaellum filamentThe archaellin subunit polymerised into the rotating filament. Archaellin glycosylation is not required: it modifies the filament without being part of the assembly machinery.
48SF_ARCHAELLUM_SIGNAL_PEPTIDASEarchaellin class III signal peptidaseRemoves the class III signal peptide from prearchaellins; unprocessed archaellins are not assembled (PMID 14622420). The enzyme is a shared component, not part of the finished structure: PibD also processes archaeal type IV pilins and other class III substrates (PMID 12813086), so the function contributes no machine specificity to the call.
49SF_ARCHAELLUM_STATORarchaellum FlaF/FlaG stator complexThe membrane-anchored FlaF/FlaG complex that holds the motor against the cell envelope during rotation (PMID 34912317).
50SF_ARCHAELLUM_MOTORarchaellum FlaI/FlaH motor complexThe cytoplasmic FlaI hexameric ATPase that powers assembly and rotation, together with the KaiC-like FlaH that regulates it. FlaI is homologous to the assembly ATPases of archaeal type IV pili.
51SF_ARCHAELLUM_PLATFORMarchaellum FlaJ membrane platformThe polytopic membrane protein on which the motor assembles. FlaJ is homologous to the platform proteins of archaeal type IV pili.
52SF_ARCHAELLUM_SWITCH_COMPLEXeuryarchaeal FlaC/D/E switch complexThe euryarchaeal cytoplasmic ring that receives chemotaxis input through CheF and acts as the switch complex (PMID 32416640). It is required for archaellation in Methanococcus maripaludis (PMID 17887963) but absent or unassigned in Methanomicrobiales, most Methanosarcinales and every crenarchaeal and thaumarchaeal archaellum, so it is accessory to the core machinery. Rotational switching is outside the claim.
53SF_ARCHAELLUM_FLAX_RINGcrenarchaeal FlaX ringThe crenarchaeal cytoplasmic ring that scaffolds the motor and binds FlaI. It is required in Sulfolobus acidocaldarius (PMID 22081969) but has no KEGG orthology, so it is accessory: no architecture may depend on a function the reference frame cannot measure.
54SF_T2SS_OUTER_MEMBRANE_SECRETINType II secretion outer-membrane secretinThe GspD channel through which folded substrates cross the outer membrane. The GspS pilotin that targets it in some lineages is not required: it is absent from systems that assemble a secretin without it.
55SF_T2SS_INNER_MEMBRANE_PLATFORMType II secretion inner-membrane platformThe GspC, GspF, GspL and GspM proteins that span the inner membrane, connect the secretin to the ATPase and are jointly required. GspN is excluded as a non-universal accessory protein.
56SF_T2SS_SECRETION_ATPASEType II secretion ATPaseThe cytoplasmic GspE ATPase that powers pseudopilus extension.
57SF_T2SS_PSEUDOPILUSType II secretion pseudopilusThe major pseudopilin GspG together with the minor pseudopilins GspH, GspI, GspJ and GspK, whose tip complex primes elongation of the piston that pushes substrate through the secretin.
58SF_T2SS_PREPILIN_PEPTIDASEType II secretion pseudopilin maturationCleavage and N-methylation of the class III pseudopilin leader peptides, without which no pseudopilus can be polymerised. The enzyme is a shared component: the same protein also processes type IVa pilins, so this function contributes no specificity to either machine and the apparatus is identified by its other four functions.
structural_system61 rows · 5 columns
system_pkfunction_pksystem_idnamedescription
11SYS_SF_FLAGELLAR_EXPORT_GATEFlhA/FlhB/FliPQR export gateThe five jointly required proteins of the flagellar type III secretion export gate.
22SYS_SF_FLAGELLAR_EXPORT_ATPASEFliI/FliH export ATPase complexThe export ATPase and its regulatory partner, jointly required.
33SYS_SF_FLAGELLAR_MS_RINGFliF MS ringSingle-protein ring.
44SYS_SF_FLAGELLAR_RODFliE/FlgBCFG rodThe proximal and distal rod proteins together with the rod-MS ring junction, jointly required.
55SYS_SF_FLAGELLAR_C_RINGFliG/FliM/FliN switch complexThe three jointly required switch proteins.
66SYS_SF_FLAGELLAR_HOOKFlgE hookSingle-protein hook.
77SYS_SF_FLAGELLAR_HOOK_FILAMENT_JUNCTIONFlgK/FlgL junctionBoth hook-associated proteins are jointly required.
88SYS_SF_FLAGELLAR_FILAMENTflagellin filament with FliD capFlagellin and the distal cap, jointly required.
99SYS_SF_FLAGELLAR_STATOR_MOTABMotA/MotB stator unit familyThe MotAB stator family, which includes the proton-driven MotAB units of Escherichia coli and the sodium-driven PomAB units of Vibrio. KEGG assigns both to K02556/K02557, so this system evidences a stator without evidencing its coupling ion; see inst/doc/proposal-structural-gifts.md.
1010SYS_SF_FLAGELLAR_OUTER_RINGFlgH/FlgI L and P ringsBoth envelope bushings are jointly required.
1111SYS_T4AP_PREPILIN_PEPTIDASEPilD prepilin peptidaseSingle bifunctional protein.
1212SYS_T4AP_MAJOR_PILINtype IVa pilin subunitOne pilin protein.
1313SYS_T4AP_ASSEMBLY_ATPASE_PILBPilB extension ATPaseThe PilB-type assembly ATPase of Pseudomonas and Myxococcus systems.
1413SYS_T4AP_ASSEMBLY_ATPASE_PILFPilF extension ATPaseThe PilF-type assembly ATPase of Neisseria and Thermus systems; a non-interchangeable orthologue serving the same function.
1514SYS_T4AP_PLATFORMPilC platform proteinSingle polytopic membrane protein.
1615SYS_T4AP_ALIGNMENT_COMPLEXPilM/N/O/P alignment subcomplexAll four proteins are jointly required to span the envelope.
1716SYS_T4AP_SECRETINPilQ secretinSingle outer membrane channel.
1817SYS_T4AP_RETRACTION_ATPASEPilT retraction ATPasePilT. The paralogue PilU is not accepted here: it cannot retract a pilus on its own, so it is not evidence of the retraction function.
1918SYS_LPTBCFGLptB/C/F/G inner-membrane complexLptB, LptC, LptF and LptG are jointly required. A protein annotated to both the component-specific LptF and LptG markers may satisfy both roles, preserving naturally fused permease architectures without collapsing the roles.
2019SYS_LPTALptA periplasmic bridge proteinLptA supplies the dedicated soluble bridge component.
2120SYS_LPTDELptD/E outer-membrane complexLptD and LptE are jointly required by the canonical architecture. LptD alone is not accepted as evidence of this system.
2221SYS_WTA_MNAAMnaA-class UDP-GlcNAc 2-epimeraseA non-hydrolysing UDP-GlcNAc 2-epimerase supplies the UDP-ManNAc donor required by the linkage unit.
2322SYS_WTA_TAGOABTagO/TagA/TagB linkage-unit systemTagO, TagA and TagB are jointly required to initiate and construct the conserved undecaprenyl-linked disaccharide-glycerol-phosphate unit.
2423SYS_WTA_TAGDTagD CDP-glycerol synthaseTagD supplies CDP-glycerol for the linkage-unit glycerol-phosphate step.
2524SYS_WTA_TARIJTarI/TarJ CDP-ribitol supply systemTarI and TarJ are jointly required to form the activated CDP-ribitol donor.
2625SYS_RIBITOL_WTA_STAPH_TARFLStaphylococcus TarF/TarL systemEquivalog-resolved TarF and TarL roles are jointly required; broader TagF-like or generic TarL evidence is not accepted for this architecture.
2726SYS_RIBITOL_WTA_W23_TARKLW23 TarK/TarL systemThe W23-specific TarK primase and TarL polymerase roles are jointly required.
2827SYS_WTA_TAGGHTagG/TagH exporterThe permease TagG and ATPase TagH are jointly required for the wall-teichoic-acid exporter.
2928SYS_WTA_LCPLCP-family attachment ligaseAt least one accepted LCP-family ligase supplies the attachment function; individual paralog identities are not required.
3029SYS_LTA_YPFPYpfP/UgtP diglucosyldiacylglycerol synthaseThe processive glycolipid glycosyltransferase supplies the named disaccharide anchor; a generic glycolipid-synthesis KO is not accepted as a shortcut.
3130SYS_LTA_LTAALtaA glycolipid flippaseThe LTA-specific MFS flippase presents the diglucosyldiacylglycerol anchor at the outer leaflet of the cytoplasmic membrane.
3231SYS_LTA_LTASLtaS polymeraseThe LtaS-family enzyme polymerizes the glycerol-phosphate chain; K19005 is not accepted because it does not resolve the required architecture.
3332SYS_T6SS_TSSLMTssL/TssM membrane complexTssL and TssM are jointly required. Their KEGG orthologies also contain the IcmH/DotU and IcmF proteins of the Legionella type IVB system, so neither is evidence of a type VI apparatus outside the complete architecture.
3433SYS_T6SS_TSSJTssJ lipoproteinSingle outer-membrane lipoprotein.
3534SYS_T6SS_BASEPLATETssE/TssF/TssG/TssK baseplateAll four baseplate proteins are jointly required.
3635SYS_T6SS_VGRGVgrG spikeThe VgrG spike protein.
3736SYS_T6SS_HCPHcp tubeThe Hcp tube protein.
3837SYS_T6SS_SHEATHTssB/TssC sheathThe small and large sheath subunits are jointly required.
3938SYS_T6SS_TSSATssA coordinatorSingle protein.
4039SYS_T6SS_CLPVClpV (TssH) ATPaseSingle AAA+ ATPase.
4140SYS_T3SS_SCTRSTUVSctR/S/T/U/V export apparatusThe five jointly required export-apparatus proteins. They are homologues of flagellar FliP/Q/R, FlhB and FlhA, and only injectisome-specific accessions are accepted for them.
4241SYS_T3SS_SCTNSctN ATPaseThe injectisome ATPase. The flagellar FliI accession is not accepted.
4342SYS_T3SS_SCTDJSctD/SctJ ringsBoth ring proteins are jointly required.
4443SYS_T3SS_SCTCSctC secretinSingle secretin. The type II secretion and type IV pilus secretins are not accepted.
4544SYS_T3SS_SCTQSctQ platform proteinSingle protein.
4645SYS_T3SS_SCTISctI inner rodSingle protein.
4746SYS_T3SS_NEEDLESctF needleThe needle filament subunit of animal-associated injectisomes.
4846SYS_T3SS_HRP_PILUSHrp pilusThe Hrp pilin of plant-associated injectisomes; a non-homologous alternative to the needle subunit. Only the Xanthomonas HrpE and Pseudomonas HrpA pilins have an accepted marker, so a Ralstonia-type HrpY pilus is an under-call.
4947SYS_ARCHAELLUM_ARCHAELLINarchaellinOne archaellin protein; genomes with several archaellin genes need only one.
5048SYS_ARCHAELLUM_FLAK_PIBDarchaeal FlaK/PibD peptidaseThe archaeal class III signal peptidase: FlaK in Methanococcales, the broad-specificity PibD elsewhere.
5148SYS_ARCHAELLUM_PILDbacterial-type PilD peptidaseThe bacterial prepilin peptidase of archaellum-encoding Chloroflexota, reported as the processing enzyme outside the SAR202 clade (PMID 40962902). Accepted at putative confidence because processing of archaellin by PilD is inferred, not demonstrated.
5249SYS_ARCHAELLUM_STATOR_FLAFGFlaF/FlaG statorBoth stator proteins are jointly required.
5350SYS_ARCHAELLUM_MOTOR_FLAHIFlaI/FlaH motorThe ATPase and its regulator are jointly required.
5451SYS_ARCHAELLUM_PLATFORM_FLAJFlaJ platformSingle-protein platform.
5552SYS_ARCHAELLUM_SWITCH_FLACDEFlaC/FlaD/FlaE switch complexThe three switch proteins, jointly required. The haloarchaeal FlaCE fusion supports both FlaC and FlaE.
5653SYS_ARCHAELLUM_FLAXFlaX ringSingle-protein ring.
5754SYS_T2SS_GSPDGspD secretinSingle outer-membrane secretin. The type III secretion and type IV pilus secretins have their own accessions and are not accepted here.
5855SYS_T2SS_GSPCFLMGspC/F/L/M inner-membrane platformAll four platform proteins are jointly required.
5956SYS_T2SS_GSPEGspE ATPaseSingle cytoplasmic ATPase. The type IVa pilus PilB and PilF ATPases are not accepted for it.
6057SYS_T2SS_GSPGHIJKGspG/H/I/J/K pseudopilusThe major and four minor pseudopilins are jointly required.
6158SYS_T2SS_PEPTIDASEclass III prepilin peptidaseOne bifunctional peptidase/N-methyltransferase. GspO and PilD are the same enzyme under two KEGG names rather than alternative implementations, so both accessions are accepted on one component.
structural_component110 rows · 5 columns
component_pksystem_pkcomponent_idnamedescription
11COMP_SF_FLHAFlhA export gate proteinLargest export gate component.
21COMP_SF_FLHBFlhB export gate proteinExport substrate specificity switch.
31COMP_SF_FLIPFliP export gate proteinExport gate channel component.
41COMP_SF_FLIQFliQ export gate proteinExport gate channel component.
51COMP_SF_FLIRFliR export gate proteinExport gate channel component.
62COMP_SF_FLIIFliI export ATPaseFlagellum-specific ATPase.
72COMP_SF_FLIHFliH ATPase regulatorNegative regulator and docking partner of FliI.
83COMP_SF_FLIFFliF MS ring proteinForms the MS ring.
94COMP_SF_FLIEFliE rod-MS ring junctionJoins the rod to the MS ring.
104COMP_SF_FLGBFlgB proximal rod proteinProximal rod.
114COMP_SF_FLGCFlgC proximal rod proteinProximal rod.
124COMP_SF_FLGFFlgF proximal rod proteinProximal rod.
134COMP_SF_FLGGFlgG distal rod proteinDistal rod.
145COMP_SF_FLIGFliG switch proteinRotor protein contacting the stator.
155COMP_SF_FLIMFliM switch proteinBinds the chemotaxis response regulator.
165COMP_SF_FLINFliN switch proteinC ring structural protein.
176COMP_SF_FLGEFlgE hook proteinPolymerises into the hook.
187COMP_SF_FLGKFlgK hook-associated protein 1Proximal junction.
197COMP_SF_FLGLFlgL hook-associated protein 3Distal junction.
208COMP_SF_FLICflagellinThe filament subunit.
218COMP_SF_FLIDFliD filament capHook-associated protein 2; the distal capping plate.
229COMP_SF_MOTAMotA-family stator A subunitIon-conducting stator subunit. The accession does not distinguish proton-driven MotA from sodium-driven PomA.
239COMP_SF_MOTBMotB-family stator B subunitPeptidoglycan-binding stator subunit. The accession does not distinguish MotB from PomB.
2410COMP_SF_FLGHFlgH L-ring proteinOuter membrane bushing.
2510COMP_SF_FLGIFlgI P-ring proteinPeptidoglycan bushing.
2611COMP_T4AP_PILDPilD prepilin peptidaseLeader peptidase and N-methyltransferase.
2712COMP_T4AP_PILINtype IVa major pilinThe polymerised fibre subunit.
2813COMP_T4AP_PILBPilB assembly ATPaseExtension motor.
2914COMP_T4AP_PILFPilF assembly ATPaseExtension motor.
3015COMP_T4AP_PILCPilC platform proteinInner membrane platform.
3116COMP_T4AP_PILMPilM cytoplasmic actin-like proteinAlignment subcomplex.
3216COMP_T4AP_PILNPilN inner membrane proteinAlignment subcomplex.
3316COMP_T4AP_PILOPilO inner membrane proteinAlignment subcomplex.
3416COMP_T4AP_PILPPilP periplasmic lipoproteinAlignment subcomplex.
3517COMP_T4AP_PILQPilQ secretinOuter membrane channel.
3618COMP_T4AP_PILTPilT retraction ATPaseDepolymerisation motor.
3719COMP_LPTBLptB ATPaseCytoplasmic ATPase that powers lipopolysaccharide extraction.
3819COMP_LPTCLptC connectorInner-membrane complex component that connects LptBFG to the periplasmic bridge.
3919COMP_LPTFLptF permeaseOne of the two jointly required transmembrane components of the extractor.
4019COMP_LPTGLptG permeaseOne of the two jointly required transmembrane components of the extractor.
4120COMP_LPTALptA bridge proteinDedicated soluble periplasmic component of the trans-envelope bridge.
4221COMP_LPTDLptD translocon beta-barrelOuter-membrane beta-barrel component of the translocon.
4321COMP_LPTELptE translocon lipoproteinLipoprotein partner within the canonical LptD/E translocon.
4422COMP_WTA_MNAAUDP-GlcNAc 2-epimeraseNon-hydrolysing epimerase that produces UDP-ManNAc; the activity may be supplied by MnaA/WecB-class proteins.
4523COMP_WTA_TAGOTagO-class linkage initiatorTransfers GlcNAc-1-phosphate to the polyprenyl-phosphate carrier. The accepted orthology is shared with WecA/Rfe and is specific to the activity, not to WTA by itself.
4623COMP_WTA_TAGATagA mannosaminyltransferaseAdds N-acetylmannosamine to the lipid-linked GlcNAc linkage precursor.
4723COMP_WTA_TAGBTagB glycerol-phosphate primaseAdds the conserved glycerol-phosphate unit to the WTA linkage precursor.
4824COMP_WTA_TAGDTagD glycerol-3-phosphate cytidylyltransferaseForms CDP-glycerol for linkage-unit construction.
4925COMP_WTA_TARITarI ribitol-phosphate cytidylyltransferaseForms CDP-ribitol from ribitol 5-phosphate and CTP.
5025COMP_WTA_TARJTarJ ribitol-5-phosphate dehydrogenaseSupplies ribitol 5-phosphate for CDP-ribitol formation.
5126COMP_WTA_STAPH_TARFStaphylococcus TarF transferaseStaphylococcus aureus-type glycerol-phosphate adaptor transferase, accepted only through the equivalog-grade profile.
5226COMP_WTA_STAPH_TARLStaphylococcus TarL polymeraseStaphylococcus-type bifunctional ribitol-phosphate primase and polymerase, accepted only through the genus-resolved equivalog profile.
5327COMP_WTA_W23_TARKW23-type TarK primaseRibitol-phosphate primase that distinguishes the W23-type architecture.
5427COMP_WTA_W23_TARLW23-type TarL polymeraseRibitol-phosphate polymerase required alongside TarK in the W23-type architecture.
5528COMP_WTA_TAGGTagG exporter permeaseMembrane permease component of the WTA ABC exporter.
5628COMP_WTA_TAGHTagH exporter ATPaseATP-binding component of the WTA ABC exporter.
5729COMP_WTA_LCPLCP-family WTA attachment ligaseTransfers polyprenyl-linked teichoic acid to peptidoglycan; the accepted orthology covers the substitutable TagT/TagU/TagV family.
5830COMP_LTA_YPFPYpfP/UgtP-family diglucosyldiacylglycerol synthaseProcessive glycosyltransferase that makes the glycolipid anchor named by the GIFT.
5931COMP_LTA_LTAALtaA glycolipid flippaseLTA-biosynthesis MFS flippase for the diglucosyldiacylglycerol anchor.
6032COMP_LTA_LTASLtaS poly(glycerol-phosphate) synthasePolymerase that transfers glycerol-phosphate units from phosphatidylglycerol to the extracellular LTA chain.
6133COMP_T6SS_TSSLTssLInner-membrane anchor of the membrane complex.
6233COMP_T6SS_TSSMTssMEnvelope-spanning core of the membrane complex.
6334COMP_T6SS_TSSJTssJOuter-membrane lipoprotein.
6435COMP_T6SS_TSSETssEBaseplate wedge protein related to phage gp25.
6535COMP_T6SS_TSSFTssFBaseplate wedge protein.
6635COMP_T6SS_TSSGTssGBaseplate wedge protein.
6735COMP_T6SS_TSSKTssKConnects the baseplate to the membrane complex.
6836COMP_T6SS_VGRGVgrG (TssI)Spike protein.
6937COMP_T6SS_HCPHcp (TssD)Tube protein.
7038COMP_T6SS_TSSBTssBSmall sheath subunit.
7138COMP_T6SS_TSSCTssCLarge sheath subunit.
7239COMP_T6SS_TSSATssATube and sheath polymerisation coordinator.
7340COMP_T6SS_CLPVClpV (TssH)Sheath-disassembly ATPase.
7441COMP_T3SS_SCTRSctRExport-apparatus protein; FliP homologue.
7541COMP_T3SS_SCTSSctSExport-apparatus protein; FliQ homologue.
7641COMP_T3SS_SCTTSctTExport-apparatus protein; FliR homologue.
7741COMP_T3SS_SCTUSctUExport-apparatus switch protein; FlhB homologue.
7841COMP_T3SS_SCTVSctVExport-gate protein; FlhA homologue.
7942COMP_T3SS_SCTNSctNExport ATPase; FliI homologue.
8043COMP_T3SS_SCTDSctDOuter of the two inner-membrane rings.
8143COMP_T3SS_SCTJSctJInner-membrane ring lipoprotein.
8244COMP_T3SS_SCTCSctCOuter-membrane secretin.
8345COMP_T3SS_SCTQSctQSorting-platform protein.
8446COMP_T3SS_SCTISctIInner rod protein.
8547COMP_T3SS_SCTFSctFNeedle filament subunit.
8648COMP_T3SS_HRP_PILINHrp pilinMajor subunit of the Hrp pilus.
8749COMP_ARCHAELLUM_ARCHAELLINarchaellin (ArlB)The polymerised filament subunit.
8850COMP_ARCHAELLUM_FLAK_PIBDFlaK/PibD class III signal peptidase (ArlK)Archaeal prearchaellin peptidase.
8951COMP_ARCHAELLUM_PILDPilD-type prepilin peptidaseBacterial class III signal peptidase.
9052COMP_ARCHAELLUM_FLAFFlaF stator protein (ArlF)Membrane-anchored stator protein.
9152COMP_ARCHAELLUM_FLAGFlaG stator protein (ArlG)Membrane-anchored stator protein; a paralogue of FlaF.
9253COMP_ARCHAELLUM_FLAHFlaH KaiC-like regulator (ArlH)Regulates FlaI and is essential for assembly.
9353COMP_ARCHAELLUM_FLAIFlaI motor ATPase (ArlI)Powers assembly and rotation.
9454COMP_ARCHAELLUM_FLAJFlaJ membrane platform (ArlJ)Polytopic membrane platform.
9555COMP_ARCHAELLUM_FLACFlaC switch protein (ArlC)Switch complex subunit.
9655COMP_ARCHAELLUM_FLADFlaD switch protein (ArlD)Switch complex subunit.
9755COMP_ARCHAELLUM_FLAEFlaE switch protein (ArlE)Switch complex subunit.
9856COMP_ARCHAELLUM_FLAXFlaX ring protein (ArlX)Crenarchaeal motor scaffold.
9957COMP_T2SS_GSPDGspD secretinOuter-membrane channel through which folded substrate passes.
10058COMP_T2SS_GSPCGspCLinks the inner-membrane platform to the secretin.
10158COMP_T2SS_GSPFGspFPolytopic inner-membrane platform protein.
10258COMP_T2SS_GSPLGspLBinds the ATPase to the platform.
10358COMP_T2SS_GSPMGspMStabilises the platform with GspL.
10459COMP_T2SS_GSPEGspESecretion ATPase.
10560COMP_T2SS_GSPGGspG major pseudopilinThe subunit polymerised into the pseudopilus.
10660COMP_T2SS_GSPHGspH minor pseudopilinTip-complex pseudopilin.
10760COMP_T2SS_GSPIGspI minor pseudopilinTip-complex pseudopilin.
10860COMP_T2SS_GSPJGspJ minor pseudopilinTip-complex pseudopilin.
10960COMP_T2SS_GSPKGspK minor pseudopilinTip-complex pseudopilin.
11061COMP_T2SS_PEPTIDASEclass III prepilin peptidaseCleaves and N-methylates pseudopilin leaders. Shared with the type IVa pilus.
structural_component_marker188 rows · 8 columns
component_pkmarker_pkevidence_typeconfidencesourcenotesbasisreference
1435orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
2436orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
2463orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18Fused FliR-FlhB protein; the same accession also supports COMP_SF_FLIR, which is what a fused protein means.not_assessedNULL
3446orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
4447orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
5448orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
5463orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18Fused FliR-FlhB protein; the same accession also supports COMP_SF_FLHB.not_assessedNULL
6443orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
7442orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
8440orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
9439orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
10426orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
11427orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
12429orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
13430orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
14441orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
15444orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
16445orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
17428orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
18433orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
19434orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
20437orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
21438orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
22449orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18KEGG assigns Vibrio cholerae PomA (VC_0892) to this orthologue alongside Escherichia coli MotA, so it evidences a stator but not its coupling ion.not_assessedNULL
23450orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18KEGG assigns Vibrio cholerae PomB (VC_0893) to this orthologue alongside Escherichia coli MotB.not_assessedNULL
24431orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
25432orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
26454orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
27451orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
27455orthologyambiguousKEGG orthology, verified against KEGG REST 2026-08-18PilE is the major pilin in Neisseria but a minor pilin in Pseudomonas, so this accession does not by itself establish that the protein is the major subunit. Accepted as an alternative marker at reduced confidence so that Neisseria-type systems are not called absent, and the weaker term is reported on any call that rests on it.not_assessedNULL
28452orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
29456orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
30453orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
31457orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
32458orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
33459orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
34460orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
35461orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
36462orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
411362orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02LptA-specific orthology; the broader LptA/LptD_N profiles are not admitted.not_assessedNULL
371363orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02LptB-specific orthology, not a generic ABC ATPase marker.not_assessedNULL
381364orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02LptC-specific orthology. LptC remains required because bypass depends on residue-level LptF suppressors that this marker cannot resolve.not_assessedNULL
421365orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02LptD-specific orthology; historical aliases Imp and OstA do not widen the accepted function.not_assessedNULL
431366orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02LptE-specific orthology; required only in the canonical architecture represented here.not_assessedNULL
391367orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02Component-specific LptF orthology; a combined LptF/LptG family is not admitted.not_assessedNULL
401368orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02Component-specific LptG orthology; a combined LptF/LptG family is not admitted.not_assessedNULL
411369sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. LptA-specific periplasmic bridge profile.not_assessedNULL
411370sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. Enterobacterales LptA profile.not_assessedNULL
371371sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. LptB-specific ATPase profile.not_assessedNULL
371372sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. Gammaproteobacterial LptB profile.not_assessedNULL
381373sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. LptC-specific connector profile.not_assessedNULL
381374sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. Enterobacterales LptC profile.not_assessedNULL
391375sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. LptF-specific permease profile, separated from LptG by NCBIfam.not_assessedNULL
401376sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. LptG-specific permease profile, separated from LptF by NCBIfam.not_assessedNULL
421377sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. Gammaproteobacterial LptD profile.not_assessedNULL
421378sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. Alternative Gammaproteobacterial LptD profile.not_assessedNULL
431379sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. Enterobacterales LptE profile; the broader Pfam-equivalent profile is not admitted.not_assessedNULL
441380orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02Activity-level UDP-GlcNAc 2-epimerase marker; it is not WTA-specific and is accepted only as one required role in the complete architecture.not_assessedNULL
451381orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02Shared TagO/WecA/Rfe activity marker; it never establishes WTA alone.not_assessedNULL
461382orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02TagA/TarA linkage-unit mannosaminyltransferase orthology.not_assessedNULL
471383orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02TagB/TarB linkage-unit glycerol-phosphate primase orthology.not_assessedNULL
481384orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02TagD glycerol-3-phosphate cytidylyltransferase orthology.not_assessedNULL
491385orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02TarI CDP-ribitol synthase orthology.not_assessedNULL
501386orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02TarJ ribitol-5-phosphate dehydrogenase orthology.not_assessedNULL
511387sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-02family_type=equivalog. Staphylococcus aureus TarF profile; K21591 and broad TagF-family profiles are not admitted as alternatives.not_assessedNULL
521388sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-02family_type=equivalog. Staphylococcus TarL profile; K18704 alone is not admitted for this lineage-resolved role.not_assessedNULL
531389orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02TarK ribitol-phosphate primase orthology; required together with TarL.not_assessedNULL
541390orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02TarL ribitol-phosphate polymerase orthology; required together with TarK so it cannot identify the W23 design alone.not_assessedNULL
551391orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02TagG WTA-export permease orthology.not_assessedNULL
561392orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02TagH WTA-export ATPase orthology.not_assessedNULL
571393orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-02TagT/TagU/TagV LCP-family teichoic-acid attachment orthology; accepted only inside the complete architecture.not_assessedNULL
581394sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-02family_type=equivalog. Processive diglucosyldiacylglycerol synthase profile; K03429 is not admitted as an alternative.not_assessedNULL
591395sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-02family_type=equivalog. LTA-biosynthesis MFS flippase profile for the diglucosyldiacylglycerol anchor.not_assessedNULL
601396sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-02family_type=equivalog. LtaS poly(glycerol-phosphate) synthase profile; the broader K19005 orthology is deliberately not admitted.not_assessedNULL
611397orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03The orthology also contains IcmH/DotU of the Legionella type IVB system; it is evidence only inside the complete architecture.not_assessedNULL
611398sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. DotU family type VI secretion system protein; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
621399orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03The orthology also contains IcmF of the Legionella type IVB system; it is evidence only inside the complete architecture.not_assessedNULL
621400sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type VI secretion system membrane subunit TssM; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
631401orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03VasD orthology; 99 of 100 sampled frame proteins pass the TssJ equivalog TIGR03352.1. K11918 is not accepted: none of 100 sampled proteins pass it.not_assessedNULL
631402sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type VI secretion system lipoprotein TssJ; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
641403orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03ImpF orthology; 89 of 100 sampled frame proteins pass the TssE equivalog TIGR03357.1.not_assessedNULL
641404orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03KEGG names this orthology only as a type VI secretion system protein. Accepted for TssE because 96 of 100 sampled frame proteins pass the TssE equivalog TIGR03357.1; see data-raw/reference/secretion-system-marker-audit.tsv.not_assessedNULL
641405orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03HsiF3-type orthology. Accepted for TssE because all 75 frame proteins pass the TssE equivalog TIGR03357.1.not_assessedNULL
641406sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type VI secretion system baseplate subunit TssE; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
651407orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Type VI-specific orthology.not_assessedNULL
651408sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type VI secretion system baseplate subunit TssF; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
661409orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Type VI-specific orthology.not_assessedNULL
661410sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type VI secretion system baseplate subunit TssG; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
671411orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Type VI-specific orthology.not_assessedNULL
671412sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type VI secretion system baseplate subunit TssK; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
681413orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03No admitted NCBIfam profile exists for VgrG: the TssI/VgrG profiles are subfamily_domain grade.not_assessedNULL
691414orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03No admitted NCBIfam profile exists for Hcp: the TssD profiles are subfamily or domain grade.not_assessedNULL
701415orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Type VI-specific orthology.not_assessedNULL
701416sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type VI secretion system contractile sheath small subunit; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
711417orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Type VI-specific orthology.not_assessedNULL
711418sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type VI secretion system contractile sheath large subunit; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
721419orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03ImpA orthology; 73 of 100 sampled frame proteins pass a TssA equivalog.not_assessedNULL
721420orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03VasJ orthology. Accepted for TssA because 95 of 100 sampled frame proteins pass a TssA equivalog; Vibrio cholerae TssA sits here and not under K11902.not_assessedNULL
721421sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type VI secretion system protein TssA; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
721422sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type VI secretion system protein TssA; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
731423orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Type VI-specific orthology.not_assessedNULL
731424sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type VI secretion system ATPase TssH; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
741425orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology; the flagellar homologue has its own accession, which is not accepted here.not_assessedNULL
741426orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology; the flagellar homologue has its own accession, which is not accepted here.not_assessedNULL
741427sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type III secretion system export apparatus subunit SctR; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
751428orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology; the flagellar homologue has its own accession, which is not accepted here.not_assessedNULL
751429orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology; the flagellar homologue has its own accession, which is not accepted here.not_assessedNULL
751430sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type III secretion system export apparatus subunit SctS; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
761431orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology; the flagellar homologue has its own accession, which is not accepted here.not_assessedNULL
761432orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology; the flagellar homologue has its own accession, which is not accepted here.not_assessedNULL
761433sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type III secretion system export apparatus subunit SctT; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
771434orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology; the flagellar homologue has its own accession, which is not accepted here.not_assessedNULL
771435orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology; the flagellar homologue has its own accession, which is not accepted here.not_assessedNULL
771436sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type III secretion system export apparatus subunit SctU; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
781437orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology; the flagellar homologue has its own accession, which is not accepted here.not_assessedNULL
781438sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type III secretion system export apparatus subunit SctV; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
791439orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology; the flagellar homologue has its own accession, which is not accepted here.not_assessedNULL
791440orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology; the flagellar homologue has its own accession, which is not accepted here.not_assessedNULL
791441sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type III secretion system ATPase SctN; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
801442orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology.not_assessedNULL
801443orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology.not_assessedNULL
801444sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type III secretion system inner membrane ring subunit SctD; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
801445sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. PrgH/EprH family type III secretion apparatus protein; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
811446orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology; the flagellar homologue has its own accession, which is not accepted here.not_assessedNULL
811447orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology; the flagellar homologue has its own accession, which is not accepted here.not_assessedNULL
811448sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type III secretion system inner membrane ring lipoprotein SctJ; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
821449orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology.not_assessedNULL
821450orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology.not_assessedNULL
821451sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type III secretion system outer membrane ring subunit SctC; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
831452orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology; the flagellar homologue has its own accession, which is not accepted here.not_assessedNULL
831453sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type III secretion system cytoplasmic ring protein SctQ; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
841454orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology.not_assessedNULL
841455orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03PrgJ inner rod of Inv-Mxi-Spa systems.not_assessedNULL
841456orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03EscI inner rod of LEE systems.not_assessedNULL
841457orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03HrpB2 inner rod of Hrp systems.not_assessedNULL
841458sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type III secretion system inner rod subunit SctI; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
851459orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Injectisome-specific orthology.not_assessedNULL
851460sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type III secretion system needle filament subunit SctF; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
851461sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type III secretion system needle complex protein; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
861462orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Xanthomonas-type HrpE pilin.not_assessedNULL
861463sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog_domain. Type III secretion system major pilin HrpA; no hit in the flagellated, secretion-free control proteomes.not_assessedNULL
871464orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03All 27 frame proteins match the archaeal-type flagellin family PF01917.not_assessedNULL
871465orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Defined as flaB, flgA; flgA here is the historical haloarchaeal archaellin gene name, not bacterial FlgA (K02386). 752 of 758 frame proteins match PF01917 and none matches the FlgA P-ring chaperone family PF13144.not_assessedNULL
881471orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Covers euryarchaeal FlaK (Methanococcus maripaludis MMP0555) and the broad-specificity PibD (Sulfolobus solfataricus SSO0131, Haloferax volcanii HVO_2993). In each of the 22 archaellum-encoding Methanococcales it also collects the pilin-specific peptidase EppA, which does not process archaellins (PMID 17114255); every one of those genomes also carries a protein passing the FlaK equivalog, so no frame call rests on EppA.referencePMID:17114255
881476sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Preflagellin peptidase FlaK, Methanococcales range; passes one K07991 protein in each of the 22 archaellum-encoding Methanococcales and none of the co-assigned EppA proteins.not_assessedNULL
89454orthologyputativeKEGG orthology, verified against KEGG REST 2026-10-03Bacterial prepilin peptidase, assigned in no archaeon of the frame. Accepted only as the archaellin peptidase of archaellum-encoding bacteria, which carry no archaeal-type peptidase orthology; that it processes archaellin is the inference of PMID 40962902, not a measurement.referencePMID:40962902
901466orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03NULLnot_assessedNULL
901477sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Archaellum stator protein ArlF; Methanobacteriota range, so it does not reach crenarchaeal or thaumarchaeal FlaF.not_assessedNULL
911467orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03NULLnot_assessedNULL
911478sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Archaellum stator protein ArlG; Methanobacteriota range, so it does not reach crenarchaeal or thaumarchaeal FlaG.not_assessedNULL
921468orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03NULLnot_assessedNULL
921479sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Archaellum protein ArlH, Archaea range.not_assessedNULL
931469orthologyputativeKEGG orthology, verified against KEGG REST 2026-10-03The orthology also collects archaeal type IV pilus and bindosome ATPases: of 885 K07332 proteins in archaellum-encoding archaea only 268 pass the FlaI equivalog, and 17 pass the bindosome BasE profile. Accepted only inside the conjunction, where 252 of 256 archaellum-encoding archaea carry a protein passing the equivalog, and at putative confidence because the accession alone cannot separate FlaI from its pilus homologues.not_assessedNULL
931480sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Archaellum ATPase FlaI; passes no K07332 protein that a bindosome or pilus contrast profile claims.not_assessedNULL
941470orthologyputativeKEGG orthology, verified against KEGG REST 2026-10-03The orthology also collects archaeal type IV pilus and bindosome platforms, including UpsF and BasF: of 858 K07333 proteins in archaellum-encoding archaea only 267 pass an ArlJ equivalog. Accepted only inside the conjunction, where 253 of 256 archaellum-encoding archaea carry a protein passing an ArlJ equivalog, and at putative confidence for the same reason as K07332.not_assessedNULL
941481sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Archaellar assembly protein ArlJ, Methanobacteriota range.not_assessedNULL
941482sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Archaellar assembly protein ArlJ, Methanobacteriati range.not_assessedNULL
941483sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Archaellar assembly protein ArlJ, Thermoproteati range.not_assessedNULL
951472orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03NULLnot_assessedNULL
951475orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Fused FlaCE protein; the same accession also supports COMP_ARCHAELLUM_FLAE, which is what a fused protein means.not_assessedNULL
961473orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03None of the 93 archaellum-encoding haloarchaea in the frame carries this orthology, so the accessory switch complex is reported incomplete in them.not_assessedNULL
971474orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03NULLnot_assessedNULL
971475orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Fused FlaCE protein; the same accession also supports COMP_ARCHAELLUM_FLAC.not_assessedNULL
981484sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Archaellum motor scaffold protein FlaX, Sulfolobaceae range, 25 RefSeq hits. No KEGG orthology exists, so the reference frame cannot measure it.not_assessedNULL
991485orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03GspD-specific orthology. KEGG assigns no K02453 to Vibrio cholerae N16961, whose epsD region carries an authentic frameshift; the resulting incomplete call reports a disrupted secretin rather than a missing marker.not_assessedNULL
991486sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type II secretion system secretin GspD; no hit in the monoderm and Campylobacterota control proteomes.not_assessedNULL
1001487orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03GspC-specific orthology. It is the weakest marker in the inventory, absent from 335 of the 504 frame genomes one function short, across 108 genera. GspC is retained as required because it is biologically required and the misses are not clade-systematic.not_assessedNULL
1001488sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type II secretion system protein GspC; no hit in the monoderm and Campylobacterota control proteomes.not_assessedNULL
1011489orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Gsp-specific orthology; the homologous type IVa pilus protein has its own accession, which is not accepted here.not_assessedNULL
1011490sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type II secretion system inner membrane protein GspF; no hit in the monoderm and Campylobacterota control proteomes.not_assessedNULL
1021491orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Gsp-specific orthology; the homologous type IVa pilus protein has its own accession, which is not accepted here.not_assessedNULL
1021492sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type II secretion system protein GspL; no hit in the monoderm and Campylobacterota control proteomes.not_assessedNULL
1031493orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Gsp-specific orthology; the homologous type IVa pilus protein has its own accession, which is not accepted here.not_assessedNULL
1031494sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type II secretion system protein GspM; no hit in the monoderm and Campylobacterota control proteomes.not_assessedNULL
1041495orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Gsp-specific orthology; the homologous type IVa pilus protein has its own accession, which is not accepted here.not_assessedNULL
1041496sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type II secretion system ATPase GspE; no hit in the monoderm and Campylobacterota control proteomes.not_assessedNULL
1051497orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Gsp-specific orthology; the homologous type IVa pilus protein has its own accession, which is not accepted here.not_assessedNULL
1051498sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type II secretion system major pseudopilin GspG; no hit in the monoderm and Campylobacterota control proteomes.not_assessedNULL
1061499orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Gsp-specific orthology; the homologous type IVa pilus protein has its own accession, which is not accepted here.not_assessedNULL
1061500sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type II secretion system minor pseudopilin GspH; no hit in the monoderm and Campylobacterota control proteomes.not_assessedNULL
1071501orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Gsp-specific orthology; the homologous type IVa pilus protein has its own accession, which is not accepted here.not_assessedNULL
1071502sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type II secretion system minor pseudopilin GspI; no hit in the monoderm and Campylobacterota control proteomes.not_assessedNULL
1081503orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Gsp-specific orthology; the homologous type IVa pilus protein has its own accession, which is not accepted here.not_assessedNULL
1081504sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type II secretion system minor pseudopilin GspJ; no hit in the monoderm and Campylobacterota control proteomes.not_assessedNULL
1091505orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03Gsp-specific orthology; the homologous type IVa pilus protein has its own accession, which is not accepted here.not_assessedNULL
1091506sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-03family_type=equivalog. Type II secretion system minor pseudopilin GspK; no hit in the monoderm and Campylobacterota control proteomes.not_assessedNULL
1101507orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03GspO orthology. GspO and PilD are the same class III peptidase under two KEGG names; GspO is assigned in 331 frame genomes against PilD in 4,102, with 51 carrying both.not_assessedNULL
110454orthologycuratedKEGG orthology, verified against KEGG REST 2026-10-03PilD orthology, accepted here as the shared component that processes both type IVa pilins and type II pseudopilins (PMID 1309616). 1,319 of the 1,536 complete frame architectures reach this role through PilD alone. Its use by type_iva_pilus and archaellum is unchanged, and it contributes no specificity to any of them.referencePMID:1309616
gift_circuit5 rows · 6 columns
circuit_pkgift_pkcircuit_idnamedescriptionstatus
132CIRCUIT_CHEMOTAXIS_COREcore chemotaxis signalling pathwayReceptor, kinase core, response regulator and adaptation, with signal termination accessory.curated
233CIRCUIT_ASPARTATE_CHEMORECEPTIONaspartate chemoreception pathwayThe Tar receptor feeding the shared chemotaxis kinase, response and adaptation functions. The three downstream functions are the same curated rows the core pathway uses, not copies of them.curated
334CIRCUIT_PHO_PHOR_PHOBPhoR/PhoB phosphate regulonThe enterobacterial and pseudomonad form of the phosphate starvation two-component system.curated
434CIRCUIT_PHO_PHOR_PHOPPhoR/PhoP phosphate regulonThe Bacillus-type form, sharing the sensor with the PhoR/PhoB circuit and differing in the cognate response regulator.curated
5161CIRCUIT_SERINE_CHEMORECEPTIONTsr serine chemoreception circuitTsr-family serine input and the shared chemotaxis kinase, response and adaptation functions.curated
circuit_function19 rows · 4 columns
circuit_pkfunction_pkordinalrequired
1111
1221
1331
1441
1550
2611
2221
2331
2441
3711
3821
31030
4711
4921
41030
51111
5221
5331
5441
regulatory_function11 rows · 4 columns
function_pkfunction_idnamedescription
1RF_CHEMOTAXIS_RECEPTIONchemoreceptor signal receptionDetection of a chemoeffector by a methyl-accepting chemoreceptor and its conversion into a conformational signal at the receptor's conserved cytoplasmic tip. The function is satisfied by any chemoreceptor; which chemoeffector is detected is a separate, narrower claim needing its own evidence.
2RF_CHEMOTAXIS_KINASE_COREchemotaxis kinase coreAutophosphorylation of the CheA histidine kinase under receptor control, which requires the CheW coupling protein to build the receptor-CheW-CheA array. CheV, a CheW-response regulator hybrid found alongside CheW in some Firmicutes, is not accepted as a substitute because it does not replace CheW in the systems where both occur.
3RF_CHEMOTAXIS_RESPONSE_REGULATORchemotaxis response regulatorPhosphotransfer from CheA to the CheY response regulator, the diffusible messenger that carries the signal to the flagellar switch.
4RF_CHEMOTAXIS_ADAPTATIONchemoreceptor adaptationReversible methylation of the chemoreceptor, which resets sensitivity so that the system responds to gradients rather than to absolute concentrations. Both the methyltransferase and the methylesterase are needed for the cycle to run in both directions.
5RF_CHEMOTAXIS_SIGNAL_TERMINATIONchemotaxis signal terminationDephosphorylation of CheY-P, which sets the response's decay time. It is curated as accessory because CheY-P also autodephosphorylates, and because the phosphatases are distributed unevenly: a genome without one still transduces a chemotactic signal, more slowly.
6RF_ASPARTATE_RECEPTIONL-aspartate chemoreceptor signal receptionDetection of L-aspartate by the Tar chemoreceptor and its conversion into a signal at the receptor's cytoplasmic tip. This is a strictly narrower function than RF_CHEMOTAXIS_RECEPTION and takes strictly narrower evidence: a generic methyl-accepting chemotaxis protein accession is deliberately not accepted.
7RF_PHO_SIGNAL_RECEPTIONphosphate-limitation signal receptionAutophosphorylation of the PhoR sensor histidine kinase in response to phosphate limitation. The same sensor serves both curated circuits, which differ in their cognate response regulator.
8RF_PHO_RESPONSE_PHOBPhoB transcriptional responsePhosphotransfer from PhoR to the PhoB response regulator, which activates Pho box promoters. This is the enterobacterial and pseudomonad form of the regulon's output.
9RF_PHO_RESPONSE_PHOPPhoP transcriptional responsePhosphotransfer from PhoR to the PhoP response regulator of the Bacillus-type phosphate regulon. K07660, the response regulator of the magnesium-sensing PhoP/PhoQ system, is a different protein that happens to share the gene name and is deliberately not accepted.
10RF_PHO_PHOSPHATE_STATUSphosphate status transduction complexThe PstSCAB transporter with PhoU, the complex through which the cell's phosphate status reaches PhoR. It is curated as accessory rather than required because it is independently a transport capability, and requiring it here would curate the same biology twice.
11RF_SERINE_RECEPTIONTsr-family L-serine chemoreceptor signal receptionDetection of L-serine by a Tsr-family receptor and transmission to the chemotaxis kinase. This function requires a Tsr-specific equivalog; the broadly assigned Tsr-like KO does not establish ligand identity.
regulatory_system14 rows · 5 columns
system_pkfunction_pksystem_idnamedescription
11SYS_RF_CHEMOTAXIS_RECEPTOR_GENERICgeneric methyl-accepting chemoreceptorA chemoreceptor identified only by its conserved signalling architecture. It evidences that the genome encodes a receptor feeding the pathway, and nothing about what that receptor detects.
21SYS_RF_CHEMOTAXIS_RECEPTOR_CHARACTERISEDcharacterised chemoreceptorA chemoreceptor whose accepted orthology or equivalog marker is anchored on a characterised ligand or stimulus. Any one of them satisfies the reception function of the core pathway; Escherichia coli K-12 carries no generic-MCP orthologue and would otherwise be called receptor-less.
32SYS_RF_CHEMOTAXIS_KINASECheA/CheW kinase coreThe histidine kinase and its coupling protein, jointly required.
43SYS_RF_CHEMOTAXIS_CHEYCheY response regulatorSingle protein.
54SYS_RF_CHEMOTAXIS_ADAPTATIONCheR/CheB methylation cycleThe methyltransferase and the methylesterase, jointly required.
65SYS_RF_CHEMOTAXIS_CHEZCheZ phosphataseThe enterobacterial CheY-P phosphatase.
75SYS_RF_CHEMOTAXIS_CHECCheC phosphataseA CheY-P phosphatase unrelated in sequence to CheZ, found in Bacillus and many archaea. A non-homologous replacement rather than a homologue.
85SYS_RF_CHEMOTAXIS_CHEXCheX phosphataseA third, again unrelated, CheY-P phosphatase family.
96SYS_RF_ASPARTATE_RECEPTORTar aspartate chemoreceptorThe Tar orthologue group, anchored on the characterised aspartate and maltose sensor of Escherichia coli and Salmonella.
107SYS_RF_PHO_SENSORPhoR sensor histidine kinaseSingle protein.
118SYS_RF_PHO_PHOBPhoB response regulatorSingle protein.
129SYS_RF_PHO_PHOPPhoP response regulatorSingle protein.
1310SYS_RF_PST_PHOUPstSCAB-PhoU complexThe four transporter subunits and PhoU, jointly required.
1411SYS_RF_TSR_SERINETsr serine receptorA Tsr-family chemoreceptor evidenced by an equivalog-grade profile.
regulatory_component20 rows · 5 columns
component_pksystem_pkcomponent_idnamedescription
11COMP_RF_MCPmethyl-accepting chemotaxis proteinAny chemoreceptor with the conserved signalling domain.
22COMP_RF_CHARACTERISED_RECEPTORcharacterised chemoreceptorA chemoreceptor whose accepted orthology or equivalog marker is anchored on a known stimulus.
33COMP_RF_CHEACheA histidine kinaseAutophosphorylating kinase.
43COMP_RF_CHEWCheW coupling proteinCouples receptor to kinase.
54COMP_RF_CHEYCheY response regulatorDiffusible messenger.
65COMP_RF_CHERCheR methyltransferaseAdds receptor methyl groups.
75COMP_RF_CHEBCheB methylesteraseRemoves receptor methyl groups.
86COMP_RF_CHEZCheZ phosphataseCheY-P phosphatase.
97COMP_RF_CHECCheC phosphataseCheY-P phosphatase.
108COMP_RF_CHEXCheX phosphataseCheY-P phosphatase.
119COMP_RF_TARTar aspartate chemoreceptorThe aspartate-sensing receptor itself.
1210COMP_RF_PHORPhoR sensor histidine kinasePhosphate-limitation sensor.
1311COMP_RF_PHOBPhoB response regulatorPho box activator.
1412COMP_RF_PHOPPhoP response regulatorBacillus-type Pho regulon activator.
1513COMP_RF_PSTSPstS phosphate-binding proteinPeriplasmic binding protein.
1613COMP_RF_PSTCPstC permeaseTransporter permease.
1713COMP_RF_PSTAPstA permeaseTransporter permease.
1813COMP_RF_PSTBPstB ATP-binding proteinTransporter ATPase.
1913COMP_RF_PHOUPhoUConveys transporter occupancy to PhoR.
2014COMP_RF_TSR_SERINETsr serine chemoreceptorPeriplasmic serine sensing and cytoplasmic CheA control.
regulatory_component_marker25 rows · 8 columns
component_pkmarker_pkevidence_typeconfidencesourcenotesbasisreference
1470orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18Identifies the conserved cytoplasmic signalling architecture, not the periplasmic sensing domain. A single genome may carry dozens: Vibrio cholerae has 34 and Pseudomonas aeruginosa 21. It therefore supports the core signal-transduction claim and no ligand-specific claim.not_assessedNULL
2479orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18Tsr, serine chemoreceptor.not_assessedNULL
2480orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18Tar, aspartate and maltose chemoreceptor.not_assessedNULL
2481orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18Trg, ribose and galactose chemoreceptor.not_assessedNULL
2482orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18Tap, dipeptide chemoreceptor.not_assessedNULL
2478orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18Aer, redox and aerotaxis receptor.not_assessedNULL
3471orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
4472orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
5476orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
6464orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
7475orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
8477orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
9474orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
10473orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
11480orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18The orthologue group is anchored on the characterised aspartate and maltose sensor. K03406 is deliberately not accepted here: it identifies the signalling domain shared by every chemoreceptor and cannot single out an aspartate sensor.not_assessedNULL
12483orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18Single copy in every reference genome checked that carries it (Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, Salmonella Typhi, Vibrio cholerae), and absent from Campylobacter jejuni, Helicobacter pylori, Mycobacterium tuberculosis and Lactococcus lactis. The group is not absorbing paralogous histidine kinases.not_assessedNULL
13484orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18Single copy in Escherichia coli, Pseudomonas aeruginosa, Salmonella Typhi and Vibrio cholerae; absent from Bacillus subtilis, which uses the K07658 regulator instead. The two regulator groups are mutually exclusive across the genomes checked.not_assessedNULL
14485orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18BSU29110 in Bacillus subtilis, immediately adjacent to the K07636 sensor BSU29100, which is the cognate pair. Not to be confused with K07660, the response regulator of the magnesium-sensing PhoP/PhoQ system, which is present in Escherichia coli and Salmonella and is a different protein with the same gene name.not_assessedNULL
15469orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
16466orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
17467orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
18465orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
19468orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
201576sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0 equivalog; compared with UniProt P02942 and KEGG K05874, 2026-10-04family_type=equivalog. Tsr-specific profile separates it from the Tar profile NF011622.0. KO K05874 collects multiple Tsr-like paralogues in some genomes and is not accepted for this ligand-specific function.not_assessedNULL
21576sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0 equivalog; compared with UniProt P02942 and KEGG K05874, 2026-10-04family_type=equivalog. A Tsr-specific receptor is also a chemoreceptor; accepting it here keeps serine_chemoreception a subset of core chemotaxis signal transduction.not_assessedNULL
gift_mechanism7 rows · 6 columns
mechanism_pkgift_pkmechanism_idnamedescriptionstatus
135MECH_TYPE_I_RMtype I restriction-modification systemRecognition, host protection and restriction, all three required.curated
236MECH_TYPE_I_E_CRISPRtype I-E CRISPR-Cas protein machineryCascade surveillance and Cas3 interference, with spacer acquisition accessory. The CRISPR array itself is outside what protein markers can evidence.curated
3130MECH_MER_HGmer operon mercury detoxificationReduction of Hg(II) to Hg(0) by MerA, required, with metal delivery, mercury-responsive induction and organomercurial lysis accessory.curated
4139MECH_MG_GLYOXALASEglutathione-dependent glyoxalase mechanismGlyoxalase I and glyoxalase II are both required to convert methylglyoxal to D-lactate and regenerate glutathione.curated
5140MECH_SUPEROXIDE_COMPLETEcomplete superoxide-to-water detoxificationOne superoxide-removal system and one hydrogen-peroxide-removal system are both required.curated
6162MECH_BETA_LACTAM_HYDROLYSISbeta-lactamase hydrolysisHydrolysis of a beta-lactam ring by any one of the four Ambler enzyme classes.curated
7163MECH_CHLORAMPHENICOL_ACETYLATIONchloramphenicol O-acetylationO-acetylation of chloramphenicol using acetyl-CoA by either CAT type.curated
mechanism_function16 rows · 4 columns
mechanism_pkfunction_pkordinalrequired
1111
1221
1331
2411
2521
2630
3711
3820
3930
31040
41111
41221
51311
51421
61511
71611
defense_function16 rows · 4 columns
function_pkfunction_idnamedescription
1DF_TYPE_I_RM_SPECIFICITYtype I restriction-modification target recognitionRecognition of the system's bipartite target sequence by the HsdS specificity subunit, which directs both the methyltransferase and the endonuclease. Which sequence is recognised is not claimed: HsdS specificity comes from variable target recognition domains that an orthology group does not resolve.
2DF_TYPE_I_RM_MODIFICATIONtype I restriction-modification host protectionAdenine methylation of the host's own target sites by HsdM, without which the system would cleave the genome that encodes it.
3DF_TYPE_I_RM_RESTRICTIONtype I restriction-modification DNA cleavageATP-dependent translocation and double-strand cleavage of unmethylated invading DNA by HsdR. It is required: a genome carrying only HsdM and HsdS has a methylation capability, which is real biology, but it defends against nothing and is not this claim.
4DF_CRISPR_I_E_SURVEILLANCEtype I-E Cascade surveillance complexThe five-subunit Cascade complex that binds crRNA and scans DNA for a matching protospacer. All five subunits are jointly required; the complex does not assemble without them.
5DF_CRISPR_I_E_INTERFERENCE_NUCLEASEtype I-E interference nucleaseRecruitment of the Cas3 nuclease-helicase by target-bound Cascade, and processive degradation of the target. K07475, which identifies only the HD nuclease module of a split Cas3, is not accepted: it does not evidence the complete nuclease-helicase.
6DF_CRISPR_ADAPTATIONCRISPR spacer acquisitionIntegration of new spacers by the Cas1-Cas2 integrase complex. It is accessory because a system can interfere using the spacers it already has, and cas1/cas2 are lost from many otherwise intact loci.
7DF_MER_HG_REDUCTIONmercuric ion reductionTwo-electron reduction of Hg(II) to elemental Hg(0) by the NADPH-dependent flavin disulfide oxidoreductase MerA, which removes the thiol-reactive species from the cytoplasm and releases a volatile product. It is the only required function of the mechanism: a genome carrying merA detoxifies the Hg(II) that reaches it, and how much reaches it is not something a genome sequence states.
8DF_MER_HG_DELIVERYmercuric ion delivery to the reductaseCapture of Hg(II) outside the cytoplasm and its passage across the inner membrane to MerA, by MerT with its periplasmic binding partner MerP, or by MerC or MerE alone. Accessory, because the transporters vary between lineages while merA does not, and because mercury reaches the cytoplasm without them.
9DF_MER_HG_INDUCTIONmercury-responsive induction of the operonActivation of the operon promoter by the Hg(II)-sensing MerR-family activator, which holds the promoter in a repressed complex until it binds the metal. It belongs to this mechanism rather than being a regulatory GIFT because its only output is this operon, and it is accessory because MerA reduces mercury whether or not a curatable activator is present. MerD (K19057) is deliberately not accepted as evidence: it modulates MerR-driven transcription as a co-regulator rather than activating the promoter itself, and as an alternative on this component it would let a genome carrying no activator claim induction.
10DF_MER_ORGANOMERCURIAL_LYSISorganomercurial carbon-mercury bond lysisProtonolysis of the carbon-mercury bond of an organomercurial such as phenylmercury by the lyase MerB, releasing Hg(II) for MerA to reduce. Accessory: it widens the range of mercury species the mechanism handles, it is absent from most mer operons, and whether broad-spectrum resistance should instead be a second mechanism is an open question rather than a decided one.
11DF_MG_GLYOXALASE_Imethylglyoxal capture as S-lactoylglutathioneGlyoxalase I converts the spontaneously formed methylglyoxal-glutathione hemithioacetal to S-lactoylglutathione. The chemistry is reverse RHEA:19069. This function alone has not regenerated glutathione and is not the complete mechanism.
12DF_MG_GLYOXALASE_IIS-lactoylglutathione hydrolysisGlyoxalase II hydrolyses S-lactoylglutathione to D-lactate and regenerates glutathione, forward RHEA:25245. D-lactate oxidation is downstream metabolism and is not required.
13DF_SUPEROXIDE_REMOVALsuperoxide conversion to hydrogen peroxideRemoval of superoxide by dismutation, RHEA:20696. Fe/Mn and Cu/Zn SODs are alternative systems. The function deliberately excludes nickel SOD without its maturation protease and superoxide reductase without a curated electron-delivery architecture.
14DF_PEROXIDE_REMOVALhydrogen peroxide removalRemoval of the hydrogen peroxide produced by the first function. Catalases use RHEA:20309; the AhpC/AhpF alternative is represented by the generic hydroperoxide chemistry RHEA:62620 and requires both proteins. A generic peroxiredoxin alone is insufficient.
15DF_BETA_LACTAM_HYDROLYSISbeta-lactam ring hydrolysisHydrolysis of the beta-lactam ring, the class-level chemistry of RHEA:20401. No specific penicillin, cephalosporin or carbapenem spectrum is claimed.
16DF_CHLORAMPHENICOL_ACETYLATIONchloramphenicol O-acetylationAcetyl-CoA-dependent conversion of chloramphenicol to chloramphenicol 3-acetate, RHEA:18421.
defense_system26 rows · 5 columns
system_pkfunction_pksystem_idnamedescription
11SYS_DF_HSDSHsdS specificity subunitSingle protein.
22SYS_DF_HSDMHsdM methyltransferaseSingle protein.
33SYS_DF_HSDRHsdR restriction subunitSingle protein.
44SYS_DF_CASCADE_I_Etype I-E CascadeCasA, CasB, CasC, CasD and CasE, jointly required.
55SYS_DF_CAS3Cas3 nuclease-helicaseSingle fused protein.
66SYS_DF_CAS1_CAS2Cas1-Cas2 integraseBoth proteins jointly required.
77SYS_DF_MERAMerA mercuric reductaseSingle catalytic protein.
88SYS_DF_MERTPMerT-MerP transport pairThe inner-membrane transporter and its periplasmic binding protein, jointly required.
98SYS_DF_MERCMerC transporterSingle protein, an alternative to MerT-MerP.
108SYS_DF_MEREMerE transporterSingle protein, an alternative to MerT-MerP and the one that also carries organomercurials.
119SYS_DF_MERRMerR activatorSingle protein.
1210SYS_DF_MERBMerB organomercurial lyaseSingle catalytic protein.
1311SYS_DF_MG_GLOAGloA glyoxalase ISingle catalytic protein.
1412SYS_DF_MG_GLOBGloB glyoxalase IISingle catalytic protein.
1513SYS_DF_SOD_FEMNFe/Mn superoxide dismutaseSingle catalytic protein; the KO does not distinguish iron from manganese but both catalyse the same reaction.
1613SYS_DF_SOD_CUZNCu/Zn superoxide dismutaseSingle catalytic protein.
1714SYS_DF_CATALASEmonofunctional catalaseSingle catalytic protein.
1814SYS_DF_KATGcatalase-peroxidase KatGSingle catalytic protein with catalase activity.
1914SYS_DF_MN_CATALASEmanganese catalaseSingle catalytic protein.
2014SYS_DF_AHPCFAhpC-AhpF peroxide-removal systemThe peroxiredoxin catalytic subunit and its NADH-dependent reductase are jointly required.
2115SYS_DF_BLA_CLASS_AAmbler class A beta-lactamaseSerine-dependent beta-lactamase enzyme; one catalytic protein.
2215SYS_DF_BLA_CLASS_BAmbler class B beta-lactamaseZinc-dependent beta-lactamase enzyme; one catalytic protein.
2315SYS_DF_BLA_CLASS_CAmbler class C beta-lactamaseSerine-dependent beta-lactamase enzyme; one catalytic protein.
2415SYS_DF_BLA_CLASS_DAmbler class D beta-lactamaseSerine-dependent beta-lactamase enzyme; one catalytic protein.
2516SYS_DF_CAT_TYPE_Achloramphenicol acetyltransferase type AOne chloramphenicol O-acetyltransferase protein.
2616SYS_DF_CAT_TYPE_Bchloramphenicol acetyltransferase type BOne chloramphenicol O-acetyltransferase protein.
defense_component33 rows · 5 columns
component_pksystem_pkcomponent_idnamedescription
11COMP_DF_HSDSHsdS specificity subunitDirects the complex to its target sequence.
22COMP_DF_HSDMHsdM methyltransferaseProtects host target sites.
33COMP_DF_HSDRHsdR restriction subunitTranslocates and cleaves.
44COMP_DF_CASACasA/Cse1PAM recognition and Cas3 recruitment.
54COMP_DF_CASBCasB/Cse2R-loop stabilisation.
64COMP_DF_CASCCasC/Cas7Backbone of the complex.
74COMP_DF_CASDCasD/Cas5crRNA 5' handle binding.
84COMP_DF_CASECasE/Cas6ecrRNA processing endoribonuclease.
95COMP_DF_CAS3Cas3 nuclease-helicaseDegrades the target.
106COMP_DF_CAS1Cas1 integraseSpacer integration.
116COMP_DF_CAS2Cas2Integrase partner.
127COMP_DF_MERAMerA mercuric reductaseReduces Hg(II) to Hg(0).
138COMP_DF_MERTMerT inner-membrane transporterPasses Hg(II) to the cytoplasm.
148COMP_DF_MERPMerP periplasmic binding proteinCaptures Hg(II) and hands it to MerT.
159COMP_DF_MERCMerC transporterAlternative inner-membrane mercury transporter.
1610COMP_DF_MEREMerE transporterAlternative transporter, permeable to organomercurials as well as Hg(II).
1711COMP_DF_MERRMerR activatorBinds Hg(II) and activates the operon promoter.
1812COMP_DF_MERBMerB organomercurial lyaseCleaves the carbon-mercury bond.
1913COMP_DF_MG_GLOAGloA glyoxalase IForms S-lactoylglutathione from the methylglyoxal-glutathione adduct.
2014COMP_DF_MG_GLOBGloB glyoxalase IIHydrolyses S-lactoylglutathione and regenerates glutathione.
2115COMP_DF_SOD_FEMNFe/Mn superoxide dismutaseDismutates superoxide.
2216COMP_DF_SOD_CUZNCu/Zn superoxide dismutaseDismutates superoxide.
2317COMP_DF_CATALASEcatalaseDismutates hydrogen peroxide.
2418COMP_DF_KATGcatalase-peroxidaseRemoves hydrogen peroxide through its catalase activity.
2519COMP_DF_MN_CATALASEmanganese catalaseDismutates hydrogen peroxide without heme.
2620COMP_DF_AHPCAhpC peroxiredoxin catalytic subunitReduces peroxide and becomes oxidised.
2720COMP_DF_AHPFAhpF NADH-dependent reductaseRegenerates reduced AhpC.
2821COMP_DF_BLA_CLASS_Aclass A beta-lactamaseCatalyses hydrolysis of a beta-lactam ring; family-level substrate spectrum is not asserted.
2922COMP_DF_BLA_CLASS_Bclass B beta-lactamaseCatalyses hydrolysis of a beta-lactam ring; family-level substrate spectrum is not asserted.
3023COMP_DF_BLA_CLASS_Cclass C beta-lactamaseCatalyses hydrolysis of a beta-lactam ring; family-level substrate spectrum is not asserted.
3124COMP_DF_BLA_CLASS_Dclass D beta-lactamaseCatalyses hydrolysis of a beta-lactam ring; family-level substrate spectrum is not asserted.
3225COMP_DF_CAT_TYPE_Atype A chloramphenicol O-acetyltransferaseAcetylates chloramphenicol at the 3-O position.
3326COMP_DF_CAT_TYPE_Btype B chloramphenicol O-acetyltransferaseAcetylates chloramphenicol at the 3-O position.
defense_component_marker96 rows · 8 columns
component_pkmarker_pkevidence_typeconfidencesourcenotesbasisreference
1487orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18The orthologue group is defined as the type I restriction enzyme S subunit, so it separates type I from types II, III and IV. It does not resolve which target sequence the variable target recognition domains specify.not_assessedNULL
2488orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18Defined as the type I restriction enzyme M protein.not_assessedNULL
3486orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18Defined as the type I restriction enzyme R subunit.not_assessedNULL
4493orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
5492orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
6494orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
7495orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
8496orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
9489orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18The fused endonuclease-helicase. K07475, the standalone HD nuclease module of a split Cas3, is not accepted as evidence of the complete function.not_assessedNULL
10491orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
11490orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-18NULLnot_assessedNULL
12949orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-19Defined as mercuric reductase, EC 1.16.1.1.not_assessedNULL
12956sequence_familyhigh-confidenceInterPro/NCBIfam, retrieved 2026-08-19An alternative to the orthology group, not a second requirement. InterPro IPR021179 is the integrated entry; the InterPro accession itself is not curated, because gifter's evidence layer has no InterPro namespace and would store an accession it can never match.not_assessedNULL
13951orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-19NULLnot_assessedNULL
14952orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-19NULLnot_assessedNULL
15954orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-19NULLnot_assessedNULL
16955orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-19NULLnot_assessedNULL
17953orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-19K19057 (MerD) is not accepted here: it is a co-regulator that modulates MerR-driven transcription, not an alternative activator.not_assessedNULL
18950orthologycuratedKEGG orthology, verified against KEGG REST 2026-08-19NF033555 (NCBIfam, organomercurial lyase MerB) names the enzyme more specifically but is not curated: it is not integrated into InterPro and gifter's evidence layer recognises no NCBIfam NF namespace.not_assessedNULL
19996orthologycuratedKEGG orthology, Rhea release 141 and PMID 21143325, verified 2026-08-20Specific glyoxalase-I chemistry. Broad aldo-keto reductases and Hsp31/DJ-1 families are deliberately not accepted.referencePMID:21143325
20997orthologycuratedKEGG orthology, Rhea release 141 and PMID 21143325, verified 2026-08-20Accepted only as the second required function after GloA context establishes S-lactoylglutathione formation.referencePMID:21143325
21998orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-20Iron and manganese enzymes catalyse the same RHEA:20696 chemistry.not_assessedNULL
22999orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-20Cu/Zn superoxide dismutase is an alternative complete system for the first required function.not_assessedNULL
231000orthologycuratedKEGG orthology, Rhea release 141 and PMID 22609271, verified 2026-08-20Exact hydrogen-peroxide dismutation activity.referencePMID:22609271
241001orthologycuratedKEGG orthology, Rhea release 141 and PMID 15547258, verified 2026-08-20Catalase-peroxidase EC 1.11.1.21 includes the RHEA:20309 catalase reaction.referencePMID:15547258
251002orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-20Non-heme alternative catalysing the same hydrogen-peroxide dismutation.not_assessedNULL
261003orthologycuratedKEGG orthology, Rhea release 141 and PMID 22609271, verified 2026-08-20Accepted only in the two-component AhpC-AhpF system; K03386 alone does not satisfy peroxide removal here.referencePMID:22609271
271004orthologycuratedKEGG orthology and PMID 22609271, verified 2026-08-20Required reductase partner for the curated AhpC system.referencePMID:22609271
301508orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class C enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281509orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
291510orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class B enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311511orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281512orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281513orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281514orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281515orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281516orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
291517orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class B enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
291518orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class B enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
291519orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class B enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311520orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311521orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311522orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311523orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311524orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281525orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281526orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281527orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281528orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311529orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311530orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311531orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311532orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
301533orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class C enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
301534orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class C enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281535orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311536orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
291537orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class B enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
301538orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class C enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
301539orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class C enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311540orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311541orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311542orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311543orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311544orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
301545orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class C enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
301546orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class C enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
291547orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class B enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281548orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281549orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281550orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281551orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311552orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311553orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311554orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311555orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311556orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
301557orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class C enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
301558orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class C enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311559orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311560orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311561orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311562orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311563orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311564orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311565orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311566orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281567orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311568orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
311569orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class D enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281570orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
281571orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class A enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
291572orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class B enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
291573orthologycuratedKEGG orthology and Rhea release 141; checked against data-raw/reference/ko-reaction-specificity.tsv, 2026-10-04Ambler class B enzyme, not a metallo-beta-lactamase-fold signature. The named allele, where present, is evidence for class-level hydrolysis only, not its drug spectrum.not_assessedNULL
321574orthologycuratedKEGG orthology and Rhea release 141, verified 2026-10-04Specific chloramphenicol O-acetyltransferase. Type B belongs to a wider hexapeptide acyltransferase family, but this KO is assigned EC 2.3.1.28; reassess if its definition widens.not_assessedNULL
331575orthologycuratedKEGG orthology and Rhea release 141, verified 2026-10-04Specific chloramphenicol O-acetyltransferase. Type B belongs to a wider hexapeptide acyltransferase family, but this KO is assigned EC 2.3.1.28; reassess if its definition widens.not_assessedNULL
marker1576 rows · 5 columns
marker_pknamespaceaccessionnamedescription
1KOK00764amidophosphoribosyltransferaseKEGG orthology marker.
2KOK01945phosphoribosylamine--glycine ligaseKEGG orthology marker.
3KOK11787multifunctional purine biosynthesis proteinKEGG orthology marker supporting multiple catalytic components.
4KOK11788multifunctional purine biosynthesis proteinKEGG orthology marker supporting multiple catalytic components.
5KOK13713fusion protein PurCDKEGG orthology marker supporting two catalytic components.
6KOK00601phosphoribosylglycinamide formyltransferaseKEGG orthology marker.
7KOK11175phosphoribosylglycinamide formyltransferaseKEGG orthology marker.
8KOK01492purine biosynthesis transformylaseKEGG orthology marker supporting multiple catalytic components.
9KOK08289phosphoribosylglycinamide formyltransferase 2KEGG orthology marker.
10KOK01952phosphoribosylformylglycinamidine synthaseKEGG orthology marker for the large single-protein architecture.
11KOK23269FGAM synthase componentKEGG orthology marker for a required complex component.
12KOK23264FGAM synthase componentKEGG orthology marker for a required complex component.
13KOK23265FGAM synthase componentKEGG orthology marker shared by alternative complex architectures.
14KOK23270FGAM synthase componentKEGG orthology marker for a required complex component.
15KOK01933phosphoribosylformylglycinamidine cyclo-ligaseKEGG orthology marker.
16KOK01587phosphoribosylaminoimidazole carboxylaseKEGG orthology marker supporting multiple catalytic components.
17KOK11808phosphoribosylaminoimidazole carboxylaseKEGG orthology marker.
18KOK01589N5-CAIR synthetaseKEGG orthology marker.
19KOK01588N5-CAIR mutaseKEGG orthology marker.
20KOK01923SAICAR synthetaseKEGG orthology marker.
21KOK01756adenylosuccinate lyaseKEGG orthology marker supporting reactions in both reference GIFTs.
22KOK00602bifunctional AICAR transformylase and IMP cyclohydrolaseKEGG orthology marker supporting two catalytic components.
23KOK06863FAICAR synthetaseKEGG orthology marker.
24KOK11176IMP cyclohydrolaseKEGG orthology marker.
25KOK01939adenylosuccinate synthaseKEGG orthology marker.
26KOK00088IMP dehydrogenaseKEGG orthology marker for the first guanylate-branch reaction.
27KOK01951GMP synthase (glutamine-hydrolyzing)KEGG orthology marker for guanylate-branch GMP formation.
28KOK11540carbamoyl-phosphate synthase / aspartate carbamoyltransferase / dihydroorotaseMultifunctional KEGG orthology marker supporting three M00051 reactions.
29KOK11541carbamoyl-phosphate synthase / aspartate carbamoyltransferaseMultifunctional KEGG orthology marker supporting two M00051 reactions.
30KOK01465dihydroorotaseKEGG orthology marker.
31KOK01954carbamoyl-phosphate synthaseKEGG orthology marker for the single-protein architecture.
32KOK01955carbamoyl-phosphate synthase large subunitKEGG orthology marker for a required complex component.
33KOK01956carbamoyl-phosphate synthase small subunitKEGG orthology marker for a required complex component.
34KOK00609aspartate carbamoyltransferase catalytic subunitKEGG orthology marker for a required complex component.
35KOK00608aspartate carbamoyltransferaseKEGG orthology marker for the single-protein architecture.
36KOK00226dihydroorotate dehydrogenase (fumarate)KEGG orthology marker.
37KOK00254dihydroorotate dehydrogenase (quinone)KEGG orthology marker.
38KOK17828dihydroorotate dehydrogenase (NAD+) catalytic subunitKEGG orthology marker.
39KOK02823dihydroorotate dehydrogenase electron transfer subunitKEGG orthology marker for a required complex component.
40KOK13421uridine monophosphate synthetaseBifunctional KEGG orthology marker supporting two M00051 reactions.
41KOK00762orotate phosphoribosyltransferaseKEGG orthology marker.
42KOK01591orotidine 5'-phosphate decarboxylaseKEGG orthology marker.
43KOK01937CTP synthaseKEGG orthology marker for cytidylate formation.
44KOK00058D-3-phosphoglycerate dehydrogenaseKEGG orthology marker.
45KOK00831phosphoserine aminotransferaseKEGG orthology marker.
46KOK28205phosphoserine transaminaseKEGG orthology marker.
47KOK01079phosphoserine phosphataseKEGG orthology marker.
48KOK02203phosphoserine / homoserine phosphotransferaseBifunctional KEGG orthology marker supporting two catalytic components.
49KOK22305phosphoserine phosphataseKEGG orthology marker.
50KOK25528phosphoserine phosphataseKEGG orthology marker.
51KOK00600glycine hydroxymethyltransferaseKEGG orthology marker.
52KOK00928aspartate kinaseKEGG orthology marker.
53KOK12524bifunctional aspartokinase / homoserine dehydrogenase 1Bifunctional KEGG orthology marker supporting two catalytic components.
54KOK12525bifunctional aspartokinase / homoserine dehydrogenase 2Bifunctional KEGG orthology marker supporting two catalytic components.
55KOK12526bifunctional diaminopimelate decarboxylase / aspartate kinaseBifunctional KEGG orthology marker carrying aspartate kinase activity.
56KOK00133aspartate-semialdehyde dehydrogenaseKEGG orthology marker.
57KOK00003homoserine dehydrogenaseKEGG orthology marker.
58KOK00872homoserine kinaseKEGG orthology marker.
59KOK02204homoserine kinase type IIKEGG orthology marker.
60KOK01733threonine synthaseKEGG orthology marker.
61KOK00651homoserine O-succinyltransferase / O-acetyltransferaseKEGG orthology marker carrying both acyl chemistries.
62KOK00641homoserine O-acetyltransferase / O-succinyltransferaseKEGG orthology marker carrying both acyl chemistries.
63KOK01739cystathionine gamma-synthaseKEGG orthology marker.
64KOK27857plant cystathionine gamma-synthaseKEGG orthology marker.
65KOK01760cystathionine beta-lyaseKEGG orthology marker.
66KOK14155cystathionine beta-lyaseKEGG orthology marker.
67KOK00548cobalamin-dependent methionine synthaseKEGG orthology marker.
68KOK24042methionine synthase / methylenetetrahydrofolate reductaseKEGG orthology marker carrying cobalamin-dependent methionine synthase activity.
69KOK00549cobalamin-independent methionine synthaseKEGG orthology marker.
70KOK01740O-acetylhomoserine (thiol)-lyaseKEGG orthology marker.
71KOK10764O-succinylhomoserine sulfhydrylaseKEGG orthology marker.
72KOK17069O-acetylhomoserine / O-acetylserine sulfhydrylaseKEGG orthology marker supporting two catalytic components.
73KOK00640serine O-acetyltransferaseKEGG orthology marker.
74KOK23304serine O-acetyltransferaseKEGG orthology marker.
75KOK01738cysteine synthaseKEGG orthology marker.
76KOK13034cyanoalanine synthase / cysteine synthaseKEGG orthology marker carrying cysteine synthase activity.
77KOK01697cystathionine beta-synthaseKEGG orthology marker.
78KOK10150cysteine synthase / cystathionine beta-synthaseKEGG orthology marker carrying cystathionine beta-synthase activity.
79KOK01758cystathionine gamma-lyaseKEGG orthology marker.
80KOK17216cystathionine beta-synthase (O-acetyl-L-serine)KEGG orthology marker.
81KOK17217cystathionine gamma-lyase / homocysteine desulfhydraseKEGG orthology marker.
82KOK01805xylA; xylose isomeraseKEGG orthology marker.
83KOK00854xylB; xylulokinaseKEGG orthology marker.
84KOK01804araA; L-arabinose isomeraseKEGG orthology marker.
85KOK00853araB; L-ribulokinaseKEGG orthology marker.
86KOK24707ribulokinaseKEGG orthology marker.
87KOK03077araD; L-ribulose-5-phosphate 4-epimeraseKEGG orthology marker.
88KOK01818fucI; L-fucose/D-arabinose isomeraseKEGG orthology marker.
89KOK00879fucK; L-fuculokinaseKEGG orthology marker.
90KOK01628fucA; L-fuculose-phosphate aldolaseKEGG orthology marker.
91KOK01813rhaA; L-rhamnose isomeraseKEGG orthology marker.
92KOK01820rhaA; L-rhamnose isomerase / sugar isomeraseKEGG orthology marker.
93KOK00848rhaB; rhamnulokinaseKEGG orthology marker.
94KOK01629rhaD; rhamnulose-1-phosphate aldolaseKEGG orthology marker.
95KOK01785galM; aldose 1-epimeraseKEGG orthology marker.
96KOK00849galK; galactokinaseKEGG orthology marker.
97KOK00965galT; UDPglucose--hexose-1-phosphate uridylyltransferaseKEGG orthology marker.
98KOK01784galE; UDP-glucose 4-epimeraseKEGG orthology marker.
99KOK17716capD; UDP-glucose 4-epimeraseKEGG orthology marker.
100KOK00884NAGK; N-acetylglucosamine kinaseKEGG orthology marker.
101KOK28207nagK; N-acetylglucosamine kinaseKEGG orthology marker.
102KOK28208murK; N-acetylmuramate/N-acetylglucosamine kinaseKEGG orthology marker.
103KOK01443nagA; N-acetylglucosamine-6-phosphate deacetylaseKEGG orthology marker.
104KOK02564nagB; glucosamine-6-phosphate deaminaseKEGG orthology marker.
105KOK01639nanA; N-acetylneuraminate lyaseKEGG orthology marker.
106KOK00885nanK; N-acylmannosamine kinaseKEGG orthology marker.
107KOK13967nanEK; N-acetylmannosamine-6-phosphate 2-epimerase / kinaseKEGG orthology marker.
108KOK01788nanE; N-acylglucosamine-6-phosphate 2-epimeraseKEGG orthology marker.
109KOK01812uxaC; glucuronate isomeraseKEGG orthology marker.
110KOK00041uxaB; tagaturonate reductaseKEGG orthology marker.
111KOK01685uxaA; altronate hydrolaseKEGG orthology marker.
112KOK16849uxaA1; altronate dehydratase small subunitKEGG orthology marker.
113KOK16850uxaA2; altronate dehydratase large subunitKEGG orthology marker.
114KOK00874kdgK; 2-dehydro-3-deoxygluconokinaseKEGG orthology marker.
115KOK01625eda; 2-dehydro-3-deoxyphosphogluconate aldolaseKEGG orthology marker.
116KOK17463dgaF; 2-dehydro-3-deoxy-phosphogluconate aldolaseKEGG orthology marker.
117KOK28887kdgA; 2-dehydro-3-deoxy-phosphogluconate aldolaseKEGG orthology marker.
118KOK00040uxuB; fructuronate reductaseKEGG orthology marker.
119KOK01686uxuA; mannonate dehydrataseKEGG orthology marker.
120KOK08323rspA; mannonate dehydrataseKEGG orthology marker.
121KOK10543xylF; D-xylose transport system substrate-binding proteinKEGG orthology marker.
122KOK10544xylH; D-xylose transport system permease proteinKEGG orthology marker.
123KOK10545xylG; D-xylose transport system ATP-binding proteinKEGG orthology marker.
124KOK10537araF; L-arabinose transport system substrate-binding proteinKEGG orthology marker.
125KOK10538araH; L-arabinose transport system permease proteinKEGG orthology marker.
126KOK10539araG; L-arabinose transport system ATP-binding proteinKEGG orthology marker.
127KOK25045xacG; L-arabinose/D-xylose transport system substrate-binding proteinKEGG orthology marker.
128KOK25046xacH; L-arabinose/D-xylose transport system permease proteinKEGG orthology marker.
129KOK25047xacI; L-arabinose/D-xylose transport system permease proteinKEGG orthology marker.
130KOK01209alpha-L-arabinofuranosidase orthologueKEGG orthology marker.
131KOK15921alpha-L-arabinofuranosidase orthologueKEGG orthology marker.
132KOK20844alpha-L-arabinofuranosidase orthologueKEGG orthology marker.
133CAZYGH2CAZy family GH2CAZy sequence family; activity assignment from dbCAN.
134CAZYGH3CAZy family GH3CAZy sequence family; activity assignment from dbCAN.
135CAZYGH43CAZy family GH43CAZy sequence family; activity assignment from dbCAN.
136CAZYGH5CAZy family GH5CAZy sequence family; activity assignment from dbCAN.
137CAZYGH51CAZy family GH51CAZy sequence family; activity assignment from dbCAN.
138CAZYGH54CAZy family GH54CAZy sequence family; activity assignment from dbCAN.
139CAZYGH62CAZy family GH62CAZy sequence family; activity assignment from dbCAN.
140KOK01181endo-1,4-beta-xylanase orthologueKEGG orthology marker.
141CAZYGH10CAZy family GH10CAZy sequence family; activity assignment from dbCAN.
142CAZYGH11CAZy family GH11CAZy sequence family; activity assignment from dbCAN.
143CAZYGH141CAZy family GH141CAZy sequence family; activity assignment from dbCAN.
144CAZYGH30CAZy family GH30CAZy sequence family; activity assignment from dbCAN.
145CAZYGH44CAZy family GH44CAZy sequence family; activity assignment from dbCAN.
146CAZYGH8CAZy family GH8CAZy sequence family; activity assignment from dbCAN.
147CAZYGH9CAZy family GH9CAZy sequence family; activity assignment from dbCAN.
148CAZYGH98CAZy family GH98CAZy sequence family; activity assignment from dbCAN.
149KOK01198xylan 1,4-beta-xylosidase orthologueKEGG orthology marker.
150KOK15920xylan 1,4-beta-xylosidase orthologueKEGG orthology marker.
151KOK22268xylan 1,4-beta-xylosidase orthologueKEGG orthology marker.
152CAZYGH1CAZy family GH1CAZy sequence family; activity assignment from dbCAN.
153CAZYGH116CAZy family GH116CAZy sequence family; activity assignment from dbCAN.
154CAZYGH120CAZy family GH120CAZy sequence family; activity assignment from dbCAN.
155CAZYGH39CAZy family GH39CAZy sequence family; activity assignment from dbCAN.
156CAZYGH52CAZy family GH52CAZy sequence family; activity assignment from dbCAN.
157KOK01176alpha-amylase orthologueKEGG orthology marker.
158KOK07405alpha-amylase orthologueKEGG orthology marker.
159CAZYGH119CAZy family GH119CAZy sequence family; activity assignment from dbCAN.
160CAZYGH126CAZy family GH126CAZy sequence family; activity assignment from dbCAN.
161CAZYGH13CAZy family GH13CAZy sequence family; activity assignment from dbCAN.
162CAZYGH57CAZy family GH57CAZy sequence family; activity assignment from dbCAN.
163KOK01200pullulanase orthologueKEGG orthology marker.
164KOK01187alpha-glucosidase orthologueKEGG orthology marker.
165CAZYGH122CAZy family GH122CAZy sequence family; activity assignment from dbCAN.
166CAZYGH31CAZy family GH31CAZy sequence family; activity assignment from dbCAN.
167CAZYGH4CAZy family GH4CAZy sequence family; activity assignment from dbCAN.
168CAZYGH63CAZy family GH63CAZy sequence family; activity assignment from dbCAN.
169CAZYGH76CAZy family GH76CAZy sequence family; activity assignment from dbCAN.
170CAZYGH97CAZy family GH97CAZy sequence family; activity assignment from dbCAN.
171KOK05972AXE1; acetylxylan esteraseKEGG orthology marker.
172CAZYCE1CAZy family CE1CAZy sequence family; activity assignment from dbCAN.
173CAZYCE2CAZy family CE2CAZy sequence family; activity assignment from dbCAN.
174CAZYCE3CAZy family CE3CAZy sequence family; activity assignment from dbCAN.
175CAZYCE4CAZy family CE4CAZy sequence family; activity assignment from dbCAN.
176CAZYCE5CAZy family CE5CAZy sequence family; activity assignment from dbCAN.
177CAZYCE6CAZy family CE6CAZy sequence family; activity assignment from dbCAN.
178CAZYCE7CAZy family CE7CAZy sequence family; activity assignment from dbCAN.
179CAZYCE12CAZy family CE12CAZy sequence family; activity assignment from dbCAN.
180CAZYGH10_e0dbCAN-sub cluster GH10_e0dbCAN-sub eCAMI cluster of CAZy family GH10.
181CAZYGH10_e10dbCAN-sub cluster GH10_e10dbCAN-sub eCAMI cluster of CAZy family GH10.
182CAZYGH10_e101dbCAN-sub cluster GH10_e101dbCAN-sub eCAMI cluster of CAZy family GH10.
183CAZYGH10_e103dbCAN-sub cluster GH10_e103dbCAN-sub eCAMI cluster of CAZy family GH10.
184CAZYGH10_e105dbCAN-sub cluster GH10_e105dbCAN-sub eCAMI cluster of CAZy family GH10.
185CAZYGH10_e109dbCAN-sub cluster GH10_e109dbCAN-sub eCAMI cluster of CAZy family GH10.
186CAZYGH10_e112dbCAN-sub cluster GH10_e112dbCAN-sub eCAMI cluster of CAZy family GH10.
187CAZYGH10_e118dbCAN-sub cluster GH10_e118dbCAN-sub eCAMI cluster of CAZy family GH10.
188CAZYGH10_e12dbCAN-sub cluster GH10_e12dbCAN-sub eCAMI cluster of CAZy family GH10.
189CAZYGH10_e130dbCAN-sub cluster GH10_e130dbCAN-sub eCAMI cluster of CAZy family GH10.
190CAZYGH10_e134dbCAN-sub cluster GH10_e134dbCAN-sub eCAMI cluster of CAZy family GH10.
191CAZYGH10_e135dbCAN-sub cluster GH10_e135dbCAN-sub eCAMI cluster of CAZy family GH10.
192CAZYGH10_e137dbCAN-sub cluster GH10_e137dbCAN-sub eCAMI cluster of CAZy family GH10.
193CAZYGH10_e141dbCAN-sub cluster GH10_e141dbCAN-sub eCAMI cluster of CAZy family GH10.
194CAZYGH10_e143dbCAN-sub cluster GH10_e143dbCAN-sub eCAMI cluster of CAZy family GH10.
195CAZYGH10_e144dbCAN-sub cluster GH10_e144dbCAN-sub eCAMI cluster of CAZy family GH10.
196CAZYGH10_e148dbCAN-sub cluster GH10_e148dbCAN-sub eCAMI cluster of CAZy family GH10.
197CAZYGH10_e170dbCAN-sub cluster GH10_e170dbCAN-sub eCAMI cluster of CAZy family GH10.
198CAZYGH10_e188dbCAN-sub cluster GH10_e188dbCAN-sub eCAMI cluster of CAZy family GH10.
199CAZYGH10_e19dbCAN-sub cluster GH10_e19dbCAN-sub eCAMI cluster of CAZy family GH10.
200CAZYGH10_e191dbCAN-sub cluster GH10_e191dbCAN-sub eCAMI cluster of CAZy family GH10.
201CAZYGH10_e20dbCAN-sub cluster GH10_e20dbCAN-sub eCAMI cluster of CAZy family GH10.
202CAZYGH10_e204dbCAN-sub cluster GH10_e204dbCAN-sub eCAMI cluster of CAZy family GH10.
203CAZYGH10_e21dbCAN-sub cluster GH10_e21dbCAN-sub eCAMI cluster of CAZy family GH10.
204CAZYGH10_e225dbCAN-sub cluster GH10_e225dbCAN-sub eCAMI cluster of CAZy family GH10.
205CAZYGH10_e25dbCAN-sub cluster GH10_e25dbCAN-sub eCAMI cluster of CAZy family GH10.
206CAZYGH10_e250dbCAN-sub cluster GH10_e250dbCAN-sub eCAMI cluster of CAZy family GH10.
207CAZYGH10_e3dbCAN-sub cluster GH10_e3dbCAN-sub eCAMI cluster of CAZy family GH10.
208CAZYGH10_e30dbCAN-sub cluster GH10_e30dbCAN-sub eCAMI cluster of CAZy family GH10.
209CAZYGH10_e38dbCAN-sub cluster GH10_e38dbCAN-sub eCAMI cluster of CAZy family GH10.
210CAZYGH10_e40dbCAN-sub cluster GH10_e40dbCAN-sub eCAMI cluster of CAZy family GH10.
211CAZYGH10_e43dbCAN-sub cluster GH10_e43dbCAN-sub eCAMI cluster of CAZy family GH10.
212CAZYGH10_e5dbCAN-sub cluster GH10_e5dbCAN-sub eCAMI cluster of CAZy family GH10.
213CAZYGH10_e50dbCAN-sub cluster GH10_e50dbCAN-sub eCAMI cluster of CAZy family GH10.
214CAZYGH10_e52dbCAN-sub cluster GH10_e52dbCAN-sub eCAMI cluster of CAZy family GH10.
215CAZYGH10_e53dbCAN-sub cluster GH10_e53dbCAN-sub eCAMI cluster of CAZy family GH10.
216CAZYGH10_e58dbCAN-sub cluster GH10_e58dbCAN-sub eCAMI cluster of CAZy family GH10.
217CAZYGH10_e6dbCAN-sub cluster GH10_e6dbCAN-sub eCAMI cluster of CAZy family GH10.
218CAZYGH10_e60dbCAN-sub cluster GH10_e60dbCAN-sub eCAMI cluster of CAZy family GH10.
219CAZYGH10_e64dbCAN-sub cluster GH10_e64dbCAN-sub eCAMI cluster of CAZy family GH10.
220CAZYGH10_e67dbCAN-sub cluster GH10_e67dbCAN-sub eCAMI cluster of CAZy family GH10.
221CAZYGH10_e75dbCAN-sub cluster GH10_e75dbCAN-sub eCAMI cluster of CAZy family GH10.
222CAZYGH10_e77dbCAN-sub cluster GH10_e77dbCAN-sub eCAMI cluster of CAZy family GH10.
223CAZYGH10_e78dbCAN-sub cluster GH10_e78dbCAN-sub eCAMI cluster of CAZy family GH10.
224CAZYGH10_e8dbCAN-sub cluster GH10_e8dbCAN-sub eCAMI cluster of CAZy family GH10.
225CAZYGH10_e83dbCAN-sub cluster GH10_e83dbCAN-sub eCAMI cluster of CAZy family GH10.
226CAZYGH10_e85dbCAN-sub cluster GH10_e85dbCAN-sub eCAMI cluster of CAZy family GH10.
227CAZYGH10_e88dbCAN-sub cluster GH10_e88dbCAN-sub eCAMI cluster of CAZy family GH10.
228CAZYGH10_e90dbCAN-sub cluster GH10_e90dbCAN-sub eCAMI cluster of CAZy family GH10.
229CAZYGH10_e96dbCAN-sub cluster GH10_e96dbCAN-sub eCAMI cluster of CAZy family GH10.
230CAZYGH10_e97dbCAN-sub cluster GH10_e97dbCAN-sub eCAMI cluster of CAZy family GH10.
231CAZYGH10_e98dbCAN-sub cluster GH10_e98dbCAN-sub eCAMI cluster of CAZy family GH10.
232CAZYGH11_e0dbCAN-sub cluster GH11_e0dbCAN-sub eCAMI cluster of CAZy family GH11.
233CAZYGH11_e10dbCAN-sub cluster GH11_e10dbCAN-sub eCAMI cluster of CAZy family GH11.
234CAZYGH11_e11dbCAN-sub cluster GH11_e11dbCAN-sub eCAMI cluster of CAZy family GH11.
235CAZYGH11_e13dbCAN-sub cluster GH11_e13dbCAN-sub eCAMI cluster of CAZy family GH11.
236CAZYGH11_e14dbCAN-sub cluster GH11_e14dbCAN-sub eCAMI cluster of CAZy family GH11.
237CAZYGH11_e15dbCAN-sub cluster GH11_e15dbCAN-sub eCAMI cluster of CAZy family GH11.
238CAZYGH11_e16dbCAN-sub cluster GH11_e16dbCAN-sub eCAMI cluster of CAZy family GH11.
239CAZYGH11_e17dbCAN-sub cluster GH11_e17dbCAN-sub eCAMI cluster of CAZy family GH11.
240CAZYGH11_e2dbCAN-sub cluster GH11_e2dbCAN-sub eCAMI cluster of CAZy family GH11.
241CAZYGH11_e20dbCAN-sub cluster GH11_e20dbCAN-sub eCAMI cluster of CAZy family GH11.
242CAZYGH11_e22dbCAN-sub cluster GH11_e22dbCAN-sub eCAMI cluster of CAZy family GH11.
243CAZYGH11_e23dbCAN-sub cluster GH11_e23dbCAN-sub eCAMI cluster of CAZy family GH11.
244CAZYGH11_e24dbCAN-sub cluster GH11_e24dbCAN-sub eCAMI cluster of CAZy family GH11.
245CAZYGH11_e39dbCAN-sub cluster GH11_e39dbCAN-sub eCAMI cluster of CAZy family GH11.
246CAZYGH11_e42dbCAN-sub cluster GH11_e42dbCAN-sub eCAMI cluster of CAZy family GH11.
247CAZYGH11_e5dbCAN-sub cluster GH11_e5dbCAN-sub eCAMI cluster of CAZy family GH11.
248CAZYGH11_e7dbCAN-sub cluster GH11_e7dbCAN-sub eCAMI cluster of CAZy family GH11.
249CAZYGH11_e8dbCAN-sub cluster GH11_e8dbCAN-sub eCAMI cluster of CAZy family GH11.
250CAZYGH16_e14dbCAN-sub cluster GH16_e14dbCAN-sub eCAMI cluster of CAZy family GH16.
251CAZYGH26_e54dbCAN-sub cluster GH26_e54dbCAN-sub eCAMI cluster of CAZy family GH26.
252CAZYGH30_e138dbCAN-sub cluster GH30_e138dbCAN-sub eCAMI cluster of CAZy family GH30.
253CAZYGH30_e145dbCAN-sub cluster GH30_e145dbCAN-sub eCAMI cluster of CAZy family GH30.
254CAZYGH30_e48dbCAN-sub cluster GH30_e48dbCAN-sub eCAMI cluster of CAZy family GH30.
255CAZYGH30_e78dbCAN-sub cluster GH30_e78dbCAN-sub eCAMI cluster of CAZy family GH30.
256CAZYGH43_e261dbCAN-sub cluster GH43_e261dbCAN-sub eCAMI cluster of CAZy family GH43.
257CAZYGH5_e130dbCAN-sub cluster GH5_e130dbCAN-sub eCAMI cluster of CAZy family GH5.
258CAZYGH5_e141dbCAN-sub cluster GH5_e141dbCAN-sub eCAMI cluster of CAZy family GH5.
259CAZYGH5_e243dbCAN-sub cluster GH5_e243dbCAN-sub eCAMI cluster of CAZy family GH5.
260CAZYGH5_e29dbCAN-sub cluster GH5_e29dbCAN-sub eCAMI cluster of CAZy family GH5.
261CAZYGH5_e319dbCAN-sub cluster GH5_e319dbCAN-sub eCAMI cluster of CAZy family GH5.
262CAZYGH5_e55dbCAN-sub cluster GH5_e55dbCAN-sub eCAMI cluster of CAZy family GH5.
263CAZYGH5_e77dbCAN-sub cluster GH5_e77dbCAN-sub eCAMI cluster of CAZy family GH5.
264CAZYGH51_e9dbCAN-sub cluster GH51_e9dbCAN-sub eCAMI cluster of CAZy family GH51.
265CAZYGH8_e19dbCAN-sub cluster GH8_e19dbCAN-sub eCAMI cluster of CAZy family GH8.
266CAZYGH8_e37dbCAN-sub cluster GH8_e37dbCAN-sub eCAMI cluster of CAZy family GH8.
267CAZYGH8_e9dbCAN-sub cluster GH8_e9dbCAN-sub eCAMI cluster of CAZy family GH8.
268CAZYGH9_e16dbCAN-sub cluster GH9_e16dbCAN-sub eCAMI cluster of CAZy family GH9.
269CAZYGH98_e0dbCAN-sub cluster GH98_e0dbCAN-sub eCAMI cluster of CAZy family GH98.
270CAZYGH120_e0dbCAN-sub cluster GH120_e0dbCAN-sub eCAMI cluster of CAZy family GH120.
271CAZYGH3_e0dbCAN-sub cluster GH3_e0dbCAN-sub eCAMI cluster of CAZy family GH3.
272CAZYGH3_e165dbCAN-sub cluster GH3_e165dbCAN-sub eCAMI cluster of CAZy family GH3.
273CAZYGH3_e21dbCAN-sub cluster GH3_e21dbCAN-sub eCAMI cluster of CAZy family GH3.
274CAZYGH3_e32dbCAN-sub cluster GH3_e32dbCAN-sub eCAMI cluster of CAZy family GH3.
275CAZYGH3_e50dbCAN-sub cluster GH3_e50dbCAN-sub eCAMI cluster of CAZy family GH3.
276CAZYGH3_e73dbCAN-sub cluster GH3_e73dbCAN-sub eCAMI cluster of CAZy family GH3.
277CAZYGH3_e88dbCAN-sub cluster GH3_e88dbCAN-sub eCAMI cluster of CAZy family GH3.
278CAZYGH39_e131dbCAN-sub cluster GH39_e131dbCAN-sub eCAMI cluster of CAZy family GH39.
279CAZYGH39_e264dbCAN-sub cluster GH39_e264dbCAN-sub eCAMI cluster of CAZy family GH39.
280CAZYGH39_e57dbCAN-sub cluster GH39_e57dbCAN-sub eCAMI cluster of CAZy family GH39.
281CAZYGH39_e74dbCAN-sub cluster GH39_e74dbCAN-sub eCAMI cluster of CAZy family GH39.
282CAZYGH43_e264dbCAN-sub cluster GH43_e264dbCAN-sub eCAMI cluster of CAZy family GH43.
283CAZYGH43_e285dbCAN-sub cluster GH43_e285dbCAN-sub eCAMI cluster of CAZy family GH43.
284CAZYGH43_e330dbCAN-sub cluster GH43_e330dbCAN-sub eCAMI cluster of CAZy family GH43.
285CAZYGH43_e398dbCAN-sub cluster GH43_e398dbCAN-sub eCAMI cluster of CAZy family GH43.
286CAZYGH43_e459dbCAN-sub cluster GH43_e459dbCAN-sub eCAMI cluster of CAZy family GH43.
287CAZYGH43_e53dbCAN-sub cluster GH43_e53dbCAN-sub eCAMI cluster of CAZy family GH43.
288CAZYGH43_e59dbCAN-sub cluster GH43_e59dbCAN-sub eCAMI cluster of CAZy family GH43.
289CAZYGH43_e67dbCAN-sub cluster GH43_e67dbCAN-sub eCAMI cluster of CAZy family GH43.
290CAZYGH5_e288dbCAN-sub cluster GH5_e288dbCAN-sub eCAMI cluster of CAZy family GH5.
291CAZYGH51_e4dbCAN-sub cluster GH51_e4dbCAN-sub eCAMI cluster of CAZy family GH51.
292CAZYGH52_e0dbCAN-sub cluster GH52_e0dbCAN-sub eCAMI cluster of CAZy family GH52.
293CAZYGH43_e0dbCAN-sub cluster GH43_e0dbCAN-sub eCAMI cluster of CAZy family GH43.
294CAZYGH43_e118dbCAN-sub cluster GH43_e118dbCAN-sub eCAMI cluster of CAZy family GH43.
295CAZYGH43_e124dbCAN-sub cluster GH43_e124dbCAN-sub eCAMI cluster of CAZy family GH43.
296CAZYGH43_e159dbCAN-sub cluster GH43_e159dbCAN-sub eCAMI cluster of CAZy family GH43.
297CAZYGH43_e173dbCAN-sub cluster GH43_e173dbCAN-sub eCAMI cluster of CAZy family GH43.
298CAZYGH43_e188dbCAN-sub cluster GH43_e188dbCAN-sub eCAMI cluster of CAZy family GH43.
299CAZYGH43_e194dbCAN-sub cluster GH43_e194dbCAN-sub eCAMI cluster of CAZy family GH43.
300CAZYGH43_e2dbCAN-sub cluster GH43_e2dbCAN-sub eCAMI cluster of CAZy family GH43.
301CAZYGH43_e239dbCAN-sub cluster GH43_e239dbCAN-sub eCAMI cluster of CAZy family GH43.
302CAZYGH43_e259dbCAN-sub cluster GH43_e259dbCAN-sub eCAMI cluster of CAZy family GH43.
303CAZYGH43_e311dbCAN-sub cluster GH43_e311dbCAN-sub eCAMI cluster of CAZy family GH43.
304CAZYGH43_e327dbCAN-sub cluster GH43_e327dbCAN-sub eCAMI cluster of CAZy family GH43.
305CAZYGH43_e429dbCAN-sub cluster GH43_e429dbCAN-sub eCAMI cluster of CAZy family GH43.
306CAZYGH43_e52dbCAN-sub cluster GH43_e52dbCAN-sub eCAMI cluster of CAZy family GH43.
307CAZYGH43_e532dbCAN-sub cluster GH43_e532dbCAN-sub eCAMI cluster of CAZy family GH43.
308CAZYGH43_e79dbCAN-sub cluster GH43_e79dbCAN-sub eCAMI cluster of CAZy family GH43.
309CAZYGH43_e84dbCAN-sub cluster GH43_e84dbCAN-sub eCAMI cluster of CAZy family GH43.
310CAZYGH51_e0dbCAN-sub cluster GH51_e0dbCAN-sub eCAMI cluster of CAZy family GH51.
311CAZYGH51_e1dbCAN-sub cluster GH51_e1dbCAN-sub eCAMI cluster of CAZy family GH51.
312CAZYGH51_e19dbCAN-sub cluster GH51_e19dbCAN-sub eCAMI cluster of CAZy family GH51.
313CAZYGH51_e26dbCAN-sub cluster GH51_e26dbCAN-sub eCAMI cluster of CAZy family GH51.
314CAZYGH51_e31dbCAN-sub cluster GH51_e31dbCAN-sub eCAMI cluster of CAZy family GH51.
315CAZYGH51_e34dbCAN-sub cluster GH51_e34dbCAN-sub eCAMI cluster of CAZy family GH51.
316CAZYGH51_e35dbCAN-sub cluster GH51_e35dbCAN-sub eCAMI cluster of CAZy family GH51.
317CAZYGH51_e36dbCAN-sub cluster GH51_e36dbCAN-sub eCAMI cluster of CAZy family GH51.
318CAZYGH51_e47dbCAN-sub cluster GH51_e47dbCAN-sub eCAMI cluster of CAZy family GH51.
319CAZYGH51_e51dbCAN-sub cluster GH51_e51dbCAN-sub eCAMI cluster of CAZy family GH51.
320CAZYGH51_e65dbCAN-sub cluster GH51_e65dbCAN-sub eCAMI cluster of CAZy family GH51.
321CAZYGH54_e0dbCAN-sub cluster GH54_e0dbCAN-sub eCAMI cluster of CAZy family GH54.
322CAZYGH62_e0dbCAN-sub cluster GH62_e0dbCAN-sub eCAMI cluster of CAZy family GH62.
323CAZYGH62_e1dbCAN-sub cluster GH62_e1dbCAN-sub eCAMI cluster of CAZy family GH62.
324CAZYGH62_e9dbCAN-sub cluster GH62_e9dbCAN-sub eCAMI cluster of CAZy family GH62.
325CAZYGH119_e2dbCAN-sub cluster GH119_e2dbCAN-sub eCAMI cluster of CAZy family GH119.
326CAZYGH13_e124dbCAN-sub cluster GH13_e124dbCAN-sub eCAMI cluster of CAZy family GH13.
327CAZYGH13_e13dbCAN-sub cluster GH13_e13dbCAN-sub eCAMI cluster of CAZy family GH13.
328CAZYGH13_e139dbCAN-sub cluster GH13_e139dbCAN-sub eCAMI cluster of CAZy family GH13.
329CAZYGH13_e143dbCAN-sub cluster GH13_e143dbCAN-sub eCAMI cluster of CAZy family GH13.
330CAZYGH13_e146dbCAN-sub cluster GH13_e146dbCAN-sub eCAMI cluster of CAZy family GH13.
331CAZYGH13_e160dbCAN-sub cluster GH13_e160dbCAN-sub eCAMI cluster of CAZy family GH13.
332CAZYGH13_e172dbCAN-sub cluster GH13_e172dbCAN-sub eCAMI cluster of CAZy family GH13.
333CAZYGH13_e173dbCAN-sub cluster GH13_e173dbCAN-sub eCAMI cluster of CAZy family GH13.
334CAZYGH13_e18dbCAN-sub cluster GH13_e18dbCAN-sub eCAMI cluster of CAZy family GH13.
335CAZYGH13_e183dbCAN-sub cluster GH13_e183dbCAN-sub eCAMI cluster of CAZy family GH13.
336CAZYGH13_e19dbCAN-sub cluster GH13_e19dbCAN-sub eCAMI cluster of CAZy family GH13.
337CAZYGH13_e205dbCAN-sub cluster GH13_e205dbCAN-sub eCAMI cluster of CAZy family GH13.
338CAZYGH13_e206dbCAN-sub cluster GH13_e206dbCAN-sub eCAMI cluster of CAZy family GH13.
339CAZYGH13_e23dbCAN-sub cluster GH13_e23dbCAN-sub eCAMI cluster of CAZy family GH13.
340CAZYGH13_e240dbCAN-sub cluster GH13_e240dbCAN-sub eCAMI cluster of CAZy family GH13.
341CAZYGH13_e245dbCAN-sub cluster GH13_e245dbCAN-sub eCAMI cluster of CAZy family GH13.
342CAZYGH13_e248dbCAN-sub cluster GH13_e248dbCAN-sub eCAMI cluster of CAZy family GH13.
343CAZYGH13_e25dbCAN-sub cluster GH13_e25dbCAN-sub eCAMI cluster of CAZy family GH13.
344CAZYGH13_e302dbCAN-sub cluster GH13_e302dbCAN-sub eCAMI cluster of CAZy family GH13.
345CAZYGH13_e303dbCAN-sub cluster GH13_e303dbCAN-sub eCAMI cluster of CAZy family GH13.
346CAZYGH13_e307dbCAN-sub cluster GH13_e307dbCAN-sub eCAMI cluster of CAZy family GH13.
347CAZYGH13_e329dbCAN-sub cluster GH13_e329dbCAN-sub eCAMI cluster of CAZy family GH13.
348CAZYGH13_e34dbCAN-sub cluster GH13_e34dbCAN-sub eCAMI cluster of CAZy family GH13.
349CAZYGH13_e345dbCAN-sub cluster GH13_e345dbCAN-sub eCAMI cluster of CAZy family GH13.
350CAZYGH13_e346dbCAN-sub cluster GH13_e346dbCAN-sub eCAMI cluster of CAZy family GH13.
351CAZYGH13_e348dbCAN-sub cluster GH13_e348dbCAN-sub eCAMI cluster of CAZy family GH13.
352CAZYGH13_e354dbCAN-sub cluster GH13_e354dbCAN-sub eCAMI cluster of CAZy family GH13.
353CAZYGH13_e380dbCAN-sub cluster GH13_e380dbCAN-sub eCAMI cluster of CAZy family GH13.
354CAZYGH13_e381dbCAN-sub cluster GH13_e381dbCAN-sub eCAMI cluster of CAZy family GH13.
355CAZYGH13_e386dbCAN-sub cluster GH13_e386dbCAN-sub eCAMI cluster of CAZy family GH13.
356CAZYGH13_e387dbCAN-sub cluster GH13_e387dbCAN-sub eCAMI cluster of CAZy family GH13.
357CAZYGH13_e389dbCAN-sub cluster GH13_e389dbCAN-sub eCAMI cluster of CAZy family GH13.
358CAZYGH13_e406dbCAN-sub cluster GH13_e406dbCAN-sub eCAMI cluster of CAZy family GH13.
359CAZYGH13_e409dbCAN-sub cluster GH13_e409dbCAN-sub eCAMI cluster of CAZy family GH13.
360CAZYGH13_e413dbCAN-sub cluster GH13_e413dbCAN-sub eCAMI cluster of CAZy family GH13.
361CAZYGH13_e419dbCAN-sub cluster GH13_e419dbCAN-sub eCAMI cluster of CAZy family GH13.
362CAZYGH13_e42dbCAN-sub cluster GH13_e42dbCAN-sub eCAMI cluster of CAZy family GH13.
363CAZYGH13_e443dbCAN-sub cluster GH13_e443dbCAN-sub eCAMI cluster of CAZy family GH13.
364CAZYGH13_e446dbCAN-sub cluster GH13_e446dbCAN-sub eCAMI cluster of CAZy family GH13.
365CAZYGH13_e462dbCAN-sub cluster GH13_e462dbCAN-sub eCAMI cluster of CAZy family GH13.
366CAZYGH13_e465dbCAN-sub cluster GH13_e465dbCAN-sub eCAMI cluster of CAZy family GH13.
367CAZYGH13_e47dbCAN-sub cluster GH13_e47dbCAN-sub eCAMI cluster of CAZy family GH13.
368CAZYGH13_e484dbCAN-sub cluster GH13_e484dbCAN-sub eCAMI cluster of CAZy family GH13.
369CAZYGH13_e486dbCAN-sub cluster GH13_e486dbCAN-sub eCAMI cluster of CAZy family GH13.
370CAZYGH13_e491dbCAN-sub cluster GH13_e491dbCAN-sub eCAMI cluster of CAZy family GH13.
371CAZYGH13_e493dbCAN-sub cluster GH13_e493dbCAN-sub eCAMI cluster of CAZy family GH13.
372CAZYGH13_e497dbCAN-sub cluster GH13_e497dbCAN-sub eCAMI cluster of CAZy family GH13.
373CAZYGH13_e5dbCAN-sub cluster GH13_e5dbCAN-sub eCAMI cluster of CAZy family GH13.
374CAZYGH13_e500dbCAN-sub cluster GH13_e500dbCAN-sub eCAMI cluster of CAZy family GH13.
375CAZYGH13_e61dbCAN-sub cluster GH13_e61dbCAN-sub eCAMI cluster of CAZy family GH13.
376CAZYGH14_e6dbCAN-sub cluster GH14_e6dbCAN-sub eCAMI cluster of CAZy family GH14.
377CAZYGH57_e11dbCAN-sub cluster GH57_e11dbCAN-sub eCAMI cluster of CAZy family GH57.
378CAZYGH57_e15dbCAN-sub cluster GH57_e15dbCAN-sub eCAMI cluster of CAZy family GH57.
379CAZYGH57_e30dbCAN-sub cluster GH57_e30dbCAN-sub eCAMI cluster of CAZy family GH57.
380CAZYGH57_e63dbCAN-sub cluster GH57_e63dbCAN-sub eCAMI cluster of CAZy family GH57.
381CAZYGH13_e113dbCAN-sub cluster GH13_e113dbCAN-sub eCAMI cluster of CAZy family GH13.
382CAZYGH13_e122dbCAN-sub cluster GH13_e122dbCAN-sub eCAMI cluster of CAZy family GH13.
383CAZYGH13_e221dbCAN-sub cluster GH13_e221dbCAN-sub eCAMI cluster of CAZy family GH13.
384CAZYGH13_e234dbCAN-sub cluster GH13_e234dbCAN-sub eCAMI cluster of CAZy family GH13.
385CAZYGH13_e250dbCAN-sub cluster GH13_e250dbCAN-sub eCAMI cluster of CAZy family GH13.
386CAZYGH13_e276dbCAN-sub cluster GH13_e276dbCAN-sub eCAMI cluster of CAZy family GH13.
387CAZYGH13_e347dbCAN-sub cluster GH13_e347dbCAN-sub eCAMI cluster of CAZy family GH13.
388CAZYGH13_e392dbCAN-sub cluster GH13_e392dbCAN-sub eCAMI cluster of CAZy family GH13.
389CAZYGH31_e102dbCAN-sub cluster GH31_e102dbCAN-sub eCAMI cluster of CAZy family GH31.
390CAZYGH31_e177dbCAN-sub cluster GH31_e177dbCAN-sub eCAMI cluster of CAZy family GH31.
391CAZYGH31_e22dbCAN-sub cluster GH31_e22dbCAN-sub eCAMI cluster of CAZy family GH31.
392CAZYGH31_e39dbCAN-sub cluster GH31_e39dbCAN-sub eCAMI cluster of CAZy family GH31.
393CAZYGH31_e41dbCAN-sub cluster GH31_e41dbCAN-sub eCAMI cluster of CAZy family GH31.
394CAZYGH31_e42dbCAN-sub cluster GH31_e42dbCAN-sub eCAMI cluster of CAZy family GH31.
395CAZYGH31_e56dbCAN-sub cluster GH31_e56dbCAN-sub eCAMI cluster of CAZy family GH31.
396CAZYGH31_e7dbCAN-sub cluster GH31_e7dbCAN-sub eCAMI cluster of CAZy family GH31.
397CAZYGH31_e73dbCAN-sub cluster GH31_e73dbCAN-sub eCAMI cluster of CAZy family GH31.
398CAZYGH31_e78dbCAN-sub cluster GH31_e78dbCAN-sub eCAMI cluster of CAZy family GH31.
399CAZYGH31_e82dbCAN-sub cluster GH31_e82dbCAN-sub eCAMI cluster of CAZy family GH31.
400CAZYGH4_e14dbCAN-sub cluster GH4_e14dbCAN-sub eCAMI cluster of CAZy family GH4.
401CAZYGH4_e6dbCAN-sub cluster GH4_e6dbCAN-sub eCAMI cluster of CAZy family GH4.
402CAZYGH63_e1dbCAN-sub cluster GH63_e1dbCAN-sub eCAMI cluster of CAZy family GH63.
403CAZYGH97_e22dbCAN-sub cluster GH97_e22dbCAN-sub eCAMI cluster of CAZy family GH97.
404CAZYGH13_e108dbCAN-sub cluster GH13_e108dbCAN-sub eCAMI cluster of CAZy family GH13.
405CAZYGH13_e130dbCAN-sub cluster GH13_e130dbCAN-sub eCAMI cluster of CAZy family GH13.
406CAZYGH13_e165dbCAN-sub cluster GH13_e165dbCAN-sub eCAMI cluster of CAZy family GH13.
407CAZYGH13_e180dbCAN-sub cluster GH13_e180dbCAN-sub eCAMI cluster of CAZy family GH13.
408CAZYGH13_e278dbCAN-sub cluster GH13_e278dbCAN-sub eCAMI cluster of CAZy family GH13.
409CAZYGH13_e300dbCAN-sub cluster GH13_e300dbCAN-sub eCAMI cluster of CAZy family GH13.
410CAZYGH13_e315dbCAN-sub cluster GH13_e315dbCAN-sub eCAMI cluster of CAZy family GH13.
411CAZYGH13_e349dbCAN-sub cluster GH13_e349dbCAN-sub eCAMI cluster of CAZy family GH13.
412CAZYGH13_e94dbCAN-sub cluster GH13_e94dbCAN-sub eCAMI cluster of CAZy family GH13.
413CAZYCE1_e20dbCAN-sub cluster CE1_e20dbCAN-sub eCAMI cluster of CAZy family CE1.
414CAZYCE1_e4dbCAN-sub cluster CE1_e4dbCAN-sub eCAMI cluster of CAZy family CE1.
415CAZYCE12_e45dbCAN-sub cluster CE12_e45dbCAN-sub eCAMI cluster of CAZy family CE12.
416CAZYCE4_e262dbCAN-sub cluster CE4_e262dbCAN-sub eCAMI cluster of CAZy family CE4.
417CAZYCE4_e58dbCAN-sub cluster CE4_e58dbCAN-sub eCAMI cluster of CAZy family CE4.
418CAZYCE5_e24dbCAN-sub cluster CE5_e24dbCAN-sub eCAMI cluster of CAZy family CE5.
419CAZYCE6_e2dbCAN-sub cluster CE6_e2dbCAN-sub eCAMI cluster of CAZy family CE6.
420CAZYCE6_e3dbCAN-sub cluster CE6_e3dbCAN-sub eCAMI cluster of CAZy family CE6.
421CAZYCE7_e11dbCAN-sub cluster CE7_e11dbCAN-sub eCAMI cluster of CAZy family CE7.
422CAZYCE7_e23dbCAN-sub cluster CE7_e23dbCAN-sub eCAMI cluster of CAZy family CE7.
423CAZYCE7_e33dbCAN-sub cluster CE7_e33dbCAN-sub eCAMI cluster of CAZy family CE7.
424KOK01387microbial collagenase orthologueKEGG orthology marker.
425PFAMPF01752Collagenase, peptidase family M9Pfam domain marker.
426KOK02387flagellar basal-body rod protein FlgBKEGG orthology marker.
427KOK02388flagellar basal-body rod protein FlgCKEGG orthology marker.
428KOK02390flagellar hook protein FlgEKEGG orthology marker.
429KOK02391flagellar basal-body rod protein FlgFKEGG orthology marker.
430KOK02392flagellar basal-body rod protein FlgGKEGG orthology marker.
431KOK02393flagellar L-ring protein FlgHKEGG orthology marker.
432KOK02394flagellar P-ring protein FlgIKEGG orthology marker.
433KOK02396flagellar hook-associated protein 1KEGG orthology marker.
434KOK02397flagellar hook-associated protein 3 FlgLKEGG orthology marker.
435KOK02400flagellar biosynthesis protein FlhAKEGG orthology marker.
436KOK02401flagellar biosynthesis protein FlhBKEGG orthology marker.
437KOK02406flagellinKEGG orthology marker.
438KOK02407flagellar hook-associated protein 2KEGG orthology marker.
439KOK02408flagellar hook-basal body complex protein FliEKEGG orthology marker.
440KOK02409flagellar M-ring protein FliFKEGG orthology marker.
441KOK02410flagellar motor switch protein FliGKEGG orthology marker.
442KOK02411flagellar assembly protein FliHKEGG orthology marker.
443KOK02412flagellum-specific ATP synthase [EC:7.4.2.8]KEGG orthology marker.
444KOK02416flagellar motor switch protein FliMKEGG orthology marker.
445KOK02417flagellar motor switch protein FliNKEGG orthology marker.
446KOK02419flagellar biosynthesis protein FliPKEGG orthology marker.
447KOK02420flagellar biosynthesis protein FliQKEGG orthology marker.
448KOK02421flagellar biosynthesis protein FliRKEGG orthology marker.
449KOK02556chemotaxis protein MotAKEGG orthology marker.
450KOK02557chemotaxis protein MotBKEGG orthology marker.
451KOK02650type IV pilus assembly protein PilAKEGG orthology marker.
452KOK02652type IV pilus assembly protein PilBKEGG orthology marker.
453KOK02653type IV pilus assembly protein PilCKEGG orthology marker.
454KOK02654leader peptidase (prepilin peptidase) / N-methyltransferase [EC:3.4.23.43 2.1.1.-]KEGG orthology marker.
455KOK02655type IV pilus assembly protein PilEKEGG orthology marker.
456KOK02656type IV pilus assembly protein PilFKEGG orthology marker.
457KOK02662type IV pilus assembly protein PilMKEGG orthology marker.
458KOK02663type IV pilus assembly protein PilNKEGG orthology marker.
459KOK02664type IV pilus assembly protein PilOKEGG orthology marker.
460KOK02665type IV pilus assembly protein PilPKEGG orthology marker.
461KOK02666type IV pilus assembly protein PilQKEGG orthology marker.
462KOK02669twitching motility protein PilTKEGG orthology marker.
463KOK13820flagellar biosynthesis protein FliR/FlhBKEGG orthology marker.
464KOK00575chemotaxis protein methyltransferase CheR [EC:2.1.1.80]KEGG orthology marker.
465KOK02036phosphate transport system ATP-binding protein [EC:7.3.2.1]KEGG orthology marker.
466KOK02037phosphate transport system permease proteinKEGG orthology marker.
467KOK02038phosphate transport system permease proteinKEGG orthology marker.
468KOK02039phosphate transport system proteinKEGG orthology marker.
469KOK02040phosphate transport system substrate-binding proteinKEGG orthology marker.
470KOK03406methyl-accepting chemotaxis proteinKEGG orthology marker.
471KOK03407two-component system, chemotaxis family, sensor kinase CheA [EC:2.7.13.3]KEGG orthology marker.
472KOK03408purine-binding chemotaxis protein CheWKEGG orthology marker.
473KOK03409chemotaxis protein CheXKEGG orthology marker.
474KOK03410chemotaxis protein CheCKEGG orthology marker.
475KOK03412two-component system, chemotaxis family, protein-glutamate methylesterase/glutaminase [EC:3.1.1.61 3.5.1.44]KEGG orthology marker.
476KOK03413two-component system, chemotaxis family, chemotaxis protein CheYKEGG orthology marker.
477KOK03414chemotaxis protein CheZKEGG orthology marker.
478KOK03776aerotaxis receptorKEGG orthology marker.
479KOK05874methyl-accepting chemotaxis protein I, serine sensor receptorKEGG orthology marker.
480KOK05875methyl-accepting chemotaxis protein II, aspartate sensor receptorKEGG orthology marker.
481KOK05876methyl-accepting chemotaxis protein III, ribose and galactose sensor receptorKEGG orthology marker.
482KOK05877methyl-accepting chemotaxis protein IV, peptide sensor receptorKEGG orthology marker.
483KOK07636two-component system, OmpR family, phosphate regulon sensor histidine kinase PhoR [EC:2.7.13.3]KEGG orthology marker.
484KOK07657two-component system, OmpR family, phosphate regulon response regulator PhoBKEGG orthology marker.
485KOK07658two-component system, OmpR family, alkaline phosphatase synthesis response regulator PhoPKEGG orthology marker.
486KOK01153type I restriction enzyme, R subunit [EC:3.1.21.3]KEGG orthology marker.
487KOK01154type I restriction enzyme, S subunit [EC:3.1.21.3]KEGG orthology marker.
488KOK03427type I restriction enzyme M protein [EC:2.1.1.72]KEGG orthology marker.
489KOK07012CRISPR-associated endonuclease/helicase Cas3 [EC:3.1.-.- 5.6.2.4]KEGG orthology marker.
490KOK09951CRISPR-associated protein Cas2KEGG orthology marker.
491KOK15342CRISP-associated protein Cas1KEGG orthology marker.
492KOK19046CRISPR system Cascade subunit CasBKEGG orthology marker.
493KOK19123CRISPR system Cascade subunit CasAKEGG orthology marker.
494KOK19124CRISPR system Cascade subunit CasCKEGG orthology marker.
495KOK19125CRISPR system Cascade subunit CasDKEGG orthology marker.
496KOK19126CRISPR system Cascade subunit CasEKEGG orthology marker.
497KOK00161pyruvate dehydrogenase E1 component subunit alphaKEGG orthology marker.
498KOK00162pyruvate dehydrogenase E1 component subunit betaKEGG orthology marker.
499KOK00163pyruvate dehydrogenase E1 componentKEGG orthology marker for the fused single-polypeptide E1.
500KOK00627pyruvate dehydrogenase E2 componentKEGG orthology marker.
501KOK00382dihydrolipoyl dehydrogenaseKEGG orthology marker shared with other 2-oxo acid dehydrogenase complexes.
502KOK00169pyruvate:ferredoxin oxidoreductase alpha subunitKEGG orthology marker.
503KOK00170pyruvate:ferredoxin oxidoreductase beta subunitKEGG orthology marker.
504KOK00171pyruvate:ferredoxin oxidoreductase delta subunitKEGG orthology marker.
505KOK00172pyruvate:ferredoxin oxidoreductase gamma subunitKEGG orthology marker.
506KOK03737pyruvate-ferredoxin/flavodoxin oxidoreductaseKEGG orthology marker for the fused NifJ-type protein.
507KOK00656formate C-acetyltransferaseKEGG orthology marker.
508KOK04069pyruvate formate-lyase activating enzymeKEGG orthology marker.
509KOK00625phosphate acetyltransferaseKEGG orthology marker.
510KOK13788phosphate acetyltransferaseKEGG orthology marker for a second phosphotransacetylase group.
511KOK15024putative phosphotransacetylaseKEGG orthology marker retained from KEGG M00579.
512KOK00925acetate kinaseKEGG orthology marker.
513KOK00626acetyl-CoA C-acetyltransferaseKEGG orthology marker; chain-length-generic thiolase.
514KOK000743-hydroxybutyryl-CoA dehydrogenaseKEGG orthology marker; the group also carries the phenylacetate and fatty acid beta-oxidation dehydrogenases.
515KOK01715short-chain-enoyl-CoA hydrataseKEGG orthology marker; chain-length-generic.
516KOK00248butyryl-CoA dehydrogenaseKEGG orthology marker; the group also carries the generic short-chain acyl-CoA dehydrogenase.
517TIGRFAMTIGR03948butyryl-CoA:acetate CoA-transferaseNCBIfam sequence family marker. Built around the characterised activity rather than the fold, and the only marker in any namespace that identifies the enzyme releasing butanoate rather than a generic CoA transfer.
518KOK00048lactaldehyde reductaseKEGG orthology marker.
519KOK01699propanediol dehydratase large subunitKEGG orthology marker.
520KOK13919propanediol dehydratase medium subunitKEGG orthology marker.
521KOK13920propanediol dehydratase small subunitKEGG orthology marker.
522KOK13922propionaldehyde dehydrogenaseKEGG orthology marker.
523KOK13923phosphate propanoyltransferaseKEGG orthology marker.
524KOK19697propionate kinase PduWKEGG orthology marker.
525KOK00932propionate kinase TdcDKEGG orthology marker.
526KOK01026propionate CoA-transferaseKEGG orthology marker.
527KOK20626lactoyl-CoA dehydratase alpha subunitKEGG orthology marker.
528KOK20627lactoyl-CoA dehydratase beta subunitKEGG orthology marker.
529KOK20143acryloyl-CoA reductaseKEGG orthology marker.
530KOK00016L-lactate dehydrogenaseKEGG orthology marker.
531KOK22373lactate racemaseKEGG orthology marker.
532KOK22212malolactic enzymeKEGG orthology marker.
533KOK01643citrate lyase alpha subunitKEGG orthology marker.
534KOK01644citrate lyase beta subunitKEGG orthology marker.
535KOK01646citrate lyase acyl-carrier subunitKEGG orthology marker.
536KOK01910citrate lyase ligaseKEGG orthology marker.
537KOK01571oxaloacetate decarboxylase alpha subunitKEGG orthology marker.
538KOK01003soluble oxaloacetate decarboxylaseKEGG orthology marker.
539KOK04072bifunctional acetaldehyde/alcohol dehydrogenaseKEGG orthology marker.
540KOK01652acetolactate synthase large subunitKEGG orthology marker.
541KOK01575acetolactate decarboxylaseKEGG orthology marker.
542KOK01497GTP cyclohydrolase IIKEGG orthology marker.
543KOK146523,4-dihydroxy 2-butanone 4-phosphate synthase / GTP cyclohydrolase IIKEGG orthology marker.
544KOK01498diaminohydroxyphosphoribosylaminopyrimidine deaminaseKEGG orthology marker.
545KOK11752diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductaseKEGG orthology marker.
546KOK000825-amino-6-(5-phosphoribosylamino)uracil reductaseKEGG orthology marker.
547KOK20861FMN hydrolase / 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphataseKEGG orthology marker.
548KOK20862FMN hydrolase / 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphataseKEGG orthology marker.
549KOK210635-amino-6-(5-phospho-D-ribitylamino)uracil phosphataseKEGG orthology marker.
550KOK210645-amino-6-(5-phospho-D-ribitylamino)uracil phosphataseKEGG orthology marker.
551KOK20860FMN hydrolase / 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphataseKEGG orthology marker.
552KOK028583,4-dihydroxy 2-butanone 4-phosphate synthaseKEGG orthology marker.
553KOK007946,7-dimethyl-8-ribityllumazine synthaseKEGG orthology marker.
554KOK00793riboflavin synthaseKEGG orthology marker.
555KOK01665para-aminobenzoate synthetase component IKEGG orthology marker.
556KOK13950para-aminobenzoate synthetaseKEGG orthology marker.
557KOK03342para-aminobenzoate synthetase / 4-amino-4-deoxychorismate lyaseKEGG orthology marker.
558KOK026194-amino-4-deoxychorismate lyaseKEGG orthology marker.
559KOK01495GTP cyclohydrolase IAKEGG orthology marker.
560KOK09007GTP cyclohydrolase IBKEGG orthology marker.
561KOK22391GTP cyclohydrolase IKEGG orthology marker.
562KOK08310dihydroneopterin triphosphate diphosphataseKEGG orthology marker.
563KOK19965dihydroneopterin triphosphate pyrophosphohydrolaseKEGG orthology marker.
564KOK016337,8-dihydroneopterin aldolase/epimerase/oxygenaseKEGG orthology marker.
565KOK13939dihydroneopterin aldolase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / dihydropteroate synthaseKEGG orthology marker.
566KOK13940dihydroneopterin aldolase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinaseKEGG orthology marker.
567KOK009502-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinaseKEGG orthology marker.
568KOK139412-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / dihydropteroate synthaseKEGG orthology marker.
569KOK00796dihydropteroate synthaseKEGG orthology marker.
570KOK11754dihydrofolate synthase / folylpolyglutamate synthaseKEGG orthology marker.
571KOK20457dihydrofolate synthaseKEGG orthology marker.
572KOK00287dihydrofolate reductaseKEGG orthology marker.
573KOK13998dihydrofolate reductase / thymidylate synthaseKEGG orthology marker.
574KOK03147phosphomethylpyrimidine synthaseKEGG orthology marker.
575KOK00941hydroxymethylpyrimidine/phosphomethylpyrimidine kinaseKEGG orthology marker.
576KOK14153hydroxymethylpyrimidine kinase / phosphomethylpyrimidine kinase / thiamine-phosphate diphosphorylaseKEGG orthology marker.
577KOK21219hydroxymethylpyrimidine kinase / phosphomethylpyrimidine kinase / thiamine-phosphate diphosphorylaseKEGG orthology marker.
578KOK031502-iminoacetate synthaseKEGG orthology marker.
579KOK03149thiazole synthaseKEGG orthology marker.
580KOK03153glycine oxidaseKEGG orthology marker.
581KOK00788thiamine-phosphate pyrophosphorylaseKEGG orthology marker.
582KOK00878hydroxyethylthiazole kinaseKEGG orthology marker.
583KOK006063-methyl-2-oxobutanoate hydroxymethyltransferaseKEGG orthology marker.
584KOK000772-dehydropantoate 2-reductaseKEGG orthology marker.
585KOK00053ketol-acid reductoisomeraseKEGG orthology marker.
586KOK01579aspartate 1-decarboxylaseKEGG orthology marker.
587KOK01918pantoate--beta-alanine ligaseKEGG orthology marker.
588KOK13799pantoate ligase / CMP/dCMP kinaseKEGG orthology marker.
589KOK06215pyridoxal 5'-phosphate synthase pdxS subunitKEGG orthology marker.
590KOK08681pyridoxal 5'-phosphate synthase pdxT subunitKEGG orthology marker.
591KOK03472D-erythrose 4-phosphate dehydrogenaseKEGG orthology marker.
592KOK03473erythronate-4-phosphate dehydrogenaseKEGG orthology marker.
593KOK000974-hydroxythreonine-4-phosphate dehydrogenaseKEGG orthology marker.
594KOK03474pyridoxine 5-phosphate synthaseKEGG orthology marker.
595KOK00275pyridoxamine 5'-phosphate oxidaseKEGG orthology marker.
596KOK006528-amino-7-oxononanoate synthaseKEGG orthology marker.
597KOK00833adenosylmethionine---8-amino-7-oxononanoate aminotransferaseKEGG orthology marker.
598KOK19562bifunctional dethiobiotin synthetase / spermidine---8-amino-7-oxononanoate transaminaseKEGG orthology marker.
599KOK01935dethiobiotin synthetaseKEGG orthology marker.
600KOK01012biotin synthaseKEGG orthology marker.
601KOK19563lysine---8-amino-7-oxononanoate aminotransferaseKEGG orthology marker.
602KOK00278L-aspartate oxidaseKEGG orthology marker.
603KOK03517quinolinate synthaseKEGG orthology marker.
604KOK06989aspartate dehydrogenaseKEGG orthology marker.
605KOK00767nicotinate-nucleotide pyrophosphorylase (carboxylating)KEGG orthology marker.
606KOK00969nicotinate-nucleotide adenylyltransferaseKEGG orthology marker.
607KOK06210nicotinamide mononucleotide adenylyltransferaseKEGG orthology marker.
608KOK01916NAD+ synthaseKEGG orthology marker.
609KOK01950NAD+ synthase (glutamine-hydrolysing)KEGG orthology marker.
610KOK00763nicotinate phosphoribosyltransferaseKEGG orthology marker.
611KOK02303uroporphyrin-III C-methyltransferaseKEGG orthology marker.
612KOK13542uroporphyrinogen III methyltransferase / synthaseKEGG orthology marker.
613KOK02302uroporphyrin-III C-methyltransferase / precorrin-2 dehydrogenase / sirohydrochlorin ferrochelataseKEGG orthology marker.
614KOK02304precorrin-2 dehydrogenase / sirohydrochlorin ferrochelataseKEGG orthology marker.
615KOK24866precorrin-2 dehydrogenaseKEGG orthology marker.
616KOK02190sirohydrochlorin cobaltochelataseKEGG orthology marker.
617KOK03795sirohydrochlorin cobaltochelataseKEGG orthology marker.
618KOK22011sirohydrochlorin cobalto/nickelchelataseKEGG orthology marker.
619KOK03394precorrin-2/cobalt-factor-2 C20-methyltransferaseKEGG orthology marker.
620KOK05934precorrin-3B C17-methyltransferase / cobalt-factor III methyltransferaseKEGG orthology marker.
621KOK13541cobalt-precorrin 5A hydrolase / cobalt-factor III methyltransferase / precorrin-3B C17-methyltransferaseKEGG orthology marker.
622KOK21479cobalt-factor III methyltransferaseKEGG orthology marker.
623KOK05936precorrin-4/cobalt-precorrin-4 C11-methyltransferaseKEGG orthology marker.
624KOK02189cobalt-precorrin 5A hydrolaseKEGG orthology marker.
625KOK02188cobalt-precorrin-5B (C1)-methyltransferaseKEGG orthology marker.
626KOK05895precorrin-6A/cobalt-precorrin-6A reductaseKEGG orthology marker.
627KOK02191cobalt-precorrin-6B (C15)-methyltransferaseKEGG orthology marker.
628KOK00595precorrin-6B C5,15-methyltransferase / cobalt-precorrin-6B C5,C15-methyltransferaseKEGG orthology marker.
629KOK03399cobalt-precorrin-7 (C5)-methyltransferaseKEGG orthology marker.
630KOK06042precorrin-8X/cobalt-precorrin-8 methylmutaseKEGG orthology marker.
631KOK02224cobyrinic acid a,c-diamide synthaseKEGG orthology marker.
632KOK13540precorrin-2 C20-methyltransferase / precorrin-3B C17-methyltransferaseKEGG orthology marker.
633KOK02229precorrin-3B synthaseKEGG orthology marker.
634KOK02228precorrin-6A synthaseKEGG orthology marker.
635KOK02230cobaltochelatase CobNKEGG orthology marker.
636KOK09882cobaltochelatase CobSKEGG orthology marker.
637KOK09883cobaltochelatase CobTKEGG orthology marker.
638KOK00798cob(I)alamin adenosyltransferaseKEGG orthology marker.
639KOK19221cob(I)alamin adenosyltransferaseKEGG orthology marker.
640KOK02232adenosylcobyric acid synthaseKEGG orthology marker.
641KOK02227adenosylcobinamide-phosphate synthaseKEGG orthology marker.
642KOK02225cobalamin biosynthesis protein CobCKEGG orthology marker.
643KOK02231adenosylcobinamide kinase / adenosylcobinamide-phosphate guanylyltransferaseKEGG orthology marker.
644KOK19712adenosylcobinamide-phosphate guanylyltransferaseKEGG orthology marker.
645KOK00768nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferaseKEGG orthology marker.
646KOK02226alpha-ribazole phosphataseKEGG orthology marker.
647KOK22316ribonuclease H / adenosylcobalamin/alpha-ribazole phosphataseKEGG orthology marker.
648KOK02233adenosylcobinamide-GDP ribazoletransferaseKEGG orthology marker.
649KOK047195,6-dimethylbenzimidazole synthaseKEGG orthology marker.
650KOK02552menaquinone-specific isochorismate synthaseKEGG orthology marker.
651KOK02361isochorismate synthaseKEGG orthology marker.
652KOK025512-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthaseKEGG orthology marker.
653KOK086802-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthaseKEGG orthology marker.
654KOK02549o-succinylbenzoate synthaseKEGG orthology marker.
655KOK01911o-succinylbenzoate---CoA ligaseKEGG orthology marker.
656KOK01661naphthoate synthaseKEGG orthology marker.
657KOK192221,4-dihydroxy-2-naphthoyl-CoA hydrolaseKEGG orthology marker.
658KOK025481,4-dihydroxy-2-naphthoate polyprenyltransferaseKEGG orthology marker.
659KOK03183demethylmenaquinone methyltransferase / 2-methoxy-6-polyprenyl-1,4-benzoquinol methylaseKEGG orthology marker.
660KOK11782chorismate dehydrataseKEGG orthology marker.
661KOK18285aminodeoxyfutalosine synthaseKEGG orthology marker.
662KOK18286aminodeoxyfutalosine deaminaseKEGG orthology marker.
663KOK20810aminodeoxyfutalosine deaminaseKEGG orthology marker.
664KOK11783futalosine hydrolaseKEGG orthology marker.
665KOK11784cyclic dehypoxanthinyl futalosine synthaseKEGG orthology marker.
666KOK117855,8-dihydroxy-2-naphthoate synthaseKEGG orthology marker.
667KOK01647citrate synthaseKEGG orthology marker.
668KOK05942citrate (Re)-synthaseKEGG orthology marker.
669KOK016592-methylcitrate synthase and citrate synthaseKEGG orthology marker.
670KOK01681aconitate hydrataseKEGG orthology marker.
671KOK01682aconitate hydratase 2KEGG orthology marker.
672KOK27802aconitate hydratase AKEGG orthology marker.
673KOK00031isocitrate dehydrogenase (NADP+)KEGG orthology marker.
674KOK00030isocitrate dehydrogenase (NAD+)KEGG orthology marker.
675KOK001642-oxoglutarate dehydrogenase E1 componentKEGG orthology marker.
676KOK006582-oxoglutarate dehydrogenase E2 componentKEGG orthology marker.
677KOK001742-oxoglutarate/2-oxoacid ferredoxin oxidoreductase subunit alphaKEGG orthology marker.
678KOK001752-oxoglutarate/2-oxoacid ferredoxin oxidoreductase subunit betaKEGG orthology marker.
679KOK01902succinyl-CoA synthetase alpha subunitKEGG orthology marker.
680KOK01903succinyl-CoA synthetase beta subunitKEGG orthology marker.
681KOK01899succinyl-CoA ligase alpha subunitKEGG orthology marker.
682KOK01900succinyl-CoA ligase beta subunitKEGG orthology marker.
683KOK01616multifunctional 2-oxoglutarate metabolism enzymeKEGG orthology marker.
684KOK00139succinate-semialdehyde dehydrogenase (NAD+)KEGG orthology marker.
685KOK17761succinate-semialdehyde dehydrogenase, mitochondrialKEGG orthology marker.
686KOK08324succinate-semialdehyde dehydrogenase, sadKEGG orthology marker.
687KOK00135succinate-semialdehyde dehydrogenase, gabDKEGG orthology marker.
688KOK00239succinate dehydrogenase or fumarate reductase flavoprotein subunitKEGG orthology marker.
689KOK00240succinate dehydrogenase or fumarate reductase iron-sulfur subunitKEGG orthology marker.
690KOK00234succinate dehydrogenase (ubiquinone) flavoprotein subunitKEGG orthology marker.
691KOK00235succinate dehydrogenase (ubiquinone) iron-sulfur subunitKEGG orthology marker.
692KOK00244fumarate reductase flavoprotein subunitKEGG orthology marker.
693KOK00245fumarate reductase iron-sulfur subunitKEGG orthology marker.
694KOK01679fumarate hydratase, class IIKEGG orthology marker.
695KOK01676fumarate hydratase, class IKEGG orthology marker.
696KOK01677fumarate hydratase subunit alphaKEGG orthology marker.
697KOK01678fumarate hydratase subunit betaKEGG orthology marker.
698KOK00024malate dehydrogenaseKEGG orthology marker.
699KOK00025malate dehydrogenase, cytoplasmicKEGG orthology marker.
700KOK00026malate dehydrogenase, mitochondrialKEGG orthology marker.
701KOK00116malate dehydrogenase (quinone)KEGG orthology marker.
702KOK016263-deoxy-7-phosphoheptulonate synthaseKEGG orthology marker.
703KOK038563-deoxy-7-phosphoheptulonate synthase, class IIKEGG orthology marker.
704KOK138533-deoxy-7-phosphoheptulonate synthase / chorismate mutaseKEGG orthology marker.
705KOK017353-dehydroquinate synthaseKEGG orthology marker.
706KOK13829shikimate kinase / 3-dehydroquinate synthaseKEGG orthology marker.
707KOK037853-dehydroquinate dehydratase IKEGG orthology marker.
708KOK037863-dehydroquinate dehydratase IIKEGG orthology marker.
709KOK138323-dehydroquinate dehydratase / shikimate dehydrogenaseKEGG orthology marker.
710KOK00014shikimate dehydrogenaseKEGG orthology marker.
711KOK05887quinate/shikimate dehydrogenase YdiBKEGG orthology marker.
712KOK00891shikimate kinaseKEGG orthology marker.
713KOK008003-phosphoshikimate 1-carboxyvinyltransferaseKEGG orthology marker.
714KOK24018cyclohexadienyl/prephenate dehydrogenase / 3-phosphoshikimate 1-carboxyvinyltransferaseKEGG orthology marker.
715KOK01736chorismate synthaseKEGG orthology marker.
716KOK01851salicylate biosynthesis isochorismate synthase PchAKEGG orthology marker.
717KOK04782isochorismate pyruvate lyase PchBKEGG orthology marker.
718KOK04781salicylate synthase MbtI, Irp9, YbtSKEGG orthology marker.
719KOK00466tryptophan 2-monooxygenase IaaMKEGG orthology marker.
720KOK21801indoleacetamide hydrolase IaaHKEGG orthology marker.
721KOK01426amidaseKEGG orthology marker.
722TIGRFAMTIGR00507shikimate dehydrogenaseNCBIfam sequence family marker for AroE, integrated as InterPro IPR011342. Built to find the prokaryotic enzyme and the equivalent domain of the fungal and plant multifunctional proteins.
723KOK00260glutamate dehydrogenaseKEGG orthology marker.
724KOK00261glutamate dehydrogenase (NAD(P)+)KEGG orthology marker.
725KOK00262glutamate dehydrogenase (NADP+)KEGG orthology marker.
726KOK00265glutamate synthase (NADPH) large chainKEGG orthology marker.
727KOK00266glutamate synthase (NADPH) small chainKEGG orthology marker.
728KOK00284glutamate synthase (ferredoxin)KEGG orthology marker.
729KOK00301sarcosine oxidaseKEGG orthology marker.
730KOK00302sarcosine oxidase, subunit alphaKEGG orthology marker.
731KOK00303sarcosine oxidase, subunit betaKEGG orthology marker.
732KOK00304sarcosine oxidase, subunit deltaKEGG orthology marker.
733KOK00305sarcosine oxidase, subunit gammaKEGG orthology marker.
734KOK00309dimethylglycine oxidaseKEGG orthology marker.
735KOK00315dimethylglycine dehydrogenaseKEGG orthology marker.
736KOK00362nitrite reductase (NADH) large subunitKEGG orthology marker.
737KOK00363nitrite reductase (NADH) small subunitKEGG orthology marker.
738KOK00365urate oxidaseKEGG orthology marker.
739KOK00366ferredoxin-nitrite reductaseKEGG orthology marker.
740KOK00367ferredoxin-nitrate reductaseKEGG orthology marker.
741KOK00372assimilatory nitrate reductase catalytic subunitKEGG orthology marker.
742KOK00479glycine betaine monooxygenase AKEGG orthology marker.
743KOK01428urease subunit alphaKEGG orthology marker.
744KOK01429urease subunit betaKEGG orthology marker.
745KOK01430urease subunit gammaKEGG orthology marker.
746KOK01466allantoinaseKEGG orthology marker.
747KOK01470creatinine amidohydrolaseKEGG orthology marker.
748KOK01477allantoicaseKEGG orthology marker.
749KOK01483ureidoglycolate lyaseKEGG orthology marker.
750KOK01915glutamine synthetaseKEGG orthology marker.
751KOK02083allantoate deiminaseKEGG orthology marker.
752KOK03119taurine dioxygenaseKEGG orthology marker.
753KOK03851taurine-pyruvate aminotransferaseKEGG orthology marker.
754KOK03852sulfoacetaldehyde acetyltransferaseKEGG orthology marker.
755KOK071275-hydroxyisourate hydrolaseKEGG orthology marker.
756KOK07255taurine dehydrogenase small subunitKEGG orthology marker.
757KOK07256taurine dehydrogenase large subunitKEGG orthology marker.
758KOK08688creatinaseKEGG orthology marker.
759KOK10831taurine transport system ATP-binding proteinKEGG orthology marker.
760KOK134845-hydroxyisourate hydrolase / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylaseKEGG orthology marker.
761KOK14048urease subunit gamma/betaKEGG orthology marker.
762KOK14977(S)-ureidoglycine aminohydrolaseKEGG orthology marker.
763KOK15228methylamine dehydrogenase light chainKEGG orthology marker.
764KOK15229methylamine dehydrogenase heavy chainKEGG orthology marker.
765KOK15551taurine transport system substrate-binding proteinKEGG orthology marker.
766KOK15552taurine transport system permease proteinKEGG orthology marker.
767KOK16838urate oxidase / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylaseKEGG orthology marker.
768KOK16839FAD-dependent urate hydroxylaseKEGG orthology marker.
769KOK16842allantoinaseKEGG orthology marker.
770KOK17735carnitine 3-dehydrogenaseKEGG orthology marker.
771KOK21832glycine betaine monooxygenase BKEGG orthology marker.
772KOK21833N,N-dimethylglycine/sarcosine dehydrogenaseKEGG orthology marker.
773KOK21834N,N-dimethylglycine/sarcosine dehydrogenase ferredoxin subunitKEGG orthology marker.
774KOK22443carnitine monooxygenase subunitKEGG orthology marker.
775KOK22444carnitine monooxygenase subunitKEGG orthology marker.
776KOK26138nitrite reductase [NAD(P)H] small subunitKEGG orthology marker.
777KOK26139nitrite reductase [NAD(P)H] large subunitKEGG orthology marker.
778KOK27497carnitine 3-dehydrogenase / betainyl-CoA thioesteraseKEGG orthology marker.
779KOK278373-dehydrocarnitine:acetyl-CoA trimethylamine transferaseKEGG orthology marker.
780KOK05549benzoate/toluate 1,2-dioxygenase subunit alphaKEGG orthology marker.
781KOK05550benzoate/toluate 1,2-dioxygenase subunit betaKEGG orthology marker.
782KOK05783dihydroxycyclohexadiene carboxylate dehydrogenaseKEGG orthology marker.
783KOK05599anthranilate 1,2-dioxygenase (deaminating, decarboxylating) large subunitKEGG orthology marker.
784KOK05600anthranilate 1,2-dioxygenase (deaminating, decarboxylating) small subunitKEGG orthology marker.
785KOK16319anthranilate 1,2-dioxygenase large subunitKEGG orthology marker.
786KOK16320anthranilate 1,2-dioxygenase small subunitKEGG orthology marker.
787KOK16249phenol/toluene 2-monooxygenase P0 componentKEGG orthology marker.
788KOK16243phenol/toluene 2-monooxygenase (NADH) P1/A1KEGG orthology marker.
789KOK16244phenol/toluene 2-monooxygenase (NADH) P2/A2KEGG orthology marker.
790KOK16242phenol/toluene 2-monooxygenase (NADH) P3/A3KEGG orthology marker.
791KOK16245phenol/toluene 2-monooxygenase (NADH) P4/A4KEGG orthology marker.
792KOK16246phenol/toluene 2-monooxygenase (NADH) P5/A5KEGG orthology marker.
793KOK03381catechol 1,2-dioxygenaseKEGG orthology marker.
794KOK01856muconate cycloisomeraseKEGG orthology marker.
795KOK03464muconolactone D-isomeraseKEGG orthology marker.
796KOK010553-oxoadipate enol-lactonaseKEGG orthology marker.
797KOK147273-oxoadipate enol-lactonase / 4-carboxymuconolactone decarboxylaseKEGG orthology marker.
798KOK010313-oxoadipate CoA-transferase, alpha subunitKEGG orthology marker.
799KOK010323-oxoadipate CoA-transferase, beta subunitKEGG orthology marker.
800KOK026153-oxoadipyl-CoA/3-oxo-5,6-didehydrosuberyl-CoA thiolaseKEGG orthology marker.
801KOK00446catechol 2,3-dioxygenaseKEGG orthology marker.
802TIGRFAMTIGR03211catechol 2,3-dioxygenaseNCBIfam sequence family marker.
803KOK102162-hydroxymuconate-semialdehyde hydrolaseKEGG orthology marker.
804KOK10217aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenaseKEGG orthology marker.
805KOK018214-oxalocrotonate tautomeraseKEGG orthology marker.
806KOK016172-oxo-3-hexenedioate decarboxylaseKEGG orthology marker.
807KOK025542-keto-4-pentenoate hydrataseKEGG orthology marker.
808KOK183642-oxopent-4-enoate/cis-2-oxohex-4-enoate hydrataseKEGG orthology marker.
809KOK016664-hydroxy 2-oxovalerate aldolaseKEGG orthology marker.
810KOK183654-hydroxy-2-oxovalerate/4-hydroxy-2-oxohexanoate aldolaseKEGG orthology marker.
811KOK04073acetaldehyde dehydrogenaseKEGG orthology marker.
812KOK18366acetaldehyde/propanal dehydrogenaseKEGG orthology marker.
813KOK01912phenylacetate-CoA ligaseKEGG orthology marker.
814TIGRFAMTIGR02155phenylacetate--CoA ligase PaaKNCBIfam sequence family marker.
815KOK02609ring-1,2-phenylacetyl-CoA epoxidase subunit PaaAKEGG orthology marker.
816KOK02610ring-1,2-phenylacetyl-CoA epoxidase subunit PaaBKEGG orthology marker.
817KOK02611ring-1,2-phenylacetyl-CoA epoxidase subunit PaaCKEGG orthology marker.
818KOK02612ring-1,2-phenylacetyl-CoA epoxidase subunit PaaDKEGG orthology marker.
819KOK02613ring-1,2-phenylacetyl-CoA epoxidase subunit PaaEKEGG orthology marker.
820KOK158662-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomeraseKEGG orthology marker.
821KOK02618oxepin-CoA hydrolase / 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenaseKEGG orthology marker.
822KOK01692enoyl-CoA hydrataseKEGG orthology marker.
823KOK057083-phenylpropionate/trans-cinnamate dioxygenase subunit alphaKEGG orthology marker.
824KOK057093-phenylpropionate/trans-cinnamate dioxygenase subunit betaKEGG orthology marker.
825KOK057112,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenaseKEGG orthology marker.
826KOK057123-(3-hydroxy-phenyl)propionate hydroxylaseKEGG orthology marker.
827KOK057132,3-dihydroxyphenylpropionate 1,2-dioxygenaseKEGG orthology marker.
828KOK057142-hydroxy-6-oxonona-2,4-dienedioate hydrolaseKEGG orthology marker.
829KOK01695tryptophan synthase alpha chainKEGG orthology marker.
830KOK01696tryptophan synthase beta chainKEGG orthology marker.
831KOK06001tryptophan synthase beta chainKEGG orthology marker.
832KOK01694tryptophan synthaseKEGG orthology marker.
833KOK017033-isopropylmalate/(R)-2-methylmalate dehydratase large subunitKEGG orthology marker.
834KOK017043-isopropylmalate/(R)-2-methylmalate dehydratase small subunitKEGG orthology marker.
835KOK017023-isopropylmalate dehydrataseKEGG orthology marker.
836KOK01940argininosuccinate synthaseKEGG orthology marker.
837KOK01693imidazoleglycerol-phosphate dehydrataseKEGG orthology marker.
838KOK01089imidazoleglycerol-phosphate dehydratase / histidinol-phosphataseKEGG orthology marker.
839KOK01914aspartate--ammonia ligaseKEGG orthology marker.
840KOK00766anthranilate phosphoribosyltransferaseKEGG orthology marker.
841KOK13497anthranilate synthase/phosphoribosyltransferaseKEGG orthology marker.
842KOK00821acetylornithine/N-succinyldiaminopimelate aminotransferaseKEGG orthology marker.
843KOK14267N-succinyldiaminopimelate aminotransferaseKEGG orthology marker.
844KOK01953asparagine synthase (glutamine-hydrolysing)KEGG orthology marker.
845KOK05822tetrahydrodipicolinate N-acetyltransferaseKEGG orthology marker.
846KOK03340diaminopimelate dehydrogenaseKEGG orthology marker.
847KOK04517prephenate dehydrogenaseKEGG orthology marker.
848KOK14187chorismate mutase / prephenate dehydrogenaseKEGG orthology marker.
849KOK04092chorismate mutaseKEGG orthology marker.
850KOK14170chorismate mutase / prephenate dehydrataseKEGG orthology marker.
851KOK04093chorismate mutaseKEGG orthology marker.
852KOK04516chorismate mutaseKEGG orthology marker.
853KOK06208chorismate mutaseKEGG orthology marker.
854KOK06209chorismate mutaseKEGG orthology marker.
855KOK00286pyrroline-5-carboxylate reductaseKEGG orthology marker.
856KOK04486histidinol-phosphatase (PHP family)KEGG orthology marker.
857KOK05602histidinol-phosphataseKEGG orthology marker.
858KOK18649inositol-phosphate phosphatase / L-galactose 1-phosphate phosphatase / histidinol-phosphataseKEGG orthology marker.
859KOK28842histidinol-phosphataseKEGG orthology marker.
860KOK00930acetylglutamate kinaseKEGG orthology marker.
861KOK22478bifunctional N-acetylglutamate synthase/kinaseKEGG orthology marker.
862KOK12659N-acetyl-gamma-glutamyl-phosphate reductase / acetylglutamate kinaseKEGG orthology marker.
863KOK00931glutamate 5-kinaseKEGG orthology marker.
864KOK12657delta-1-pyrroline-5-carboxylate synthetaseKEGG orthology marker.
865KOK00832aromatic-amino-acid transaminaseKEGG orthology marker.
866KOK05821aromatic amino acid aminotransferase IIKEGG orthology marker.
867KOK00812aspartate aminotransferaseKEGG orthology marker.
868KOK00813aspartate aminotransferaseKEGG orthology marker.
869KOK11358aspartate aminotransferaseKEGG orthology marker.
870KOK00826branched-chain amino acid aminotransferaseKEGG orthology marker.
871KOK01586diaminopimelate decarboxylaseKEGG orthology marker.
872KOK00620glutamate N-acetyltransferase / amino-acid N-acetyltransferaseKEGG orthology marker.
873KOK01778diaminopimelate epimeraseKEGG orthology marker.
874KOK01814phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomeraseKEGG orthology marker.
875KOK24017phosphoribosyl isomerase AKEGG orthology marker.
876KOK01438acetylornithine deacetylaseKEGG orthology marker.
877KOK14677aminoacylaseKEGG orthology marker.
878KOK006742,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferaseKEGG orthology marker.
879KOK00818acetylornithine aminotransferaseKEGG orthology marker.
880KOK00259alanine dehydrogenaseKEGG orthology marker.
881KOK19244alanine dehydrogenaseKEGG orthology marker.
882KOK00765ATP phosphoribosyltransferaseKEGG orthology marker.
883KOK09011(R)-citramalate synthaseKEGG orthology marker.
884KOK14260alanine-synthesizing transaminaseKEGG orthology marker.
885KOK14261alanine-synthesizing transaminaseKEGG orthology marker.
886KOK00814alanine transaminaseKEGG orthology marker.
887KOK00835valine--pyruvate aminotransferaseKEGG orthology marker.
888KOK00611ornithine carbamoyltransferaseKEGG orthology marker.
889KOK00147glutamate-5-semialdehyde dehydrogenaseKEGG orthology marker.
890KOK01496phosphoribosyl-AMP cyclohydrolaseKEGG orthology marker.
891KOK11755phosphoribosyl-AMP cyclohydrolase / phosphoribosyl-ATP pyrophosphohydrolaseKEGG orthology marker.
892KOK14152phosphoribosyl-ATP pyrophosphohydrolase / phosphoribosyl-AMP cyclohydrolase / histidinol dehydrogenaseKEGG orthology marker.
893KOK05823N-acetyldiaminopimelate deacetylaseKEGG orthology marker.
894KOK016492-isopropylmalate synthaseKEGG orthology marker.
895KOK01817phosphoribosylanthranilate isomeraseKEGG orthology marker.
896KOK13498indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomeraseKEGG orthology marker.
897KOK13501anthranilate synthase / indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomeraseKEGG orthology marker.
898KOK00145N-acetyl-gamma-glutamyl-phosphate reductaseKEGG orthology marker.
899KOK00211prephenate dehydrogenase (NADP+)KEGG orthology marker.
900KOK01713cyclohexadienyl dehydrataseKEGG orthology marker.
901KOK04518prephenate dehydrataseKEGG orthology marker.
902KOK05359arogenate/prephenate dehydrataseKEGG orthology marker.
903KOK01657anthranilate synthase component IKEGG orthology marker.
904KOK01658anthranilate synthase component IIKEGG orthology marker.
905KOK13503anthranilate synthaseKEGG orthology marker.
906KOK01656anthranilate synthase / indole-3-glycerol phosphate synthaseKEGG orthology marker.
907KOK01439succinyl-diaminopimelate desuccinylaseKEGG orthology marker.
908KOK01523phosphoribosyl-ATP pyrophosphohydrolaseKEGG orthology marker.
909KOK01609indole-3-glycerol phosphate synthaseKEGG orthology marker.
910KOK00817histidinol-phosphate aminotransferaseKEGG orthology marker.
911KOK10206LL-diaminopimelate aminotransferaseKEGG orthology marker.
912KOK01755argininosuccinate lyaseKEGG orthology marker.
913KOK14681argininosuccinate lyase / amino-acid N-acetyltransferaseKEGG orthology marker.
914KOK00618amino-acid N-acetyltransferaseKEGG orthology marker.
915KOK00619amino-acid N-acetyltransferaseKEGG orthology marker.
916KOK14682amino-acid N-acetyltransferaseKEGG orthology marker.
917KOK22477N-acetylglutamate synthaseKEGG orthology marker.
918KOK02500imidazole glycerol-phosphate synthase subunit HisFKEGG orthology marker.
919KOK02501imidazole glycerol-phosphate synthase subunit HisHKEGG orthology marker.
920KOK01663imidazole glycerol-phosphate synthaseKEGG orthology marker.
921KOK01687dihydroxy-acid dehydrataseKEGG orthology marker.
922KOK00841aminotransferaseKEGG orthology marker.
923KOK000523-isopropylmalate dehydrogenaseKEGG orthology marker.
924KOK00013histidinol dehydrogenaseKEGG orthology marker.
925KOK017144-hydroxy-tetrahydrodipicolinate synthaseKEGG orthology marker.
926KOK002154-hydroxy-tetrahydrodipicolinate reductaseKEGG orthology marker.
927KOK00926carbamate kinaseKEGG orthology marker.
928KOK01777proline racemaseKEGG orthology marker.
929KOK10670glycine/sarcosine/betaine reductase complex component AKEGG orthology marker.
930KOK10671glycine reductase complex component B subunit alpha and betaKEGG orthology marker.
931KOK10672glycine reductase complex component B subunit gammaKEGG orthology marker.
932KOK21576glycine/sarcosine/betaine reductase complex component C subunit alphaKEGG orthology marker.
933KOK21577glycine/sarcosine/betaine reductase complex component C subunit betaKEGG orthology marker.
934KOK10793D-proline reductase (dithiol) PrdAKEGG orthology marker.
935KOK10794D-proline reductase (dithiol) PrdBKEGG orthology marker.
936KOK01712urocanate hydrataseKEGG orthology marker.
937KOK01580glutamate decarboxylaseKEGG orthology marker.
938KOK17989L-serine/L-threonine ammonia-lyaseKEGG orthology marker.
939KOK01667tryptophanaseKEGG orthology marker.
940KOK01478arginine deiminaseKEGG orthology marker.
941KOK01745histidine ammonia-lyaseKEGG orthology marker.
942KOK01754threonine dehydrataseKEGG orthology marker.
943KOK01479formiminoglutamaseKEGG orthology marker.
944KOK01468imidazolonepropionaseKEGG orthology marker.
945KOK01761methionine-gamma-lyaseKEGG orthology marker.
946KOK20021L-cysteine desulfidaseKEGG orthology marker.
947KOK26607putative L-cysteine desulfidaseKEGG orthology marker.
948KOK28981L-cysteine desulfidaseKEGG orthology marker.
949KOK00520merA; mercuric reductase [EC:1.16.1.1]KEGG orthology marker.
950KOK00221E4.99.1.2; alkylmercury lyase [EC:4.99.1.2]KEGG orthology marker.
951KOK08363merT; mercuric ion transport proteinKEGG orthology marker.
952KOK08364merP; periplasmic mercuric ion binding proteinKEGG orthology marker.
953KOK08365merR; MerR family transcriptional regulator, mercuric resistance operon regulatory proteinKEGG orthology marker.
954KOK19058merC; mercuric ion transport proteinKEGG orthology marker.
955KOK19059merE; mercuric ion transport proteinKEGG orthology marker.
956TIGRFAMTIGR02053mercury(II) reductaseNCBIfam sequence family marker for MerA, integrated as InterPro IPR021179. Built around the mercuric reductase itself rather than the wider pyridine nucleotide-disulfide oxidoreductase fold its catalytic core belongs to.
957KOK01637icl; isocitrate lyaseKEGG orthology marker.
958KOK01638aceB; malate synthaseKEGG orthology marker. K01639 is not an alternative: it is N-acetylneuraminate lyase.
959KOK02588nifH; nitrogenase iron proteinKEGG orthology marker.
960KOK02586nifD; nitrogenase molybdenum-iron protein alpha chainKEGG orthology marker.
961KOK02591nifK; nitrogenase molybdenum-iron protein beta chainKEGG orthology marker.
962KOK02585nifB; nitrogen fixation protein NifBKEGG orthology marker.
963KOK02587nifE; nitrogenase molybdenum-cofactor synthesis protein NifEKEGG orthology marker.
964KOK02592nifN, vnfN; nitrogenase cofactor synthesis protein NifN/VnfNKEGG orthology marker shared by the molybdenum and vanadium cofactor scaffolds.
965KOK22899vnfH; vanadium nitrogenase iron proteinKEGG orthology marker.
966KOK22896vnfD; vanadium-dependent nitrogenase alpha chainKEGG orthology marker.
967KOK22897vnfK; vanadium-dependent nitrogenase beta chainKEGG orthology marker.
968KOK22898vnfG; vanadium nitrogenase delta subunitKEGG orthology marker.
969KOK22903vnfE; nitrogenase vanadium-cofactor synthesis protein VnfEKEGG orthology marker.
970KOK00958sat, met3; sulfate adenylyltransferaseKEGG orthology marker.
971KOK00956cysN; sulfate adenylyltransferase subunit 1KEGG orthology marker.
972KOK00957cysD; sulfate adenylyltransferase subunit 2KEGG orthology marker.
973KOK00955cysNC; bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinaseKEGG orthology marker.
974KOK00860cysC; adenylylsulfate kinaseKEGG orthology marker.
975EC1.8.4.8phosphoadenylyl-sulfate reductase (thioredoxin)Reaction-specific activity marker used because KO K00390 also covers EC 1.8.4.10.
976EC1.8.4.10adenylyl-sulfate reductase (thioredoxin)Reaction-specific activity marker used because KO K00390 also covers EC 1.8.4.8.
977KOK00380cysJ; sulfite reductase (NADPH) flavoprotein alpha-componentKEGG orthology marker.
978KOK00381cysI; sulfite reductase (NADPH) hemoprotein beta-componentKEGG orthology marker.
979KOK00392sir; sulfite reductase (ferredoxin)KEGG orthology marker.
980KOK00836ectB; diaminobutyrate-2-oxoglutarate transaminaseKEGG orthology marker specific to the first ectoine-tail reaction.
981KOK06718ectA; L-2,4-diaminobutyric acid acetyltransferaseKEGG orthology marker.
982KOK06720ectC; L-ectoine synthaseKEGG orthology marker.
983KOK01599hemE; uroporphyrinogen decarboxylaseKEGG orthology marker.
984KOK00228hemF; coproporphyrinogen III oxidaseKEGG orthology marker for the oxygen-dependent enzyme.
985KOK02495hemN; oxygen-independent coproporphyrinogen III oxidaseKEGG orthology marker.
986KOK00230hemG; menaquinone-dependent protoporphyrinogen oxidaseKEGG orthology marker.
987KOK00231hemY; protoporphyrinogen/coproporphyrinogen III oxidaseKEGG orthology marker with two reaction-specific uses.
988KOK08973hemJ; protoporphyrinogen IX oxidaseKEGG orthology marker.
989KOK01772hemH; protoporphyrin/coproporphyrin ferrochelataseKEGG orthology marker with two reaction-specific uses.
990KOK00435hemQ; hydrogen peroxide-dependent heme synthaseKEGG orthology marker.
991KOK01252entB; bifunctional isochorismate lyase and aryl carrier proteinKEGG orthology marker with two component-specific uses.
992KOK00216entA; 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenaseKEGG orthology marker.
993KOK02362entD; enterobactin synthetase component D and phosphopantetheinyl transferaseKEGG orthology marker.
994KOK02363entE; 2,3-dihydroxybenzoate aryl-carrier-protein ligaseKEGG orthology marker.
995KOK02364entF; serine-activating enterobactin synthetase component FKEGG orthology marker.
996KOK01759gloA; lactoylglutathione lyaseKEGG orthology marker for glyoxalase I.
997KOK01069gloB; hydroxyacylglutathione hydrolaseKEGG orthology marker for glyoxalase II.
998KOK04564sodA/sodB; superoxide dismutase, Fe-Mn familyKEGG orthology marker.
999KOK04565sodC; superoxide dismutase, Cu-Zn familyKEGG orthology marker.
1000KOK03781katE; catalaseKEGG orthology marker.
1001KOK03782katG; catalase-peroxidaseKEGG orthology marker.
1002KOK07217manganese catalaseKEGG orthology marker.
1003KOK03386ahpC; peroxiredoxin 2/4 family catalytic subunitKEGG orthology marker accepted only with AhpF for this mechanism.
1004KOK03387ahpF; NADH-dependent peroxiredoxin subunit FKEGG orthology marker accepted only with AhpC for this mechanism.
1005KOK00108betA; choline dehydrogenaseKEGG orthology marker.
1006KOK11440gbsB; choline dehydrogenaseKEGG orthology marker for the Gram-positive architecture.
1007KOK00499choline monooxygenaseKEGG orthology marker.
1008KOK17755choline oxidaseKEGG orthology marker whose enzyme catalyses both route reactions.
1009KOK00130betB/gbsA; betaine-aldehyde dehydrogenaseKEGG orthology marker specific to the aldehyde at the requested boundary.
1010KOK00589MET1; uroporphyrin-III C-methyltransferaseKEGG orthology marker.
1011KOK02496hemX; uroporphyrin-III C-methyltransferaseKEGG orthology marker.
1012KOK13543hemDX; uroporphyrinogen III methyltransferase / synthaseKEGG orthology marker whose fusion supplies the methyltransferase reaction.
1013KOK03794sirB; sirohydrochlorin ferrochelataseKEGG orthology marker specific to EC 4.99.1.4.
1014CAZYAA10CAZy family AA10CAZy sequence family; activity assignment from dbCAN.
1015CAZYAA10_e1dbCAN-sub cluster AA10_e1dbCAN-sub eCAMI cluster of CAZy family AA10.
1016CAZYAA10_e12dbCAN-sub cluster AA10_e12dbCAN-sub eCAMI cluster of CAZy family AA10.
1017CAZYAA10_e44dbCAN-sub cluster AA10_e44dbCAN-sub eCAMI cluster of CAZy family AA10.
1018CAZYAA10_e49dbCAN-sub cluster AA10_e49dbCAN-sub eCAMI cluster of CAZy family AA10.
1019CAZYAA10_e58dbCAN-sub cluster AA10_e58dbCAN-sub eCAMI cluster of CAZy family AA10.
1020CAZYAA10_e66dbCAN-sub cluster AA10_e66dbCAN-sub eCAMI cluster of CAZy family AA10.
1021CAZYGH109CAZy family GH109CAZy sequence family; activity assignment from dbCAN.
1022CAZYGH109_e0dbCAN-sub cluster GH109_e0dbCAN-sub eCAMI cluster of CAZy family GH109.
1023CAZYGH109_e1dbCAN-sub cluster GH109_e1dbCAN-sub eCAMI cluster of CAZy family GH109.
1024CAZYGH151_e0dbCAN-sub cluster GH151_e0dbCAN-sub eCAMI cluster of CAZy family GH151.
1025CAZYGH18CAZy family GH18CAZy sequence family; activity assignment from dbCAN.
1026CAZYGH18_e1dbCAN-sub cluster GH18_e1dbCAN-sub eCAMI cluster of CAZy family GH18.
1027CAZYGH18_e104dbCAN-sub cluster GH18_e104dbCAN-sub eCAMI cluster of CAZy family GH18.
1028CAZYGH18_e111dbCAN-sub cluster GH18_e111dbCAN-sub eCAMI cluster of CAZy family GH18.
1029CAZYGH18_e121dbCAN-sub cluster GH18_e121dbCAN-sub eCAMI cluster of CAZy family GH18.
1030CAZYGH18_e14dbCAN-sub cluster GH18_e14dbCAN-sub eCAMI cluster of CAZy family GH18.
1031CAZYGH18_e147dbCAN-sub cluster GH18_e147dbCAN-sub eCAMI cluster of CAZy family GH18.
1032CAZYGH18_e148dbCAN-sub cluster GH18_e148dbCAN-sub eCAMI cluster of CAZy family GH18.
1033CAZYGH18_e151dbCAN-sub cluster GH18_e151dbCAN-sub eCAMI cluster of CAZy family GH18.
1034CAZYGH18_e154dbCAN-sub cluster GH18_e154dbCAN-sub eCAMI cluster of CAZy family GH18.
1035CAZYGH18_e164dbCAN-sub cluster GH18_e164dbCAN-sub eCAMI cluster of CAZy family GH18.
1036CAZYGH18_e175dbCAN-sub cluster GH18_e175dbCAN-sub eCAMI cluster of CAZy family GH18.
1037CAZYGH18_e177dbCAN-sub cluster GH18_e177dbCAN-sub eCAMI cluster of CAZy family GH18.
1038CAZYGH18_e184dbCAN-sub cluster GH18_e184dbCAN-sub eCAMI cluster of CAZy family GH18.
1039CAZYGH18_e187dbCAN-sub cluster GH18_e187dbCAN-sub eCAMI cluster of CAZy family GH18.
1040CAZYGH18_e19dbCAN-sub cluster GH18_e19dbCAN-sub eCAMI cluster of CAZy family GH18.
1041CAZYGH18_e193dbCAN-sub cluster GH18_e193dbCAN-sub eCAMI cluster of CAZy family GH18.
1042CAZYGH18_e196dbCAN-sub cluster GH18_e196dbCAN-sub eCAMI cluster of CAZy family GH18.
1043CAZYGH18_e2dbCAN-sub cluster GH18_e2dbCAN-sub eCAMI cluster of CAZy family GH18.
1044CAZYGH18_e20dbCAN-sub cluster GH18_e20dbCAN-sub eCAMI cluster of CAZy family GH18.
1045CAZYGH18_e211dbCAN-sub cluster GH18_e211dbCAN-sub eCAMI cluster of CAZy family GH18.
1046CAZYGH18_e224dbCAN-sub cluster GH18_e224dbCAN-sub eCAMI cluster of CAZy family GH18.
1047CAZYGH18_e231dbCAN-sub cluster GH18_e231dbCAN-sub eCAMI cluster of CAZy family GH18.
1048CAZYGH18_e236dbCAN-sub cluster GH18_e236dbCAN-sub eCAMI cluster of CAZy family GH18.
1049CAZYGH18_e253dbCAN-sub cluster GH18_e253dbCAN-sub eCAMI cluster of CAZy family GH18.
1050CAZYGH18_e258dbCAN-sub cluster GH18_e258dbCAN-sub eCAMI cluster of CAZy family GH18.
1051CAZYGH18_e26dbCAN-sub cluster GH18_e26dbCAN-sub eCAMI cluster of CAZy family GH18.
1052CAZYGH18_e260dbCAN-sub cluster GH18_e260dbCAN-sub eCAMI cluster of CAZy family GH18.
1053CAZYGH18_e263dbCAN-sub cluster GH18_e263dbCAN-sub eCAMI cluster of CAZy family GH18.
1054CAZYGH18_e272dbCAN-sub cluster GH18_e272dbCAN-sub eCAMI cluster of CAZy family GH18.
1055CAZYGH18_e285dbCAN-sub cluster GH18_e285dbCAN-sub eCAMI cluster of CAZy family GH18.
1056CAZYGH18_e287dbCAN-sub cluster GH18_e287dbCAN-sub eCAMI cluster of CAZy family GH18.
1057CAZYGH18_e3dbCAN-sub cluster GH18_e3dbCAN-sub eCAMI cluster of CAZy family GH18.
1058CAZYGH18_e325dbCAN-sub cluster GH18_e325dbCAN-sub eCAMI cluster of CAZy family GH18.
1059CAZYGH18_e327dbCAN-sub cluster GH18_e327dbCAN-sub eCAMI cluster of CAZy family GH18.
1060CAZYGH18_e334dbCAN-sub cluster GH18_e334dbCAN-sub eCAMI cluster of CAZy family GH18.
1061CAZYGH18_e338dbCAN-sub cluster GH18_e338dbCAN-sub eCAMI cluster of CAZy family GH18.
1062CAZYGH18_e342dbCAN-sub cluster GH18_e342dbCAN-sub eCAMI cluster of CAZy family GH18.
1063CAZYGH18_e347dbCAN-sub cluster GH18_e347dbCAN-sub eCAMI cluster of CAZy family GH18.
1064CAZYGH18_e348dbCAN-sub cluster GH18_e348dbCAN-sub eCAMI cluster of CAZy family GH18.
1065CAZYGH18_e354dbCAN-sub cluster GH18_e354dbCAN-sub eCAMI cluster of CAZy family GH18.
1066CAZYGH18_e373dbCAN-sub cluster GH18_e373dbCAN-sub eCAMI cluster of CAZy family GH18.
1067CAZYGH18_e392dbCAN-sub cluster GH18_e392dbCAN-sub eCAMI cluster of CAZy family GH18.
1068CAZYGH18_e4dbCAN-sub cluster GH18_e4dbCAN-sub eCAMI cluster of CAZy family GH18.
1069CAZYGH18_e401dbCAN-sub cluster GH18_e401dbCAN-sub eCAMI cluster of CAZy family GH18.
1070CAZYGH18_e428dbCAN-sub cluster GH18_e428dbCAN-sub eCAMI cluster of CAZy family GH18.
1071CAZYGH18_e431dbCAN-sub cluster GH18_e431dbCAN-sub eCAMI cluster of CAZy family GH18.
1072CAZYGH18_e521dbCAN-sub cluster GH18_e521dbCAN-sub eCAMI cluster of CAZy family GH18.
1073CAZYGH18_e66dbCAN-sub cluster GH18_e66dbCAN-sub eCAMI cluster of CAZy family GH18.
1074CAZYGH18_e672dbCAN-sub cluster GH18_e672dbCAN-sub eCAMI cluster of CAZy family GH18.
1075CAZYGH18_e69dbCAN-sub cluster GH18_e69dbCAN-sub eCAMI cluster of CAZy family GH18.
1076CAZYGH18_e72dbCAN-sub cluster GH18_e72dbCAN-sub eCAMI cluster of CAZy family GH18.
1077CAZYGH18_e77dbCAN-sub cluster GH18_e77dbCAN-sub eCAMI cluster of CAZy family GH18.
1078CAZYGH18_e80dbCAN-sub cluster GH18_e80dbCAN-sub eCAMI cluster of CAZy family GH18.
1079CAZYGH18_e81dbCAN-sub cluster GH18_e81dbCAN-sub eCAMI cluster of CAZy family GH18.
1080CAZYGH18_e83dbCAN-sub cluster GH18_e83dbCAN-sub eCAMI cluster of CAZy family GH18.
1081CAZYGH18_e830dbCAN-sub cluster GH18_e830dbCAN-sub eCAMI cluster of CAZy family GH18.
1082CAZYGH18_e834dbCAN-sub cluster GH18_e834dbCAN-sub eCAMI cluster of CAZy family GH18.
1083CAZYGH18_e91dbCAN-sub cluster GH18_e91dbCAN-sub eCAMI cluster of CAZy family GH18.
1084CAZYGH18_e95dbCAN-sub cluster GH18_e95dbCAN-sub eCAMI cluster of CAZy family GH18.
1085CAZYGH19CAZy family GH19CAZy sequence family; activity assignment from dbCAN.
1086CAZYGH19_e1dbCAN-sub cluster GH19_e1dbCAN-sub eCAMI cluster of CAZy family GH19.
1087CAZYGH19_e113dbCAN-sub cluster GH19_e113dbCAN-sub eCAMI cluster of CAZy family GH19.
1088CAZYGH19_e143dbCAN-sub cluster GH19_e143dbCAN-sub eCAMI cluster of CAZy family GH19.
1089CAZYGH19_e169dbCAN-sub cluster GH19_e169dbCAN-sub eCAMI cluster of CAZy family GH19.
1090CAZYGH19_e18dbCAN-sub cluster GH19_e18dbCAN-sub eCAMI cluster of CAZy family GH19.
1091CAZYGH19_e27dbCAN-sub cluster GH19_e27dbCAN-sub eCAMI cluster of CAZy family GH19.
1092CAZYGH19_e5dbCAN-sub cluster GH19_e5dbCAN-sub eCAMI cluster of CAZy family GH19.
1093CAZYGH19_e81dbCAN-sub cluster GH19_e81dbCAN-sub eCAMI cluster of CAZy family GH19.
1094CAZYGH20CAZy family GH20CAZy sequence family; activity assignment from dbCAN.
1095CAZYGH20_e0dbCAN-sub cluster GH20_e0dbCAN-sub eCAMI cluster of CAZy family GH20.
1096CAZYGH20_e1dbCAN-sub cluster GH20_e1dbCAN-sub eCAMI cluster of CAZy family GH20.
1097CAZYGH20_e10dbCAN-sub cluster GH20_e10dbCAN-sub eCAMI cluster of CAZy family GH20.
1098CAZYGH20_e105dbCAN-sub cluster GH20_e105dbCAN-sub eCAMI cluster of CAZy family GH20.
1099CAZYGH20_e107dbCAN-sub cluster GH20_e107dbCAN-sub eCAMI cluster of CAZy family GH20.
1100CAZYGH20_e114dbCAN-sub cluster GH20_e114dbCAN-sub eCAMI cluster of CAZy family GH20.
1101CAZYGH20_e12dbCAN-sub cluster GH20_e12dbCAN-sub eCAMI cluster of CAZy family GH20.
1102CAZYGH20_e13dbCAN-sub cluster GH20_e13dbCAN-sub eCAMI cluster of CAZy family GH20.
1103CAZYGH20_e132dbCAN-sub cluster GH20_e132dbCAN-sub eCAMI cluster of CAZy family GH20.
1104CAZYGH20_e137dbCAN-sub cluster GH20_e137dbCAN-sub eCAMI cluster of CAZy family GH20.
1105CAZYGH20_e143dbCAN-sub cluster GH20_e143dbCAN-sub eCAMI cluster of CAZy family GH20.
1106CAZYGH20_e146dbCAN-sub cluster GH20_e146dbCAN-sub eCAMI cluster of CAZy family GH20.
1107CAZYGH20_e167dbCAN-sub cluster GH20_e167dbCAN-sub eCAMI cluster of CAZy family GH20.
1108CAZYGH20_e18dbCAN-sub cluster GH20_e18dbCAN-sub eCAMI cluster of CAZy family GH20.
1109CAZYGH20_e182dbCAN-sub cluster GH20_e182dbCAN-sub eCAMI cluster of CAZy family GH20.
1110CAZYGH20_e214dbCAN-sub cluster GH20_e214dbCAN-sub eCAMI cluster of CAZy family GH20.
1111CAZYGH20_e22dbCAN-sub cluster GH20_e22dbCAN-sub eCAMI cluster of CAZy family GH20.
1112CAZYGH20_e35dbCAN-sub cluster GH20_e35dbCAN-sub eCAMI cluster of CAZy family GH20.
1113CAZYGH20_e45dbCAN-sub cluster GH20_e45dbCAN-sub eCAMI cluster of CAZy family GH20.
1114CAZYGH20_e49dbCAN-sub cluster GH20_e49dbCAN-sub eCAMI cluster of CAZy family GH20.
1115CAZYGH20_e51dbCAN-sub cluster GH20_e51dbCAN-sub eCAMI cluster of CAZy family GH20.
1116CAZYGH20_e57dbCAN-sub cluster GH20_e57dbCAN-sub eCAMI cluster of CAZy family GH20.
1117CAZYGH20_e61dbCAN-sub cluster GH20_e61dbCAN-sub eCAMI cluster of CAZy family GH20.
1118CAZYGH20_e70dbCAN-sub cluster GH20_e70dbCAN-sub eCAMI cluster of CAZy family GH20.
1119CAZYGH20_e71dbCAN-sub cluster GH20_e71dbCAN-sub eCAMI cluster of CAZy family GH20.
1120CAZYGH20_e74dbCAN-sub cluster GH20_e74dbCAN-sub eCAMI cluster of CAZy family GH20.
1121CAZYGH20_e77dbCAN-sub cluster GH20_e77dbCAN-sub eCAMI cluster of CAZy family GH20.
1122CAZYGH20_e80dbCAN-sub cluster GH20_e80dbCAN-sub eCAMI cluster of CAZy family GH20.
1123CAZYGH20_e93dbCAN-sub cluster GH20_e93dbCAN-sub eCAMI cluster of CAZy family GH20.
1124CAZYGH20_e95dbCAN-sub cluster GH20_e95dbCAN-sub eCAMI cluster of CAZy family GH20.
1125CAZYGH20_e97dbCAN-sub cluster GH20_e97dbCAN-sub eCAMI cluster of CAZy family GH20.
1126CAZYGH29CAZy family GH29CAZy sequence family; activity assignment from dbCAN.
1127CAZYGH29_e1dbCAN-sub cluster GH29_e1dbCAN-sub eCAMI cluster of CAZy family GH29.
1128CAZYGH29_e124dbCAN-sub cluster GH29_e124dbCAN-sub eCAMI cluster of CAZy family GH29.
1129CAZYGH29_e126dbCAN-sub cluster GH29_e126dbCAN-sub eCAMI cluster of CAZy family GH29.
1130CAZYGH29_e13dbCAN-sub cluster GH29_e13dbCAN-sub eCAMI cluster of CAZy family GH29.
1131CAZYGH29_e149dbCAN-sub cluster GH29_e149dbCAN-sub eCAMI cluster of CAZy family GH29.
1132CAZYGH29_e17dbCAN-sub cluster GH29_e17dbCAN-sub eCAMI cluster of CAZy family GH29.
1133CAZYGH29_e29dbCAN-sub cluster GH29_e29dbCAN-sub eCAMI cluster of CAZy family GH29.
1134CAZYGH29_e30dbCAN-sub cluster GH29_e30dbCAN-sub eCAMI cluster of CAZy family GH29.
1135CAZYGH29_e53dbCAN-sub cluster GH29_e53dbCAN-sub eCAMI cluster of CAZy family GH29.
1136CAZYGH29_e70dbCAN-sub cluster GH29_e70dbCAN-sub eCAMI cluster of CAZy family GH29.
1137CAZYGH29_e79dbCAN-sub cluster GH29_e79dbCAN-sub eCAMI cluster of CAZy family GH29.
1138CAZYGH29_e8dbCAN-sub cluster GH29_e8dbCAN-sub eCAMI cluster of CAZy family GH29.
1139CAZYGH29_e81dbCAN-sub cluster GH29_e81dbCAN-sub eCAMI cluster of CAZy family GH29.
1140CAZYGH29_e85dbCAN-sub cluster GH29_e85dbCAN-sub eCAMI cluster of CAZy family GH29.
1141CAZYGH33CAZy family GH33CAZy sequence family; activity assignment from dbCAN.
1142CAZYGH33_e105dbCAN-sub cluster GH33_e105dbCAN-sub eCAMI cluster of CAZy family GH33.
1143CAZYGH33_e121dbCAN-sub cluster GH33_e121dbCAN-sub eCAMI cluster of CAZy family GH33.
1144CAZYGH33_e129dbCAN-sub cluster GH33_e129dbCAN-sub eCAMI cluster of CAZy family GH33.
1145CAZYGH33_e130dbCAN-sub cluster GH33_e130dbCAN-sub eCAMI cluster of CAZy family GH33.
1146CAZYGH33_e131dbCAN-sub cluster GH33_e131dbCAN-sub eCAMI cluster of CAZy family GH33.
1147CAZYGH33_e132dbCAN-sub cluster GH33_e132dbCAN-sub eCAMI cluster of CAZy family GH33.
1148CAZYGH33_e135dbCAN-sub cluster GH33_e135dbCAN-sub eCAMI cluster of CAZy family GH33.
1149CAZYGH33_e163dbCAN-sub cluster GH33_e163dbCAN-sub eCAMI cluster of CAZy family GH33.
1150CAZYGH33_e197dbCAN-sub cluster GH33_e197dbCAN-sub eCAMI cluster of CAZy family GH33.
1151CAZYGH33_e22dbCAN-sub cluster GH33_e22dbCAN-sub eCAMI cluster of CAZy family GH33.
1152CAZYGH33_e41dbCAN-sub cluster GH33_e41dbCAN-sub eCAMI cluster of CAZy family GH33.
1153CAZYGH33_e5dbCAN-sub cluster GH33_e5dbCAN-sub eCAMI cluster of CAZy family GH33.
1154CAZYGH33_e66dbCAN-sub cluster GH33_e66dbCAN-sub eCAMI cluster of CAZy family GH33.
1155CAZYGH33_e75dbCAN-sub cluster GH33_e75dbCAN-sub eCAMI cluster of CAZy family GH33.
1156CAZYGH33_e77dbCAN-sub cluster GH33_e77dbCAN-sub eCAMI cluster of CAZy family GH33.
1157CAZYGH33_e9dbCAN-sub cluster GH33_e9dbCAN-sub eCAMI cluster of CAZy family GH33.
1158CAZYGH33_e91dbCAN-sub cluster GH33_e91dbCAN-sub eCAMI cluster of CAZy family GH33.
1159CAZYGH95CAZy family GH95CAZy sequence family; activity assignment from dbCAN.
1160CAZYGH95_e0dbCAN-sub cluster GH95_e0dbCAN-sub eCAMI cluster of CAZy family GH95.
1161CAZYGH95_e2dbCAN-sub cluster GH95_e2dbCAN-sub eCAMI cluster of CAZy family GH95.
1162CAZYGH95_e21dbCAN-sub cluster GH95_e21dbCAN-sub eCAMI cluster of CAZy family GH95.
1163CAZYGH95_e26dbCAN-sub cluster GH95_e26dbCAN-sub eCAMI cluster of CAZy family GH95.
1164CAZYGH95_e3dbCAN-sub cluster GH95_e3dbCAN-sub eCAMI cluster of CAZy family GH95.
1165KOK01183chitinase orthologueKEGG orthology marker.
1166KOK01186sialidase orthologueKEGG orthology marker.
1167KOK01204alpha-N-acetylgalactosaminidase orthologueKEGG orthology marker.
1168KOK01206alpha-L-fucosidase orthologueKEGG orthology marker.
1169KOK01207beta-N-acetylhexosaminidase orthologueKEGG orthology marker.
1170KOK13381bifunctional chitinase/lysozyme orthologueKEGG orthology marker.
1171KOK15923alpha-L-fucosidase 2 orthologueKEGG orthology marker.
1172KOK23550sialidase NanH orthologueKEGG orthology marker.
1173CAZYCE8CAZy family CE8CAZy sequence family; activity assignment from dbCAN.
1174CAZYCE8_e1dbCAN-sub cluster CE8_e1dbCAN-sub eCAMI cluster of CAZy family CE8.
1175CAZYCE8_e105dbCAN-sub cluster CE8_e105dbCAN-sub eCAMI cluster of CAZy family CE8.
1176CAZYCE8_e14dbCAN-sub cluster CE8_e14dbCAN-sub eCAMI cluster of CAZy family CE8.
1177CAZYCE8_e16dbCAN-sub cluster CE8_e16dbCAN-sub eCAMI cluster of CAZy family CE8.
1178CAZYCE8_e19dbCAN-sub cluster CE8_e19dbCAN-sub eCAMI cluster of CAZy family CE8.
1179CAZYCE8_e22dbCAN-sub cluster CE8_e22dbCAN-sub eCAMI cluster of CAZy family CE8.
1180CAZYCE8_e24dbCAN-sub cluster CE8_e24dbCAN-sub eCAMI cluster of CAZy family CE8.
1181CAZYCE8_e30dbCAN-sub cluster CE8_e30dbCAN-sub eCAMI cluster of CAZy family CE8.
1182CAZYCE8_e32dbCAN-sub cluster CE8_e32dbCAN-sub eCAMI cluster of CAZy family CE8.
1183CAZYCE8_e38dbCAN-sub cluster CE8_e38dbCAN-sub eCAMI cluster of CAZy family CE8.
1184CAZYCE8_e43dbCAN-sub cluster CE8_e43dbCAN-sub eCAMI cluster of CAZy family CE8.
1185CAZYCE8_e47dbCAN-sub cluster CE8_e47dbCAN-sub eCAMI cluster of CAZy family CE8.
1186CAZYCE8_e52dbCAN-sub cluster CE8_e52dbCAN-sub eCAMI cluster of CAZy family CE8.
1187CAZYCE8_e6dbCAN-sub cluster CE8_e6dbCAN-sub eCAMI cluster of CAZy family CE8.
1188CAZYCE8_e61dbCAN-sub cluster CE8_e61dbCAN-sub eCAMI cluster of CAZy family CE8.
1189CAZYCE8_e62dbCAN-sub cluster CE8_e62dbCAN-sub eCAMI cluster of CAZy family CE8.
1190CAZYCE8_e78dbCAN-sub cluster CE8_e78dbCAN-sub eCAMI cluster of CAZy family CE8.
1191CAZYCE8_e84dbCAN-sub cluster CE8_e84dbCAN-sub eCAMI cluster of CAZy family CE8.
1192CAZYCE8_e99dbCAN-sub cluster CE8_e99dbCAN-sub eCAMI cluster of CAZy family CE8.
1193CAZYGH28CAZy family GH28CAZy sequence family; activity assignment from dbCAN.
1194CAZYGH28_e0dbCAN-sub cluster GH28_e0dbCAN-sub eCAMI cluster of CAZy family GH28.
1195CAZYGH28_e1dbCAN-sub cluster GH28_e1dbCAN-sub eCAMI cluster of CAZy family GH28.
1196CAZYGH28_e107dbCAN-sub cluster GH28_e107dbCAN-sub eCAMI cluster of CAZy family GH28.
1197CAZYGH28_e120dbCAN-sub cluster GH28_e120dbCAN-sub eCAMI cluster of CAZy family GH28.
1198CAZYGH28_e125dbCAN-sub cluster GH28_e125dbCAN-sub eCAMI cluster of CAZy family GH28.
1199CAZYGH28_e130dbCAN-sub cluster GH28_e130dbCAN-sub eCAMI cluster of CAZy family GH28.
1200CAZYGH28_e200dbCAN-sub cluster GH28_e200dbCAN-sub eCAMI cluster of CAZy family GH28.
1201CAZYGH28_e250dbCAN-sub cluster GH28_e250dbCAN-sub eCAMI cluster of CAZy family GH28.
1202CAZYGH28_e29dbCAN-sub cluster GH28_e29dbCAN-sub eCAMI cluster of CAZy family GH28.
1203CAZYGH28_e295dbCAN-sub cluster GH28_e295dbCAN-sub eCAMI cluster of CAZy family GH28.
1204CAZYGH28_e45dbCAN-sub cluster GH28_e45dbCAN-sub eCAMI cluster of CAZy family GH28.
1205CAZYGH28_e56dbCAN-sub cluster GH28_e56dbCAN-sub eCAMI cluster of CAZy family GH28.
1206CAZYGH28_e58dbCAN-sub cluster GH28_e58dbCAN-sub eCAMI cluster of CAZy family GH28.
1207CAZYGH28_e61dbCAN-sub cluster GH28_e61dbCAN-sub eCAMI cluster of CAZy family GH28.
1208CAZYGH28_e67dbCAN-sub cluster GH28_e67dbCAN-sub eCAMI cluster of CAZy family GH28.
1209CAZYGH28_e70dbCAN-sub cluster GH28_e70dbCAN-sub eCAMI cluster of CAZy family GH28.
1210CAZYGH28_e75dbCAN-sub cluster GH28_e75dbCAN-sub eCAMI cluster of CAZy family GH28.
1211CAZYGH28_e86dbCAN-sub cluster GH28_e86dbCAN-sub eCAMI cluster of CAZy family GH28.
1212CAZYGH28_e98dbCAN-sub cluster GH28_e98dbCAN-sub eCAMI cluster of CAZy family GH28.
1213CAZYGH4_e30dbCAN-sub cluster GH4_e30dbCAN-sub eCAMI cluster of CAZy family GH4.
1214CAZYGH4_e34dbCAN-sub cluster GH4_e34dbCAN-sub eCAMI cluster of CAZy family GH4.
1215KOK01051pectinesterase orthologueKEGG orthology marker.
1216KOK01184polygalacturonase orthologueKEGG orthology marker.
1217KOK01213exo-polygalacturonase orthologueKEGG orthology marker.
1218KOK22933exo-polygalacturonase LplD orthologueKEGG orthology marker.
1219KOK01728pectate lyase orthologueKEGG orthology marker.
1220KOK19551pectate lyase C orthologueKEGG orthology marker.
1221KOK01731pectate disaccharide-lyase PelW orthologueKEGG orthology marker.
1222KOK22994pectate disaccharide-lyase PelX orthologueKEGG orthology marker.
1223KOK01730oligogalacturonide lyase orthologueKEGG orthology marker.
1224KOK018154-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase orthologueKEGG orthology marker.
1225KOK000652-dehydro-3-deoxy-D-gluconate 5-dehydrogenase orthologueKEGG orthology marker.
1226KOK01732pectin lyase orthologueKEGG orthology marker.
1227CAZYPL1CAZy family PL1CAZy sequence family; activity assignment from dbCAN.
1228CAZYPL10CAZy family PL10CAZy sequence family; activity assignment from dbCAN.
1229CAZYPL2CAZy family PL2CAZy sequence family; activity assignment from dbCAN.
1230CAZYPL3CAZy family PL3CAZy sequence family; activity assignment from dbCAN.
1231CAZYPL9CAZy family PL9CAZy sequence family; activity assignment from dbCAN.
1232CAZYPL10_e2dbCAN-sub cluster PL10_e2dbCAN-sub eCAMI cluster of CAZy family PL10.
1233CAZYPL10_e5dbCAN-sub cluster PL10_e5dbCAN-sub eCAMI cluster of CAZy family PL10.
1234CAZYPL1_e103dbCAN-sub cluster PL1_e103dbCAN-sub eCAMI cluster of CAZy family PL1.
1235CAZYPL1_e108dbCAN-sub cluster PL1_e108dbCAN-sub eCAMI cluster of CAZy family PL1.
1236CAZYPL1_e124dbCAN-sub cluster PL1_e124dbCAN-sub eCAMI cluster of CAZy family PL1.
1237CAZYPL1_e163dbCAN-sub cluster PL1_e163dbCAN-sub eCAMI cluster of CAZy family PL1.
1238CAZYPL1_e18dbCAN-sub cluster PL1_e18dbCAN-sub eCAMI cluster of CAZy family PL1.
1239CAZYPL1_e2dbCAN-sub cluster PL1_e2dbCAN-sub eCAMI cluster of CAZy family PL1.
1240CAZYPL1_e20dbCAN-sub cluster PL1_e20dbCAN-sub eCAMI cluster of CAZy family PL1.
1241CAZYPL1_e3dbCAN-sub cluster PL1_e3dbCAN-sub eCAMI cluster of CAZy family PL1.
1242CAZYPL1_e36dbCAN-sub cluster PL1_e36dbCAN-sub eCAMI cluster of CAZy family PL1.
1243CAZYPL1_e4dbCAN-sub cluster PL1_e4dbCAN-sub eCAMI cluster of CAZy family PL1.
1244CAZYPL1_e51dbCAN-sub cluster PL1_e51dbCAN-sub eCAMI cluster of CAZy family PL1.
1245CAZYPL1_e53dbCAN-sub cluster PL1_e53dbCAN-sub eCAMI cluster of CAZy family PL1.
1246CAZYPL1_e60dbCAN-sub cluster PL1_e60dbCAN-sub eCAMI cluster of CAZy family PL1.
1247CAZYPL1_e67dbCAN-sub cluster PL1_e67dbCAN-sub eCAMI cluster of CAZy family PL1.
1248CAZYPL1_e68dbCAN-sub cluster PL1_e68dbCAN-sub eCAMI cluster of CAZy family PL1.
1249CAZYPL1_e73dbCAN-sub cluster PL1_e73dbCAN-sub eCAMI cluster of CAZy family PL1.
1250CAZYPL1_e75dbCAN-sub cluster PL1_e75dbCAN-sub eCAMI cluster of CAZy family PL1.
1251CAZYPL1_e79dbCAN-sub cluster PL1_e79dbCAN-sub eCAMI cluster of CAZy family PL1.
1252CAZYPL1_e88dbCAN-sub cluster PL1_e88dbCAN-sub eCAMI cluster of CAZy family PL1.
1253CAZYPL2_e0dbCAN-sub cluster PL2_e0dbCAN-sub eCAMI cluster of CAZy family PL2.
1254CAZYPL3_e0dbCAN-sub cluster PL3_e0dbCAN-sub eCAMI cluster of CAZy family PL3.
1255CAZYPL3_e10dbCAN-sub cluster PL3_e10dbCAN-sub eCAMI cluster of CAZy family PL3.
1256CAZYPL3_e12dbCAN-sub cluster PL3_e12dbCAN-sub eCAMI cluster of CAZy family PL3.
1257CAZYPL3_e16dbCAN-sub cluster PL3_e16dbCAN-sub eCAMI cluster of CAZy family PL3.
1258CAZYPL3_e18dbCAN-sub cluster PL3_e18dbCAN-sub eCAMI cluster of CAZy family PL3.
1259CAZYPL3_e8dbCAN-sub cluster PL3_e8dbCAN-sub eCAMI cluster of CAZy family PL3.
1260CAZYPL3_e9dbCAN-sub cluster PL3_e9dbCAN-sub eCAMI cluster of CAZy family PL3.
1261CAZYPL9_e23dbCAN-sub cluster PL9_e23dbCAN-sub eCAMI cluster of CAZy family PL9.
1262CAZYPL9_e31dbCAN-sub cluster PL9_e31dbCAN-sub eCAMI cluster of CAZy family PL9.
1263CAZYPL9_e8dbCAN-sub cluster PL9_e8dbCAN-sub eCAMI cluster of CAZy family PL9.
1264CAZYPL2_e1dbCAN-sub cluster PL2_e1dbCAN-sub eCAMI cluster of CAZy family PL2.
1265CAZYPL9_e1dbCAN-sub cluster PL9_e1dbCAN-sub eCAMI cluster of CAZy family PL9.
1266CAZYPL1_e16dbCAN-sub cluster PL1_e16dbCAN-sub eCAMI cluster of CAZy family PL1.
1267CAZYPL1_e165dbCAN-sub cluster PL1_e165dbCAN-sub eCAMI cluster of CAZy family PL1.
1268CAZYPL1_e25dbCAN-sub cluster PL1_e25dbCAN-sub eCAMI cluster of CAZy family PL1.
1269CAZYPL1_e33dbCAN-sub cluster PL1_e33dbCAN-sub eCAMI cluster of CAZy family PL1.
1270CAZYPL1_e71dbCAN-sub cluster PL1_e71dbCAN-sub eCAMI cluster of CAZy family PL1.
1271CAZYPL1_e8dbCAN-sub cluster PL1_e8dbCAN-sub eCAMI cluster of CAZy family PL1.
1272KOK15783doeA; ectoine hydrolaseKEGG orthology marker.
1273KOK15784doeB; N2-acetyl-L-2,4-diaminobutanoate deacetylaseKEGG orthology marker.
1274KOK10674ectD; ectoine hydroxylaseKEGG orthology marker.
1275KOK19266lactaldehyde dehydrogenaseKEGG orthology marker.
1276KOK07248aldA; lactaldehyde dehydrogenase / glycolaldehyde dehydrogenaseKEGG orthology marker supporting a promiscuous aldehyde dehydrogenase.
1277NCBIFAMNF000689.1ferrochelataseNCBIfam equivalog-grade profile. ferrochelatase, EC 4.98.1.1. Built from NCBI Protein Cluster (PRK); 20040 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1278NCBIFAMNF001209.0metX homoserine O-acetyltransferase MetXNCBIfam equivalog-grade profile. homoserine O-acetyltransferase MetX, EC 2.3.1.31. Built from NCBI Protein Cluster (PRK); 37806 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1279NCBIFAMNF002537.0phosphoadenylyl-sulfate reductaseNCBIfam equivalog-grade profile. phosphoadenylyl-sulfate reductase, EC 1.8.4.8. Built from NCBI Protein Cluster (PRK); 54479 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1280NCBIFAMNF003776.0metA homoserine O-succinyltransferase MetANCBIfam equivalog-grade profile. homoserine O-succinyltransferase MetA, EC 2.3.1.46. Built from NCBI Protein Cluster (PRK); 1211 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1281NCBIFAMNF004057.0precorrin-8X methylmutaseNCBIfam equivalog-grade profile. precorrin-8X methylmutase, EC 5.4.99.61. Built from NCBI Protein Cluster (PRK); 454 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1282NCBIFAMNF004058.0cobalt-factor II C(20)-methyltransferaseNCBIfam equivalog-grade profile. cobalt-factor II C(20)-methyltransferase, EC 2.1.1.151. Built from NCBI Protein Cluster (PRK); 431 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1283NCBIFAMNF004059.0cobalt-factor II C(20)-methyltransferaseNCBIfam equivalog-grade profile. cobalt-factor II C(20)-methyltransferase, EC 2.1.1.151. Built from NCBI Protein Cluster (PRK); 663 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1284NCBIFAMNF004060.0cobalt-factor II C(20)-methyltransferaseNCBIfam equivalog-grade profile. cobalt-factor II C(20)-methyltransferase, EC 2.1.1.151. Built from NCBI Protein Cluster (PRK); 265 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1285NCBIFAMNF004061.0cobalt-factor II C(20)-methyltransferaseNCBIfam equivalog-grade profile. cobalt-factor II C(20)-methyltransferase, EC 2.1.1.151. Built from NCBI Protein Cluster (PRK); 1761 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1286NCBIFAMNF004062.0cobalt-factor II C(20)-methyltransferaseNCBIfam equivalog-grade profile. cobalt-factor II C(20)-methyltransferase, EC 2.1.1.151. Built from NCBI Protein Cluster (PRK); 54 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1287NCBIFAMNF004063.0cobalt-factor II C(20)-methyltransferaseNCBIfam equivalog-grade profile. cobalt-factor II C(20)-methyltransferase, EC 2.1.1.151. Built from NCBI Protein Cluster (PRK); 419 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1288NCBIFAMNF004423.0precorrin-3B C(17)-methyltransferaseNCBIfam equivalog-grade profile. precorrin-3B C(17)-methyltransferase, EC 2.1.1.131. Built from NCBI Protein Cluster (PRK); 59 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1289NCBIFAMNF004614.0precorrin-2 C(20)-methyltransferaseNCBIfam equivalog-grade profile. precorrin-2 C(20)-methyltransferase, EC 2.1.1.130. Built from NCBI Protein Cluster (PRK); 353 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1290NCBIFAMNF004619.0precorrin-8X methylmutaseNCBIfam equivalog-grade profile. precorrin-8X methylmutase, EC 5.4.99.61. Built from NCBI Protein Cluster (PRK); 639 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1291NCBIFAMNF004647.0precorrin-2 C(20)-methyltransferaseNCBIfam equivalog-grade profile. precorrin-2 C(20)-methyltransferase, EC 2.1.1.130. Built from NCBI Protein Cluster (PRK); 18994 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1292NCBIFAMNF004648.0precorrin-3B C(17)-methyltransferaseNCBIfam equivalog-grade profile. precorrin-3B C(17)-methyltransferase, EC 2.1.1.131. Built from NCBI Protein Cluster (PRK); 1928 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1293NCBIFAMNF004901.0cobalt-precorrin-8 methylmutaseNCBIfam equivalog-grade profile. cobalt-precorrin-8 methylmutase, EC 5.4.99.60. Built from NCBI Protein Cluster (PRK); 238 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1294NCBIFAMNF005074.0isocitrate lyaseNCBIfam equivalog-grade profile. isocitrate lyase, EC 4.1.3.1. Built from NCBI Protein Cluster (PRK); 9029 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1295NCBIFAMNF005492.0phosphoribosylaminoimidazolecarboxamide formyltransferaseNCBIfam equivalog-grade profile. phosphoribosylaminoimidazolecarboxamide formyltransferase, EC 2.1.2.3. Built from NCBI Protein Cluster (PRK); 5354 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1296NCBIFAMNF005967.0cobalt-precorrin-6A reductaseNCBIfam equivalog-grade profile. cobalt-precorrin-6A reductase, EC 1.3.1.106. Built from NCBI Protein Cluster (PRK); 1789 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1297NCBIFAMNF005968.0cobalt-precorrin-6A reductaseNCBIfam equivalog-grade profile. cobalt-precorrin-6A reductase, EC 1.3.1.106. Built from NCBI Protein Cluster (PRK); 27257 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1298NCBIFAMNF005969.0cobalt-precorrin-6A reductaseNCBIfam equivalog-grade profile. cobalt-precorrin-6A reductase, EC 1.3.1.106. Built from NCBI Protein Cluster (PRK); 5566 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1299NCBIFAMNF005970.0cobalt-precorrin-6A reductaseNCBIfam equivalog-grade profile. cobalt-precorrin-6A reductase, EC 1.3.1.106. Built from NCBI Protein Cluster (PRK); 1154 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1300NCBIFAMNF005971.0cobalt-precorrin-6A reductaseNCBIfam equivalog-grade profile. cobalt-precorrin-6A reductase, EC 1.3.1.106. Built from NCBI Protein Cluster (PRK); 81 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1301NCBIFAMNF006136.0precorrin-8X methylmutaseNCBIfam equivalog-grade profile. precorrin-8X methylmutase, EC 5.4.99.61. Built from NCBI Protein Cluster (PRK); 19152 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1302NCBIFAMNF006137.0cobalt-precorrin-8 methylmutaseNCBIfam equivalog-grade profile. cobalt-precorrin-8 methylmutase, EC 5.4.99.60. Built from NCBI Protein Cluster (PRK); 1967 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1303NCBIFAMNF006449.0metX homoserine O-succinyltransferase MetXNCBIfam equivalog-grade profile. homoserine O-succinyltransferase MetX, EC 2.3.1.46. Built from NCBI Protein Cluster (PRK); 2062 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1304NCBIFAMNF006916.0succinic semialdehyde dehydrogenaseNCBIfam equivalog-grade profile. succinic semialdehyde dehydrogenase, EC 1.2.1.79. Built from NCBI Protein Cluster (PRK); 17569 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1305NCBIFAMNF007604.0entD enterobactin synthase subunit EntDNCBIfam equivalog-grade profile. enterobactin synthase subunit EntD, EC 6.3.2.14. Built from NCBI Protein Cluster (PRK); 4482 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1306NCBIFAMNF007605.2entF enterobactin non-ribosomal peptide synthetase EntFNCBIfam equivalog-grade profile. enterobactin non-ribosomal peptide synthetase EntF, EC 6.3.2.14. Built from NCBI Protein Cluster (PRK); 11422 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1307NCBIFAMNF008220.0L-fucose isomeraseNCBIfam equivalog-grade profile. L-fucose isomerase, EC 5.3.1.25. Built from NCBI Protein Cluster (PRK); 9680 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1308NCBIFAMNF008759.0serA phosphoglycerate dehydrogenaseNCBIfam equivalog-grade profile. phosphoglycerate dehydrogenase, EC 1.1.1.95. Built from NCBI Protein Cluster (PRK); 19517 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1309NCBIFAMNF008841.0protoporphyrinogen oxidaseNCBIfam equivalog-grade profile. protoporphyrinogen oxidase, EC 1.3.3.4. Built from NCBI Protein Cluster (PRK); 2928 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1310NCBIFAMNF008843.0protoporphyrinogen oxidaseNCBIfam equivalog-grade profile. protoporphyrinogen oxidase, EC 1.3.3.4. Built from NCBI Protein Cluster (PRK); 86 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1311NCBIFAMNF008845.0hemY protoporphyrinogen oxidaseNCBIfam equivalog-grade profile. protoporphyrinogen oxidase, EC 1.3.3.4. Built from NCBI Protein Cluster (PRK); 5976 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1312NCBIFAMNF008907.0multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunitNCBIfam equivalog-grade profile. multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit, EC 4.1.1.71. Built from NCBI Protein Cluster (PRK); 71314 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1313NCBIFAMNF009081.0protoporphyrinogen oxidaseNCBIfam equivalog-grade profile. protoporphyrinogen oxidase, EC 1.3.3.4. Built from NCBI Protein Cluster (PRK); 2030 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1314NCBIFAMNF009259.0bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinaseNCBIfam equivalog-grade profile. bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase, EC 2.7.1.49. Built from NCBI Protein Cluster (PRK); 2147 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1315NCBIFAMNF011645.0aceA isocitrate lyaseNCBIfam equivalog-grade profile. isocitrate lyase, EC 4.1.3.1. Built from NCBI Protein Cluster (PRK); 26011 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1316NCBIFAMNF012017.0cobalt-precorrin-4 methyltransferaseNCBIfam equivalog-grade profile. cobalt-precorrin-4 methyltransferase, EC 2.1.1.271. Built from NCBI Protein Cluster (PRK); 1764 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1317NCBIFAMTIGR00109.1hemH ferrochelataseNCBIfam equivalog-grade profile. ferrochelatase, EC 4.98.1.1. Built from JCVI; 70512 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1318NCBIFAMTIGR00562.1hemG protoporphyrinogen oxidaseNCBIfam equivalog-grade profile. protoporphyrinogen oxidase, EC 1.3.3.4. Built from JCVI; 35757 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1319NCBIFAMTIGR00715.1cobK precorrin-6A reductaseNCBIfam equivalog-grade profile. precorrin-6A reductase, EC 1.3.1.54. Built from JCVI; 32358 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1320NCBIFAMTIGR00718.1sdaAA L-serine ammonia-lyase alpha chainNCBIfam equivalog-grade profile for the alpha subunit of the split iron-sulfur enzyme; release hmm_PGAP/20.0.
1321NCBIFAMTIGR00719.1sdaAB L-serine ammonia-lyase beta chainNCBIfam equivalog-grade profile for the beta subunit of the split iron-sulfur enzyme; release hmm_PGAP/20.0.
1322NCBIFAMTIGR00720.1sdaA single-chain L-serine ammonia-lyaseNCBIfam equivalog-grade profile for the complete single-chain iron-sulfur enzyme; release hmm_PGAP/20.0.
1323NCBIFAMTIGR01001.2metA homoserine O-succinyltransferase MetANCBIfam equivalog-grade profile. homoserine O-succinyltransferase MetA, EC 2.3.1.46. Built from JCVI; 4449 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1324NCBIFAMTIGR01089.1fucI L-fucose isomeraseNCBIfam equivalog-grade profile. L-fucose isomerase, EC 5.3.1.25. Built from JCVI; 9572 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1325NCBIFAMTIGR01327.1serA phosphoglycerate dehydrogenaseNCBIfam equivalog-grade profile. phosphoglycerate dehydrogenase, EC 1.1.1.95. Built from JCVI; 36301 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1326NCBIFAMTIGR01346.1aceA isocitrate lyaseNCBIfam equivalog-grade profile. isocitrate lyase, EC 4.1.3.1. Built from JCVI; 26266 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1327NCBIFAMTIGR01465.1cobM precorrin-4 C(11)-methyltransferaseNCBIfam equivalog-grade profile. precorrin-4 C(11)-methyltransferase, EC 2.1.1.133. Built from JCVI; 36952 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1328NCBIFAMTIGR01466.1cobJ precorrin-3B C(17)-methyltransferaseNCBIfam equivalog_domain-grade profile. precorrin-3B C(17)-methyltransferase, EC 2.1.1.131. Built from JCVI; 45145 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1329NCBIFAMTIGR01467.1cobI precorrin-2 C(20)-methyltransferaseNCBIfam equivalog-grade profile. precorrin-2 C(20)-methyltransferase, EC 2.1.1.130. Built from JCVI; 36417 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1330NCBIFAMTIGR01608.1citD citrate lyase acyl carrier proteinNCBIfam equivalog-grade profile. citrate lyase acyl carrier protein, EC 4.1.3.6. Built from JCVI; 4816 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1331NCBIFAMTIGR02057.1cysH phosphoadenosine phosphosulfate reductaseNCBIfam equivalog-grade profile. phosphoadenosine phosphosulfate reductase, EC 1.8.4.8. Built from JCVI; 8875 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1332NCBIFAMTIGR03216.12-hydroxymuconic semialdehyde dehydrogenaseNCBIfam equivalog-grade profile. 2-hydroxymuconic semialdehyde dehydrogenase, EC 1.2.1.85. Built from JCVI; 6400 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1333NCBIFAMNF040708.3ahbA siroheme decarboxylase subunit alphaNCBIfam equivalog-grade profile. siroheme decarboxylase subunit alpha, EC 4.1.1.111. Built from NCBIFAM; 1773 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0. The profile KEGG has no counterpart for: K22225 names the decarboxylase without separating its two subunits.
1334NCBIFAMNF040707.3ahbB siroheme decarboxylase subunit betaNCBIfam equivalog-grade profile. siroheme decarboxylase subunit beta, EC 4.1.1.111. Built from NCBIFAM; 8656 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0. The sister profile of NF040708.3, and the reason a heterodimer can be evidenced at all.
1335NCBIFAMTIGR04546.1ahbC 12,18-didecarboxysiroheme deacetylaseNCBIfam equivalog-grade profile. 12,18-didecarboxysiroheme deacetylase, the radical SAM enzyme KEGG calls AhbC. Built from JCVI; 575 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0. No EC number is assigned to the activity.
1336NCBIFAMTIGR04545.1ahbD heme b synthaseNCBIfam equivalog-grade profile. heme b synthase, EC 1.3.98.6, the radical SAM enzyme KEGG calls AhbD. Built from JCVI; 622 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1337KOK22226ahbC; Fe-coproporphyrin III synthaseKEGG orthology marker.
1338KOK22227ahbD; AdoMet-dependent heme synthaseKEGG orthology marker.
1339NCBIFAMTIGR02067.1hisN histidinol-phosphataseNCBIfam equivalog-grade profile. histidinol-phosphatase, EC 3.1.3.15. Built from TIGR02067 (his_9_HisN); 23807 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1340NCBIFAMNF005996.1hisJ histidinol-phosphataseNCBIfam equivalog-grade profile. histidinol-phosphatase HisJ, EC 3.1.3.15. Built from NCBI Protein Cluster (PRK08123); 6700 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1341NCBIFAMNF052360.1histidinol-phosphatase, HolPasePseu familyNCBIfam equivalog-grade profile. histidinol-phosphatase, EC 3.1.3.15. 8656 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1342NCBIFAMNF052359.1histidinol-phosphatase, Neisseriaceae familyNCBIfam equivalog-grade profile. histidinol-phosphatase, EC 3.1.3.15. Taxonomic range Neisseriaceae; 337 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1343NCBIFAMTIGR01261.1hisB N-terminal histidinol-phosphatase domainNCBIfam equivalog_domain-grade profile. histidinol-phosphatase, EC 3.1.3.15. Built from TIGR01261 (hisB_Nterm), the phosphatase domain of the bifunctional HisB protein; 19756 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1344NCBIFAMNF001611.0phosphoribosyl-ATP diphosphataseNCBIfam equivalog-grade profile. phosphoribosyl-ATP diphosphatase, EC 3.6.1.31. Built from NCBI Protein Cluster (PRK00400.1-3); 16612 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1345NCBIFAMNF001613.0phosphoribosyl-ATP diphosphataseNCBIfam equivalog-grade profile. phosphoribosyl-ATP diphosphatase, EC 3.6.1.31. Built from NCBI Protein Cluster (PRK00400.1-5); 8106 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1346NCBIFAMNF001610.0phosphoribosyl-ATP diphosphataseNCBIfam equivalog-grade profile. phosphoribosyl-ATP diphosphatase, EC 3.6.1.31. Built from NCBI Protein Cluster (PRK00400.1-1); 7731 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1347NCBIFAMTIGR03188.1hisE phosphoribosyl-ATP diphosphatase domainNCBIfam equivalog_domain-grade profile. phosphoribosyl-ATP diphosphatase, EC 3.6.1.31. Built from TIGR03188 (histidine_hisI); 58388 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1348KOK02804nagE; N-acetylglucosamine PTS system EIICBA or EIICB componentKEGG orthology marker.
1349KOK02803nagEb; N-acetylglucosamine PTS system EIIB componentKEGG orthology marker.
1350NCBIFAMNF007608.0nagE PTS N-acetylglucosamine transporter subunit IIABCNCBIfam equivalog-grade profile. PTS N-acetyl glucosamine transporter subunit IIABC, EC 2.7.1.193. Built from NCBI Protein Cluster (PRK10255); 3362 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1351NCBIFAMTIGR01998.1nagE N-acetylglucosamine-specific PTS transporter subunit IIBCNCBIfam equivalog_domain-grade profile. N-acetylglucosamine-specific PTS transporter subunit IIBC, EC 2.7.1.193. Built from TIGR01998; 23373 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1352NCBIFAMTIGR00502.1nagB glucosamine-6-phosphate deaminaseNCBIfam equivalog-grade profile. glucosamine-6-phosphate deaminase, EC 3.5.99.6. Built from TIGR00502; 35984 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1353NCBIFAMNF001685.0nagB glucosamine-6-phosphate deaminaseNCBIfam equivalog-grade profile. glucosamine-6-phosphate deaminase, EC 3.5.99.6. Built from NCBI Protein Cluster (PRK00443); 2406 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1354NCBIFAMNF001682.0glucosamine-6-phosphate deaminase, Caryophanales familyNCBIfam equivalog-grade profile. glucosamine-6-phosphate deaminase, EC 3.5.99.6. Built from NCBI Protein Cluster (PRK00443); taxonomic range Caryophanales; 257 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1355NCBIFAMNF009022.0glucosamine-6-phosphate deaminaseNCBIfam equivalog-grade profile. glucosamine-6-phosphate deaminase, EC 3.5.99.6. Built from NCBI Protein Cluster (PRK12358); 2302 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1356NCBIFAMNF041128.1glmD glucosamine-6-phosphate deaminaseNCBIfam equivalog-grade profile. glucosamine-6-phosphate deaminase, EC 3.5.99.6. Taxonomic range Thermococcaceae; 39 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1357NCBIFAMNF046059.1nagB-II glucosamine-6-phosphate deaminase NagB-IINCBIfam equivalog-grade profile. glucosamine-6-phosphate deaminase NagB-II, EC 3.5.99.6. Taxonomic range Pseudomonadota; 763 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1358NCBIFAMNF009835.0nagK N-acetylglucosamine kinaseNCBIfam equivalog-grade profile. N-acetylglucosamine kinase, EC 2.7.1.59. Built from NCBI Protein Cluster (PRK13310); 6570 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1359NCBIFAMNF046058.1nagK N-acetylglucosamine kinaseNCBIfam equivalog-grade profile. N-acetylglucosamine kinase, EC 2.7.1.59. Taxonomic range Pseudomonadota; 993 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1360NCBIFAMTIGR00221.1nagA N-acetylglucosamine-6-phosphate deacetylaseNCBIfam equivalog-grade profile. N-acetylglucosamine-6-phosphate deacetylase, EC 3.5.1.25. Built from TIGR00221; 71976 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1361NCBIFAMNF008371.0nagA N-acetylglucosamine-6-phosphate deacetylaseNCBIfam equivalog-grade profile. N-acetylglucosamine-6-phosphate deacetylase, EC 3.5.1.25. Built from NCBI Protein Cluster (PRK11170); 7117 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1362KOK09774LPS export system protein LptAKEGG orthology marker.
1363KOK06861LPS export ATP-binding protein LptBKEGG orthology marker.
1364KOK11719LPS export system protein LptCKEGG orthology marker.
1365KOK04744LPS-assembly protein LptDKEGG orthology marker.
1366KOK03643LPS-assembly lipoprotein LptEKEGG orthology marker.
1367KOK07091LPS export system permease protein LptFKEGG orthology marker.
1368KOK11720LPS export system permease protein LptGKEGG orthology marker.
1369NCBIFAMTIGR03002.1lptA lipopolysaccharide transport periplasmic proteinNCBIfam equivalog-grade profile. LptA periplasmic bridge protein; 18220 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1370NCBIFAMNF008143.0lptA lipopolysaccharide ABC transporter substrate-binding proteinNCBIfam equivalog-grade profile. LptA profile restricted to Enterobacterales; 1615 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1371NCBIFAMTIGR04406.1lptB LPS export ABC transporter ATP-binding proteinNCBIfam equivalog-grade profile. LptB ATP-binding component; 30612 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1372NCBIFAMNF008144.0lptB LPS export ABC transporter ATP-binding proteinNCBIfam equivalog-grade profile. LptB profile restricted to Gammaproteobacteria; 5351 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1373NCBIFAMTIGR04409.1lptC LPS export ABC transporter periplasmic proteinNCBIfam equivalog-grade profile. LptC inner-membrane connector; 28890 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1374NCBIFAMNF008142.0lptC LPS export ABC transporter periplasmic proteinNCBIfam equivalog-grade profile. LptC profile restricted to Enterobacterales; 1960 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1375NCBIFAMTIGR04407.1lptF LPS export ABC transporter permeaseNCBIfam equivalog-grade profile. Component-specific LptF permease profile; 27649 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1376NCBIFAMTIGR04408.1lptG LPS export ABC transporter permeaseNCBIfam equivalog-grade profile. Component-specific LptG permease profile; 28899 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1377NCBIFAMNF002997.0lptD LPS assembly outer membrane complex proteinNCBIfam equivalog-grade profile. LptD profile restricted to Gammaproteobacteria; 9959 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1378NCBIFAMNF003358.0lptD LPS-assembly proteinNCBIfam equivalog-grade profile. A second LptD profile restricted to Gammaproteobacteria; 1113 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1379NCBIFAMNF008062.1lptE LPS assembly lipoproteinNCBIfam equivalog-grade profile. LptE profile restricted to Enterobacterales; 2899 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1380KOK01791UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing)KEGG orthology marker; the WecB/MnaA-class activity supplies UDP-ManNAc but is not WTA-specific by itself.
1381KOK02851UDP-GlcNAc:polyprenyl-phosphate GlcNAc-1-phosphate transferaseKEGG orthology marker shared by wecA, tagO and rfe.
1382KOK05946TagA/TarA linkage-unit mannosaminyltransferaseKEGG orthology marker for N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase.
1383KOK21285TagB/TarB teichoic acid glycerol-phosphate primaseKEGG orthology marker.
1384KOK00980TagD glycerol-3-phosphate cytidylyltransferaseKEGG orthology marker.
1385KOK21030TarI D-ribitol-5-phosphate cytidylyltransferaseKEGG orthology marker.
1386KOK05352TarJ ribitol-5-phosphate 2-dehydrogenaseKEGG orthology marker.
1387NCBIFAMNF041712.1teichoic acid glycerol-phosphate transferase TarFNCBIfam equivalog-grade profile restricted to Staphylococcus aureus; 393 RefSeq protein hits in release hmm_PGAP/20.0.
1388NCBIFAMNF041713.1teichoic acid ribitol-phosphate polymerase TarLNCBIfam equivalog-grade profile restricted to Staphylococcus; 1254 RefSeq protein hits in release hmm_PGAP/20.0.
1389KOK21592TarK teichoic acid ribitol-phosphate primaseKEGG orthology marker.
1390KOK18704TarL CDP-ribitol ribitolphosphotransferase / teichoic acid ribitol-phosphate polymeraseKEGG orthology marker.
1391KOK09692TagG teichoic acid transport system permeaseKEGG orthology marker.
1392KOK09693TagH teichoic acid transport system ATP-binding proteinKEGG orthology marker.
1393KOK01005TagT/TagU/TagV polyisoprenyl-teichoic acid--peptidoglycan transferaseKEGG orthology marker for an LCP-family attachment enzyme.
1394NCBIFAMNF010134.0diglucosyldiacylglycerol synthaseNCBIfam equivalog-grade processive glycolipid glycosyltransferase profile restricted to Staphylococcaceae in its seed scope; 1035 RefSeq protein hits in release hmm_PGAP/20.0.
1395NCBIFAMNF047396.1lipoteichoic acid biosynthesis MFS flippase LtaANCBIfam equivalog-grade LtaA profile restricted to Staphylococcaceae in its seed scope; 1045 RefSeq protein hits in release hmm_PGAP/20.0.
1396NCBIFAMNF053595.1lipoteichoic acid synthase LtaSNCBIfam equivalog-grade LtaS profile restricted to Caryophanales in its seed scope; 5195 RefSeq protein hits in release hmm_PGAP/20.0.
1397KOK11892type VI secretion system protein ImpKKEGG orthology marker.
1398NCBIFAMNF005444.0DotU family type VI secretion system proteinNCBIfam equivalog-grade profile. DotU family type VI secretion system protein; 3843 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1399KOK11891type VI secretion system protein ImpLKEGG orthology marker.
1400NCBIFAMTIGR03348.1tssM type VI secretion system membrane subunit TssMNCBIfam equivalog-grade profile. Type VI secretion system membrane subunit TssM; 40259 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1401KOK11906type VI secretion system protein VasDKEGG orthology marker.
1402NCBIFAMTIGR03352.1tssJ type VI secretion system lipoprotein TssJNCBIfam equivalog-grade profile. Type VI secretion system lipoprotein TssJ; 21904 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1403KOK11897type VI secretion system protein ImpFKEGG orthology marker.
1404KOK11905type VI secretion system proteinKEGG orthology marker.
1405KOK11919type VI secretion system lysozyme-related proteinKEGG orthology marker.
1406NCBIFAMTIGR03357.1tssE type VI secretion system baseplate subunit TssENCBIfam equivalog-grade profile. Type VI secretion system baseplate subunit TssE; 20269 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1407KOK11896type VI secretion system protein ImpGKEGG orthology marker.
1408NCBIFAMTIGR03359.1tssF type VI secretion system baseplate subunit TssFNCBIfam equivalog-grade profile. Type VI secretion system baseplate subunit TssF; 43714 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1409KOK11895type VI secretion system protein ImpHKEGG orthology marker.
1410NCBIFAMTIGR03347.1tssG type VI secretion system baseplate subunit TssGNCBIfam equivalog-grade profile. Type VI secretion system baseplate subunit TssG; 34908 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1411KOK11893type VI secretion system protein ImpJKEGG orthology marker.
1412NCBIFAMTIGR03353.2tssK type VI secretion system baseplate subunit TssKNCBIfam equivalog-grade profile. Type VI secretion system baseplate subunit TssK; 33692 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1413KOK11904type VI secretion system secreted protein VgrGKEGG orthology marker.
1414KOK11903type VI secretion system secreted protein HcpKEGG orthology marker.
1415KOK11901type VI secretion system protein ImpBKEGG orthology marker.
1416NCBIFAMTIGR03358.1tssB type VI secretion system contractile sheath small subunitNCBIfam equivalog-grade profile. Type VI secretion system contractile sheath small subunit; 19285 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1417KOK11900type VI secretion system protein ImpCKEGG orthology marker.
1418NCBIFAMTIGR03355.1tssC type VI secretion system contractile sheath large subunitNCBIfam equivalog-grade profile. Type VI secretion system contractile sheath large subunit; 29271 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1419KOK11902type VI secretion system protein ImpAKEGG orthology marker.
1420KOK11910type VI secretion system protein VasJKEGG orthology marker.
1421NCBIFAMTIGR03362.1tssA type VI secretion system protein TssANCBIfam equivalog-grade profile. Type VI secretion system protein TssA; 17997 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1422NCBIFAMTIGR03363.1tssA type VI secretion system protein TssANCBIfam equivalog-grade profile. Type VI secretion system protein TssA; 16453 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1423KOK11907type VI secretion system protein VasGKEGG orthology marker.
1424NCBIFAMTIGR03345.1tssH type VI secretion system ATPase TssHNCBIfam equivalog-grade profile. Type VI secretion system ATPase TssH; 46985 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1425KOK03226type III secretion protein RKEGG orthology marker.
1426KOK22507type III secretion system export apparatus proteinKEGG orthology marker.
1427NCBIFAMTIGR01102.1sctR type III secretion system export apparatus subunit SctRNCBIfam equivalog-grade profile. Type III secretion system export apparatus subunit SctR; 6534 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1428KOK03227type III secretion protein SKEGG orthology marker.
1429KOK22508type III secretion system export apparatus proteinKEGG orthology marker.
1430NCBIFAMTIGR01403.1sctS type III secretion system export apparatus subunit SctSNCBIfam equivalog-grade profile. Type III secretion system export apparatus subunit SctS; 3989 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1431KOK03228type III secretion protein TKEGG orthology marker.
1432KOK22509type III secretion system export apparatus proteinKEGG orthology marker.
1433NCBIFAMTIGR01401.1sctT type III secretion system export apparatus subunit SctTNCBIfam equivalog-grade profile. Type III secretion system export apparatus subunit SctT; 9335 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1434KOK03229type III secretion protein UKEGG orthology marker.
1435KOK22510type III secretion system export apparatus switch proteinKEGG orthology marker.
1436NCBIFAMTIGR01404.2sctU type III secretion system export apparatus subunit SctUNCBIfam equivalog-grade profile. Type III secretion system export apparatus subunit SctU; 6828 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1437KOK03230type III secretion protein VKEGG orthology marker.
1438NCBIFAMTIGR01399.1sctV type III secretion system export apparatus subunit SctVNCBIfam equivalog-grade profile. Type III secretion system export apparatus subunit SctV; 9928 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1439KOK03224ATP synthase in type III secretion protein NKEGG orthology marker.
1440KOK22506type III secretion system ATPaseKEGG orthology marker.
1441NCBIFAMTIGR02546.1sctN type III secretion system ATPase SctNNCBIfam equivalog-grade profile. Type III secretion system ATPase SctN; 5266 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1442KOK03220type III secretion protein DKEGG orthology marker.
1443KOK22488type III secretion system proteinKEGG orthology marker.
1444NCBIFAMTIGR02500.1sctD type III secretion system inner membrane ring subunit SctDNCBIfam equivalog-grade profile. Type III secretion system inner membrane ring subunit SctD; 4702 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1445NCBIFAMTIGR02554.1PrgH/EprH family type III secretion apparatus proteinNCBIfam equivalog-grade profile. PrgH/EprH family type III secretion apparatus protein; 1967 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1446KOK03222type III secretion protein JKEGG orthology marker.
1447KOK22505type III secretion system inner membrane ring proteinKEGG orthology marker.
1448NCBIFAMTIGR02544.1sctJ type III secretion system inner membrane ring lipoprotein SctJNCBIfam equivalog-grade profile. Type III secretion system inner membrane ring lipoprotein SctJ; 9558 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1449KOK03219type III secretion protein CKEGG orthology marker.
1450KOK22504type III secretion system outer membrane ring proteinKEGG orthology marker.
1451NCBIFAMTIGR02516.1sctC type III secretion system outer membrane ring subunit SctCNCBIfam equivalog-grade profile. Type III secretion system outer membrane ring subunit SctC; 10609 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1452KOK03225type III secretion protein QKEGG orthology marker.
1453NCBIFAMTIGR02551.1sctQ type III secretion system cytoplasmic ring protein SctQNCBIfam equivalog-grade profile. Type III secretion system cytoplasmic ring protein SctQ; 9309 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1454KOK04053type III secretion protein IKEGG orthology marker.
1455KOK22487type III secretion system proteinKEGG orthology marker.
1456KOK23661type III secretion system proteinKEGG orthology marker.
1457KOK18374type III secretion inner rod protein HrpB2KEGG orthology marker.
1458NCBIFAMNF038054.1sctI type III secretion system inner rod subunit SctINCBIfam equivalog-grade profile. Type III secretion system inner rod subunit SctI; 1182 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1459KOK03221type III secretion protein FKEGG orthology marker.
1460NCBIFAMTIGR02105.1sctF type III secretion system needle filament subunit SctFNCBIfam equivalog-grade profile. Type III secretion system needle filament subunit SctF; 1403 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1461NCBIFAMNF011854.0type III secretion system needle complex proteinNCBIfam equivalog-grade profile. Type III secretion system needle complex protein; 414 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1462KOK18375type III secretion hrp pilus HrpEKEGG orthology marker.
1463NCBIFAMNF053530.1type III secretion system major pilin HrpANCBIfam equivalog_domain-grade profile. Type III secretion system major pilin HrpA; 432 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1464KOK07324archaeal flagellin FlaAKEGG orthology marker.
1465KOK07325archaeal flagellin FlaBKEGG orthology marker.
1466KOK07329archaeal flagellar protein FlaFKEGG orthology marker.
1467KOK07330archaeal flagellar protein FlaGKEGG orthology marker.
1468KOK07331archaeal flagellar protein FlaHKEGG orthology marker.
1469KOK07332archaeal flagellar protein FlaIKEGG orthology marker.
1470KOK07333archaeal flagellar protein FlaJKEGG orthology marker.
1471KOK07991archaeal preflagellin peptidase FlaK [EC:3.4.23.52]KEGG orthology marker.
1472KOK07822archaeal flagellar protein FlaCKEGG orthology marker.
1473KOK07327archaeal flagellar protein FlaDKEGG orthology marker.
1474KOK07328archaeal flagellar protein FlaEKEGG orthology marker.
1475KOK23986archaeal flagellar protein FlaCEKEGG orthology marker.
1476NCBIFAMNF040695.1preflagellin peptidase FlaKNCBIfam equivalog-grade profile. preflagellin peptidase FlaK; 35 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1477NCBIFAMNF052590.1archaellum stator protein ArlFNCBIfam equivalog-grade profile. archaellum stator protein ArlF; 554 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1478NCBIFAMNF052591.1archaellum stator protein ArlGNCBIfam equivalog-grade profile. archaellum stator protein ArlG; 711 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1479NCBIFAMNF052589.1archaellum protein ArlHNCBIfam equivalog-grade profile. archaellum protein ArlH; 787 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1480NCBIFAMNF058587.1archaellum flagellar ATPase motor FlaINCBIfam equivalog-grade profile. archaellum flagellar ATPase motor FlaI; 982 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1481NCBIFAMNF004703.2archaellar assembly protein ArlJ/FlaJNCBIfam equivalog-grade profile. archaellar assembly protein ArlJ/FlaJ; 205 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1482NCBIFAMNF004704.2archaellar assembly protein ArlJ/FlaJNCBIfam equivalog-grade profile. archaellar assembly protein ArlJ/FlaJ; 741 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1483NCBIFAMNF004705.1archaellar assembly protein ArlJ/FlaJNCBIfam equivalog-grade profile. archaellar assembly protein ArlJ/FlaJ; 84 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1484NCBIFAMNF058591.1archaellum flagellar motor scaffold protein FlaXNCBIfam equivalog-grade profile. archaellum flagellar motor scaffold protein FlaX; 25 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1485KOK02453general secretion pathway protein DKEGG orthology marker.
1486NCBIFAMTIGR02517.1gspD type II secretion system secretin GspDNCBIfam equivalog-grade profile. Type II secretion system secretin GspD; 33545 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1487KOK02452general secretion pathway protein CKEGG orthology marker.
1488NCBIFAMTIGR01713.1gspC type II secretion system protein GspCNCBIfam equivalog-grade profile. Type II secretion system protein GspC; 9033 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1489KOK02455general secretion pathway protein FKEGG orthology marker.
1490NCBIFAMTIGR02120.1gspF type II secretion system inner membrane protein GspFNCBIfam equivalog-grade profile. Type II secretion system inner membrane protein GspF; 21091 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1491KOK02461general secretion pathway protein LKEGG orthology marker.
1492NCBIFAMTIGR01709.2gspL type II secretion system protein GspLNCBIfam equivalog-grade profile. Type II secretion system protein GspL; 29376 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1493KOK02462general secretion pathway protein MKEGG orthology marker.
1494NCBIFAMNF040576.1gspM type II secretion system protein GspMNCBIfam equivalog-grade profile. Type II secretion system protein GspM; 4720 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1495KOK02454general secretion pathway protein EKEGG orthology marker.
1496NCBIFAMTIGR02533.1gspE type II secretion system ATPase GspENCBIfam equivalog-grade profile. Type II secretion system ATPase GspE; 22823 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1497KOK02456general secretion pathway protein GKEGG orthology marker.
1498NCBIFAMTIGR01710.1gspG type II secretion system major pseudopilin GspGNCBIfam equivalog-grade profile. Type II secretion system major pseudopilin GspG; 22392 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1499KOK02457general secretion pathway protein HKEGG orthology marker.
1500NCBIFAMTIGR01708.2gspH type II secretion system minor pseudopilin GspHNCBIfam equivalog-grade profile. Type II secretion system minor pseudopilin GspH; 10806 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1501KOK02458general secretion pathway protein IKEGG orthology marker.
1502NCBIFAMTIGR01707.1gspI type II secretion system minor pseudopilin GspINCBIfam equivalog-grade profile. Type II secretion system minor pseudopilin GspI; 16423 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1503KOK02459general secretion pathway protein JKEGG orthology marker.
1504NCBIFAMTIGR01711.1gspJ type II secretion system minor pseudopilin GspJNCBIfam equivalog-grade profile. Type II secretion system minor pseudopilin GspJ; 13422 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1505KOK02460general secretion pathway protein KKEGG orthology marker.
1506NCBIFAMNF037980.1gspK type II secretion system minor pseudopilin GspKNCBIfam equivalog-grade profile. Type II secretion system minor pseudopilin GspK; 23881 RefSeq protein hits in NCBIfam release hmm_PGAP/20.0.
1507KOK02464general secretion pathway protein OKEGG orthology marker.
1508KOK01467ampC; beta-lactamase class CKEGG orthology marker for a class C beta-lactamase; EC 3.5.2.6, RHEA:20401.
1509KOK17836penP; beta-lactamase class AKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1510KOK17837bla2, blm, ccrA, blaB; metallo-beta-lactamase class BKEGG orthology marker for a class B beta-lactamase; EC 3.5.2.6, RHEA:20401.
1511KOK17838oxa; beta-lactamase class DKEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1512KOK18698blaTEM; beta-lactamase class A TEMKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1513KOK18699blaSHV; beta-lactamase class A SHVKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1514KOK18766blaZ; beta-lactamase class A BlaZKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1515KOK18767blaCTX-M; beta-lactamase class A CTX-MKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1516KOK18768blaKPC; beta-lactamase class A KPCKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1517KOK18780blaNDM; metallo-beta-lactamase class B NDMKEGG orthology marker for a class B beta-lactamase; EC 3.5.2.6, RHEA:20401.
1518KOK18781blaVIM; metallo-beta-lactamase class B VIMKEGG orthology marker for a class B beta-lactamase; EC 3.5.2.6, RHEA:20401.
1519KOK18782blaIMP; metallo-beta-lactamase class B IMPKEGG orthology marker for a class B beta-lactamase; EC 3.5.2.6, RHEA:20401.
1520KOK18790blaOXA-1; beta-lactamase class D OXA-1KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1521KOK18791blaOXA-2; beta-lactamase class D OXA-2KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1522KOK18792blaOXA-10; beta-lactamase class D OXA-10KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1523KOK18793blaOXA-23; beta-lactamase class D OXA-23KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1524KOK18794blaOXA-51; beta-lactamase class D OXA-51KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1525KOK18795blaCARB-1; beta-lactamase class A CARB-1, PSE familyKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1526KOK18796blaLEN; beta-lactamase class A LENKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1527KOK18797blaPER; beta-lactamase class A PERKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1528KOK18970blaGES; beta-lactamase class A GESKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1529KOK18971blaOXA-24; beta-lactamase class D OXA-24KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1530KOK18972blaOXA-58; beta-lactamase class D OXA-58KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1531KOK18973blaOXA-50; beta-lactamase class D OXA-50KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1532KOK18976blaOXA-48; beta-lactamase class D OXA-48KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1533KOK19095blaCMY-1; beta-lactamase class C CMY-1KEGG orthology marker for a class C beta-lactamase; EC 3.5.2.6, RHEA:20401.
1534KOK19096blaCMY-2; beta-lactamase class C CMY-2KEGG orthology marker for a class C beta-lactamase; EC 3.5.2.6, RHEA:20401.
1535KOK19097blaVEB; beta-lactamase class A VEBKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1536KOK19098blaOXA-9; beta-lactamase class D OXA-9KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1537KOK19099blaGIM; metallo-beta-lactamase class B GIMKEGG orthology marker for a class B beta-lactamase; EC 3.5.2.6, RHEA:20401.
1538KOK19100blaDHA; beta-lactamase class C DHAKEGG orthology marker for a class C beta-lactamase; EC 3.5.2.6, RHEA:20401.
1539KOK19101blaFOX; beta-lactamase class C FOXKEGG orthology marker for a class C beta-lactamase; EC 3.5.2.6, RHEA:20401.
1540KOK19209blaOXA-42; beta-lactamase class D OXA-42KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1541KOK19210blaOXA-61; beta-lactamase class D OXA-61KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1542KOK19211blaOXA-62; beta-lactamase class D OXA-62KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1543KOK19212blaOXA-63; beta-lactamase class D OXA-63KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1544KOK19213blaOXA-12; beta-lactamase class D OXA-12KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1545KOK19214blaACC; beta-lactamase class C ACCKEGG orthology marker for a class C beta-lactamase; EC 3.5.2.6, RHEA:20401.
1546KOK19215blaACT_MIR; beta-lactamase class C ACT/MIRKEGG orthology marker for a class C beta-lactamase; EC 3.5.2.6, RHEA:20401.
1547KOK19216blaIND; metallo-beta-lactamase class B INDKEGG orthology marker for a class B beta-lactamase; EC 3.5.2.6, RHEA:20401.
1548KOK19217blaCARB-17; beta-lactamase class A CARB-17KEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1549KOK19218blaCARB-5; beta-lactamase class A CARB-5, RTG familyKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1550KOK19316blaIMI; beta-lactamase class A IMIKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1551KOK19317blaBEL; beta-lactamase class A BELKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1552KOK19318blaOXA-213; beta-lactamase class D OXA-213KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1553KOK19319blaOXA-134; beta-lactamase class D OXA-134KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1554KOK19320blaOXA-211; beta-lactamase class D OXA-211KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1555KOK19321blaOXA-214; beta-lactamase class D OXA-214KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1556KOK19322blaOXA-229; beta-lactamase class D OXA-229KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1557KOK20319blaADC; beta-lactamase class C ADCKEGG orthology marker for a class C beta-lactamase; EC 3.5.2.6, RHEA:20401.
1558KOK20320blaPDC; beta-lactamase class C PDCKEGG orthology marker for a class C beta-lactamase; EC 3.5.2.6, RHEA:20401.
1559KOK21266blaOXA-286; beta-lactamase class D OXA-286KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1560KOK21276blaOXA-22; beta-lactamase class D OXA-22KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1561KOK21277blaOXA-60; beta-lactamase class D OXA-60KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1562KOK22331blaOXA-184; beta-lactamase class D OXA-184KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1563KOK22332blaOXA-548; beta-lactamase class D OXA-548KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1564KOK22333blaOXA-493; beta-lactamase class D OXA-493KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1565KOK22334blaOXA-464; beta-lactamase class D OXA-464KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1566KOK22335blaOXA-114; beta-lactamase class D OXA-114KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1567KOK22346blaSME; beta-lactamase class A SMEKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1568KOK22351blaOXA-209; beta-lactamase class D OXA-209KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1569KOK22352blaOXA-29; beta-lactamase class D OXA-29KEGG orthology marker for a class D beta-lactamase; EC 3.5.2.6, RHEA:20401.
1570KOK24153blaOXY; beta-lactamase class A OXYKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1571KOK24159blaLAP; beta-lactamase class A LAPKEGG orthology marker for a class A beta-lactamase; EC 3.5.2.6, RHEA:20401.
1572KOK24161blaGOP; beta-lactamase class B GOBKEGG orthology marker for a class B beta-lactamase; EC 3.5.2.6, RHEA:20401.
1573KOK24162blaBlaB; beta-lactamase class B BlaBKEGG orthology marker for a class B beta-lactamase; EC 3.5.2.6, RHEA:20401.
1574KOK19271chloramphenicol O-acetyltransferase type AKEGG orthology marker for EC 2.3.1.28, RHEA:18421.
1575KOK00638chloramphenicol O-acetyltransferase type BKEGG orthology marker for EC 2.3.1.28, RHEA:18421.
1576NCBIFAMNF011615.0Tsr serine chemoreceptorNCBIfam hmm_PGAP/20.0 equivalog-grade Tsr profile; separated from Tar.
component_marker1405 rows · 8 columns
component_pkmarker_pkevidence_typeconfidencesourcenotesbasisreference
11orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
22orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
23orthologycuratedKEGG M00048 2026-08-17Multifunctional protein.kegg_reaction_linkNULL
24orthologycuratedKEGG M00048 2026-08-17Multifunctional protein.kegg_reaction_linkNULL
25orthologycuratedKEGG M00048 2026-08-17Fusion protein.kegg_reaction_linkNULL
36orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
37orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
33orthologycuratedKEGG M00048 2026-08-17Multifunctional protein.kegg_reaction_linkNULL
38orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
49orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
510orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
611orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
712orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
813orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
914orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
1013orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
1115orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
113orthologycuratedKEGG M00048 2026-08-17Multifunctional protein.kegg_reaction_linkNULL
114orthologycuratedKEGG M00048 2026-08-17Multifunctional protein.kegg_reaction_linkNULL
1216orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
1217orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
1318orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
1419orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
1520orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
1516orthologycuratedKEGG M00048 2026-08-17Multifunctional protein.kegg_reaction_linkNULL
155orthologycuratedKEGG M00048 2026-08-17Fusion protein.kegg_reaction_linkNULL
1621orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
1722orthologycuratedKEGG M00048 2026-08-17Bifunctional protein.kegg_reaction_linkNULL
178orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
1823orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
1922orthologycuratedKEGG M00048 2026-08-17Bifunctional protein.kegg_reaction_linkNULL
1924orthologycuratedKEGG M00048 2026-08-17NULLkegg_reaction_linkNULL
2025orthologycuratedKEGG M00049 2026-08-17Only the IMP-to-adenylosuccinate reaction is used.kegg_reaction_linkNULL
2121orthologycuratedKEGG M00049 2026-08-17Only the adenylosuccinate-to-AMP reaction is used.kegg_reaction_linkNULL
2226orthologycuratedKEGG M00050 2026-08-17Only the IMP-to-XMP reaction is used; downstream shared nucleotide phosphorylation is excluded.kegg_reaction_linkNULL
2327orthologycuratedKEGG M00050 2026-08-17The complete glutamine-dependent XMP-to-GMP reaction is used.kegg_reaction_linkNULL
2428orthologycuratedKEGG M00051 2026-08-17Multifunctional CAD protein; only the carbamoyl-phosphate synthase reaction is used here.kegg_reaction_linkNULL
2429orthologycuratedKEGG M00051 2026-08-17Multifunctional protein; only the carbamoyl-phosphate synthase reaction is used here.kegg_reaction_linkNULL
2431orthologycuratedKEGG M00051 2026-08-17Single-protein carbamoyl-phosphate synthase architecture.kegg_reaction_linkNULL
2532orthologycuratedKEGG M00051 2026-08-17Required large subunit.kegg_reaction_linkNULL
2633orthologycuratedKEGG M00051 2026-08-17Required small subunit.kegg_reaction_linkNULL
2728orthologycuratedKEGG M00051 2026-08-17Multifunctional CAD protein; only the aspartate carbamoyltransferase reaction is used here.kegg_reaction_linkNULL
2729orthologycuratedKEGG M00051 2026-08-17Multifunctional protein; only the aspartate carbamoyltransferase reaction is used here.kegg_reaction_linkNULL
2735orthologycuratedKEGG M00051 2026-08-17Single-protein aspartate carbamoyltransferase architecture.kegg_reaction_linkNULL
2834orthologycuratedKEGG M00051 2026-08-17Required catalytic subunit.kegg_reaction_linkNULL
2928orthologycuratedKEGG M00051 2026-08-17Multifunctional CAD protein; only the dihydroorotase reaction is used here.kegg_reaction_linkNULL
2930orthologycuratedKEGG M00051 2026-08-17Single-protein dihydroorotase architecture.kegg_reaction_linkNULL
3036orthologycuratedKEGG M00051 2026-08-17Fumarate-dependent reaction R01867.kegg_reaction_linkNULL
3137orthologycuratedKEGG M00051 2026-08-17Quinone-dependent reaction R01868.kegg_reaction_linkNULL
3238orthologycuratedKEGG M00051 2026-08-17NAD-dependent reaction R01869.kegg_reaction_linkNULL
3339orthologycuratedKEGG 2026-08-17PyrK subunit of the class 1B holoenzyme; annotated to the same KEGG reaction R01869.kegg_reaction_linkNULL
3440orthologycuratedKEGG M00051 2026-08-17Bifunctional UMP synthase; only the orotate phosphoribosyltransferase reaction is used here.kegg_reaction_linkNULL
3441orthologycuratedKEGG M00051 2026-08-17Single-function orotate phosphoribosyltransferase.kegg_reaction_linkNULL
3540orthologycuratedKEGG M00051 2026-08-17Bifunctional UMP synthase; only the orotidine 5'-phosphate decarboxylase reaction is used here.kegg_reaction_linkNULL
3542orthologycuratedKEGG M00051 2026-08-17Single-function orotidine 5'-phosphate decarboxylase.kegg_reaction_linkNULL
3643orthologycuratedKEGG M00052 2026-08-17The complete glutamine-dependent UTP-to-CTP reaction is used; shared nucleotide phosphorylation is excluded.kegg_reaction_linkNULL
3744orthologycuratedKEGG M00020 2026-08-17NULLkegg_reaction_linkNULL
3845orthologycuratedKEGG M00020 2026-08-17NULLkegg_reaction_linkNULL
3846orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-27Second orthology group for the reaction, restricted to Thermococcales and Desulfurococcales. KEGG names it phosphoserine transaminase, declares EC 2.6.1.52 and GO:0004648, assigns it R04173 alone -- so it is narrower than K00831, which also carries the pyridoxal phosphate reaction R05085 -- and places it in no glyoxylate map. Ambiguous rather than curated because UniProt names the characterised member Q5JDI4 TK1548 a probable serine--glyoxylate aminotransferase with no EC, and its founding publication is about phosphoglycolate removal; the two readings share a class V aminotransferase fold. None of the 50 genomes carrying it carries K00831 and 49 carry serA and a phosphatase, which is the signature of a non-homologous replacement, but co-occurrence is genomic context and gifter does not evidence claims that way.kegg_reaction_linkNULL
3947orthologycuratedKEGG M00020 2026-08-17NULLkegg_reaction_linkNULL
3948orthologycuratedKEGG M00020 2026-08-17Bifunctional protein; the homoserine kinase activity is used by threonine biosynthesis.kegg_reaction_linkNULL
3949orthologycuratedKEGG M00020 2026-08-17NULLkegg_reaction_linkNULL
3950orthologycuratedKEGG M00020 2026-08-17NULLkegg_reaction_linkNULL
4051orthologycuratedKEGG R00945 2026-08-17Used in the serine-to-glycine direction; no KEGG module covers this capability.kegg_reaction_linkNULL
4152orthologycuratedKEGG M00018 2026-08-17NULLkegg_reaction_linkNULL
4153orthologycuratedKEGG M00018 2026-08-17Bifunctional protein; only the aspartate kinase reaction is used here.kegg_reaction_linkNULL
4154orthologycuratedKEGG M00018 2026-08-17Bifunctional protein; only the aspartate kinase reaction is used here.kegg_reaction_linkNULL
4155orthologycuratedKEGG M00018 2026-08-17Bifunctional protein carrying EC 2.7.2.4; listed by M00018 but omitted from M00017, which is a KEGG inconsistency.kegg_reaction_linkNULL
4256orthologycuratedKEGG M00018 2026-08-17NULLkegg_reaction_linkNULL
4357orthologycuratedKEGG M00018 2026-08-17NULLkegg_reaction_linkNULL
4353orthologycuratedKEGG M00018 2026-08-17Bifunctional protein; only the homoserine dehydrogenase reaction is used here.kegg_reaction_linkNULL
4354orthologycuratedKEGG M00018 2026-08-17Bifunctional protein; only the homoserine dehydrogenase reaction is used here.kegg_reaction_linkNULL
4457orthologycuratedKEGG M00018 2026-08-17KEGG annotates the same orthologue to both cofactor reactions.kegg_reaction_linkNULL
4453orthologycuratedKEGG M00018 2026-08-17Bifunctional protein; only the homoserine dehydrogenase reaction is used here.kegg_reaction_linkNULL
4454orthologycuratedKEGG M00018 2026-08-17Bifunctional protein; only the homoserine dehydrogenase reaction is used here.kegg_reaction_linkNULL
4558orthologycuratedKEGG M00018 2026-08-17NULLkegg_reaction_linkNULL
4559orthologycuratedKEGG M00018 2026-08-17NULLkegg_reaction_linkNULL
4548orthologycuratedKEGG M00018 2026-08-17Bifunctional protein; the phosphoserine phosphatase activity is used by serine biosynthesis.kegg_reaction_linkNULL
4660orthologycuratedKEGG M00018 2026-08-17NULLkegg_reaction_linkNULL
4761orthologycuratedKEGG M00017 2026-08-17KEGG assigns both R01776 and R01777 to this orthologue, so the acyl specificity is not recoverable at KO resolution.kegg_reaction_linkNULL
4762orthologycuratedKEGG M00017 2026-08-17KEGG assigns both R01776 and R01777 to this orthologue, so the acyl specificity is not recoverable at KO resolution.kegg_reaction_linkNULL
4862orthologycuratedKEGG M00017 2026-08-17KEGG assigns both R01776 and R01777 to this orthologue, so the acyl specificity is not recoverable at KO resolution.kegg_reaction_linkNULL
4861orthologycuratedKEGG M00017 2026-08-17KEGG assigns both R01776 and R01777 to this orthologue, so the acyl specificity is not recoverable at KO resolution.kegg_reaction_linkNULL
4963orthologycuratedKEGG M00017 2026-08-17NULLkegg_reaction_linkNULL
5063orthologycuratedKEGG R03217 2026-08-17KEGG annotates the same orthologue to the O-acetylhomoserine chemistry.kegg_reaction_linkNULL
5164orthologycuratedKEGG M00017 2026-08-17NULLkegg_reaction_linkNULL
5265orthologycuratedKEGG M00017 2026-08-17NULLkegg_reaction_linkNULL
5266orthologycuratedKEGG M00017 2026-08-17NULLkegg_reaction_linkNULL
5371orthologycuratedKEGG R01288 2026-08-17MetZ is the dedicated O-succinylhomoserine sulfhydrylase. K01739 is rejected here although KEGG annotates MetB to R01288: the sulfhydrylase side activity of a cystathionine gamma-synthase is not evidence that a genome assimilates sulfide directly, and accepting it would make every transsulfuration genome positive for this GIFT.kegg_reaction_linkNULL
5470orthologycuratedKEGG R01287 2026-08-17Direct sulfhydrylation; absent from KEGG module M00017.kegg_reaction_linkNULL
5472orthologycuratedKEGG R01287 2026-08-17Bifunctional sulfhydrylase; the O-acetylserine activity is used by cysteine biosynthesis.ec_matchNULL
5567orthologycuratedKEGG M00017 2026-08-17NULLkegg_reaction_linkNULL
5568orthologycuratedKEGG M00017 2026-08-17Bifunctional protein; only the methionine synthase reaction is used here.kegg_reaction_linkNULL
5669orthologycuratedKEGG M00017 2026-08-17NULLkegg_reaction_linkNULL
5773orthologycuratedKEGG M00021 2026-08-17NULLkegg_reaction_linkNULL
5774orthologycuratedKEGG M00021 2026-08-17NULLkegg_reaction_linkNULL
5875orthologycuratedKEGG M00021 2026-08-17NULLkegg_reaction_linkNULL
5876orthologycuratedKEGG M00021 2026-08-17Bifunctional protein; only the cysteine synthase reaction is used here.kegg_reaction_linkNULL
5872orthologycuratedKEGG M00021 2026-08-17Bifunctional sulfhydrylase; the O-acetylhomoserine activity is used by methionine biosynthesis.kegg_reaction_linkNULL
5977orthologycuratedKEGG M00338 2026-08-17NULLkegg_reaction_linkNULL
5978orthologycuratedKEGG M00338 2026-08-17Multifunctional protein; only the cystathionine beta-synthase reaction is used here.kegg_reaction_linkNULL
6080orthologycuratedKEGG M00609 2026-08-17Cysteine-forming step of M00609; the four SAM-cycle steps of that module are excluded.kegg_reaction_linkNULL
6179orthologycuratedKEGG M00338 2026-08-17NULLkegg_reaction_linkNULL
6181orthologycuratedKEGG M00609 2026-08-17KEGG assigns both orthologues to R01001; they are alternative evidence for one reaction.kegg_reaction_linkNULL
6282orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
6383orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
6484orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
6585orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
6586orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
6687orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
6788orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
6889orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
6990orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
7091orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
7092orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
7193orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
7294orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
7395orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
7496orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
7597orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
7698orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
7699orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
77100orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
77101orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
77102orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Cell wall recycling kinase acting on the same chemistry.kegg_reaction_linkNULL
78103orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
79104orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
80105orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
81106orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
81107orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Bifunctional nanEK supports components in two reactions.kegg_reaction_linkNULL
82108orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
82107orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Bifunctional nanEK supports components in two reactions.kegg_reaction_linkNULL
83109orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
84110orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
85114orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
86115orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
86116orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
86117orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
87109orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
88118orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
89119orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
89120orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
90111orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
91112orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
92113orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
93121orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18NULLunsupportedNULL
94122orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18NULLunsupportedNULL
95123orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLec_matchNULL
96127orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18Dual-specificity system, characterised on both pentoses.unsupportedNULL
97128orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18Dual-specificity system, characterised on both pentoses.unsupportedNULL
98129orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18Dual-specificity system, characterised on both pentoses.unsupportedNULL
99124orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18NULLunsupportedNULL
100125orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18NULLunsupportedNULL
101126orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLec_matchNULL
102127orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18Dual-specificity system, characterised on both pentoses.unsupportedNULL
103128orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18Dual-specificity system, characterised on both pentoses.unsupportedNULL
104129orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18Dual-specificity system, characterised on both pentoses.unsupportedNULL
105130orthologycuratedKEGG orthology, verified 2026-08-18NULLec_matchNULL
105131orthologycuratedKEGG orthology, verified 2026-08-18NULLec_matchNULL
105132orthologycuratedKEGG orthology, verified 2026-08-18NULLec_matchNULL
105133sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 11 distinct characterised activities in dbCAN.ec_matchNULL
105134sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 19 distinct characterised activities in dbCAN.ec_matchNULL
105135sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 8 distinct characterised activities in dbCAN.ec_matchNULL
105136sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 28 distinct characterised activities in dbCAN.ec_matchNULL
105137sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 6 distinct characterised activities in dbCAN.ec_matchNULL
105138sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 3 distinct characterised activities in dbCAN.ec_matchNULL
105139sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 1 characterised activity in dbCAN.ec_matchNULL
106140orthologycuratedKEGG orthology, verified 2026-08-18NULLec_matchNULL
106141sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 7 distinct characterised activities in dbCAN.ec_matchNULL
106142sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 2 distinct characterised activities in dbCAN.ec_matchNULL
106143sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 2 distinct characterised activities in dbCAN.ec_matchNULL
106144sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 9 distinct characterised activities in dbCAN.ec_matchNULL
106135sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 8 distinct characterised activities in dbCAN.ec_matchNULL
106145sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 4 distinct characterised activities in dbCAN.ec_matchNULL
106136sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 28 distinct characterised activities in dbCAN.ec_matchNULL
106137sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 6 distinct characterised activities in dbCAN.ec_matchNULL
106146sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 7 distinct characterised activities in dbCAN.ec_matchNULL
106147sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 9 distinct characterised activities in dbCAN.ec_matchNULL
106148sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 2 distinct characterised activities in dbCAN.ec_matchNULL
107149orthologycuratedKEGG orthology, verified 2026-08-18NULLec_matchNULL
107150orthologycuratedKEGG orthology, verified 2026-08-18NULLec_matchNULL
107151orthologycuratedKEGG orthology, verified 2026-08-18NULLec_matchNULL
107152sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 30 distinct characterised activities in dbCAN.ec_matchNULL
107141sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 7 distinct characterised activities in dbCAN.ec_matchNULL
107142sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 2 distinct characterised activities in dbCAN.ec_matchNULL
107153sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 5 distinct characterised activities in dbCAN.ec_matchNULL
107154sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 1 characterised activity in dbCAN.ec_matchNULL
107133sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 11 distinct characterised activities in dbCAN.ec_matchNULL
107134sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 19 distinct characterised activities in dbCAN.ec_matchNULL
107144sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 9 distinct characterised activities in dbCAN.ec_matchNULL
107155sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 6 distinct characterised activities in dbCAN.ec_matchNULL
107135sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 8 distinct characterised activities in dbCAN.ec_matchNULL
107136sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 28 distinct characterised activities in dbCAN.ec_matchNULL
107137sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 6 distinct characterised activities in dbCAN.ec_matchNULL
107156sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 1 characterised activity in dbCAN.ec_matchNULL
107138sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 3 distinct characterised activities in dbCAN.ec_matchNULL
108157orthologycuratedKEGG orthology, verified 2026-08-18NULLec_matchNULL
108158orthologycuratedKEGG orthology, verified 2026-08-18NULLec_matchNULL
108159sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 1 characterised activity in dbCAN.ec_matchNULL
108160sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 1 characterised activity in dbCAN.ec_matchNULL
108161sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 34 distinct characterised activities in dbCAN.ec_matchNULL
108162sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 7 distinct characterised activities in dbCAN.ec_matchNULL
109163orthologycuratedKEGG orthology, verified 2026-08-18NULLec_matchNULL
109161sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 34 distinct characterised activities in dbCAN.ec_matchNULL
109162sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 7 distinct characterised activities in dbCAN.ec_matchNULL
110164orthologycuratedKEGG orthology, verified 2026-08-18NULLec_matchNULL
110165sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 1 characterised activity in dbCAN.ec_matchNULL
110161sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 34 distinct characterised activities in dbCAN.ec_matchNULL
110166sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 14 distinct characterised activities in dbCAN.ec_matchNULL
110167sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 7 distinct characterised activities in dbCAN.ec_matchNULL
110168sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 5 distinct characterised activities in dbCAN.ec_matchNULL
110169sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 2 distinct characterised activities in dbCAN.ec_matchNULL
110170sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 5 distinct characterised activities in dbCAN.ec_matchNULL
111171orthologycuratedKEGG orthology, verified 2026-08-18NULLec_matchNULL
111172sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 5 distinct characterised activities in dbCAN.ec_matchNULL
111173sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 3 distinct characterised activities in dbCAN.ec_matchNULL
111174sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 2 distinct characterised activities in dbCAN.ec_matchNULL
111175sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 6 distinct characterised activities in dbCAN.ec_matchNULL
111176sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 3 distinct characterised activities in dbCAN.ec_matchNULL
111177sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 1 characterised activity in dbCAN.ec_matchNULL
111178sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 3 distinct characterised activities in dbCAN.ec_matchNULL
111179sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping, retrieved 2026-08-18Family carries 3 distinct characterised activities in dbCAN.ec_matchNULL
106180sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106181sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106182sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-189 of 9 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106183sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106184sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106185sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106186sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106187sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 7 EC-annotated members carry EC 3.2.1.8 (71%); contains CAZy subfamily GH43_16.ec_matchNULL
106188sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-188 of 11 EC-annotated members carry EC 3.2.1.8 (73%); contains CAZy subfamily GH43_12.ec_matchNULL
106189sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-188 of 8 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106190sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106191sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1822 of 22 EC-annotated members carry EC 3.2.1.8 (100%); contains CAZy subfamily GH43_12.ec_matchNULL
106192sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106193sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1829 of 34 EC-annotated members carry EC 3.2.1.8 (85%); contains CAZy subfamily GH43_16;GH5_1.ec_matchNULL
106194sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106195sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106196sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106197sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106198sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106199sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106200sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106201sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106202sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106203sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1813 of 13 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106204sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106205sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106206sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 6 EC-annotated members carry EC 3.2.1.8 (67%); contains CAZy subfamily GH5_1.ec_matchNULL
106207sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1815 of 15 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106208sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106209sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106210sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1831 of 31 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106211sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106212sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106213sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106214sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-186 of 9 EC-annotated members carry EC 3.2.1.8 (67%).ec_matchNULL
106215sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106216sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106217sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-189 of 9 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106218sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-189 of 9 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106219sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1844 of 44 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106220sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106221sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106222sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-187 of 7 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106223sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106224sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%); contains CAZy subfamily GH43_16.ec_matchNULL
106225sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1821 of 21 EC-annotated members carry EC 3.2.1.8 (100%); contains CAZy subfamily GH43_1;GH43_12.ec_matchNULL
106226sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106227sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106228sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1832 of 32 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106229sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106230sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106231sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1828 of 28 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106232sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1820 of 20 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106233sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106234sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1859 of 59 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106235sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106236sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1829 of 29 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106237sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-18104 of 104 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106238sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106239sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1812 of 12 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106240sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1812 of 12 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106241sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106242sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1866 of 71 EC-annotated members carry EC 3.2.1.8 (93%).ec_matchNULL
106243sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1818 of 18 EC-annotated members carry EC 3.2.1.8 (100%); contains CAZy subfamily GH5_53.ec_matchNULL
106244sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106245sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106246sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.8 (100%); contains CAZy subfamily GH5_53.ec_matchNULL
106247sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1810 of 12 EC-annotated members carry EC 3.2.1.8 (83%); contains CAZy subfamily GH16_21.ec_matchNULL
106248sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1837 of 37 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106249sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1866 of 66 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106252sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%); contains CAZy subfamily GH30_7.ec_matchNULL
106253sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%); contains CAZy subfamily GH30_8;GH43_10.ec_matchNULL
106255sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1816 of 24 EC-annotated members carry EC 3.2.1.8 (67%); contains CAZy subfamily GH30_8.ec_matchNULL
106257sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%); contains CAZy subfamily GH5_21.ec_matchNULL
106259sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%); contains CAZy subfamily GH43_10;GH5_21.ec_matchNULL
106261sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 4 EC-annotated members carry EC 3.2.1.8 (50%); contains CAZy subfamily GH5_4.ec_matchNULL
106265sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-186 of 11 EC-annotated members carry EC 3.2.1.8 (55%).ec_matchNULL
106266sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 5 EC-annotated members carry EC 3.2.1.8 (60%); contains CAZy subfamily GH5_55.ec_matchNULL
106267sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
106269sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.8 (100%).ec_matchNULL
107270sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.37 (100%).ec_matchNULL
107271sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1892 of 131 EC-annotated members carry EC 3.2.1.37 (70%).ec_matchNULL
107273sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-188 of 8 EC-annotated members carry EC 3.2.1.37 (100%).ec_matchNULL
107275sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.37 (100%).ec_matchNULL
107276sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1831 of 31 EC-annotated members carry EC 3.2.1.37 (100%).ec_matchNULL
107277sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1815 of 18 EC-annotated members carry EC 3.2.1.37 (83%).ec_matchNULL
107278sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.37 (100%).ec_matchNULL
107279sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.37 (100%).ec_matchNULL
107280sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.37 (100%).ec_matchNULL
107281sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1810 of 10 EC-annotated members carry EC 3.2.1.37 (100%).ec_matchNULL
107282sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 8 EC-annotated members carry EC 3.2.1.37 (50%); contains CAZy subfamily GH43_35.ec_matchNULL
107283sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1820 of 23 EC-annotated members carry EC 3.2.1.37 (87%); contains CAZy subfamily GH43_11;GH43_12.ec_matchNULL
107284sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-186 of 8 EC-annotated members carry EC 3.2.1.37 (75%); contains CAZy subfamily GH43_11;GH43_12;GH43_13.ec_matchNULL
107285sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 4 EC-annotated members carry EC 3.2.1.37 (50%); contains CAZy subfamily GH43_2.ec_matchNULL
107286sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.37 (100%); contains CAZy subfamily GH43_12;GH43_13.ec_matchNULL
107287sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1819 of 23 EC-annotated members carry EC 3.2.1.37 (83%); contains CAZy subfamily GH43_1;GH43_10;GH43_29;GH43_32;GH43_33;GH43_34;GH5_21.ec_matchNULL
107288sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 4 EC-annotated members carry EC 3.2.1.37 (50%); contains CAZy subfamily GH43_10;GH43_17;GH43_26;GH43_29;GH43_30.ec_matchNULL
107289sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 4 EC-annotated members carry EC 3.2.1.37 (50%); contains CAZy subfamily GH43_12.ec_matchNULL
107290sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 4 EC-annotated members carry EC 3.2.1.37 (50%); contains CAZy subfamily GH5_22.ec_matchNULL
107292sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-188 of 8 EC-annotated members carry EC 3.2.1.37 (100%).ec_matchNULL
105293sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_10;GH43_12.ec_matchNULL
105294sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_10;GH43_16.ec_matchNULL
105295sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-187 of 7 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_12.ec_matchNULL
105296sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_19;GH43_29;GH43_34.ec_matchNULL
105297sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_18;GH43_20;PL1_2.ec_matchNULL
105298sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_10;GH43_16.ec_matchNULL
105299sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_8;GH43_9.ec_matchNULL
105300sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_10.ec_matchNULL
105301sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_10;GH43_16.ec_matchNULL
105302sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_12.ec_matchNULL
105256sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1811 of 15 EC-annotated members carry EC 3.2.1.55 (73%); contains CAZy subfamily GH43_10;GH43_16;GH43_34.ec_matchNULL
105282sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 8 EC-annotated members carry EC 3.2.1.55 (50%); contains CAZy subfamily GH43_35.ec_matchNULL
105303sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 4 EC-annotated members carry EC 3.2.1.55 (50%); contains CAZy subfamily GH43_17;GH43_23;GH43_26;GH43_34.ec_matchNULL
105304sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_2;GH43_29;GH43_34.ec_matchNULL
105285sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 4 EC-annotated members carry EC 3.2.1.55 (50%); contains CAZy subfamily GH43_2.ec_matchNULL
105305sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_12.ec_matchNULL
105306sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_36.ec_matchNULL
105307sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_10;GH43_29.ec_matchNULL
105288sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 4 EC-annotated members carry EC 3.2.1.55 (50%); contains CAZy subfamily GH43_10;GH43_17;GH43_26;GH43_29;GH43_30.ec_matchNULL
105289sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 4 EC-annotated members carry EC 3.2.1.55 (50%); contains CAZy subfamily GH43_12.ec_matchNULL
105308sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_20.ec_matchNULL
105309sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_18;GH43_20;GH43_34.ec_matchNULL
105310sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1836 of 36 EC-annotated members carry EC 3.2.1.55 (100%).ec_matchNULL
105311sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.55 (100%).ec_matchNULL
105312sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1826 of 26 EC-annotated members carry EC 3.2.1.55 (100%).ec_matchNULL
105313sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-187 of 7 EC-annotated members carry EC 3.2.1.55 (100%).ec_matchNULL
105314sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.55 (100%).ec_matchNULL
105315sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.55 (100%).ec_matchNULL
105316sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1810 of 10 EC-annotated members carry EC 3.2.1.55 (100%).ec_matchNULL
105317sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH51_2.ec_matchNULL
105291sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1820 of 31 EC-annotated members carry EC 3.2.1.55 (65%).ec_matchNULL
105318sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_18;GH43_22;GH43_29;GH43_34;GH43_4.ec_matchNULL
105319sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH51_1.ec_matchNULL
105320sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1810 of 10 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH51_1;GH51_14.ec_matchNULL
105321sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1823 of 23 EC-annotated members carry EC 3.2.1.55 (100%).ec_matchNULL
105322sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1824 of 24 EC-annotated members carry EC 3.2.1.55 (100%).ec_matchNULL
105323sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_16.ec_matchNULL
105324sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.55 (100%); contains CAZy subfamily GH43_36.ec_matchNULL
108325sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.1 (100%).ec_matchNULL
108326sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-187 of 7 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_1.ec_matchNULL
108327sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_36.ec_matchNULL
108328sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_1.ec_matchNULL
108329sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1810 of 10 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_6.ec_matchNULL
108330sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_19;GH13_32;GH13_6.ec_matchNULL
108331sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_19;GH13_28;GH13_32;GH13_42.ec_matchNULL
108332sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-189 of 17 EC-annotated members carry EC 3.2.1.1 (53%); contains CAZy subfamily GH13_20;GH13_21;GH13_39.ec_matchNULL
108333sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_5.ec_matchNULL
108334sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-187 of 7 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_5;GH13_7.ec_matchNULL
108336sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1816 of 16 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_1.ec_matchNULL
108337sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1849 of 49 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_15;GH13_24;GH13_32.ec_matchNULL
108338sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_1;GH13_2.ec_matchNULL
108339sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_32.ec_matchNULL
108340sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_28;GH13_32.ec_matchNULL
108341sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_5.ec_matchNULL
108343sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_5.ec_matchNULL
108344sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_28.ec_matchNULL
108345sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1810 of 19 EC-annotated members carry EC 3.2.1.1 (53%); contains CAZy subfamily GH13_39.ec_matchNULL
108346sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1815 of 17 EC-annotated members carry EC 3.2.1.1 (88%); contains CAZy subfamily GH13_36.ec_matchNULL
108348sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-188 of 8 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_28.ec_matchNULL
108349sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1850 of 50 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_6.ec_matchNULL
108350sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_20.ec_matchNULL
108351sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-18214 of 219 EC-annotated members carry EC 3.2.1.1 (98%); contains CAZy subfamily GH13_15;GH13_24;GH13_34.ec_matchNULL
108352sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1818 of 18 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_7.ec_matchNULL
108353sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-187 of 10 EC-annotated members carry EC 3.2.1.1 (70%); contains CAZy subfamily GH13_1;GH13_45.ec_matchNULL
108354sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_32.ec_matchNULL
108355sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-188 of 8 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_36.ec_matchNULL
108356sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-188 of 8 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_32.ec_matchNULL
108357sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-188 of 8 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_36.ec_matchNULL
108358sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1810 of 14 EC-annotated members carry EC 3.2.1.1 (71%); contains CAZy subfamily GH13_19;GH13_45;GH13_6.ec_matchNULL
108359sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1879 of 79 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_1;GH13_45.ec_matchNULL
108360sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_1.ec_matchNULL
108361sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-18153 of 163 EC-annotated members carry EC 3.2.1.1 (94%); contains CAZy subfamily GH13_5;GH13_7.ec_matchNULL
108362sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_28.ec_matchNULL
108363sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_49.ec_matchNULL
108365sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_36.ec_matchNULL
108367sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 5 EC-annotated members carry EC 3.2.1.1 (60%); contains CAZy subfamily GH13_36.ec_matchNULL
108368sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_27.ec_matchNULL
108372sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 6 EC-annotated members carry EC 3.2.1.1 (67%); contains CAZy subfamily GH13_48.ec_matchNULL
108373sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1817 of 20 EC-annotated members carry EC 3.2.1.1 (85%); contains CAZy subfamily GH13_14;GH13_5;GH13_7.ec_matchNULL
108374sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1825 of 25 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH13_28;GH13_42.ec_matchNULL
108375sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-186 of 12 EC-annotated members carry EC 3.2.1.1 (50%); contains CAZy subfamily GH13_12;GH13_14;GH13_28;GH13_41.ec_matchNULL
108377sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.1 (100%); contains CAZy subfamily GH57_7.ec_matchNULL
108379sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.1 (100%).ec_matchNULL
110381sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.20 (100%); contains CAZy subfamily GH13_38.ec_matchNULL
110383sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1814 of 14 EC-annotated members carry EC 3.2.1.20 (100%); contains CAZy subfamily GH13_17.ec_matchNULL
110384sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.20 (100%); contains CAZy subfamily GH13_16;GH13_23;GH13_30.ec_matchNULL
110385sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.20 (100%); contains CAZy subfamily GH13_23;GH13_30;GH13_40.ec_matchNULL
110386sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-187 of 9 EC-annotated members carry EC 3.2.1.20 (78%); contains CAZy subfamily GH13_16;GH13_17;GH13_23;GH13_40;GH13_48.ec_matchNULL
110347sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1815 of 22 EC-annotated members carry EC 3.2.1.20 (68%); contains CAZy subfamily GH13_20;GH13_21.ec_matchNULL
110389sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.20 (100%); contains CAZy subfamily GH31_1.ec_matchNULL
110390sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.20 (100%); contains CAZy subfamily GH31_1.ec_matchNULL
110391sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.20 (100%).ec_matchNULL
110392sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1825 of 50 EC-annotated members carry EC 3.2.1.20 (50%).ec_matchNULL
110393sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.20 (100%).ec_matchNULL
110394sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1835 of 65 EC-annotated members carry EC 3.2.1.20 (54%).ec_matchNULL
110395sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1813 of 15 EC-annotated members carry EC 3.2.1.20 (87%).ec_matchNULL
110396sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-189 of 12 EC-annotated members carry EC 3.2.1.20 (75%).ec_matchNULL
110397sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1835 of 49 EC-annotated members carry EC 3.2.1.20 (71%).ec_matchNULL
110398sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.20 (100%).ec_matchNULL
110399sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1820 of 20 EC-annotated members carry EC 3.2.1.20 (100%).ec_matchNULL
110400sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.20 (100%).ec_matchNULL
110402sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-189 of 18 EC-annotated members carry EC 3.2.1.20 (50%).ec_matchNULL
110403sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 4 EC-annotated members carry EC 3.2.1.20 (50%).ec_matchNULL
109404sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.41 (100%); contains CAZy subfamily GH13_13.ec_matchNULL
109405sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.41 (100%); contains CAZy subfamily GH13_14.ec_matchNULL
109406sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.41 (100%); contains CAZy subfamily GH13_20.ec_matchNULL
109407sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.41 (100%); contains CAZy subfamily GH13_14.ec_matchNULL
109335sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1810 of 13 EC-annotated members carry EC 3.2.1.41 (77%); contains CAZy subfamily GH13_13;GH13_3;GH13_32.ec_matchNULL
109342sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1825 of 31 EC-annotated members carry EC 3.2.1.41 (81%); contains CAZy subfamily GH13_13;GH13_14;GH13_32;GH13_37;GH13_5.ec_matchNULL
109408sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 10 EC-annotated members carry EC 3.2.1.41 (50%); contains CAZy subfamily GH13_12;GH13_41.ec_matchNULL
109409sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1812 of 12 EC-annotated members carry EC 3.2.1.41 (100%); contains CAZy subfamily GH13_14.ec_matchNULL
109410sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1810 of 10 EC-annotated members carry EC 3.2.1.41 (100%); contains CAZy subfamily GH13_14.ec_matchNULL
109411sequence_subfamilycuratedCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1818 of 18 EC-annotated members carry EC 3.2.1.41 (100%); contains CAZy subfamily GH13_12;GH13_14;GH13_41.ec_matchNULL
109364sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 6 EC-annotated members carry EC 3.2.1.41 (67%); contains CAZy subfamily GH13_20.ec_matchNULL
109366sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-186 of 11 EC-annotated members carry EC 3.2.1.41 (55%); contains CAZy subfamily GH13_14;GH13_32;GH13_41.ec_matchNULL
109371sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1815 of 17 EC-annotated members carry EC 3.2.1.41 (88%); contains CAZy subfamily GH13_14.ec_matchNULL
109412sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.41 (100%); contains CAZy subfamily GH13_14.ec_matchNULL
109378sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 7 EC-annotated members carry EC 3.2.1.41 (71%).ec_matchNULL
111413sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-183 of 3 EC-annotated members carry EC 3.1.1.72 (100%).ec_matchNULL
111414sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-187 of 7 EC-annotated members carry EC 3.1.1.72 (100%).ec_matchNULL
111415sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 5 EC-annotated members carry EC 3.1.1.72 (100%).ec_matchNULL
111418sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 4 EC-annotated members carry EC 3.1.1.72 (100%).ec_matchNULL
111419sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-186 of 8 EC-annotated members carry EC 3.1.1.72 (75%); contains CAZy subfamily GH43_10;GH43_17;GH43_28.ec_matchNULL
111420sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-185 of 5 EC-annotated members carry EC 3.1.1.72 (100%).ec_matchNULL
111421sequence_subfamilyambiguousCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-1814 of 28 EC-annotated members carry EC 3.1.1.72 (50%).ec_matchNULL
111422sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 4 EC-annotated members carry EC 3.1.1.72 (100%).ec_matchNULL
111423sequence_subfamilyhigh-confidenceCAZy subfamily via dbCAN-sub db_v5-2-9_5-5-2026 HMM profiles, derived 2026-08-184 of 4 EC-annotated members carry EC 3.1.1.72 (100%).ec_matchNULL
112424orthologycuratedKEGG, verified 2026-08-18KEGG assigns K01387 to MEROPS family M9 and to toxins that damage the extracellular matrix. Microbial only: the host collagenases MMP-1 and MMP-8 are separate orthologues.ec_matchNULL
112425sequence_familyhigh-confidenceInterPro/Pfam, retrieved 2026-08-18Pfam Collagenase, the M9 catalytic domain, described by InterPro as a family of enzymes that break down collagens. Substrate-specific at family level, unlike the broad protease families.not_assessedNULL
113497orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
114498orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
115500orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
116501orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Shared with the 2-oxoglutarate and branched-chain complexes; required here as a subunit rather than as evidence of the reaction on its own.kegg_reaction_linkNULL
117499orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18AceE-type single polypeptide; 4813 KEGG organisms complete the complex this way and would be negative if only the alpha/beta architecture were accepted.kegg_reaction_linkNULL
118500orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
119501orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
120502orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
121503orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
122505orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
123504orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
124506orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Fused four-domain protein; 2202 KEGG organisms carry it, including most gut anaerobes that carry no PorABCD.kegg_reaction_linkNULL
125507orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
126508orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18NULLunsupportedNULL
127509orthologycuratedKEGG M00579 2026-08-18NULLkegg_reaction_linkNULL
127510orthologycuratedKEGG M00579 2026-08-18Second phosphotransacetylase group of KEGG M00579.kegg_reaction_linkNULL
127511orthologycuratedKEGG M00579 2026-08-18Third group of KEGG M00579, annotated as putative; retained because the module accepts it and it adds no false positives that K00625 or K13788 do not already cover.kegg_reaction_linkNULL
128512orthologycuratedKEGG M00579 2026-08-18NULLkegg_reaction_linkNULL
129513orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18Chain-length-generic thiolase. Acceptable here only because the route also requires the substrate-specific transferase; it licenses no claim on its own.kegg_reaction_linkNULL
130514orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18The orthology group also carries paaH, fadB and mmgB. Same reasoning as the thiolase.kegg_reaction_linkNULL
131515orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18Chain-length-generic enoyl-CoA hydratase. Same reasoning as the thiolase.kegg_reaction_linkNULL
132516orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18Generic short-chain acyl-CoA dehydrogenase. Same reasoning as the thiolase.kegg_reaction_linkNULL
133517sequence_familyhigh-confidenceInterPro/NCBIfam, retrieved 2026-08-18Matches 178 proteins in 171 proteomes, led by Faecalibacterium, Roseburia, Eubacterium and Anaerostipes, and matches no Bacillus, Escherichia, Salmonella or Pseudomonas. K01034 and K01035 are deliberately refused here: KEGG assigns them EC 2.8.3.8 and EC 2.8.3.9 together, so they cannot separate butanoate release from acetoacetate degradation.not_assessedNULL
134518orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
135519orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
136520orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
137521orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
138522orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
139523orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
140524orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18PduW, the operon-encoded kinase.kegg_reaction_linkNULL
140525orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18TdcD, assigned to the same reaction R01353 and accepted as an alternative.kegg_reaction_linkNULL
141526orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18KEGG assigns the lactoyl-CoA transfer R01449 to this group alongside the propanoate transfer R00928.kegg_reaction_linkNULL
142527orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
143528orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
144529orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Assigned in 22 KEGG organisms and in 4 of the 13 that carry the transferase with both dehydratase subunits; the remaining nine are reported incomplete with this reaction named.kegg_reaction_linkNULL
145530orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18The NAD-dependent enzyme, EC 1.1.1.27. Present in 4143 of 11855 organisms and sharing only 573 of them with the quinone-dependent K29125, which is why this component evidences a direction.kegg_reaction_linkNULL
146531orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Present in 560 organisms, anaerobe-dominated. Eight of the ten genomes behind propionate_formation_acrylate carry it.kegg_reaction_linkNULL
147532orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Present in 337 organisms, almost all lactic acid bacteria.kegg_reaction_linkNULL
148533orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
149534orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
150535orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
151536orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18The acyl-carrier ligase. Required because apo-citrate lyase is inactive.unsupportedNULL
152537orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18Alpha subunit only. K01572 is assigned in one KEGG organism, so it is not usable as required evidence.unsupportedNULL
153538orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
154539orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18AdhE is bifunctional, so one accession evidences both reactions of the route.kegg_reaction_linkNULL
155539orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18The same protein as the preceding step; the alcohol dehydrogenase activity of AdhE.kegg_reaction_linkNULL
156540orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18KEGG names this group ilvB, ilvG, ilvI: it is the anabolic branched-chain amino acid synthase and is present in 9341 organisms. Recorded so that the curated chemistry is complete, and confined to a route step declared not required so that it can never carry the acetoin claim.kegg_reaction_linkNULL
157541orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Acetolactate decarboxylase, present in 1649 organisms and existing only for this pathway. The whole specificity of acetoin_formation rests here.kegg_reaction_linkNULL
158542orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
159543orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Bifunctional GTP cyclohydrolase II / 3,4-dihydroxy-2-butanone 4-phosphate synthase; carries both riboflavin ring-forming activities in one polypeptide.kegg_reaction_linkNULL
160544orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
161545orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Fungal and bacterial RibD/RibG fusion carrying both the deaminase and the reductase activity.kegg_reaction_linkNULL
162546orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
163545orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
164547orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18One of several lineage-restricted HAD-family phosphatases assigned to this step; no orthology group covers it across bacteria, which is why the step is curated as not required.kegg_reaction_linkNULL
164548orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
164549orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
164550orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
164551orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
165552orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
166543orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
167553orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
168554orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
169555orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18PabB synthase component. PabA, the glutamine amidotransferase subunit, is interchangeable with TrpG and is not required as evidence.kegg_reaction_linkNULL
169556orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18PabAB fusion.kegg_reaction_linkNULL
170557orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Fusion carrying both the synthase and the lyase activity.kegg_reaction_linkNULL
171558orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
172557orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
173559orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
173560orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18FolE2-type GTP cyclohydrolase IB, the non-homologous replacement used where FolE is absent.kegg_reaction_linkNULL
173561orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
174562orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18Nudix hydrolase assigned to this step mainly in Proteobacteria; the reaction is universal but the orthology is not, which is why the step is curated as not required.kegg_reaction_linkNULL
174563orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
175564orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
175565orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18FolBKP-type fusion.kegg_reaction_linkNULL
175566orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18FolBK-type fusion.kegg_reaction_linkNULL
176567orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
176565orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
176566orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
176568orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18FolKP-type fusion.kegg_reaction_linkNULL
177569orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
177565orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
177568orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
178570orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
178571orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
179572orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
179573orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18FolM-type alternative dihydrofolate reductase.kegg_reaction_linkNULL
180574orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
181575orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
181576orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18ThiDE fusion.kegg_reaction_linkNULL
181577orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18ThiDN fusion.kegg_reaction_linkNULL
182578orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
183579orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18ThiG is the required catalytic subunit. The ThiS/ThiF sulfur-transfer pair is deliberately not required: ThiF is homologous to MoeB and ThiI also serves tRNA thiolation, so those markers add no thiamine specificity while removing two thirds of genuine thiazole synthesis.kegg_reaction_linkNULL
184580orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
185581orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
185576orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
185577orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
186575orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
186576orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
186577orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
187582orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
188583orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
189584orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
190585orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18IlvC carries out the ketopantoate reduction in genomes lacking PanE. Accepted for this reaction, not as evidence of pantothenate synthesis on its own: the route's other three reactions supply the specificity.unsupportedNULL
191586orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
192587orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
192588orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18PanCB fusion.kegg_reaction_linkNULL
193589orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
194590orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
195591orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
196592orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
19745orthologyhigh-confidenceKEGG orthology and Rhea release 141, verified 2026-08-18The same protein that transaminates 3-phosphohydroxypyruvate in serine biosynthesis; it is bifunctional, and the marker is accepted here for this reaction rather than as evidence of pyridoxal phosphate synthesis on its own.kegg_reaction_linkNULL
198593orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
199594orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
200595orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
201596orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Accepts either the CoA or the acyl-carrier-protein thioester of pimelate; the marker does not distinguish them.kegg_reaction_linkNULL
202597orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
202598orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18BIO3-BIO1 fusion carrying both the transaminase and the dethiobiotin synthetase activity.kegg_reaction_linkNULL
203599orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
203598orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
204600orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
205601orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18The lysine-dependent transaminase used by Bacillus and many Firmicutes in place of the SAM-dependent enzyme.kegg_reaction_linkNULL
206602orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NadB also transfers electrons to fumarate anaerobically; only the oxygen-dependent reaction is curated, which is why this route is declared aerobic.kegg_reaction_linkNULL
207603orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
208604orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18KEGG assigns this orthology group to EC 1.4.1.21, whose Rhea equation ends at oxaloacetate; the reaction curated here is the iminosuccinate-forming EC 1.4.1.29 chemistry that feeds quinolinate synthase.kegg_reaction_linkNULL
209605orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
210606orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
210607orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
211608orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
212609orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
213610orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
214611orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
214612orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
215613orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18CysG serves siroheme biosynthesis in genomes that make no corrinoid at all; it is accepted for this shared reaction, and the corrin-specific steps downstream carry the claim.kegg_reaction_linkNULL
216614orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
216615orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
217613orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
218616orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18CbiK, the class II chelatase of Salmonella-type systems.kegg_reaction_linkNULL
218617orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18CbiX.kegg_reaction_linkNULL
218618orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18CfbA.kegg_reaction_linkNULL
219619orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
220620orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
220621orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18CbiGH fusion.kegg_reaction_linkNULL
220622orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18CbiH60.kegg_reaction_linkNULL
221623orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
222624orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
222621orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
223625orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
224626orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
225627orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
225628orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18CbiET fusion.kegg_reaction_linkNULL
226629orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
226628orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
227630orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
228631orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
229619orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
229632orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18CobIJ fusion.kegg_reaction_linkNULL
230633orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18The oxygen-dependent ring hydroxylase that defines the aerobic route.kegg_reaction_linkNULL
231620orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
231632orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
231621orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
232623orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
233634orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
234626orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
235628orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
236630orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
237631orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
238635orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
239636orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
240637orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
241638orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
241639orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
242640orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
243641orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18CbiB/CobD.kegg_reaction_linkNULL
243642orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18CobC-type.kegg_reaction_linkNULL
244643orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Bifunctional kinase and guanylyltransferase; the kinase half is what lets a salvager enter this route from imported cobinamide.kegg_reaction_linkNULL
244644orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18CobY, the archaeal non-homologous replacement.kegg_reaction_linkNULL
245645orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
246646orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
246647orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
247648orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
248649orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18The oxygen-dependent route to the lower ligand. Its absence does not prove the genome cannot make DMB: the anaerobic bza pathway has no orthology group and is not curated.kegg_reaction_linkNULL
249650orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
250651orthologyhigh-confidenceKEGG orthology and Rhea release 141, verified 2026-08-18EntC catalyses the same reaction for enterobactin synthesis and is the only isochorismate synthase annotated in many Bacteroidetes; accepted for the reaction, with the route's remaining steps carrying the menaquinone claim.kegg_reaction_linkNULL
251652orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
252653orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18Annotated mainly in Proteobacteria and Actinobacteria; the elimination it catalyses also proceeds without a dedicated enzyme, so the step is curated as not required.kegg_reaction_linkNULL
253654orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
254655orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
255656orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
256657orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18A hotdog-fold thioesterase with several non-homologous replacements and no orthology group covering them; the step is curated as not required.kegg_reaction_linkNULL
257658orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
258659orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Also methylates the ubiquinone precursor in genomes that make both quinones.kegg_reaction_linkNULL
259660orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
260661orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
261662orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
261663orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
262664orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
263665orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
264666orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
265667orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
266668orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
267669orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18The group cannot distinguish citrate synthase from 2-methylcitrate synthase. Accepting it keeps Bacteroides and Staphylococcus positive and adds 1292 genomes whose only member may be a 2-methylcitrate synthase. Reconsider when a 2-methylcitrate cycle GIFT is curated.kegg_reaction_linkNULL
268670orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
268671orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
268672orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Split out of K01681 by KEGG. Without it Bacillus subtilis and Mycobacterium tuberculosis are wrongly aconitase-negative.kegg_reaction_linkNULL
269673orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
270674orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
271675orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
272676orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
273501orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Shared with the pyruvate dehydrogenase complex; specificity comes from the jointly required E1 and E2.kegg_reaction_linkNULL
274677orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
275678orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
276679orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
277680orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
278681orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLec_matchNULL
279682orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLec_matchNULL
280683orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLec_matchNULL
281684orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
281685orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
281686orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Carries both the NAD- and the NADP-dependent EC numbers and is therefore accepted for both reactions.kegg_reaction_linkNULL
282687orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
282686orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
283688orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18KEGG names the group sdhA, frdA. It evidences the couple and not its direction, which is why the GIFT is an interconversion.kegg_reaction_linkNULL
284689orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
285690orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
286691orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
287692orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
288693orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
289694orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
290695orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
291696orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
292697orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
293698orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
293699orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
293700orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
294701orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
295702orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
296703orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18The class II family; 1857 bacteria and 96 archaea, and the only DAHP synthase of most Actinomycetota.kegg_reaction_linkNULL
297704orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
298705orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
299706orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Fusion carrying both this reaction and the shikimate kinase step.kegg_reaction_linkNULL
300707orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
301708orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18The commoner of the two in bacteria, 7454 against 1666; the two are non-homologous and neither is derivable from the other.kegg_reaction_linkNULL
302709orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Fusion carrying both this reaction and the shikimate dehydrogenase step.kegg_reaction_linkNULL
303710orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
303722sequence_familyhigh-confidenceInterPro/NCBIfam, retrieved 2026-08-18Added because K00014 has a taxonomic coverage hole rather than a specificity problem: Mycobacterium tuberculosis Rv2552c and Synechocystis slr1559 are annotated shikimate 5-dehydrogenase in RefSeq and carry no KO at all. A genome annotated against NCBIfam can satisfy the step that KEGG cannot see.not_assessedNULL
304709orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
305711orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18YdiB is a quinate/shikimate dehydrogenase, and Rhea records EC 1.1.1.282 against this master alongside EC 1.1.1.25, so the chemistry is right; whether YdiB carries the pathway flux in a genome that also has AroE is not something a marker can say. Adding it moves the route by 180 bacteria. K25901 qsuD is refused: EC 1.1.1.24 is the NAD(+) reaction RHEA:17741, a different master.kegg_reaction_linkNULL
306712orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18KEGG assigns both the P-loop AroK/AroL kinases and the archaeal GHMP-family shikimate kinase, such as Methanocaldococcus jannaschii MJ_1440, to this KO, so the non-homologous replacement is real but not separable at KO level and is not curated as two systems.kegg_reaction_linkNULL
307706orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Fusion carrying both this reaction and the dehydroquinate synthase step.kegg_reaction_linkNULL
308713orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
309714orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
310715orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18The best-annotated step of the pathway, 9149 bacteria and 397 archaea.kegg_reaction_linkNULL
311716orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18KEGG names it the salicylate biosynthesis isochorismate synthase, but the reaction is the same isomerisation MenF and EntC catalyse. It is curated as a system of the reaction, not of one route, so it also satisfies the menaquinone route: that adds 7 genomes to menaquinone_biosynthesis.kegg_reaction_linkNULL
312718orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18MbtI, Irp9 and YbtS convert chorismate to salicylate through an enzyme-bound isochorismate and release free isochorismate slowly; KEGG assigns them both EC 5.4.4.2 and EC 4.2.99.21, and gifter accordingly curates them as a system of each reaction rather than as a route of their own.ec_matchNULL
313717orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18The one salicylate-specific step of the route, and the marker the claim rests on. 1017 bacteria carry it, but 706 of those carry no isochorismate synthase of any kind and so cannot complete the route. PchB shares the AroQ fold with chorismate mutase and has residual mutase activity; 90.3 percent of its carriers also carry a separate chorismate mutase KO, against an 84.6 percent baseline, so it is not systematically standing in for the mutase.kegg_reaction_linkNULL
314718orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18The same protein as the isochorismate synthase system of the preceding step; a genome carrying it alone completes the route.kegg_reaction_linkNULL
315719orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18Tryptophan 2-monooxygenase, the committed and diagnostic step: 92 bacteria, almost all plant-associated Proteobacteria, and indole-3-acetamide has no bacterial fate other than hydrolysis to the auxin. This marker, not the hydrolase, carries the IAA claim.kegg_reaction_linkNULL
316720orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18The dedicated iaaH orthology group, 362 bacteria. With K00466 it completes the route in 49 bacteria.kegg_reaction_linkNULL
317721orthologyambiguousKEGG orthology and Rhea release 141, verified 2026-08-18The broad amidase signature family, 4948 bacteria, and far too wide to license an auxin claim on its own. It is accepted only as a system of this reaction, which no other GIFT uses, and only because the preceding monooxygenase already restricts the route to 92 genomes. Accepting it moves the route from 49 to 86 bacteria; refusing it would call 37 genomes that carry IaaM and an amidase negative on an annotation boundary.kegg_reaction_linkNULL
318738orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
318767orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
319768orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
320755orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
320767orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18NULLunsupportedNULL
320760orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
321767orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
321760orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
322746orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
322769orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
323748orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
324751orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
325762orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
326749orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
327743orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
328744orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
328761orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
329745orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
329761orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
330741orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
331740orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
332739orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
333736orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
334737orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
335777orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
336776orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
337742orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLec_matchNULL
338771orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLec_matchNULL
339772orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
340773orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
341735orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
342734orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
343730orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
344731orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
345733orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
346732orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
347729orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
348772orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
349773orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
350747orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
351758orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
352774orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLec_matchNULL
353775orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLec_matchNULL
354770orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLec_matchNULL
354778orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLec_matchNULL
355779orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLec_matchNULL
356778orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLec_matchNULL
357763orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
358764orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
359752orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
360753orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
361756orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18NULLunsupportedNULL
362757orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18NULLunsupportedNULL
363754orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
364765orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18NULLunsupportedNULL
365759orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLec_matchNULL
366766orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-18NULLunsupportedNULL
367750orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
368726orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
369727orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
370728orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
371725orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
371724orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
372723orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
372724orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-18NULLkegg_reaction_linkNULL
373780orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19KEGG names this orthologue a benzoate/toluate 1,2-dioxygenase. Benzoate is within the enzyme's range, so the benzoate claim is honest; the same accession may not be used to claim a methylbenzoate trait, which it could not be distinguished from.kegg_reaction_linkNULL
374781orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
375782orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
376783orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
377784orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
378785orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
379786orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
380787orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
381788orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
382789orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
383790orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19KEGG names the system a phenol/toluene 2-monooxygenase. Only the phenol reaction is claimed here; toluene hydroxylation by the same enzyme yields cresol and is not curated.kegg_reaction_linkNULL
384791orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
385792orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
386793orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19KEGG separates chlorocatechol 1,2-dioxygenase as K15253, so this accession is not carrying the chlorinated chemistry.kegg_reaction_linkNULL
387794orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
388795orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
389796orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
390797orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19The same protein also decarboxylates 4-carboxymuconolactone in the protocatechuate branch, which gifter does not curate.kegg_reaction_linkNULL
391798orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
392799orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
393800orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19The same orthologue carries the first thiolysis of the phenylacetate route, RHEA:34799, which is why the thiolysis is curated once as its own GIFT.kegg_reaction_linkNULL
394801orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19K07104, KEGG's other catechol 2,3-dioxygenase orthologue, is deliberately refused: it is assigned in 2081 KEGG genomes dominated by Bacillus, Streptococcus, Staphylococcus and Listeria, of which only 276 carry any lower meta pathway gene.kegg_reaction_linkNULL
394802sequence_familyhigh-confidenceInterPro/NCBIfam, retrieved 2026-08-19Corroborating sequence family for the same activity, used because the KO layer offers one specific and one over-broad orthologue and the family agrees with the specific one.not_assessedNULL
395803orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
396804orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
397805orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLec_matchNULL
398806orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
399807orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
400808orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
401809orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
402810orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
403811orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
404812orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
405813orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
405814sequence_familyhigh-confidenceInterPro/NCBIfam, retrieved 2026-08-19Corroborating sequence family built around PaaK specifically.not_assessedNULL
406815orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLec_matchNULL
407816orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_module_memberNULL
408817orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLec_matchNULL
409818orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_module_memberNULL
410819orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_module_memberNULL
411820orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLec_matchNULL
412821orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19PaaZ is bifunctional, so one accession evidences two consecutive reactions of the route.ec_matchNULL
413821orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19Same accession as the preceding reaction, for the same bifunctional protein.ec_matchNULL
414800orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19The same thiolase catalyses the terminal thiolysis, curated as oxoadipyl_coa_thiolysis.kegg_reaction_linkNULL
415822orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19Chain-generic enoyl-CoA hydratase orthologue; accepted because the route's specificity is established upstream.kegg_reaction_linkNULL
416514orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19Already curated for butyrate formation. A multifunctional marker supporting two unrelated routes is the intended behaviour, not a collision.kegg_reaction_linkNULL
417823orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19KEGG and NCBIfam alike name this a 3-phenylpropionate/trans-cinnamate dioxygenase. Only the phenylpropanoate substrate is claimed; cinnamate cannot be distinguished and is deliberately not curated as a trait.kegg_reaction_linkNULL
418824orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
419825orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
420826orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
421827orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
422828orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
423829orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
424830orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
424831orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
425832orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
426833orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
427834orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
428835orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
429836orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
430837orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
431838orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
432839orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
433840orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
433841orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
434842orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
434843orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
435844orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
436845orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
437585orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
438846orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
439847orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
439848orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
440849orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
440850orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
440848orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
440851orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
440852orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
440853orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
440854orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
441855orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
442856orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
442857orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
442858orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
442859orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
443838orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
444860orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
444861orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
444862orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
445863orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
446864orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
447865orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
447866orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
447867orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
447868orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
447869orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
447870orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-19NULLunsupportedNULL
448871orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
44855orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
449872orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
450873orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
451874orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
451875orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
452876orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
452877orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
453833orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
454834orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
455835orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
456878orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
457879orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
457842orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
458870orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
459880orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
459881orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
460882orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
461883orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
462884orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
462885orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-19NULLunsupportedNULL
462886orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
463887orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-19NULLunsupportedNULL
464888orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
465889orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
466864orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
467890orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
467891orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
467892orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
468893orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
469894orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
470895orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
470875orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
470896orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
470897orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
471898orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
471862orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
472899orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
473900orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
473901orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
473902orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
473850orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
474903orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
475904orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
476905orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
476897orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
476906orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
477867orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
477868orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
477869orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
478585orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
479833orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
480834orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
481907orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
482908orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
482891orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
482892orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
483909orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
483896orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
483897orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
483906orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
484910orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
485911orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
486912orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
486913orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
487914orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
487915orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
487913orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
487916orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
487917orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
487861orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
487872orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
488918orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
489919orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
490920orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
491870orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
492921orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
493870orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
494865orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
494866orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
494867orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
494868orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
494869orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
494870orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-19NULLunsupportedNULL
495922orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
496540orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
497921orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
498923orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
499923orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
500924orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
500892orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
501924orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
501892orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
502925orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
503926orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
504833orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
505834orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
506927orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
507928orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
508929orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLec_matchNULL
509930orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLec_matchNULL
510931orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLec_matchNULL
511932orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLec_matchNULL
512933orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLec_matchNULL
513934orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
514935orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
515936orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
516937orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
5171322sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-04family_type=equivalog. Full-length single-chain iron-sulfur serine dehydratase; verified against E. coli SdaA, SdaB and TdcG.ec_matchNULL
5181320sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-04family_type=equivalog. SdaAA alpha chain; cannot complete the split enzyme without the beta component.ec_matchNULL
5191321sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-10-04family_type=equivalog. SdaAB beta chain; cannot complete the split enzyme without the alpha component.ec_matchNULL
520938orthologycuratedKEGG orthology and Rhea release 141, verified 2026-10-04The KO names a single-chain L-serine/L-threonine ammonia-lyase and is kept separate from the iron-sulfur systems.kegg_reaction_linkNULL
521939orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
522940orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
523941orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
524942orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
524938orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
525943orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
526944orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
527945orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
528946orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
528947orthologyputativeKEGG orthology and Rhea release 141, verified 2026-08-19NULLunsupportedNULL
528948orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-19NULLkegg_reaction_linkNULL
529957orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-20Direct isocitrate-lyase evidence.kegg_reaction_linkNULL
530958orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-20K01639 is refused because KEGG defines it as N-acetylneuraminate lyase.kegg_reaction_linkNULL
531959orthologycuratedKEGG orthology and nitrogenase assembly literature, verified 2026-08-20NifH alone is not evidence of a complete nitrogenase.kegg_reaction_linkNULL
532960orthologycuratedKEGG orthology and nitrogenase assembly literature, verified 2026-08-20Required Mo nitrogenase catalytic chain.kegg_reaction_linkNULL
533961orthologycuratedKEGG orthology and nitrogenase assembly literature, verified 2026-08-20Required Mo nitrogenase catalytic chain.kegg_reaction_linkNULL
534962orthologyputativeKEGG orthology and nitrogenase assembly literature, verified 2026-08-20Required because NifB makes the cofactor precursor and cannot be replaced by housekeeping Fe-S assembly.unsupportedNULL
535963orthologyputativeKEGG orthology and nitrogenase assembly literature, verified 2026-08-20Required Mo-cofactor scaffold component.unsupportedNULL
536964orthologyputativeKEGG orthology and nitrogenase assembly literature, verified 2026-08-20Required Mo-cofactor scaffold component.unsupportedNULL
537965orthologycuratedKEGG orthology and nitrogenase assembly literature, verified 2026-08-20Required V nitrogenase electron-delivery component.kegg_reaction_linkNULL
538966orthologycuratedKEGG orthology and nitrogenase assembly literature, verified 2026-08-20Required V nitrogenase catalytic chain.kegg_reaction_linkNULL
539967orthologycuratedKEGG orthology and nitrogenase assembly literature, verified 2026-08-20Required V nitrogenase catalytic chain.kegg_reaction_linkNULL
540968orthologycuratedKEGG orthology and nitrogenase assembly literature, verified 2026-08-20Required V nitrogenase delta subunit.kegg_reaction_linkNULL
541962orthologyputativeKEGG orthology and nitrogenase assembly literature, verified 2026-08-20Shared precursor synthase required by all three nitrogenase cofactors.unsupportedNULL
542969orthologyputativeKEGG orthology and nitrogenase assembly literature, verified 2026-08-20Required V-cofactor scaffold component.unsupportedNULL
543964orthologyputativeKEGG orthology and nitrogenase assembly literature, verified 2026-08-20KEGG's K02592 entry is named NifN but also annotates vnfN in validated vanadium clusters.unsupportedNULL
544970orthologycuratedKEGG module M00176 and Rhea release 141, verified 2026-08-20Monomeric sulfate adenylyltransferase.kegg_reaction_linkNULL
545971orthologycuratedKEGG module M00176 and Rhea release 141, verified 2026-08-20Required with CysD.kegg_reaction_linkNULL
546972orthologycuratedKEGG module M00176 and Rhea release 141, verified 2026-08-20Required with CysN.kegg_reaction_linkNULL
547973orthologycuratedKEGG module M00176 and Rhea release 141, verified 2026-08-20Fusion supplies the CysN activity.kegg_reaction_linkNULL
548972orthologycuratedKEGG module M00176 and Rhea release 141, verified 2026-08-20Required partner of CysNC.kegg_reaction_linkNULL
549974orthologycuratedKEGG module M00176 and Rhea release 141, verified 2026-08-20Standalone APS kinase.kegg_reaction_linkNULL
550973orthologycuratedKEGG module M00176 and Rhea release 141, verified 2026-08-20Fusion supplies the APS kinase activity.kegg_reaction_linkNULL
551975activitycuratedRhea release 141 and KEGG K00390 definition, verified 2026-08-20KO K00390 is deliberately refused because it spans this activity and APS reductase.not_assessedNULL
552976activitycuratedRhea release 141 and KEGG K00390 definition, verified 2026-08-20KO K00390 is deliberately refused because it spans this activity and PAPS reductase.not_assessedNULL
553977orthologycuratedKEGG module M00176 and Rhea release 141, verified 2026-08-20Required with CysI.kegg_reaction_linkNULL
554978orthologycuratedKEGG module M00176 and Rhea release 141, verified 2026-08-20Required with CysJ.kegg_reaction_linkNULL
555979orthologycuratedKEGG module M00176 and Rhea release 141, verified 2026-08-20Ferredoxin-dependent terminal reductase.kegg_reaction_linkNULL
556980orthologycuratedKEGG M00033 and Rhea release 141, verified 2026-08-20The reaction runs opposite the Rhea master in ectoine biosynthesis.kegg_reaction_linkNULL
557981orthologycuratedKEGG M00033 and Rhea release 141, verified 2026-08-20Substrate-specific ectoine-pathway acetyltransferase.kegg_reaction_linkNULL
558982orthologycuratedKEGG M00033 and Rhea release 141, verified 2026-08-20Ectoine synthase closes the trait-specific ring.kegg_reaction_linkNULL
559983orthologycuratedKEGG M00121/M00926 and Rhea release 141, verified 2026-08-20Shared first reaction of every curated UROGEN_III-to-heme route.kegg_reaction_linkNULL
560984orthologycuratedKEGG M00121 and Rhea release 141, verified 2026-08-20Oxygen-dependent HemF.kegg_reaction_linkNULL
561985orthologycuratedKEGG M00121 and Rhea release 141, verified 2026-08-20Oxygen-independent radical-SAM HemN.kegg_reaction_linkNULL
562987orthologycuratedKEGG M00121 and Rhea release 141, verified 2026-08-20The same KO also supports its experimentally established coproporphyrinogen oxidase activity in the copro route.kegg_reaction_linkNULL
563986orthologycuratedKEGG M00121 and Rhea release 141, verified 2026-08-20KEGG maps K00230 to R09489, but Rhea 141 does not cross-reference that KEGG reaction to RHEA:27409; only the exact Rhea EC cross-reference is stored.ec_matchNULL
564988orthologycuratedKEGG M00121 and Rhea release 141, verified 2026-08-20HemJ identifies the protoporphyrinogen oxidase while Rhea leaves its electron acceptor abstract.kegg_reaction_linkNULL
565989orthologycuratedKEGG M00121 and Rhea release 141, verified 2026-08-20The same KO also supports coproferrochelatase in its separate reaction-specific component.kegg_reaction_linkNULL
566987orthologycuratedKEGG M00926, Rhea release 141 and PMID 25646457, verified 2026-08-20Multifunctional HemY marker attached to the copro-specific reaction component.kegg_reaction_linkPMID:25646457
567989orthologycuratedKEGG M00926, Rhea release 141 and PMID 25646457, verified 2026-08-20Multifunctional HemH marker attached to the copro-specific reaction component.kegg_reaction_linkPMID:25646457
568990orthologycuratedKEGG M00926, Rhea release 141 and PMID 25646457, verified 2026-08-20Hydrogen peroxide-dependent conversion of coproheme to heme b.kegg_reaction_linkPMID:25646457
569991orthologycuratedKEGG map01053 and Rhea release 141, verified 2026-08-20This component uses the isochorismate-lyase domain; the same protein's carrier domain is separately required downstream.kegg_reaction_linkNULL
570992orthologycuratedKEGG map01053 and Rhea release 141, verified 2026-08-20EntA identifies the 2,3-dihydroxybenzoate-forming dehydrogenase.kegg_reaction_linkNULL
571991orthologycuratedKEGG map01053, Rhea release 141 and PMID 10375542, verified 2026-08-20The aryl-carrier function is distinct from the same protein's upstream lyase function.kegg_reaction_linkPMID:10375542
572993orthologycuratedKEGG map01053, Rhea release 141 and PMID 10375542, verified 2026-08-20Required carrier-domain phosphopantetheinyl transferase, not an accessory annotation.kegg_reaction_linkPMID:10375542
573994orthologycuratedKEGG map01053, Rhea release 141 and PMID 10375542, verified 2026-08-20Required 2,3-dihydroxybenzoate-activating ligase.kegg_reaction_linkPMID:10375542
574995orthologycuratedKEGG map01053, Rhea release 141 and PMID 10375542, verified 2026-08-20Required serine-activating and cyclising NRPS component.kegg_reaction_linkPMID:10375542
5751005orthologycuratedKEGG M00555 and Rhea release 141, verified 2026-08-20BetA architecture represented by MetaCyc BETSYN-PWY.kegg_reaction_linkNULL
5761006orthologycuratedKEGG M00555, Rhea release 141 and PMID 8752328, verified 2026-08-20GbsB architecture represented by MetaCyc PWY-3722.kegg_reaction_linkPMID:8752328
5771007orthologycuratedKEGG M00555 and Rhea release 141, verified 2026-08-20The reaction consumes oxygen and reduced ferredoxin.kegg_reaction_linkNULL
5781008orthologycuratedKEGG M00555 and Rhea release 141, verified 2026-08-20The same choline oxidase catalyses both steps and is attached to both reaction-specific components.kegg_reaction_linkNULL
5791008orthologycuratedKEGG M00555 and Rhea release 141, verified 2026-08-20The same choline oxidase catalyses both steps and is attached to both reaction-specific components.kegg_reaction_linkNULL
5801009orthologycuratedKEGG M00555 and Rhea release 141, verified 2026-08-20K14085 is deliberately refused: ALDH7A1 spans many aldehydes and cannot identify betaine aldehyde even though KEGG includes it in M00555.kegg_reaction_linkNULL
2141010orthologycuratedKEGG M00846 and Rhea release 141, verified 2026-08-20MET1 supplies the same two-methyl-transfer conversion as the accepted CobA orthologues.kegg_reaction_linkNULL
2141011orthologycuratedKEGG M00846 and Rhea release 141, verified 2026-08-20HemX is explicitly assigned uroporphyrinogen-III C-methyltransferase activity.kegg_reaction_linkNULL
2141012orthologycuratedKEGG M00846 and Rhea release 141, verified 2026-08-20The HemDX fusion establishes the methyltransferase reaction; its uroporphyrinogen synthase activity is outside this GIFT boundary.kegg_reaction_linkNULL
581613orthologycuratedKEGG M00846, Rhea release 141 and PMID 9461500, verified 2026-08-20The maintained KO explicitly includes sirohydrochlorin ferrochelatase activity, so the same CysG observation can support all three reaction-specific components.kegg_reaction_linkPMID:9461500
582614orthologycuratedKEGG M00846, Rhea release 141 and PMID 11980703, verified 2026-08-20Met8 is bifunctional: its same observation supplies both precorrin-2 dehydrogenation and iron insertion.kegg_reaction_linkPMID:11980703
5831013orthologycuratedKEGG M00846, Rhea release 141 and PMID 12408752, verified 2026-08-20SirB is the split iron-specific chelatase. Broader CbiX-family KOs are refused because sequence alone does not resolve iron from cobalt or nickel insertion.kegg_reaction_linkPMID:12408752
5841025sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 5 distinct characterised activities in dbCAN.ec_matchNULL
5841026sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841027sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841028sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-189 of 9 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841029sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1812 of 17 EC-annotated members carry EC 3.2.1.14 (71%).ec_matchNULL
5841030sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1812 of 12 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841031sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841032sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841033sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-188 of 8 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841034sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841035sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841036sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841037sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841038sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1821 of 21 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841039sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841040sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841041sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1810 of 10 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841042sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 6 EC-annotated members carry EC 3.2.1.14 (67%).ec_matchNULL
5841043sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841044sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1825 of 25 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841045sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841046sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1818 of 18 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841047sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841048sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841049sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841050sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841051sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841052sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841053sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841054sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1858 of 58 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841055sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1822 of 22 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841056sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841057sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841058sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841059sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841060sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841061sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1824 of 24 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841062sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841063sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1821 of 21 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841064sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1812 of 12 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841065sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841066sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841067sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841068sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1863 of 63 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841069sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841070sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1847 of 47 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841071sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841072sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841073sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1841 of 45 EC-annotated members carry EC 3.2.1.14 (91%).ec_matchNULL
5841074sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841075sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841076sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841077sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841078sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841079sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1853 of 58 EC-annotated members carry EC 3.2.1.14 (91%).ec_matchNULL
5841080sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841081sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841082sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841083sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841084sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1811 of 13 EC-annotated members carry EC 3.2.1.14 (85%).ec_matchNULL
5841085sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 3 distinct characterised activities in dbCAN.ec_matchNULL
5841086sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18161 of 161 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841087sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841088sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1816 of 16 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841089sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841090sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841091sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841092sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-187 of 7 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841093sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1844 of 44 EC-annotated members carry EC 3.2.1.14 (100%).ec_matchNULL
5841165orthologycuratedKEGG orthology, verified 2026-08-21NULLec_matchNULL
5841170orthologycuratedKEGG orthology, verified 2026-08-21Bifunctional chitinase/lysozyme; the chitinase activity is the one claimed here.ec_matchNULL
5861014sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 4 distinct characterised activities in dbCAN.ec_matchNULL
5861015sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 1.14.99.53 (100%).ec_matchNULL
5861016sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 1.14.99.53 (100%).ec_matchNULL
5861017sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 1.14.99.53 (100%).ec_matchNULL
5861018sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 1.14.99.53 (100%).ec_matchNULL
5861019sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 1.14.99.53 (100%).ec_matchNULL
5861020sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 1.14.99.53 (100%).ec_matchNULL
5851094sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 4 distinct characterised activities in dbCAN.ec_matchNULL
5851095sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1812 of 12 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851096sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851097sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-189 of 9 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851098sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-189 of 15 EC-annotated members carry EC 3.2.1.52 (60%).ec_matchNULL
5851099sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1817 of 17 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851100sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851101sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1818 of 18 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851102sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851103sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-189 of 9 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851104sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851105sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851106sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851107sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851108sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851109sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851110sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851111sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851112sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851113sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1812 of 12 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851114sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1813 of 13 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851115sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851116sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1816 of 16 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851117sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851118sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851119sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851120sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1835 of 35 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851121sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851122sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851123sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851124sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1832 of 32 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851125sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.52 (100%).ec_matchNULL
5851169orthologycuratedKEGG orthology, verified 2026-08-21NULLec_matchNULL
5881024sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.51 (100%).ec_matchNULL
5881126sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 7 distinct characterised activities in dbCAN.ec_matchNULL
5881127sequence_familyputativeCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.111 (100%).unsupportedNULL
5881128sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 10 EC-annotated members carry EC 3.2.1.111 (50%).unsupportedNULL
5881129sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 4 EC-annotated members carry EC 3.2.1.111 (50%).unsupportedNULL
5881130sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.51 (100%).ec_matchNULL
5881131sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.51 (100%).ec_matchNULL
5881132sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.51 (100%).ec_matchNULL
5881133sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.51 (100%).ec_matchNULL
5881134sequence_familyputativeCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-188 of 11 EC-annotated members carry EC 3.2.1.111 (73%).unsupportedNULL
5881135sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.51 (100%).ec_matchNULL
5881136sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1858 of 58 EC-annotated members carry EC 3.2.1.51 (100%).ec_matchNULL
5881137sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1816 of 16 EC-annotated members carry EC 3.2.1.51 (100%).ec_matchNULL
5881138sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.51 (100%).ec_matchNULL
5881139sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.51 (100%).ec_matchNULL
5881140sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.51 (100%).ec_matchNULL
5881159sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 3 distinct characterised activities in dbCAN.ec_matchNULL
5881160sequence_familyputativeCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.63 (100%).unsupportedNULL
5881161sequence_familyputativeCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.63 (100%).unsupportedNULL
5881162sequence_familyputativeCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-187 of 7 EC-annotated members carry EC 3.2.1.63 (100%).unsupportedNULL
5881163sequence_familyputativeCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.63 (100%).unsupportedNULL
5881164sequence_familyputativeCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.63 (100%).unsupportedNULL
5881168orthologycuratedKEGG orthology, verified 2026-08-21NULLec_matchNULL
5881171orthologycuratedKEGG orthology, verified 2026-08-21GH95 alpha-L-fucosidase 2.ec_matchNULL
5891021sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 2 distinct characterised activities in dbCAN.ec_matchNULL
5891022sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 8 EC-annotated members carry EC 3.2.1.49 (75%).ec_matchNULL
5891023sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.49 (100%).ec_matchNULL
5891167orthologycuratedKEGG orthology, verified 2026-08-21NULLec_matchNULL
5871141sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 5 distinct characterised activities in dbCAN.ec_matchNULL
5871142sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871143sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871144sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871145sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871146sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871147sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871148sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 8 EC-annotated members carry EC 3.2.1.18 (62%).ec_matchNULL
5871149sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871150sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871151sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871152sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1818 of 18 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871153sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1817 of 17 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871154sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1834 of 34 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871155sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871156sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871157sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871158sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1826 of 26 EC-annotated members carry EC 3.2.1.18 (100%).ec_matchNULL
5871166orthologycuratedKEGG orthology, verified 2026-08-21NULLec_matchNULL
5871172orthologycuratedKEGG orthology, verified 2026-08-21NULLec_matchNULL
5901193sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 7 distinct characterised activities in dbCAN, all of them on pectin; the family is substrate-coherent but does not separate endo from exo action.ec_matchNULL
5901194sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.15 (100%).ec_matchNULL
5901195sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.15 (100%).ec_matchNULL
5901196sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.15 (100%).ec_matchNULL
5901197sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 3.2.1.15 (100%).ec_matchNULL
5901198sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-188 of 8 EC-annotated members carry EC 3.2.1.15 (100%).ec_matchNULL
5901199sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1824 of 24 EC-annotated members carry EC 3.2.1.15 (100%).ec_matchNULL
5901200sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.15 (100%).ec_matchNULL
5901201sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.15 (100%).ec_matchNULL
5901203sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 3.2.1.15 (100%).ec_matchNULL
5901204sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.15 (100%).ec_matchNULL
5901205sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1813 of 13 EC-annotated members carry EC 3.2.1.15 (100%).ec_matchNULL
5901210sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1879 of 79 EC-annotated members carry EC 3.2.1.15 (100%).ec_matchNULL
5901211sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1812 of 12 EC-annotated members carry EC 3.2.1.15 (100%).ec_matchNULL
5901212sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1810 of 10 EC-annotated members carry EC 3.2.1.15 (100%).ec_matchNULL
5901216orthologycuratedKEGG orthology, verified 2026-08-21NULLec_matchNULL
5911193sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 7 distinct characterised activities in dbCAN, all of them on pectin; the family is substrate-coherent but does not separate endo from exo action.ec_matchNULL
5911202sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.2.1.67 (100%).ec_matchNULL
5911206sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-187 of 9 EC-annotated members carry EC 3.2.1.67 (78%).ec_matchNULL
5911207sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.67 (100%).ec_matchNULL
5911208sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.67 (100%).ec_matchNULL
5911209sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.67 (100%).ec_matchNULL
5911213sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 3.2.1.67 (100%).ec_matchNULL
5911214sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.2.1.67 (100%).ec_matchNULL
5911217orthologycuratedKEGG orthology, verified 2026-08-21NULLec_matchNULL
5911218orthologycuratedKEGG orthology, verified 2026-08-21NULLec_matchNULL
5921173sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 1 characterised activity in dbCAN.ec_matchNULL
5921174sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921175sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-188 of 8 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921176sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921177sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921178sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1868 of 68 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921179sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1812 of 12 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921180sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-187 of 7 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921181sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921182sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921183sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1812 of 12 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921184sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921185sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921186sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1810 of 10 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921187sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1815 of 15 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921188sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921189sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921190sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921191sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921192sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 3.1.1.11 (100%).ec_matchNULL
5921215orthologycuratedKEGG orthology, verified 2026-08-21NULLec_matchNULL
5931219orthologycuratedKEGG orthology, verified 2026-08-21NULLec_matchNULL
5931220orthologycuratedKEGG orthology, verified 2026-08-21NULLec_matchNULL
5931227sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 4 distinct characterised activities in dbCAN: pectate lyase, exo-pectate lyase, pectin lyase and a poly-alpha-D-N-acetylgalactosaminuronate lyase on bacterial outer-membrane polysaccharide. Three of the four are the same pectin chemistry and differ only in endo versus exo action and in whether the backbone is esterified; the fourth is a different substrate, so the family is neither activity-coherent nor fully substrate-coherent.ec_matchNULL
5931229sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 2 distinct characterised activities in dbCAN, pectate lyase and exo-polygalacturonate lyase, both on pectin; the family is substrate-coherent but does not separate endo from exo action.ec_matchNULL
5931230sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 1 characterised activity in dbCAN, pectate lyase.ec_matchNULL
5931231sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 5 distinct characterised activities in dbCAN: pectate lyase, exopolygalacturonate lyase, pectin lyase, rhamnogalacturonan endolyase and a thiopeptidoglycan lyase. Four are pectin chemistry, but the peptidoglycan activity means a hit may not be acting on pectin at all.ec_matchNULL
5931228sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 1 characterised activity in dbCAN, pectate lyase.ec_matchNULL
5931232sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 2 annotated members, below the ten the curated grade requires.ec_matchNULL
5931233sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 2 annotated members, below the ten the curated grade requires.ec_matchNULL
5931234sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1817 of 17 EC-annotated members carry EC 4.2.2.2 (100%).ec_matchNULL
5931235sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1823 of 23 EC-annotated members carry EC 4.2.2.2 (100%).ec_matchNULL
5931236sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 2 annotated members, below the ten the curated grade requires.ec_matchNULL
5931237sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 2 annotated members, below the ten the curated grade requires.ec_matchNULL
5931238sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1826 of 26 EC-annotated members carry EC 4.2.2.2 (100%).ec_matchNULL
5931239sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1815 of 20 EC-annotated members carry EC 4.2.2.2 (75%).ec_matchNULL
5931240sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 2 annotated members, below the ten the curated grade requires.ec_matchNULL
5931241sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1874 of 74 EC-annotated members carry EC 4.2.2.2 (100%).ec_matchNULL
5931242sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 2 annotated members, below the ten the curated grade requires.ec_matchNULL
5931243sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1826 of 26 EC-annotated members carry EC 4.2.2.2 (100%).ec_matchNULL
5931244sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1829 of 29 EC-annotated members carry EC 4.2.2.2 (100%).ec_matchNULL
5931245sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-187 of 7 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 7 annotated members, below the ten the curated grade requires.ec_matchNULL
5931246sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 3 annotated members, below the ten the curated grade requires.ec_matchNULL
5931247sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 5 annotated members, below the ten the curated grade requires.ec_matchNULL
5931248sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1822 of 22 EC-annotated members carry EC 4.2.2.2 (100%).ec_matchNULL
5931249sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1824 of 24 EC-annotated members carry EC 4.2.2.2 (100%).ec_matchNULL
5931250sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18125 of 125 EC-annotated members carry EC 4.2.2.2 (100%).ec_matchNULL
5931251sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 2 annotated members, below the ten the curated grade requires.ec_matchNULL
5931252sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1810 of 10 EC-annotated members carry EC 4.2.2.2 (100%).ec_matchNULL
5931253sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 5 annotated members, below the ten the curated grade requires.ec_matchNULL
5931254sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 6 annotated members, below the ten the curated grade requires.ec_matchNULL
5931255sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 6 annotated members, below the ten the curated grade requires.ec_matchNULL
5931256sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 4 annotated members, below the ten the curated grade requires.ec_matchNULL
5931257sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 4 annotated members, below the ten the curated grade requires.ec_matchNULL
5931258sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-185 of 5 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 5 annotated members, below the ten the curated grade requires.ec_matchNULL
5931259sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-187 of 7 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 7 annotated members, below the ten the curated grade requires.ec_matchNULL
5931260sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-186 of 6 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 6 annotated members, below the ten the curated grade requires.ec_matchNULL
5931261sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 2 annotated members, below the ten the curated grade requires.ec_matchNULL
5931262sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-184 of 4 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 4 annotated members, below the ten the curated grade requires.ec_matchNULL
5931263sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 4.2.2.2 (100%). Agreement is complete but rests on 2 annotated members, below the ten the curated grade requires.ec_matchNULL
5941221orthologycuratedKEGG orthology, verified 2026-08-21NULLkegg_reaction_linkNULL
5941222orthologycuratedKEGG orthology, verified 2026-08-21NULLkegg_reaction_linkNULL
5941227sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 4 distinct characterised activities in dbCAN: pectate lyase, exo-pectate lyase, pectin lyase and a poly-alpha-D-N-acetylgalactosaminuronate lyase on bacterial outer-membrane polysaccharide. Three of the four are the same pectin chemistry and differ only in endo versus exo action and in whether the backbone is esterified; the fourth is a different substrate, so the family is neither activity-coherent nor fully substrate-coherent.ec_matchNULL
5941229sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 2 distinct characterised activities in dbCAN, pectate lyase and exo-polygalacturonate lyase, both on pectin; the family is substrate-coherent but does not separate endo from exo action.ec_matchNULL
5941231sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 5 distinct characterised activities in dbCAN: pectate lyase, exopolygalacturonate lyase, pectin lyase, rhamnogalacturonan endolyase and a thiopeptidoglycan lyase. Four are pectin chemistry, but the peptidoglycan activity means a hit may not be acting on pectin at all.ec_matchNULL
5941264sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 4.2.2.9 (100%). Agreement is complete but rests on 3 annotated members, below the ten the curated grade requires.ec_matchNULL
5941265sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 4.2.2.9 (100%). Agreement is complete but rests on 3 annotated members, below the ten the curated grade requires.ec_matchNULL
5951223orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-21NULLkegg_reaction_linkNULL
5961224orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-21NULLkegg_reaction_linkNULL
5971225orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-21NULLkegg_reaction_linkNULL
5981226orthologycuratedKEGG orthology, verified 2026-08-21NULLec_matchNULL
5981220orthologycuratedKEGG orthology, verified 2026-08-21NULLec_matchNULL
5981227sequence_familyambiguousCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-18Family carries 4 distinct characterised activities in dbCAN: pectate lyase, exo-pectate lyase, pectin lyase and a poly-alpha-D-N-acetylgalactosaminuronate lyase on bacterial outer-membrane polysaccharide. Three of the four are the same pectin chemistry and differ only in endo versus exo action and in whether the backbone is esterified; the fourth is a different substrate, so the family is neither activity-coherent nor fully substrate-coherent.ec_matchNULL
5981266sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1822 of 22 EC-annotated members carry EC 4.2.2.10 (100%).ec_matchNULL
5981267sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-183 of 3 EC-annotated members carry EC 4.2.2.10 (100%). Agreement is complete but rests on 3 annotated members, below the ten the curated grade requires.ec_matchNULL
5981268sequence_familycuratedCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-1824 of 24 EC-annotated members carry EC 4.2.2.10 (100%).ec_matchNULL
5981269sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 4.2.2.10 (100%). Agreement is complete but rests on 2 annotated members, below the ten the curated grade requires.ec_matchNULL
5981270sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-182 of 2 EC-annotated members carry EC 4.2.2.10 (100%). Agreement is complete but rests on 2 annotated members, below the ten the curated grade requires.ec_matchNULL
5981271sequence_familyhigh-confidenceCAZy via dbCAN db_v5-2-9_5-5-2026, retrieved 2026-08-187 of 7 EC-annotated members carry EC 4.2.2.10 (100%). Agreement is complete but rests on 7 annotated members, below the ten the curated grade requires.ec_matchNULL
5991272orthologycuratedKEGG 2026-08-22Specific to the ectoine hydrolase of the degradative operon.kegg_reaction_linkNULL
6001273orthologycuratedKEGG 2026-08-22NULLkegg_reaction_linkNULL
6011274orthologycuratedKEGG 2026-08-22Single-reaction orthologue; the hydroxylase acts on ectoine and nothing else in the database.kegg_reaction_linkNULL
6021275orthologycuratedKEGG 2026-08-22Single-reaction orthologue for EC 1.2.1.22.kegg_reaction_linkNULL
6021276orthologycuratedKEGG 2026-08-22AldA also oxidises glycolaldehyde, EC 1.2.1.21. The breadth is the enzyme's rather than the annotation's: AldA genuinely performs this reaction, and the route's input anchor states which substrate the GIFT is about.kegg_reaction_linkNULL
2801312sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. Kgd, the multifunctional 2-oxoglutarate decarboxylase that releases succinate semialdehyde. NCBIfam names the decarboxylase activity this route needs; K01616 already covers the same multifunctional protein, so the profile adds annotation coverage rather than a new claim.ec_matchNULL
1501330sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CitD, the acyl carrier (gamma) subunit alone. Attached here and to no other subunit: the profile carries the holoenzyme EC 4.1.3.6 but identifies one polypeptide, and placing it on the alpha or beta component would claim a subunit it cannot see.ec_matchNULL
5511279sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. PAPS reductase CysH. The curated reaction is the 3'-phosphoadenylyl-sulfate one, and the profile is graded for that activity.ec_matchNULL
5511331sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CysH built to prefer PAPS over APS, and explicitly separated by NCBIfam from the APS-preferring TIGR02055 and TIGR00424 groups. That separation is the reason to admit it: the curated reaction is the PAPS one.ec_matchNULL
371308sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. SerA phosphoglycerate dehydrogenase.ec_matchNULL
371325sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. The long form of SerA. NCBIfam notes that short forms, including Escherichia coli SerA, score between trusted and noise cutoffs, so this profile is a partial view of the activity and is admitted beside K00058 rather than instead of it.ec_matchNULL
2311288sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CobJ precorrin-3B C17-methyltransferase.ec_matchNULL
2311292sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CobJ precorrin-3B C17-methyltransferase.ec_matchNULL
2311328sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog_domain. CobJ. Graded equivalog_domain because the enzyme frequently occurs fused to other cobalamin enzymes; the one-function guarantee is a guarantee about the domain, which is the level the marker claims.ec_matchNULL
2821304sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. NADP-dependent succinic semialdehyde dehydrogenase, EC 1.2.1.79. This is the cofactor the curated reaction states and neither K00135 nor K08324 does.ec_matchNULL
5291294sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. Isocitrate lyase of the glyoxylate bypass.ec_matchNULL
5291315sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. AceA isocitrate lyase.ec_matchNULL
5291326sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. AceA isocitrate lyase.ec_matchNULL
481278sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. MetX in its homoserine O-acetyltransferase form, EC 2.3.1.31. gifter curates the acetyl and succinyl transfers as separate reactions while K00641 and K00651 sit on both; this profile states the acetyl activity.ec_matchNULL
2241296sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CbiJ cobalt-precorrin-6A reductase.ec_matchNULL
2241297sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CbiJ cobalt-precorrin-6A reductase.ec_matchNULL
2241298sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CbiJ cobalt-precorrin-6A reductase.ec_matchNULL
2241299sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CbiJ cobalt-precorrin-6A reductase.ec_matchNULL
2241300sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CbiJ cobalt-precorrin-6A reductase.ec_matchNULL
2271293sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CbiC cobalt-precorrin-8 methylmutase.ec_matchNULL
2271302sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CbiC cobalt-precorrin-8 methylmutase.ec_matchNULL
2291289sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CobI precorrin-2 C20-methyltransferase.ec_matchNULL
2291291sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CobI precorrin-2 C20-methyltransferase.ec_matchNULL
2291329sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CobI precorrin-2 C20-methyltransferase, separated by NCBIfam from the several closely related cobalamin methyltransferases K03394 also names.ec_matchNULL
671307sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. L-fucose isomerase. K01818 is annotated L-fucose/D-arabinose isomerase; the profile names the fucose activity the GIFT is named for.ec_matchNULL
671324sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. FucI, characterised in Escherichia coli and Bacteroides thetaiotaomicron.ec_matchNULL
2191282sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CbiL cobalt-factor II C20-methyltransferase. K03394 covers precorrin-2 and cobalt-factor-2 methylation together; the profile states the cobalt-factor II activity.ec_matchNULL
2191283sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CbiL cobalt-factor II C20-methyltransferase.ec_matchNULL
2191284sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CbiL cobalt-factor II C20-methyltransferase.ec_matchNULL
2191285sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CbiL cobalt-factor II C20-methyltransferase.ec_matchNULL
2191286sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CbiL cobalt-factor II C20-methyltransferase.ec_matchNULL
2191287sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CbiL cobalt-factor II C20-methyltransferase.ec_matchNULL
471280sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. MetA homoserine O-succinyltransferase, EC 2.3.1.46, which NCBIfam records as unrelated in sequence to the MetX succinyltransferases. States the succinyl activity that K00641 and K00651 leave joined to the acetyl one.ec_matchNULL
471303sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. MetX in its homoserine O-succinyltransferase form, EC 2.3.1.46.ec_matchNULL
471323sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. The MetA-type clade with homoserine O-succinyltransferase activity, which NCBIfam separates from the acetyltransferase members of the same family.ec_matchNULL
2321327sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CobM precorrin-4 C11-methyltransferase, separated by NCBIfam from the precorrin-3B C17-methyltransferase it is commonly conflated with.ec_matchNULL
171295sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. AICAR transformylase, EC 2.1.2.3.ec_matchNULL
2361281sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CobH precorrin-8X methylmutase. K06042 covers the precorrin-8X and cobalt-precorrin-8 mutases together; the profile states the non-cobalt one.ec_matchNULL
2361290sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CobH precorrin-8X methylmutase.ec_matchNULL
2361301sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CobH precorrin-8X methylmutase.ec_matchNULL
5651277sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. HemH ferrochelatase.ec_matchNULL
5651317sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. HemH. NCBIfam records that the family covers protoporphyrin ferrochelatase and coproporphyrin ferrochelatase together, which is the same breadth K01772 already carries, so the marker does not narrow the claim; it widens which annotations can satisfy it.ec_matchNULL
1861314sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. Bifunctional ThiD hydroxymethylpyrimidine/phosphomethylpyrimidine kinase, the same bifunctionality the curated KOs carry.ec_matchNULL
2341319sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CobK precorrin-6A reductase, characterised in Pseudomonas denitrificans. K05895 covers the precorrin-6A and cobalt-precorrin-6A reductases together; the profile states the non-cobalt one.ec_matchNULL
5621309sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. HemY-type oxygen-dependent protoporphyrinogen oxidase.ec_matchNULL
5621310sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. HemY-type oxygen-dependent protoporphyrinogen oxidase.ec_matchNULL
5621311sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. HemY-type oxygen-dependent protoporphyrinogen oxidase.ec_matchNULL
5621313sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. HemY-type oxygen-dependent protoporphyrinogen oxidase.ec_matchNULL
5621318sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. The HemY-type flavoprotein oxidase, model label proto_IX_ox and 470 positions long, matching the 468-position HemY profile NF008845.0. Its gene_symbol field reads hemG, which is a naming artefact: the Escherichia coli HemG is a small flavodoxin catalysing the quinone-dependent reaction, not this oxygen-dependent one.ec_matchNULL
2211316sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. CbiF cobalt-precorrin-4 C11-methyltransferase, EC 2.1.1.271. K05936 covers the precorrin-4 and cobalt-precorrin-4 methyltransferases together; the profile states the cobalt one.ec_matchNULL
5721305sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. EntD phosphopantetheinyl transferase alone. Attached to the EntD component only: the profile carries the aggregate EC 6.3.2.14 but identifies one subunit of the enterobactin synthetase, and the other three components keep their own evidence.ec_matchNULL
5741306sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. EntF, the serine-activating nonribosomal peptide synthetase, alone. Same reasoning as EntD: one subunit of the aggregate, attached to one component.ec_matchNULL
3961332sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. 2-hydroxymuconic semialdehyde dehydrogenase, EC 1.2.1.85, the second step of catechol meta-cleavage. K10217 is annotated for the aminomuconate and hydroxymuconate semialdehyde dehydrogenases together; the profile states the hydroxymuconate one.ec_matchNULL
6031333sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. AhbA, the alpha subunit. K22225 is deliberately absent from this component and from AhbB: KEGG assigns one accession to both subunits, so admitting it here would let a single observed gene satisfy a jointly required heterodimer. That refusal is what made this GIFT wait for a namespace that separates them.ec_matchNULL
6041334sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. AhbB, the beta subunit. Same refusal of K22225 as on AhbA, and for the same reason.ec_matchNULL
6051337orthologycuratedKEGG M00847 and Rhea release 141, verified 2026-08-23AhbC, the radical SAM enzyme converting 12,18-didecarboxysiroheme to Fe-coproporphyrin III. The orthology group names one gene and one activity, so it states this reaction despite carrying no EC number.kegg_reaction_linkNULL
6051335sequence_familyputativeNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. AhbC, corroborating the KEGG orthology with a sequence family built for the same activity. Admitted as an OR alternative so that a genome annotated only against NCBIfam can satisfy the step.unsupportedNULL
6061338orthologycuratedKEGG M00847 and Rhea release 141, verified 2026-08-23AhbD, the radical SAM enzyme converting Fe-coproporphyrin III to heme b. EC 1.3.98.6 is specific to the AdoMet-dependent conversion and does not cover the peroxide-dependent one.kegg_reaction_linkNULL
6061336sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. AhbD, corroborating the KEGG orthology with a sequence family built for the same activity.ec_matchNULL
4421339sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. HisN, the inositol-monophosphatase-family phosphatase that solves this step in Actinomycetota and elsewhere. EC 3.1.3.15 is the EC RHEA:14465 carries. Added because the phenotype benchmark scored histidine_biosynthesis at recall 0.520 against strains observed to grow without histidine, with this reaction missing in 22 of 30 sampled failures and Actinomycetota dominating them.ec_matchNULL
4421340sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. HisJ, a third unrelated family solving the same step. Attached to the standalone phosphatase component, not to the bifunctional one: HisJ is its own protein.ec_matchNULL
4421341sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. A further standalone histidinol-phosphatase family carrying EC 3.1.3.15, 8656 hits. Named for its profile rather than a gene symbol because NCBIfam assigns none.ec_matchNULL
4421342sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. The Neisseriaceae-restricted histidinol-phosphatase. Narrow by design; admitted because the grade guarantees one function and the taxonomic restriction is the profile's, not a claim gifter makes.ec_matchNULL
4431343sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog_domain. The N-terminal phosphatase domain of the bifunctional HisB protein, so it belongs on the bifunctional component beside K01089 and not on the standalone one. Its GO terms carry the imidazoleglycerol-phosphate dehydratase activity of the other domain, which is what identifies the protein as the fused form.ec_matchNULL
4821344sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. Phosphoribosyl-ATP diphosphatase, EC 3.6.1.31, the EC RHEA:22828 carries. The curated KO layer reaches 38.7% of reference genomes at best and this reaction was missing in 15 of 30 sampled histidine failures.ec_matchNULL
4821345sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. A second PRK00400-derived diphosphatase family on the same reaction.ec_matchNULL
4821346sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog. A third PRK00400-derived diphosphatase family on the same reaction.ec_matchNULL
4821347sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-23family_type=equivalog_domain. Its source identifier reads histidine_hisI, which names the cyclohydrolase gene, but its declared EC is 3.6.1.31 and not the cyclohydrolase's 3.5.4.19: in many genomes hisI denotes the fused HisIE protein. Admitted for the diphosphatase reaction on the EC, and the naming trap is recorded here so it is not re-litigated. A domain profile is the right grade for a step that occurs standalone as HisE and fused as HisIE, which is why K01523 and K11755 already sit on this component.ec_matchNULL
6071348orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-27NagE as one fused EIICBA or EIICB polypeptide, the self-sufficient form. KEGG assigns it EC 2.7.1.193, the EC RHEA:49240 carries.kegg_reaction_linkNULL
6071349orthologycuratedKEGG orthology and Rhea release 141, verified 2026-08-27The enzyme IIB chain of split N-acetylglucosamine systems, admitted on the same EC 2.7.1.193. It is substrate-specific, so it cannot license a broader claim; what it cannot show is its EIIC partner, for which no N-acetylglucosamine-specific orthology group exists in either admitted namespace. Refusing it would leave 51 genomes with GlcNAc-specific PTS evidence and no way to state it.ec_matchNULL
6071350sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-27family_type=equivalog. The fused EIIABC NagE, declaring EC 2.7.1.193. Corroborates the orthology with a sequence family built for the same activity, so a genome annotated only against NCBIfam can satisfy the step.ec_matchNULL
6071351sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-27family_type=equivalog_domain. The IIBC unit of NagE, declaring EC 2.7.1.193 and 23373 hits. A domain profile is the right grade for a transporter that occurs fused and split, which is the same reasoning that admitted TIGR03188.1 on the histidine diphosphatase.ec_matchNULL
791352sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-27family_type=equivalog. NagB, the deaminase family K02564 also names, at 35984 hits the broadest profile on the reaction. EC 3.5.99.6 is the EC RHEA:12172 carries, verified against reaction_xrefs before curating.ec_matchNULL
791357sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-27family_type=equivalog. NagB-II, a second deaminase family that K02564 does not cover, which is why this profile is the one the curation lead named. Same EC 3.5.99.6, different protein.ec_matchNULL
791353sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-27family_type=equivalog. The PRK00443 gammaproteobacterial NagB.ec_matchNULL
791354sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-27family_type=equivalog. The PRK00443 profile restricted to Caryophanales. Narrow by design; admitted because the grade guarantees one function and the taxonomic restriction is the profile's, not a claim gifter makes.ec_matchNULL
791355sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-27family_type=equivalog. A third PRK-derived deaminase family on the same reaction, domain-wide in range.ec_matchNULL
791356sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-27family_type=equivalog. GlmD, the Thermococcaceae deaminase. 39 hits and archaeal, so it changes almost nothing on a bacterial reference set; admitted because the reaction is the same one and refusing an equivalog for being rare is not a rule gifter has.ec_matchNULL
771358sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-27family_type=equivalog. NagK from PRK13310, declaring EC 2.7.1.59, the EC RHEA:17417 carries. Its GO term GO:0045127 is N-acetylglucosamine kinase activity, so profile, EC and GO agree.ec_matchNULL
771359sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-27family_type=equivalog. A second NagK family, Pseudomonadota-ranged, on the same EC. Admitted for annotation coverage: the kinase route stays the minority entry either way, which is why this change also curates the PTS route.ec_matchNULL
781360sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-27family_type=equivalog. NagA, at 71976 hits the broadest profile on the reaction and ranged across cellular organisms. EC 3.5.1.25 is the EC RHEA:22936 carries, and GO:0008448 is the deacetylase activity. Curated so that the middle step of both amino sugar capabilities is reachable in a genome annotated only against NCBIfam.ec_matchNULL
781361sequence_familyhigh-confidenceNCBIfam hmm_PGAP/20.0, retrieved 2026-08-27family_type=equivalog. The PRK11170 gammaproteobacterial NagA, same EC and same GO term.ec_matchNULL
reference_frame19 rows · 6 columns
frame_pkframe_idlabeldescriptionboundedinterpretation
1carbohydrate_degradationCarbohydrate degradationCatabolic GIFTs acting on polysaccharides, neutral monosaccharides, amino sugars or uronates.0Measures the supported repertoire in the current curated carbohydrate catalogue; it is not total carbohydrate metabolism, substrate use, growth or activity.
2plant_fibre_utilisationPlant fibre utilisationGIFTs curated with a fibre-degradation role, including polymer processing, uptake and intracellular catabolism of released sugars.0Measures encoded fibre-associated capabilities; it does not show that fibre is available, consumed or degraded in situ.
3host_glycan_foragingHost glycan foragingGIFTs acting on host-derived glycans or the sugars released from them.0Current membership covers released-sugar catabolism rather than complete mucin or host-glycan depolymerisation.
4carbon_acquisitionCarbon acquisitionGIFTs that convert an acquired substrate into central carbon metabolism.0Measures a curated catabolic repertoire, not carbon-use efficiency, growth yield, flux or environmental substrate availability.
5aromatic_catabolismAromatic catabolismGIFTs that activate, cleave or funnel aromatic rings toward central metabolism.0Counts independently meaningful aromatic-catabolic capabilities; it does not prove complete mineralisation unless the required connected GIFTs are all supported.
6nitrogen_acquisitionNitrogen acquisitionGIFTs whose curated role makes nitrogen available from inorganic or organic sources.0Measures encoded acquisition chemistry, not nitrogen limitation, uptake rate, assimilation rate or growth.
7sulfur_acquisitionSulfur acquisitionGIFTs whose curated role makes sulfur available from inorganic or organic sources.0Measures encoded acquisition chemistry, not sulfur limitation, uptake rate, assimilation rate or growth.
8fermentation_productsFermentation productsGIFTs that form a curated terminal fermentation product.0Measures the repertoire of encoded product-forming chemistry; it does not establish fermentation, secretion, product concentration or flux.
9short_chain_fatty_acidsShort-chain fatty acidsGIFTs whose curated substrate or product class is a short-chain fatty acid.0Covers formation and interconversion capabilities and must not be read as an SCFA production rate or concentration.
10vitamin_biosynthesisVitamin biosynthesisGIFTs participating in curated vitamin and cofactor biosynthetic capabilities.0Richness counts atomic capabilities, not the number of complete vitamins a genome can synthesize from environmental precursors.
11released_bioactive_productsReleased bioactive productsGIFTs whose chemistry forms a product curated as potentially bioactive when released.0The GIFT establishes product-forming chemistry only; release, concentration and an effect on a host or community are not inferred.
12chemical_detoxificationChemical detoxificationDefense GIFTs implementing a complete curated chemical-detoxification mechanism.0Measures encoded mechanisms, not exposure, expression, survival or resistance under a particular condition.
13shikimate_derived_biosynthesisShikimate-derived biosynthesisBiosynthetic GIFTs whose product carbon skeleton is derived from the shikimate pathway.0Membership describes biosynthetic family provenance; richness does not prove that every connected product pathway is complete.
14biomass_essential_anabolismBiomass-essential anabolic GIFTsAnabolic GIFTs whose declared output is a curated biomass-essential anchor.1Coverage is the fraction of assessable curated biomass-essential anabolic capabilities supported, not proof of growth without supplementation.
15amino_acid_autonomyAmino-acid autonomyBiomass-essential anabolic GIFTs in the amino-acid substrate class.1Coverage measures supported curated amino-acid anabolic capabilities, not prototrophic growth in a specified medium.
16nucleotide_autonomyNucleotide autonomyBiomass-essential anabolic GIFTs in the nucleotide substrate class.1Coverage measures supported curated nucleotide anabolic capabilities, not growth, nucleotide pool size or salvage independence.
17cofactor_autonomyCofactor autonomyBiomass-essential anabolic GIFTs in the cofactor substrate class.1Coverage measures supported curated cofactor anabolic capabilities, not cofactor sufficiency, uptake independence or growth.
18extracellular_public_goodsExtracellular processing outputsMetabolic GIFTs derived as consuming and releasing extracellular anchors.0Identifies encoded extracellular processing interfaces; public-good use, sharing and ecological benefit are not inferred.
19nutrient_uptakeNutrient uptakeMetabolic GIFTs derived as moving an extracellular anchor to a cytoplasmic anchor.0Measures curated uptake capabilities, not transport rate, substrate availability or uptake activity.
reference_frame_filter31 rows · 3 columns
frame_pkfilter_keyvalue
1modecatabolic
1facet:substrate_classpolysaccharide
1facet:substrate_classmonosaccharide
1facet:substrate_classamino_sugar
1facet:substrate_classuronate
2facet:physiological_rolefibre_degradation
3facet:physiological_rolehost_glycan_foraging
4facet:physiological_rolecarbon_acquisition
5facet:physiological_rolearomatic_ring_catabolism
6facet:physiological_rolenitrogen_acquisition
7facet:physiological_rolesulfur_acquisition
8facet:physiological_rolefermentative_end_product
9facet:substrate_classshort_chain_fatty_acid
10facet:physiological_rolevitamin_biosynthesis
11facet:physiological_rolereleased_bioactive_product
12typedefense
12facet:defense_classchemical_detoxification
13facet:biosynthetic_familyshikimate_derived_aromatic
14modeanabolic
14auxotrophy_indicatortrue
15modeanabolic
15facet:substrate_classamino_acid
15auxotrophy_indicatortrue
16modeanabolic
16facet:substrate_classnucleotide
16auxotrophy_indicatortrue
17modeanabolic
17facet:substrate_classcofactor
17auxotrophy_indicatortrue
18resource_strategypublic_good
19resource_strategyuptake
reference_frame_metric71 rows · 4 columns
frame_pkscopemetric_idrationale
1genomegift_richnessCount complete curated carbohydrate-degradation capabilities.
1genomebreadth_substrate_classSeparate polymer, neutral-sugar, amino-sugar and uronate breadth from raw richness.
1communitycommunity_richnessCount carbohydrate-degradation capabilities represented anywhere in the community.
1communityprovider_countReport redundancy separately for every carbohydrate-degradation capability.
1communityabundance_coverageWhen abundance is supplied, report how much observed abundance carries each capability.
2genomegift_richnessCount supported fibre-processing, uptake and catabolic capabilities.
2communitycommunity_richnessCount fibre-associated capabilities represented anywhere in the community.
2communityprovider_countIdentify redundant and single-provider fibre capabilities.
2networkdistributed_chain_linksIdentify extracellular fibre-processing chains completed only across genomes.
3genomegift_richnessCount supported host-glycan-associated sugar catabolic capabilities.
3communityprovider_countReport how many genomes carry each host-glycan-associated capability.
3communityabundance_coverageWhen abundance is supplied, report the observed abundance carrying each capability.
4genomegift_richnessCount complete acquired-carbon catabolic capabilities.
4genomebreadth_substrate_classCount distinct curated substrate classes represented by supported GIFTs.
4communitycommunity_richnessCount acquired-carbon capabilities represented anywhere in the community.
4communityprovider_countReport community redundancy for each acquired-carbon capability.
5genomegift_richnessCount supported aromatic entry, cleavage and funnel capabilities.
5communitycommunity_richnessCount aromatic-catabolic capabilities represented anywhere in the community.
5communityprovider_countIdentify the providers of each aromatic-catabolic capability.
5networkdistributed_chain_linksIdentify anchor-compatible aromatic chains split between genomes.
6genomegift_richnessCount complete curated nitrogen-acquisition capabilities.
6genomebreadth_substrate_classCount distinct nitrogen-bearing substrate classes represented.
6communitycommunity_richnessCount nitrogen-acquisition capabilities represented anywhere in the community.
6communityprovider_countReport provider redundancy for each nitrogen-acquisition capability.
7genomegift_richnessCount complete curated sulfur-acquisition capabilities.
7communitycommunity_richnessCount sulfur-acquisition capabilities represented anywhere in the community.
7communityprovider_countReport provider redundancy for each sulfur-acquisition capability.
8genomegift_richnessCount supported terminal product-forming capabilities.
8genomebreadth_substrate_classSeparate short-chain fatty acids, organic acids and neutral products.
8communitycommunity_richnessCount product-forming capabilities represented anywhere in the community.
8communityprovider_countReport providers without conflating presence with abundance.
9genomegift_richnessCount supported short-chain-fatty-acid formation or interconversion capabilities.
9communitycommunity_richnessCount short-chain-fatty-acid capabilities represented anywhere in the community.
9communityprovider_countReport provider redundancy for each capability.
9communityabundance_coverageWhen abundance is supplied, report how much observed abundance carries each capability.
10genomegift_richnessCount supported atomic vitamin and cofactor biosynthetic capabilities.
10communitycommunity_richnessCount vitamin-biosynthetic capabilities represented anywhere in the community.
10communityprovider_countReport providers of each independently meaningful biosynthetic capability.
11genomegift_richnessCount supported product-forming chemistries.
11communityprovider_countReport which genomes encode each product-forming capability.
11communityabundance_coverageWhen abundance is supplied, keep carrier abundance separate from capability presence.
12genomegift_richnessCount complete curated chemical-detoxification mechanisms.
12communitycommunity_richnessCount mechanisms represented anywhere in the community.
12communityprovider_countReport redundancy for each complete mechanism.
13genomegift_richnessCount supported independently meaningful shikimate-derived biosynthetic capabilities.
13communitycommunity_richnessCount shikimate-derived capabilities represented anywhere in the community.
13communityprovider_countReport providers for each shikimate-derived capability.
14genomesupported_fractionReport coverage only because this frame is curated as bounded.
14genomeassessable_fractionExpose how much of the bounded denominator could be assessed.
14communitycommunity_coverageReport bounded-frame coverage by at least one community member.
14communityprovider_countReport redundancy for each biomass-essential anabolic capability.
15genomesupported_fractionReport coverage of assessable biomass-essential amino-acid capabilities.
15genomeassessable_fractionExpose how much of the amino-acid denominator could be assessed.
15communitycommunity_coverageReport bounded amino-acid capability coverage across the community.
15communityprovider_countReport redundancy for each amino-acid anabolic capability.
16genomesupported_fractionReport coverage of assessable biomass-essential nucleotide capabilities.
16genomeassessable_fractionExpose how much of the nucleotide denominator could be assessed.
16communitycommunity_coverageReport bounded nucleotide capability coverage across the community.
16communityprovider_countReport redundancy for each nucleotide anabolic capability.
17genomesupported_fractionReport coverage of assessable biomass-essential cofactor capabilities.
17genomeassessable_fractionExpose how much of the cofactor denominator could be assessed.
17communitycommunity_coverageReport bounded cofactor capability coverage across the community.
17communityprovider_countReport redundancy for each cofactor anabolic capability.
18genomegift_richnessCount encoded extracellular processing interfaces.
18communityprovider_countReport the providers of each extracellular processing interface.
18communityabundance_coverageWhen abundance is supplied, report how much observed abundance carries each interface.
18networkhandoff_edgesReport only anchor-compatible potential handoffs across genomes.
19genomegift_richnessCount complete curated nutrient-uptake capabilities.
19communityprovider_countReport provider redundancy for each uptake capability.
19communityabundance_coverageWhen abundance is supplied, report how much observed abundance carries each uptake capability.
19networkdistributed_chain_linksTest whether extracellular supply and uptake are split across genomes.
database_change144 rows · 11 columns
change_pkchange_idreleasedchanged_atlayercategorycall_effectsummaryrationaleevidenceeffect
1DBC-20260820-NAMED-FRAMES2026.20.42026-08-20T11:35ZschemaadditionnoneNineteen named reference frames expose recurring genome and community questions through curated metadata filtersUsers could already construct frames from type, mode, facets and the derived GIFT profile, but every analysis had to restate biologically meaningful groupings and their interpretation limits. Storing reusable filter recipes makes those groupings discoverable and versioned while preserving the rule that a frame is never a hard-coded list of GIFT identifiers.Existing curated gift_type, mode, gift_facet and gift_profile semantics in database release 2026.20.3; quantitative-trait invariants and implemented metrics documented in inst/doc/proposal-quantitative-traits.md.No GIFT, route, architecture, circuit, mechanism, marker or Boolean call changes. Schema version 7 adds normalized reference-frame definitions, filters and metric recommendations. Nineteen presets resolve membership from current metadata; only biomass-essential anabolism and its amino-acid, nucleotide and cofactor subsets are declared bounded.
2DBC-20260820-COMPATIBLE-SOLUTES2026.20.22026-08-20T12:00ZgiftadditionbroadensEctoine biosynthesis and choline-to-betaine oxidation are curated as bounded compatible-solute chemistryThe claims end at L-ectoine and glycine betaine and deliberately exclude transport, regulation, intracellular concentration and osmotic-tolerance outcomes. The ectoine cut starts at the existing ASA branchpoint instead of repeating its upstream trunk. Choline oxidation reuses the existing BETAINE anchor and admits four chemically complete routes, while refusing ALDH7A1 K14085 because its aldehyde range cannot identify betaine aldehyde.Rhea release 141; KEGG M00033 and M00555; MetaCyc P101-PWY, BETSYN-PWY and PWY-3722; ectoine biochemistry PMID 31921013 and GbsAB genetics PMID 8752328, all assessed 2026-08-20. Full boundary and marker audit in inst/doc/proposal-compatible-solutes-heme-enterobactin-detoxification.md.ectoine_biosynthesis becomes callable only on EctB plus EctA plus EctC. choline_to_betaine becomes callable on BetA/BetB, GbsB/GbsA, choline-monooxygenase/BADH or choline oxidase and composes into the existing betaine chain. K14085 fires neither.
3DBC-20260820-HEME-B2026.20.22026-08-20T12:01ZgiftadditionbroadensHeme b biosynthesis is curated from the uroporphyrinogen III branchpoint through classical and coproporphyrin routesUROGEN_III is the last shared anchor before corrin, siroheme and heme chemistry diverge. Six classical minimal routes materialise independent HemF/HemN and HemY/HemG/HemJ choices, and a seventh route represents the HemY-HemH-HemQ coproporphyrin pathway. Multifunctional HemY and HemH markers attach to two reaction-specific components. The siroheme route is excluded because it has a different input boundary.Rhea release 141; KEGG M00121 and M00926; MetaCyc HEME-BIOSYNTHESIS-II, HEMESYN2-PWY and PWY-7766; HemG PMID 19583219, HemJ PMID 20823222 and the coproporphyrin route PMID 25646457, assessed 2026-08-20.heme_b_biosynthesis becomes callable on any complete route. A partial route, a ferrochelatase alone or siroheme-pathway markers remain negative. The new HEME_B anchor does not make a vitamin or respiratory-capacity claim.
4DBC-20260820-ENTEROBACTIN-SPLIT2026.20.22026-08-20T12:02ZgiftadditionbroadensEnterobactin biosynthesis is split at 2,3-dihydroxybenzoate into a reusable catecholate head and a complete assembly GIFTMetaCyc ENTBACSYN-PWY crosses a useful branchpoint. Curating its head once prevents reaction duplication and lets other catecholate products reuse it. The tail uses the aggregate Rhea EC 6.3.2.14 reaction but keeps EntB, EntD, EntE and EntF as four jointly required system components; EntB's lyase and carrier roles remain separate despite sharing one marker.Rhea release 141 RHEA:18985, RHEA:11112, RHEA:23824 and RHEA:30571; KEGG map01053 and K01252/K00216/K02362/K02363/K02364; MetaCyc ENTBACSYN-PWY; assembly enzymology PMID 10375542, assessed 2026-08-20.dihydroxybenzoate_biosynthesis composes from the existing chorismate output into enterobactin_biosynthesis through the new DIHYDROXYBENZOATE_2_3 anchor. The head can be positive without the tail; the tail requires all four assembly components and claims neither secretion nor iron acquisition.
5DBC-20260820-CHEMICAL-DETOX-EXPANSION2026.20.22026-08-20T12:03ZgiftadditionbroadensTwo complete chemical-detoxification mechanisms are added for methylglyoxal and superoxideMethylglyoxal disposal requires both glutathione-dependent glyoxalases and stops at D-lactate, before its oxidation. Superoxide detoxification requires removal of both superoxide and the hydrogen peroxide produced; SOD alone is incomplete. Alternative catalases and the complete AhpC-AhpF pair satisfy peroxide removal. Nickel SOD without its maturation protease, superoxide reductase without its electron-delivery architecture, and broad methylglyoxal reductases are not accepted.Rhea release 141 RHEA:19069, RHEA:25245, RHEA:20696, RHEA:20309 and RHEA:62620; MetaCyc PWY-5386, DETOX1-PWY and DETOX1-PWY-1; PMID 21143325, PMID 22609271, PMID 15516600 and PMID 12072973, assessed 2026-08-20.methylglyoxal_detoxification becomes callable only on GloA plus GloB. superoxide_detoxification becomes callable only on an accepted SOD plus an accepted catalase or both AhpC and AhpF. SOD alone, K00518 and K05919 remain negative.
6DBC-20260820-PHB-REFUSED2026.20.22026-08-20T12:04ZgiftclarificationnonePolyhydroxybutyrate biosynthesis is refused at the current marker specificityThe proposed acetyl-CoA-to-PHB boundary is coherent, but K03821 identifies polyhydroxyalkanoate synthases spanning different monomer and chain-length preferences. PhaA and PhaB context establishes 3-hydroxybutyryl-CoA supply but cannot make the downstream polymerase accession PHB-specific, so a positive call would exceed its genomic evidence.Rhea release 141 RHEA:15405 and RHEA:66924; KEGG K00626, K00023 and K03821; PhaC specificity studies PMID 15205419, PMID 24564904 and PMID 21261834, assessed 2026-08-20. Full audit in inst/doc/proposal-compatible-solutes-heme-enterobactin-detoxification.md.No PHB GIFT, polymer anchor, route or marker is added. Reconsider only when a maintained marker can distinguish a synthase accepting 3-hydroxybutyrate at the claimed polymer specificity, such as a validated class-specific custom HMM.
7DBC-20260820-SIROHEME-BIOSYNTHESIS2026.20.32026-08-20T10:06ZgiftadditionbroadensSiroheme biosynthesis is curated from uroporphyrinogen III through multifunctional or split enzyme systemsSiroheme is a defensible cofactor branchpoint between uroporphyrinogen III and siroheme-dependent chemistry. The route requires methylation, dehydrogenation and iron insertion. CysG supplies all three; Met8 supplies the terminal pair; split systems require an accepted methyltransferase, SirC and iron-specific SirB. RHEA:32459 consolidates the two sequential methyl transfers that MetaCyc records separately, so the route has three Rhea reactions without collapsing two different genomic requirements.Rhea release 141 RHEA:32459, RHEA:15613 and RHEA:24360; ChEBI release 253 CHEBI:60052; KEGG M00846 and K00589/K02302/K02303/K02304/K02496/K03794/K13542/K13543/K24866; MetaCyc 30.0 PWY-5194; PMID 9461500, PMID 11980703 and PMID 12408752, verified 2026-08-20. The accepted markers complete the UROGEN_III-to-siroheme tail in 4161 of 10151 bacterial and 1 of 470 archaeal KEGG genomes.siroheme_biosynthesis becomes callable on CysG alone or a complete split implementation and exposes the SIROHEME branchpoint. CbiX-family evidence that cannot resolve iron insertion remains negative, so the trait knowingly under-calls archaeal alternatives. No siroheme-dependent reductase, alternative heme route, cofactor use or phenotype is implied.
8DBC-20260820-AHB-DECARBOXYLASE-REFUSAL2026.20.32026-08-20T10:07ZmarkerclarificationnoneSiroheme-to-heme b remains refused because KO K22225 cannot prove both AhbA and AhbBThe siroheme-to-heme boundary and its three chemical reactions are coherent, and AhbC plus either AhbD or the peroxide-dependent heme synthase are product-specific. The first reaction nevertheless requires the AhbA-AhbB heterodimer. KEGG assigns both experimentally required Methanosarcina genes to K22225, so putting that accession on two components would let one observed gene satisfy both and would collapse a multisubunit system. Gene order cannot repair the evidence, and gifter has no marker-multiplicity contract.MetaCyc 30.0 PWY-7552; Rhea release 141 RHEA:19093, RHEA:37431, RHEA:56520 and RHEA:56516; KEGG M00847 and Mbar_A1459/Mbar_A1460, both K22225; PMID 24669201 and PMID 24865947. Of the current KEGG genomes carrying the full K22225-K22226-(K22227 or K25033) expression, 45 bacterial and 3 archaeal genomes have only one K22225 gene row, verified 2026-08-20.No siroheme_to_heme_b GIFT, route or Ahb marker is added, and the existing heme_b_biosynthesis boundary remains UROGEN_III through the classical routes. Reconsider only with maintained markers that distinguish AhbA from AhbB, a validated fusion-specific marker, or a general evidence contract that requires distinct observed genes for repeated accessions.
9DBC-20260817-INITIAL-CURATION2026.08.12026-08-17giftadditionnoneInitial curated release of five nucleotide biosynthesis GIFTsEstablish the reference content of gifter as biologically bounded capabilities between declared molecular anchors, derived from but not equal to KEGG modules M00048 to M00052.Rhea release 141 reaction chemistry, ChEBI release 253 anchor identity, KEGG modules M00048-M00052 for pathway organisation and orthology assignment.Baseline release. Purine core, adenylate, guanylate, pyrimidine core and cytidylate biosynthesis become callable, composing through the shared IMP anchor.
10DBC-20260817-ATCASE-PYRI2026.08.22026-08-17T17:45Zenzyme_systemcorrectionbroadensAspartate carbamoyltransferase no longer requires the PyrI regulatory subunitPyrI is an allosteric regulator, not a catalytic subunit, and class C aspartate carbamoyltransferases are catalytic trimers with no regulatory subunit. Requiring K00610 asserted a subunit that most prokaryotes do not encode. The previous definition followed the KEGG module expression (K00609+K00610,K00608), which is a pathway drawing convention rather than an evidence claim.Of 9670 KEGG organisms carrying K00609, 7863 carry neither K00610 nor K00608. Bacillus subtilis, Lactococcus lactis, Pseudomonas aeruginosa, Staphylococcus aureus and Mycobacterium tuberculosis, all de novo pyrimidine prototrophs, were called incomplete at RHEA:20013 when evaluated from their complete KEGG orthology annotation.SYS_20013_HOLOENZYME became the single-component SYS_20013_CATALYTIC, satisfied by K00609 alone; COMP_20013_REGULATORY and marker K00610 were removed. Those five reference genomes now complete the GIFT; no genome lost a previously complete call.
11DBC-20260817-DHOD-PYRK2026.08.22026-08-17T17:45Zenzyme_systemcorrectionnarrowsNAD-dependent dihydroorotate oxidation now requires the PyrK electron transfer subunitThe class 1B enzyme is a PyrDb/PyrK holoenzyme. The catalytic subunit alone cannot reduce NAD+, so accepting K17828 by itself claimed the NAD-dependent chemistry from half of the enzyme. KEGG module M00051 lists only K17828 for this step.KEGG annotates K02823 (pyrDII/PyrK) to the same reaction R01869 as K17828, and 2403 of the 2724 organisms carrying K17828 also carry K02823.SYS_13513_NAD gained the required component COMP_13513_ELECTRON accepting K02823. Genomes annotated with K17828 but not K02823 now report RHEA:13513 as unsupported and fall back to the fumarate-dependent or quinone-dependent route. None of the nine reference genomes changed.
12DBC-20260817-MARKER-AUDIT2026.08.22026-08-17T17:45ZmarkerclarificationnoneMarker layer audited against KEGG orthology; no orthologs missingConfirm whether other genomic markers are acceptable for the curated enzymes before broadening the evidence layer, and record the rejected candidates so they are not re-proposed.The accepted markers of all 27 reactions were compared against every KO that KEGG assigns to the corresponding EC number, and against the step logic of modules M00048-M00052. Twenty-six of 27 reactions matched exactly; the only difference was the regulatory K00610 retired in this release.No markers added. K06863 stays off the folate-dependent AICAR transformylase because purP is formate-dependent and modelled as RHEA:24836. K01948 (EC 6.3.4.16) remains unacceptable for the glutamine-dependent RHEA:18633. Non-KO namespaces validate and resolve correctly but were not adopted, because evaluation has no confidence filter and weaker evidence would silently change calls.
13DBC-20260817-CHANGE-HISTORY2026.08.32026-08-17T18:05ZschemaadditionnoneCuration history recorded inside the database and published in the atlasDatabase decisions were only readable in a Markdown file next to the code. Storing them as curated source tables keeps the biological history versioned with the content it describes, linked to the GIFTs it affects, and publishable with the reference atlas.Schema version 2 adds database_change and change_gift; sources are database_changes.tsv and change_gifts.tsv.No change to any GIFT call. database_changelog() reads the history, the HTML atlas gains a Changelog view, and each GIFT shows its own change history.
14DBC-20260817-AMINO-ACID-BATCH2026.09.12026-08-17T20:10ZgiftadditionbroadensNine serine, glycine, aspartate-family, cysteine and methionine biosynthesis GIFTs addedExtend gifter beyond nucleotide metabolism with the amino acid capabilities most often needed to interpret host-associated genomes, curated as bounded capabilities rather than as imported KEGG modules.KEGG modules M00016-M00021, M00338 and M00609 for orthology and pathway organisation; Rhea release 141 for reaction identity, direction and ChEBI participants; KEGG gene-to-organism links for the prevalence figures quoted in the accompanying change entries.Eleven anchors, nine GIFTs, nineteen routes and twenty-five reactions become callable. The amino acid GIFTs compose into a single acyclic chain from 3-phosphoglycerate through serine and cysteine to methionine, and from aspartate through the semialdehyde and homoserine branchpoints to threonine and methionine.
15DBC-20260817-ASPARTATE-TRUNK2026.09.12026-08-17T20:10ZgiftadditionnoneThe aspartate-to-homoserine trunk is curated once instead of twiceKEGG M00018 and M00017 both contain aspartate kinase, aspartate-semialdehyde dehydrogenase and homoserine dehydrogenase. Importing both modules as GIFTs would encode the same three reactions twice and let the two copies drift apart. The trunk is cut at the two real branchpoints instead.6569 KEGG organisms satisfy the orthology of both modules, so the duplication would be exercised in the majority of genomes carrying either. L-aspartate 4-semialdehyde is the branchpoint to lysine and diaminopimelate (M00016); L-homoserine is the branchpoint to threonine and methionine and is named in both module titles.aspartate_semialdehyde_biosynthesis and homoserine_biosynthesis carry the shared chemistry; threonine and methionine biosynthesis begin at the homoserine anchor and compose through it. The lysine and diaminopimelate branch can later attach at the semialdehyde anchor without re-cutting any existing GIFT.
16DBC-20260817-METHIONINE-SULFHYDRYLATION2026.09.12026-08-17T20:10ZgiftadditionbroadensDirect sulfhydrylation added as a methionine biosynthesis capability absent from KEGG M00017M00017 models only transsulfuration, in which cysteine donates the sulfur through cystathionine. Many prokaryotes instead incorporate inorganic sulfide directly into acylated homoserine. Following the module would call those genomes methionine auxotrophs.Among KEGG organisms carrying the complete aspartate-to-homoserine trunk and a homoserine acyltransferase, 4096 have only a direct sulfhydrylase, 985 have only the transsulfuration enzymes and 2353 have both. 3910 organisms complete methionine biosynthesis by sulfhydrylation and would be called incomplete by M00017 as written.methionine_biosynthesis_sulfhydrylation was created with the sulfide input anchor declared. It is kept separate from the transsulfuration capability because anchors are declared per GIFT and not per route, so one GIFT declaring both cysteine and sulfide inputs would over-claim the requirements of both routes.
17DBC-20260817-M00609-REDUCTION2026.09.12026-08-17T20:10ZgiftadditionbroadensM00338 and the cysteine-forming tail of M00609 merged; the SAM-cycle steps of M00609 excludedThe first four steps of M00609 are the activated methyl cycle, not cysteine biosynthesis. K17462 is a putative AdoMet-dependent methyltransferase with EC 2.1.1.- whose reaction R10404 has no Rhea master, and the SAM-to-SAH conversion it stands for is performed by hundreds of unrelated methyltransferases. Requiring it is a pathway-drawing convention, as K00610 was for aspartate carbamoyltransferase. The remaining two steps make cysteine from homocysteine, which is exactly what M00338 does by different chemistry.Of 489 KEGG organisms carrying both K17216 and K17217, only 332 carry K17462, so 157 would be called incomplete for a step that is not evidence of anything. None of the 2592 organisms carrying the M00338 pair K01697 and K01758 carries the M00609 pair, which makes the two enzyme sets taxonomically disjoint solutions to one problem rather than two traits.cysteine_biosynthesis_homocysteine carries both chemistries as the alternative routes CYS_RT_SERINE and CYS_RT_OAS. The O-acetyl-L-serine route additionally requires serine O-acetyltransferase, which M00609 omits because its diagram enters at O-acetyl-L-serine; 486 of the 489 organisms carry it, so the added requirement costs almost no sensitivity.
18DBC-20260817-HOMOCYSTEINE-INPUT-ONLY2026.09.12026-08-17T20:10ZanchorclarificationnoneL-homocysteine is declared as an input anchor only, and methionine biosynthesis is not split at itCysteine to methionine and homocysteine to cysteine is a real metabolic interconversion, so the obvious boundary choices make the anchor-derived composition graph cyclic and the database fails to build. Declaring homocysteine as an output anchor, or curating a methionine-to-homocysteine GIFT, re-creates the cycle.The source validator turns every output-anchor to input-anchor match into a directed edge and rejects cycles. With homocysteine as an output the graph closes through METHIONINE, HOMOCYSTEINE and CYSTEINE. In the organisms that use the mcc route the homocysteine consumed by cysteine biosynthesis comes from methionine salvage rather than from de novo methionine biosynthesis, so an input-only boundary is also the honest one.L-homocysteine stays internal to both methionine GIFTs and is declared only as an input of cysteine_biosynthesis_homocysteine. Any future methionine salvage or SAM-cycle GIFT must revisit this boundary before it can be added.
19DBC-20260817-GIFT-PATHWAY-LINKS2026.09.12026-08-17T20:10ZschemaadditionnoneGIFTs can be linked to related external pathways with an explicit set relationA GIFT is a curated capability between declared anchors and is deliberately not equal to any pathway record, but users arrive from the resources they already know. A reference that only named a module would imply an equivalence that is usually false, so the link stores how the boundaries compare.Schema version 3 adds gift_xref with the relation vocabulary equivalent, subset_of, superset_of, overlaps and related; the source is gift_xrefs.tsv. The namespace is open so that resources beyond KEGG can be linked.No change to any GIFT call. get_gift_pathways() and gifts_for_pathway() read the links, and the atlas shows them on each GIFT. Fourteen GIFTs are linked to KEGG modules and pathway maps; MetaCyc identifiers are accepted by the schema but not yet curated.
20DBC-20260817-SCHEMA-4-REACTION-IDENTITY2026.09.22026-08-17T21:30ZschemaadditionnoneReactions carry a stable reaction_id and an optional Rhea masterRhea coverage of polymer-acting chemistry is incomplete because a polysaccharide is a substrate class rather than a compound with a balanced equation. Requiring a Rhea master as reaction identity would have excluded most carbohydrate-active chemistry from the database. Rhea remains preferred and remains the reaction_id wherever it exists; a reaction without one must instead carry at least one cross-reference.CAZy family and characterised-activity records; absence of Rhea master reactions for endo-acting glycoside hydrolases on polymeric substrates.No change to any existing GIFT call. reaction_id equals the Rhea master for all reactions curated so far.
21DBC-20260817-SCHEMA-4-ANCHOR-COMPARTMENT2026.09.22026-08-17T21:30ZschemaadditionnoneAnchors carry a molecule key and a two-state compartment qualifierDepolymerisation, uptake and intracellular saccharification are separate ecological strategies, and distinguishing them requires saying which side of the membrane a boundary molecule sits on. Compartment is a curated boundary claim, not a genomic inference: markers identify chemistry, not localisation. The qualifier is limited to declared anchors; no other part of gifter is compartmentalised.Curation proposal inst/doc/proposal-polysaccharide-degradation.md sections 4 and 8.2; selfish versus public-goods glycan foraging literature.No change to any existing GIFT call. Every existing anchor is compartment unspecified, and graph edges between unspecified anchors remain exact.
22DBC-20260817-SCHEMA-4-GIFT-MODE2026.09.22026-08-17T21:30ZschemaadditionnoneGIFTs declare a mode and composition cycles are checked within a modeCatabolism and biosynthesis legitimately close loops through shared metabolites, so the acyclicity check that protects boundary curation would reject correct content once degradation GIFTs are added. Cycles remain forbidden within a mode, which is where they still indicate a boundary error.Worked example: GlcNAc degradation to fructose 6-phosphate against amino sugar biosynthesis from fructose 6-phosphate.No change to any existing GIFT call. All content curated so far is anabolic.
23DBC-20260818-SUGAR-DEGRADATION2026.09.32026-08-18T10:00ZgiftadditionbroadensNine monosaccharide and uronate degradation GIFTs added as the first catabolic contentMonosaccharide catabolism is the tier that connects carbohydrate degradation to central metabolism, and it is the half of the degradation model that needs no polymer chemistry. Each GIFT ends at the central metabolite the sugar actually becomes, so capabilities that yield different products are separate traits rather than routes of one trait.Rhea release 141 master reactions and KEGG orthology, every accession verified against the resource on 2026-08-18. KEGG modules M00632 and M00061 match two of the nine boundaries exactly; the other seven have no module.Nine new positive calls become possible. No existing GIFT call changes; the new content shares no reaction with the biosynthetic GIFTs.
24DBC-20260818-GNE-EXCLUDED2026.09.32026-08-18T10:00ZmarkerclarificationnarrowsThe bifunctional biosynthetic enzyme GNE is not accepted as evidence for N-acetylmannosamine kinaseGNE (K12409) carries a N-acetylmannosamine kinase domain and so catalyses the curated chemistry, but in the organisms that encode it that activity belongs to sialic acid biosynthesis rather than catabolism. Accepting it would call sialic acid degradation in genomes that only synthesise it, destroying the distinction the GIFT exists to draw.KEGG orthology entry K12409, annotated as bifunctional UDP-N-acetylglucosamine 2-epimerase / N-acetylmannosamine kinase.N-acetylneuraminate degradation is not called from GNE alone. Genomes carrying nanK or the bifunctional nanEK are unaffected.
25DBC-20260818-GALM-OPTIONAL2026.09.32026-08-18T10:00ZrouteclarificationbroadensAldose 1-epimerase is optional in the Leloir routeMutarotation between the alpha and beta anomers of D-galactose also proceeds spontaneously, so a genome lacking aldose 1-epimerase still runs the Leloir pathway. The reaction is retained at required = 0 so that it appears in the evidence trace without gating the call.Spontaneous anomerisation of reducing sugars in aqueous solution; KEGG M00632 includes galM but the pathway operates without it.Galactose degradation is called in genomes carrying galK, galT and galE but no recognised aldose 1-epimerase.
26DBC-20260818-PENTOSE-UPTAKE2026.09.42026-08-18T14:00ZgiftadditionbroadensD-xylose and L-arabinose uptake curated, and their anchors split by compartmentImport is what separates a genome that can use a sugar released by others from one that merely encodes the catabolic enzymes, and it is the first place the compartment layer carries real content. Both pentoses have substrate-specific ABC importer orthologues and a Rhea master for the translocation, so both conditions of the splitting licence are met.KEGG orthology K10543/K10544/K10545, K10537/K10538/K10539 and K25045/K25046/K25047; Rhea master reactions RHEA:29899 and RHEA:30007, both carrying explicit (out) and (in) participants.Two new positive calls become possible, and the first composition edges in the catabolic half of the database appear: uptake now feeds the matching degradation GIFT through the cytoplasmic anchor.
27DBC-20260818-UPTAKE-LICENCE2026.09.42026-08-18T14:00ZgiftclarificationnoneUptake GIFTs are curated only where transporter markers are substrate-specific and the translocation has a verified reaction identityFucose, galactose and mannose are moved mainly by promiscuous carriers: the KEGG orthologue for fucose uptake is annotated as a fucose-galactose-glucose symporter, so accepting it would attribute fucose uptake to any genome carrying that family. Sialic acid, hexuronate and N-acetylglucosamine have substrate-specific markers but no reaction identity gifter can verify, because their symporters and importers carry no EC number and no Rhea master. In both cases no uptake GIFT is curated and the substrate anchor stays compartment-unspecified, so no catabolic chain is broken by a transporter that could not be evidenced.KEGG orthology entry K02429, annotated as an MFS fucose-galactose-glucose:H+ symporter; absence of an EC number or Rhea master for K03290 (nanT), K08191 (exuT) and K10200/K10201/K10202 (ngcEFG).No call changes. Seven substrates keep an unspecified anchor and remain callable from their catabolic markers alone.
28DBC-20260818-PENTOSE-ANCHOR-IDENTITY2026.09.42026-08-18T14:00ZanchorcorrectionnoneThe pentose anchors use the generic sugar rather than a single anomerRhea represents ABC import of the generic sugar and uses one ChEBI identifier for both sides of the membrane. The anomer-specific identities previously recorded described the isomerase substrate rather than the boundary molecule, and would have made the transport and catabolic reactions appear to act on different substances.Rhea RHEA:29899 and RHEA:30007 use CHEBI:53455 and CHEBI:17535 for both the external and internal participant.No call changes; no route reaction was altered.
29DBC-20260818-POLYSACCHARIDE-TIERS2026.10.12026-08-18T18:00ZgiftadditionbroadensArabinoxylan and starch depolymerisation and saccharification curated as separate tiersEndo-acting depolymerisation and exo-acting saccharification are curated as separate GIFTs because possessing one without the other is the primary-degrader versus cross-feeder distinction, which is the main thing a carbohydrate database is asked to resolve. Polymer and oligosaccharide anchors are extracellular: a polymer cannot cross a membrane, and no oligosaccharide importer could be evidenced, so the products of their cleavage are outside the cell. Side-chain release earns its own GIFT because the released L-arabinose is itself an anchored fermentable sugar.CAZy family and activity assignments from dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping.tsv; KEGG orthology entries verified 2026-08-18. None of the six EC numbers has a Rhea master reaction.Six new positive calls become possible, and the first complete traversal from a dietary polysaccharide to central metabolism appears in the derived graph.
30DBC-20260818-CAZY-CONFIDENCE2026.10.12026-08-18T18:00ZmarkeradditionnoneCAZy families accepted as markers, with confidence derived from measured family polyspecificityA CAZy family is a sequence family, not an activity. Accepting a family as evidence for one of its activities silently attributes the others, so confidence is set from the number of distinct characterised activities the family carries in dbCAN: one activity is curated, two or three is high-confidence, four or more is ambiguous. GH5 carries 28 and GH13 carries 34, so neither is evidence for a specific chemistry on its own; GH52, GH120 and GH62 carry one each.Distinct EC counts computed directly from the pinned dbCAN mapping and recorded per marker in component_markers.notes.Calls resting only on polyspecific families report evidence_confidence = ambiguous rather than reading like curated orthology.
31DBC-20260818-CAZY-ONE-SYSTEM2026.10.12026-08-18T18:00Zenzyme_systemclarificationnoneA CAZy family and a KEGG orthologue are alternative markers of one catalytic role, not alternative enzyme systemsThe proposal suggested one enzyme system per non-homologous CAZy family. At implementation these are all single-protein hydrolases, and an annotation pipeline cannot tell whether the family hit and the orthology hit describe the same protein - they usually do. Modelling them as alternative systems would imply two enzymes where there is one. The system and component layers remain available for genuinely multi-subunit CAZyme architectures.Absence of subunit structure in the curated hydrolases; overlap between CAZy and KEGG annotation of the same protein.No call changes; the Boolean result is identical either way.
32DBC-20260818-SUBSTRATE-LEVEL-GIFTS2026.10.22026-08-18T21:00ZgiftcorrectionmixedPolysaccharide degradation is curated per substrate capability rather than per enzymatic stepThe first polysaccharide release split each substrate into single-reaction GIFTs for endo-acting depolymerisation, exo-acting saccharification and debranching. That made a GIFT equivalent to a reaction, which is the marker-checklist shape the ontology exists to avoid, and it left the question a user actually asks - can this genome degrade xylan - unanswerable by any single trait. The separation was motivated by the primary-degrader versus cross-feeder distinction, which is real, but that distinction is already carried by the incomplete-route diagnostics: a genome with only the endo-acting enzyme is now reported as incomplete with the exo-acting reaction named as missing, which is more informative than a separate positive trait because it says what is absent. Oligosaccharide intermediates return to being internal; they would be promoted back to anchors only if an oligosaccharide importer could be evidenced, which would make selfish foraging an independently meaningful capability.gifter evaluation contract: route completeness with closest-route and missing-reaction reporting. Invariant 9 of AGENTS.md, which forbids both arbitrary single-step fragments and bundles of independently meaningful capabilities.Six single-reaction GIFTs are replaced by three substrate-level capabilities. Genomes carrying a complete endo-plus-exo enzyme set keep a positive call; genomes carrying only one side of it now report an incomplete capability with the missing reaction named, where they previously reported a positive call for a fragment. Two anchors are withdrawn.
33DBC-20260818-EXO-ACTIVITY-CLAIM2026.10.32026-08-18T23:00ZgiftcorrectionnoneThe curator note for polymer saccharification no longer claims that the exo-acting enzyme cannot release a monosaccharide on its ownThe note justified requiring both activities by asserting that neither alone liberates a usable monosaccharide. The second half of that is chemically wrong. EC 3.2.1.37 is defined by IUBMB as xylan 1,4-beta-xylosidase, removing successive D-xylose residues from the non-reducing termini of xylans, so it can release D-xylose from the polymer directly; the same applies to EC 3.2.1.20 on alpha-glucan termini. The reason both reactions are required is a curation decision about what counts as evidence for effective polymer-to-monosaccharide saccharification, not a claim about what either enzyme can catalyse. Endo-acting cleavage generates the additional chain ends that make exo-acting release productive on a polymer rather than marginal.IUBMB enzyme nomenclature for EC 3.2.1.37 and EC 3.2.1.20; the curated reaction description of RXN_XYLOOLIGO_EXO already stated the correct substrate.No call changes and no route changes. The requirement is unaltered; only its stated justification is corrected.
34DBC-20260818-CAZY-SUBFAMILIES2026.11.12026-08-18T23:59ZmarkeradditionbroadensCAZy subfamily markers curated from the dbCAN-sub HMM library, with confidence from measured EC dominanceMarker policy prefers a subfamily over a polyspecific family, but the family-level substrate mapping shipped by dbCAN contains no subfamily rows, so the first polysaccharide release accepted bare families and recorded them as ambiguous. The subfamily assignments live in the dbCAN-sub HMM library, whose profile names encode the eCAMI cluster, its parent family, the official CAZy subfamilies it contains, and the EC numbers its members carry, each with a member count. Streaming the library and keeping only those names yields a 104 KB table from a 4.9 GB artifact. Confidence now comes from two measured quantities rather than one: how dominant an EC is among the EC-annotated members of a cluster, and how many members support it. Clusters whose parent family belongs to a different catalytic class are excluded, and carbohydrate-binding modules are excluded entirely because they catalyse nothing.dbCAN-sub HMM library db_v5-2-9_5-5-2026, 53411 profiles, of which 2474 carry at least one EC assignment; derived table in data-raw/reference/cazy-subfamily-ec.tsv with the extraction script alongside it.267 subfamily evidence rows added across seven catalytic components. Genomes annotated by dbCAN-sub gain calls they previously missed, and a call resting on a specific subfamily now reports curated or high-confidence where a bare family reported ambiguous. Bare families are retained as a lower-confidence fallback, so no genome loses a call.
35DBC-20260818-FACET-CLASSIFICATION2026.11.12026-08-18T23:59ZgiftadditionnoneGIFTs and anchors carry a registered facet vocabulary, and a derived profile is exposed alongside itA single free-text category could not answer questions that cut across it, and the information needed to answer them was already present in the declared anchors and the compartment layer with no way out. The facet vocabulary is registered so that a multi-valued classification cannot degenerate into free text: substrate_class is single-valued and therefore partitions the database, while physiological_role and the anchor facets are multi-valued and return supersets. Nothing in the derived profile is curated, and neither facets nor profile enter the completeness logic that produces a call.Declared anchors, anchor compartment, and the anchor-derived composition graph, all already present in the database.No call changes. The former gift.category column is replaced by the substrate_class facet.
36DBC-20260818-COLLAGEN-CLEAVAGE2026.12.12026-08-18T12:00ZgiftadditionbroadensCollagen cleavage curated as the first protein-degradation GIFT, with a protein substrate class and a host tissue degradation roleProtein degradation was proposed as a layer of eight substrate-specific traits. Applying the evidence test of the polysaccharide proposal to real markers licensed one. Collagen passes on mechanism rather than on nomenclature: EC 3.4.24.3 is defined by digestion of native collagen in the triple-helical region, an activity generic endopeptidases lack because the intact helix resists them, and KEGG assigns K01387 to MEROPS family M9 and to extracellular-matrix-damaging toxins while keeping the host collagenases MMP-1 and MMP-8 as separate orthologues. The trait therefore claims no more than its markers support. The product is anchored as collagen peptides rather than as a shared peptide pool, because a pool has no membership criterion and would connect every protein-degradation GIFT to every other one's downstream through an undefined intermediate; a shared oligopeptide tier is deferred behind peptide transporter evidence, on the same licence that keeps oligosaccharides internal. The capability needed no schema change: anchors were never restricted to small molecules, rhea_master has been nullable since schema 4, and the marker namespace vocabulary is open.KEGG orthology K01387 and EC 3.4.24.3, verified 2026-08-18; Pfam PF01752 via InterPro, retrieved 2026-08-18; Rhea searched 2026-08-18 and found to contain collagen hydroxylation, glycosylation and crosslinking but no proteolytic cleavage of the helix. Full assessment in inst/doc/proposal-protein-degradation.md.One GIFT, two anchors, one reaction, one route, one enzyme system, one component and two marker evidence rows are added. Genomes encoding a family M9 collagenase gain a positive call. Four facet terms are registered and two anchor facet definitions are broadened from glycan-only wording to cover proteins; no existing anchor is reclassified and no existing call changes.
37DBC-20260818-EVIDENCE-SPECIFICITY2026.12.12026-08-18T12:00ZgiftclarificationnoneTrait specificity may not exceed marker specificity, and seven candidate protein-degradation traits are refused under that ruleThe rule was already enforced for carbohydrate-active enzymes as marker policy, where accepting a polyspecific family such as GH5 for a cellulose component would make every mannan degrader a cellulose degrader. Stated as marker policy it reads as advice about confidence values; it is in fact a constraint on what a GIFT may be called, so it is promoted to a named invariant. The protein layer makes the constraint concrete. Elastin cleavage was refused although a named orthologue exists, because EC 3.4.24.26 defines pseudolysin as hydrolysing elastin, collagen types III and IV, fibronectin and immunoglobulin A: accepting it would attribute an elastin-specific claim to a broadly proteolytic enzyme, and would equally license a collagen call, silently equating the two traits. That is the first recorded case of an over-broad marker damaging a trait other than the one it was accepted for. Keratin cleavage was refused for want of any orthologue, keratinolysis being an assay phenotype of subtilisins rather than a clade. Albumin, actin, glutelin, tropomyosin and troponin cleavage were refused because no microbial protease orthologue exists for them; searching for those substrates returns the host structural proteins themselves.KEGG orthology and enzyme records searched 2026-08-18 for each candidate substrate. Reasoning and per-substrate outcomes in inst/doc/proposal-protein-degradation.md, section 4.No call changes. Seven candidate traits are refused rather than deferred silently, so the reasons are available when the evidence changes. AGENTS.md gains invariant 16.
38DBC-20260818-GIFT-TYPE2026.12.22026-08-18T09:10ZschemaadditionnoneGIFT becomes an umbrella concept with an explicit gift_typeA genome encodes capabilities that are not chemistry. Modelling a flagellum or a restriction-modification system as a directed route between molecular anchors would have required inventing input and output molecules that the structure does not have, and the resulting call would rest on a boundary claim nobody could defend. Making the kind of capability explicit lets each type state its own completeness contract instead.Reviewed against the existing metabolic model: every curated GIFT to date is a claim about chemistry between declared anchors, and none of the four non-metabolic capability types examined (structural, regulatory, defense, developmental) can be stated that way without fabricated anchors.All 29 existing GIFTs became gift_type = metabolic with no change to their anchors, routes, reactions, systems, components, markers, calls or traces. The anchor/route model, the composition graph and the derived profile are now metabolic-only by construction.
39DBC-20260818-FLAGELLAR-APPARATUS2026.12.22026-08-18T09:20ZgiftadditionbroadensFlagellar apparatus added as the first structural GIFTThe flagellum is the clearest case of a capability whose completeness is architectural rather than chemical: it is complete when a curated set of structural and assembly functions is jointly supported, and it has no meaningful input or output molecule. It exercises alternative architectures, multisubunit systems, a fused protein serving two components, and the evidence-specificity limit on ion coupling.KEGG orthology, verified against the KEGG REST API on 2026-08-18. Structural decomposition follows the export gate, basal body, C ring, hook, hook-filament junction, filament and stator of the characterised enterobacterial and Bacillus flagella; the L and P rings are curated as a separate diderm architecture because monoderms build a flagellum without them.flagellar_apparatus becomes callable through two architectures, ARCH_FLAGELLUM_DIDERM and ARCH_FLAGELLUM_MONODERM, sharing nine structural functions. No metabolic call changed.
40DBC-20260818-FLAGELLAR-ION-COUPLING2026.12.22026-08-18T09:25Zstructural_componentclarificationnoneProton- and sodium-driven flagellar apparatus refused at KO evidence levelNaming a GIFT for its coupling ion would claim a specificity the evidence does not carry. The specificity of a GIFT claim must not exceed the specificity of the genomic evidence supporting it, and this is the structural instance of that invariant.KEGG assigns Vibrio cholerae PomA (VC_0892) and PomB (VC_0893), the sodium-driven polar flagellar stator, to K02556 and K02557, the same orthologues as the proton-driven MotA and MotB of Escherichia coli. MotX (K21217) and MotY (K21218) are specific to the sodium-type polar T ring but evidence a scaffold rather than an ion channel, and are absent from the sodium-driven MotPS motors of alkaliphilic Bacillus.proton_driven_flagellar_apparatus and sodium_driven_flagellar_apparatus were not curated. The single flagellar_apparatus GIFT is deliberately silent about coupling ion, and the refusal is recorded in inst/doc/proposal-structural-gifts.md.
41DBC-20260818-TYPE-IVA-PILUS2026.12.22026-08-18T09:30ZgiftadditionbroadensType IVa pilus machinery added as a second structural GIFTA second structural capability with a substantially different architecture from the flagellum was needed to show that the structural model is not a flagellum-shaped special case. It also carries the accessory-function case: a pilus can be assembled by a genome that cannot retract it.KEGG orthology, verified against the KEGG REST API on 2026-08-18. Scoped to the type IVa system because the PilM/N/O/P alignment subcomplex markers are specific to it.type_iva_pilus becomes callable through ARCH_T4AP_CORE with six required functions and retraction curated as accessory. The claim is deliberately confined to encoding the assembly machinery and does not extend to twitching motility, natural competence or adhesion.
42DBC-20260818-CHEMOTAXIS-CORE2026.12.32026-08-18T11:05ZgiftadditionbroadensCore chemotaxis signal transduction added as the first regulatory GIFTThe chemotaxis pathway is the clearest case of a capability that is neither chemistry nor a structure: it is an information-transduction circuit, complete when a receptor, a kinase core, a response regulator and an adaptation cycle are jointly encoded. It was curated first because it needs no evidence the marker model lacks.KEGG orthology, verified against the KEGG REST API on 2026-08-18: K03406, K03407, K03408, K00575, K03412, K03413 and the termination phosphatases K03414, K03410, K03409. Receptor distribution was measured rather than assumed: Escherichia coli K-12 carries no K03406 orthologue, its four receptors being assigned to the characterised groups K05874, K05875, K05876 and K03776, while Pseudomonas aeruginosa carries 21 K03406 genes and Vibrio cholerae 34.chemotaxis_signal_transduction becomes callable through CIRCUIT_CHEMOTAXIS_CORE with four required functions. The reception function accepts a generic or a characterised chemoreceptor, so an Escherichia coli annotation is not called receptor-less. Signal termination is accessory with three non-homologous systems.
43DBC-20260818-CHEMOTAXIS-SPECIFICITY2026.12.32026-08-18T11:10Zregulatory_componentadditionnarrowsLigand-specific chemoreception curated as a separate claim with separate evidenceRegulatory specificity cannot exceed evidence specificity. A generic methyl-accepting chemotaxis protein identifies the conserved cytoplasmic signalling domain shared by every chemoreceptor and says nothing about the periplasmic domain that determines what is detected. Rather than leave the principle implicit, a narrower claim was curated with strictly narrower evidence.K03406 is assigned to 34 genes in Vibrio cholerae and 21 in Pseudomonas aeruginosa, so it cannot single out any one chemoeffector. K05875 is the Tar orthologue group, anchored on the characterised aspartate and maltose sensor of Escherichia coli and Salmonella.aspartate_chemoreception requires K05875 for its reception function and refuses K03406. A genome carrying only a generic chemoreceptor completes chemotaxis_signal_transduction and not aspartate_chemoreception, which is the intended behaviour.
44DBC-20260818-PHO-TWO-CIRCUITS2026.12.32026-08-18T11:20ZgiftadditionbroadensPhosphate starvation response added with two cognate-pair circuitsThe regulatory proposal recorded orthology calibration as the question blocking this trait: whether K07636 and K07657 distinguish a cognate Pho pair from a genome full of paralogous kinases and regulators. The calibration was done and the answer separated one capability into two circuits sharing a sensor.Gene counts per genome from the KEGG REST API on 2026-08-18. K07636 is single-copy in Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, Salmonella Typhi and Vibrio cholerae, and absent from Campylobacter jejuni, Helicobacter pylori, Mycobacterium tuberculosis and Lactococcus lactis. K07657 is single-copy in the four Gram-negatives and absent from Bacillus subtilis, which instead carries K07658 at BSU29110, immediately adjacent to the K07636 sensor BSU29100. The two regulator groups are mutually exclusive across the genomes checked.phosphate_starvation_response becomes callable through CIRCUIT_PHO_PHOR_PHOB and CIRCUIT_PHO_PHOR_PHOP, which share the RF_PHO_SIGNAL_RECEPTION function. K07660, the response regulator of the magnesium-sensing PhoP/PhoQ system, is refused despite sharing the gene name. PstSCAB-PhoU is accessory.
45DBC-20260818-TYPE-I-RM2026.12.32026-08-18T11:30ZgiftadditionbroadensType I restriction-modification added as the first defense GIFTA defense capability is not the sum of its convenient parts. Type I restriction-modification was curated first because it makes that explicit: the mechanism is complete only when recognition, host protection and restriction are all encoded, and the multisubunit requirement is real rather than a modelling choice.KEGG orthology, verified against the KEGG REST API on 2026-08-18. K01153, K03427 and K01154 are defined as the R, M and S subunits of a type I restriction enzyme, so the accessions separate type I from types II, III and IV. Escherichia coli K-12 carries one of each, the EcoKI system.type_i_restriction_modification becomes callable through MECH_TYPE_I_RM with three required functions. A genome carrying only HsdM and HsdS is called incomplete, missing DF_TYPE_I_RM_RESTRICTION. The target sequence recognised by HsdS is not claimed, because the variable target recognition domains are not resolved by the orthology group.
46DBC-20260818-CRISPR-ARRAY-LIMIT2026.12.32026-08-18T11:40ZgiftadditionbroadensType I-E CRISPR-Cas curated as an encoded-machinery claim, not an interference claimA CRISPR-Cas system without a CRISPR array has no guide RNAs and interferes with nothing, and an array is a repeat-spacer locus detected by structure rather than a protein annotation. gifter's evidence layer is a namespaced accession and cannot express it. Rather than pretend protein markers cover the array, or refuse the trait entirely, the claim was narrowed to what the evidence supports.KEGG orthology, verified against the KEGG REST API on 2026-08-18: K19123, K19046, K19124, K19125 and K19126 are defined as Cascade subunits CasA, CasB, CasC, CasD and CasE, and K07012 as the Cas3 endonuclease-helicase. Escherichia coli K-12 carries one of each plus K15342 and K09951.type_i_e_crispr_cas_machinery becomes callable through MECH_TYPE_I_E_CRISPR with Cascade and Cas3 required and Cas1-Cas2 adaptation accessory. The array limitation is stated in the GIFT description rather than a footnote. K07475, the HD module of a split Cas3, is refused as evidence of the complete nuclease-helicase. Extending the evidence model to genomic features is deferred to a second demonstrated need.
47DBC-20260818-SCFA-LAYER2026.13.12026-08-18T14:00ZgiftadditionbroadensShort-chain fatty acid formation curated as five GIFTs, with a sixth connecting them to existing catabolic contentgifter's catabolic layer ended at pyruvate and the deoxyhexose GIFTs ended at (S)-lactaldehyde, so the fermentation products those routes exist to explain could not be called. acetate_interconversion, butyrate_formation, propionate_formation_propanediol and propionate_formation_acrylate name the products; pyruvate_to_acetyl_coa and propanediol_formation connect them to what is already curated, so that no SCFA GIFT is an isolated node in the composition graph.KEGG module M00579 for the acetate node; KEGG orthology-to-gene links retrieved 2026-08-18 over 11856 organisms for prevalence and co-occurrence; Rhea release 141 for all eighteen reactions; ChEBI release 253 for the six new anchors; NCBIfam TIGR03948 and InterPro IPR023990 for the butyrate terminal step; KEGG reaction records for the cross-references. Full assessment in inst/doc/proposal-scfa-biosynthesis.md.Six GIFTs become callable. pyruvate_to_acetyl_coa composes with galacturonate and glucuronate degradation through PYRUVATE; propanediol_formation composes with fucose and rhamnose degradation through LACTALDEHYDE; acetate_interconversion composes into butyrate_formation through ACETATE. No existing GIFT call changes, because no existing route, system, component or marker was edited.
48DBC-20260818-BUTYRATE-MARKER-NAMESPACE2026.13.12026-08-18T14:05ZmarkeradditionbroadensThe butyrate terminal step is evidenced by NCBIfam TIGR03948, the first non-KO, non-CAZy marker in the metabolic layerKEGG orthology cannot express this trait. K01034 and K01035 carry EC 2.8.3.8 and EC 2.8.3.9 together, so the accession that would stand for butyryl-CoA:acetate CoA-transferase is the same one that stands for the acetoacetate degradation transferase of Escherichia coli. Accepting it would have equated butyrate formation with acetoacetate catabolism, which is the damage the evidence-specificity invariant describes.Of 39 KEGG genomes in canonical butyrate-producing genera, 31 complete the KO core and 9 carry any terminal KO; Faecalibacterium prausnitzii L2-6, Agathobacter rectalis ATCC 33656 and Roseburia intestinalis XB6B4 carry none, while Bacillus subtilis 168 carries both terminal KO sets. Of 366 organisms completing the KO core with phosphate butyryltransferase and butyrate kinase, 120 are Bacillus and 16 Geobacillus. TIGR03948 matches 178 proteins in 171 proteomes, led by Faecalibacterium, Roseburia, Eubacterium and Anaerostipes, and matches no Bacillus, Escherichia, Salmonella or Pseudomonas.butyrate_formation is callable at the specificity its name claims. Users supplying TIGRFAM accessions already had them recognised by the evaluator; this is the first curated row that uses one. No other GIFT is affected.
49DBC-20260818-BUTYRATE-KINASE-REFUSED2026.13.12026-08-18T14:10ZrouteclarificationnoneThe butyrate kinase route is refused and the refusal recordedPhosphate butyryltransferase and butyrate kinase are not specific to butyrate formation. They serve branched-chain acyl-CoA metabolism in aerobic Bacillota, and the non-specificity is a property of the enzymes rather than of KEGG's annotation, so no change of marker namespace repairs it.K00634 with K00929 is complete in 817 KEGG organisms and in 366 that also complete the acetyl-CoA core, of which 120 are Bacillus. At sequence-family level the picture is the same: NCBIfam TIGR02707 matches 2279 proteins with Bacillus the second most frequent genus, and TIGR02706 matches 573 with Bacillus second after Clostridium.butyrate_formation carries one route rather than two. A genome whose only butyrate-releasing enzyme is Buk is called negative, which is the honest answer at this evidence level. Revisit if a marker separates fermentative Ptb/Buk from the branched-chain acyl-CoA enzymes.
50DBC-20260818-PROPIONATE-SUCCINATE-REFUSED2026.13.12026-08-18T14:15ZgiftclarificationnoneThe succinate (Wood-Werkman) route to propionate is refused and the refusal recordedIts markers are direction-blind and taxonomically misleading. Methylmalonyl-CoA mutase and the methylmalonyl-CoA decarboxylase are the same genes KEGG module M00741 uses to degrade propanoyl-CoA, so the same evidence supports the opposite claim, and the CoA-transferase releasing propionate is not resolved by any orthology group in the organisms that matter most.Mutase with decarboxylase and a candidate CoA-transferase is complete in 177 KEGG organisms, or 293 if the methylmalonyl-CoA carboxyltransferase K17489 is also accepted; the leading genera of that set are Corynebacterium (70), Escherichia (19), Cutibacterium (16) and Klebsiella (13). Bacteroides thetaiotaomicron, the dominant gut propionate producer, is negative because it carries no transferase KO, and its K00634 with K00929 pair is the same one already refused for butyrate.Propionate is callable through the propanediol and acrylate routes only. Genomes producing propionate through succinate are called negative. Revisit when a marker resolves propionate release and separates the biosynthetic from the degradative direction.
51DBC-20260818-ACETATE-INTERCONVERSION2026.13.12026-08-18T14:20Zgiftclarificationnoneacetate_interconversion is declared mode = interconversion and declares both of its boundaries in both roles, the first use of that mode valueThe phosphotransacetylase and acetate kinase node is near-equilibrium and physiologically bidirectional, so naming it a formation and declaring only ACETYL_COA to ACETATE would assert a direction the markers do not evidence. Splitting it into a formation GIFT and an assimilation GIFT would assert a distinction the same two genes cannot make either, so the one GIFT declares both directions. The mode also keeps any future acetate-activation GIFT out of a within-mode cycle with this one.KEGG module M00579 records the acetyl-CoA to acetate direction only; the same two enzymes run towards acetyl-CoA in acetate-assimilating genomes such as Escherichia coli at high acetate, and no marker distinguishes the directions. 6582 of 11856 KEGG organisms carry the pair.The GIFT was renamed from acetate_formation, because formation names a direction its own description says the evidence cannot establish. The mode CHECK branch that had never been exercised now carries content and a stated contract. Composition from this node into butyrate_formation runs through both ACETATE and ACETYL_COA; both edges cross a mode boundary and are therefore exempt from the catabolic cycle scan, which is the intended behaviour.
52DBC-20260818-BCD-ETF-NOT-REQUIRED2026.13.12026-08-18T14:25Zenzyme_componentclarificationnoneThe electron-transfer flavoprotein is not a required component of the butanoyl-CoA dehydrogenase systemK03521 and K03522 are the generic fixA and fixB orthologues shared with nitrogen fixation. A marker present in almost every genome carries no evidence about butyrate, so requiring it would trade recall for no gain in specificity. The route's specificity comes from its terminal transferase, not from the electron carrier.K03521 and K03522 together are present in 7729 of 11856 KEGG organisms. Among the 39 genomes in canonical butyrate-producing genera, 31 complete the acetyl-CoA core but only 20 carry both flavoprotein subunits; Faecalibacterium prausnitzii L2-6 carries K03522 and no K03521.butyrate_formation is complete in genomes whose flavoprotein subunits are unannotated. The biological reading is unchanged: the complex needs the flavoprotein, and gifter is stating that it does not use it as evidence.
53DBC-20260818-INTERCONVERSION-CONTRACT2026.13.12026-08-18T15:00ZschemaadditionnoneThe interconversion mode gains a boundary contract the source validator enforcesThe mode value existed in the schema CHECK with nothing behind it and no stated meaning, which is the situation AGENTS.md forbids for a type and which is no better for a mode. Curating the first interconversion GIFT is the point at which the contract has to be written down, because the alternative is a mode whose meaning is inferred from one example.Declaring a reversible node in one direction asserts a direction the markers do not support; declaring it in both required relaxing the rule that no anchor may carry both roles. That rule was doing real work: two compartments of one molecule is the signature of transport, and losing it would stop transport being required to reach the cytoplasm. Separating the two cases by compartment identity keeps that guarantee and adds the new one.Every anchor of an interconversion GIFT must be declared as both input and output, and no other mode may declare an anchor that way. A molecule appearing in two compartments remains the signature of transport and is no longer conflated with a mirrored boundary. Enforced in R/database-build.R and covered by four fixtures in test-compartment.R. The SQL schema is unchanged at version 6: this is a source-contract rule, not a DDL change.
54DBC-20260818-ORGANIC-ACID-LAYER2026.14.12026-08-18T18:00ZgiftadditionbroadensOrganic acid and neutral fermentation product formation curated as six GIFTs, and the citric acid cycle refused as a source of anchorsThe request was to express the capacity to form fumarate, succinate, citrate and lactate. Those four are not one class and the assessment splits them. Lactate, ethanol and acetoin are fermentation end products, which a genome can be said to release and for which a directional marker exists. Citrate, fumarate and succinate are citric acid cycle intermediates, consumed by the pathway that makes them, present in every genome that has the cycle, and with no direction their markers can evidence. Malate and citrate enter as input-only boundaries of capabilities that consume them; nothing in the layer claims to produce them.59 KEGG orthology groups over the 11855 organisms carrying at least one of them, Rhea release 141 for all nine reactions, ChEBI release 253 for the five anchors. Full evidence test in inst/doc/proposal-organic-acid-formation.md.Six new GIFTs, five new anchors, nine new reactions and twelve new KO markers. The substrate_class vocabulary gains organic_acid and neutral_fermentation_product, and physiological_role fermentative_end_product is broadened from short-chain fatty acids to fermentation end products generally. propionate_formation_acrylate stops being an orphan at its input.
55DBC-20260818-LACTATE-DIRECTION2026.14.12026-08-18T18:05Zgiftclarificationnonelactate_formation is the first fermentation end product whose direction is evidenced rather than assertedThe SCFA layer had to declare acetate an interconversion because the same phosphotransacetylase and acetate kinase run the node in both directions and no marker separates them. Lactate is different, and the reason is chemical: forming lactate is a cytoplasmic NADH-consuming reduction, while consuming it feeds electrons to a quinone or a cytochrome. Those are different enzymes with different cofactors and KEGG gives them different orthology groups, so the catabolic declaration is supported by the marker rather than added on top of it.K00016 in 4143 organisms and the quinone-dependent K29125 in 3388, sharing only 573. Lactococcus lactis, Lactobacillus delbrueckii, Lactiplantibacillus plantarum, Streptococcus pyogenes, Enterococcus faecalis, Bifidobacterium longum and Bacillus subtilis carry the forming group and not the consuming one; Escherichia coli, Salmonella Typhimurium and Pseudomonas aeruginosa are the reverse.K29125, K00101, K03777 and K00102 are recorded as refused markers rather than accepted alternatives. The GIFT is declared catabolic, not interconversion.
56DBC-20260818-TCA-NOT-ANCHORABLE2026.14.12026-08-18T18:10ZanchorclarificationnoneCitric acid cycle intermediates are refused as output anchors, and succinate, fumarate and citrate formation are refused as traitsThree independent reasons, checked rather than argued. First, the markers carry no information: citrate synthase is in 8467 of 11855 organisms and adenylosuccinate lyase, which releases fumarate and which gifter already curates inside purine_core_biosynthesis and adenylate_biosynthesis, is in 11115. Second, they carry no direction: KEGG names the group that would have to evidence succinate formation sdhA, frdA, and requiring the narrow frdABCD instead calls Vibrio, Escherichia and Klebsiella positive while calling Bacteroides, Prevotella and Fibrobacter negative. Third, the cycle is a cycle: six catabolic GIFTs spanning citrate to oxaloacetate close a within-mode loop in anchor-derived composition and the build fails. There is no boundary to demote, because no acid in the cycle is only ever consumed.Running the validator's own edge derivation and .find_graph_cycle() over the current gift_anchors.tsv plus the hypothetical rows reports the catabolic cycle, and reports that declaring FUMARATE on the GIFTs whose curated reactions already involve it adds two edges from purine to pyrimidine biosynthesis that mean nothing.No SUCCINATE, FUMARATE, OXALOACETATE or 2-oxoglutarate anchor exists. MALATE and CITRATE exist as input-only anchors of capabilities that consume them, and oxaloacetate stays an internal intermediate of the citrate route. A metabolite does not need an anchor to be modelled.
57DBC-20260818-FORMATE-REFUSED2026.14.12026-08-18T18:15ZanchorclarificationnoneFormate formation is refused on the per-GIFT anchor rule rather than on evidencePyruvate formate-lyase with its activase is complete in 2843 organisms and the reaction is effectively irreversible towards formate, so the evidence is not the obstruction. gift_anchor is keyed on gift, role and ordinal, so anchors are declared per GIFT and not per route, and the lyase is one of three routes of pyruvate_to_acetyl_coa. Declaring FORMATE an output would claim that the pyruvate dehydrogenase complex and pyruvate:ferredoxin oxidoreductase produce it too. Curating a separate formate GIFT over the same reaction would duplicate a curated route.KEGG K00656 with K04069 in 2843 organisms; the three curated routes of pyruvate_to_acetyl_coa are PYR_ACOA_PDH, PYR_ACOA_PFOR and PYR_ACOA_PFL.No FORMATE anchor and no formate GIFT. The trigger for revisiting is per-route boundary anchors, or a deliberate decision to split the lyase route out of pyruvate_to_acetyl_coa into its own GIFT.
58DBC-20260818-D-LACTATE-DEFERRED2026.14.12026-08-18T18:20ZmarkerclarificationnoneD-lactate formation is deferred, and the (R)-lactate anchor is reached through the racemase insteadK03778 is specific to the right chemistry but its leading genera are Pseudomonas, Streptomyces and Burkholderia, obligate aerobes running the NAD-dependent reaction oxidatively, so it fails the direction clause without acetate's justification for accepting that failure. The organisms that actually need (R)-lactate mostly do not have it: of the ten KEGG genomes behind propionate_formation_acrylate, eight carry lactate racemase and only two carry K03778.K03778 in 3133 organisms led by Pseudomonas (224), Streptomyces (158) and Burkholderia (90). Megasphaera elsdenii, M. stantonii, M. massiliensis, M. hexanoica, Pseudocoprococcus catus and three Desulfosporosinus carry K22373 and not K03778; the two Anaerotignum genomes are the reverse.No D-lactate formation GIFT. If one is curated later the honest form is a route whose marker mapping is recorded as ambiguous, so that evidence_confidence reports the weakness at the call.
59DBC-20260818-ACETOIN-SYNTHASE-NOT-REQUIRED2026.14.12026-08-18T18:25ZrouteclarificationnoneThe acetolactate synthase step of acetoin_formation is curated but not requiredKEGG names K01652 ilvB, ilvG, ilvI: the orthology group that would evidence the condensation step is the anabolic branched-chain amino acid synthase, present in 9341 organisms, and it carries no acetoin-specific information. Acetolactate decarboxylase exists only for this pathway. This is the butyrate decision applied again: evidence the trait on the specific terminal step, not on the shared core.K01575 in 1649 organisms led by Streptococcus, Bacillus, Corynebacterium, Staphylococcus, Klebsiella, Enterobacter, Listeria, Enterococcus and Lactococcus. Requiring K01652 as well changes the call in 50 of those 1649.route_reactions.required is 0 for RHEA:25249 and the marker mapping for K01652 is recorded as ambiguous. The chemistry stays curated so that the PYRUVATE boundary is truthful.
60DBC-20260818-VITAMIN-LAYER2026.15.12026-08-18T19:00ZgiftadditionbroadensVitamin biosynthesis curated as twenty GIFTs covering B1, B2, B3, B5, B6, B7, B9, B12 and K2The capacity to produce vitamins is the largest capability the ontology could express without a schema change, and the one where the host-relevant claim depends most on where the boundary falls. Each vitamin is cut where genomes measurably differ rather than where the pathway drawing ends: folate at 4-aminobenzoate, thiamine at its two activated moieties, NAD at nicotinate D-ribonucleotide, and cobalamin at the corrin ring, the cobinamide arm and the nucleotide loop.KEGG orthology sets for 126 orthology groups intersected over all 10151 bacterial genomes in the KEGG release of 2026-08-18; Rhea release 141, which returned a master reaction for all 100 EC numbers in the layer; ChEBI release 253 for the 31 new anchors; a validation panel of 18 reference genomes spanning Enterobacteriaceae, Bacteroidetes, Clostridia, Bifidobacterium, Lactobacillaceae, Akkermansia and Propionibacterium.Twenty new callable GIFTs, 31 anchors, 26 routes, 94 reactions and 151 marker assignments. The layer partitions bacteria rather than describing all of them: 1087 of 10151 genomes complete none of the nine vitamin capabilities, 228 complete all nine, and half complete four or fewer. Every GIFT is an auxotrophy indicator in gift_profile, because each declares a biomass-essential output anchor.
61DBC-20260818-ORPHAN-STEP-RULE2026.15.12026-08-18T19:05ZrouteclarificationbroadensFour reactions that no marker identifies at the specificity of the step are curated as not requiredA reaction can be certain chemistry and still have no orthology group that covers it across bacteria. Requiring such a step converts a missing annotation into a false negative for the whole capability, and deleting it makes the route describe chemistry that does not exist. Both are worse than curating the step with required = 0 and recording why.Requiring the 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase reduces riboflavin biosynthesis from 7943 to 2682 bacterial genomes; requiring the dihydroneopterin triphosphate diphosphatase reduces folate biosynthesis from 5898 to 1634; requiring MenH and the 1,4-dihydroxy-2-naphthoyl-CoA hydrolase reduces the classical menaquinone route from 3109 to 1355.The four steps remain visible in trace_gift() and in the route tables, and are excluded from completeness. Riboflavin, folate and menaquinone calls are broader than a strict reading of the KEGG modules would give.
62DBC-20260818-B12-SPLIT2026.15.12026-08-18T19:10ZgiftclarificationnarrowsA single cobalamin biosynthesis trait is refused; corrin ring, cobinamide arm and nucleotide loop are curated as three capabilitiesMost of the prevalence of the cobalamin pathway is salvage rather than synthesis. A single trait would call corrinoid salvagers producers, which is the worst error this layer could make.4139 of 10151 bacterial genomes complete the nucleotide loop and 3044 of those encode no corrin ring at all, Escherichia coli among them. 1017 genomes complete the anaerobic ring route and 340 the aerobic one.A genome that imports cobinamide and attaches a lower ligand completes cobamide_nucleotide_loop_assembly and not corrin_ring_biosynthesis. No GIFT in the database claims cobalamin production on the strength of the loop alone.
63DBC-20260818-DMB-LOWER-LIGAND2026.15.12026-08-18T19:15ZgiftclarificationnarrowsThe lower ligand is curated as its own capability, because a cobamide without dimethylbenzimidazole is not vitamin B12The nucleotide loop attaches whichever benzimidazole, purine or phenolic ligand the genome can supply, and only 5,6-dimethylbenzimidazole makes the product the vitamin a host can use. Naming the loop after cobalamin would assert a lower ligand the evidence does not establish.Of the 1081 bacterial genomes completing ring, cobinamide arm and nucleotide loop, 538 also carry BluB. Limosilactobacillus reuteri completes the corrinoid path and carries no BluB, consistent with its reported production of a cobamide rather than of cobalamin. The anaerobic bza route to the ligand has no KEGG orthology group and is not curated, so a negative dmb_biosynthesis_aerobic call is not evidence that the genome cannot make the ligand.dmb_biosynthesis_aerobic is callable separately and composes into cobamide_nucleotide_loop_assembly through the DMB anchor.
64DBC-20260818-COFACTOR-ANCHOR-RULE2026.15.12026-08-18T19:20ZanchorclarificationnoneA cofactor may be declared an anchor only where the reaction consumes it, and cofactor activation steps are not curatedThis layer produces cofactors, so it needs a sharper form of the standing rule against cofactor anchors. Without it, tetrahydrofolate, pyridoxal 5-phosphate and NAD would become input anchors of half the database and the anabolic composition graph would stop describing biosynthesis and start describing cofactor dependence.BluB destroys FMNH2 to build the benzimidazole ring, so FMNH2 is a substrate and is declared as an input-only anchor. By contrast the flavin kinase and FMN adenylyltransferase step is complete in all 18 reference genomes, including the six that cannot make riboflavin, so it partitions nothing and tracks annotation rather than biology.Riboflavin to FAD, pantothenate to coenzyme A, thiamine phosphate to the diphosphate and folate polyglutamylation are not curated. The vitamin, not the working cofactor form, is the output boundary of every GIFT in the layer.
65DBC-20260818-ALKALINE-PHOSPHATASE-REFUSED2026.15.12026-08-18T19:25ZmarkerclarificationnoneA generic alkaline phosphatase is refused as evidence of the folate dihydroneopterin monophosphatase step, and the step is left uncuratedThe specificity of a claim may not exceed the specificity of its evidence. Accepting alkaline phosphatase here would have fired the step in every genome carrying a phosphatase and would have damaged every other trait that marker also matches.K01077 is assigned in 3202 bacterial genomes and K01113 in 2770, in both cases as a general phosphomonoesterase rather than as a folate enzyme.The folate route runs from the dihydroneopterin triphosphate diphosphatase to the aldolase without a curated monophosphatase reaction, and the route description records the gap.
66DBC-20260818-THIS-THIF-NOT-REQUIRED2026.15.12026-08-18T19:30Zenzyme_componentclarificationbroadensThe ThiS and ThiF sulfur carrier is not a required component of thiazole synthaseThiF is homologous to MoeB of molybdopterin biosynthesis and ThiI also serves tRNA thiolation, so neither marker is specific to thiamine. Requiring them would gate the trait on markers that add no thiamine specificity.Requiring ThiG together with ThiS and ThiF reduces the thiazole branch from 5396 to 1554 bacterial genomes; Bacteroides, Bifidobacterium, Akkermansia and Propionibacterium reference genomes all lack the ThiF assignment while carrying ThiG.thiazole_phosphate_biosynthesis is complete on thiazole synthase plus an imine-supplying enzyme.
67DBC-20260818-ENTC-ACCEPTED2026.15.12026-08-18T19:35ZmarkerclarificationbroadensEntC is accepted for the isochorismate synthase reaction of menaquinone biosynthesisA marker whose pathway assignment lies elsewhere is still admissible when it is accurate at the level of the reaction. What the specificity rule forbids is a marker whose chemistry is broader than the claim, and EntC catalyses exactly the reaction MenF catalyses. Route completeness supplies the menaquinone specificity.Bacteroides thetaiotaomicron annotates BT_4700 as entC and carries no menF; with MenF alone the genome is called menaquinone-negative. Accepting both raises the classical route from 2461 to 4047 genomes carrying the step, and the complete route from 1355 to 3109.Bacteroidetes genomes that make menaquinone are no longer called negative on the first step.
68DBC-20260818-CORRIN-RING-RECALL2026.15.12026-08-18T19:40ZmarkerclarificationnoneThe corrin ring capability is curated with a known recall limit caused by gene fusion, and no domain marker is accepted to repair itPropionibacterium freudenreichii, the organism industrial vitamin B12 comes from, is called incomplete for the corrin ring. Its genome carries the genes, as cysG_cbiX and cobJ_cbiE_cbiG_cbiH fusions that KEGG assigns to none of the component orthology groups. The obvious repair is a domain marker, and it is refused.Pfam PF00590 is Tetrapyrrole (Corrin/Porphyrin) Methylases, one family covering CbiE, CbiF, CbiH, CbiL, CobM and diphthine synthase; it cannot say which step a protein performs. PFREUD_07710 and PFREUD_07700 are the two fusions in question.corrin_ring_biosynthesis reports the closest route with three named missing reactions for that genome rather than a positive call on a widened marker. Precision is preserved at the cost of recall, and the cost is recorded here.
69DBC-20260818-NAD-CUT-AT-NAMN2026.15.12026-08-18T19:45ZgiftclarificationnoneNAD biosynthesis is cut at nicotinate D-ribonucleotide so that de novo synthesis and pyridine salvage share the trunk instead of duplicating itBeing able to live without niacin and being able to make the pyridine ring are different claims about a genome. Cutting at the mononucleotide lets both exist without either duplicating the adenylyltransferase and synthetase, and avoids a breaking re-cut later.6398 bacterial genomes form quinolinate from aspartate, 6921 recover nicotinate into the trunk, and 6791 carry the trunk itself. The cut follows the precedent set for L-aspartate 4-semialdehyde in the amino acid layer.Four callable GIFTs share one trunk. A genome positive for namn_salvage_nicotinate and negative for quinolinate_biosynthesis_aspartate is niacin-dependent.
70DBC-20260818-GTP-LINK-OPEN2026.15.12026-08-18T19:50ZanchorclarificationnoneGTP is declared as an input-only anchor and no GIFT is curated to link it to GMPThe architecture guide already decided this for adenylate: biosynthesis stops at AMP because phosphorylation is shared metabolism. A GMP to GTP capability would assert the opposite for guanylate, and the same gap already exists between the curated UMP output of pyrimidine core biosynthesis and the UTP input of cytidylate biosynthesis.Guanylate kinase is assigned in 9625 of 10151 bacterial genomes and nucleoside-diphosphate kinase in 8897, so the trait would be complete in 84 per cent of bacteria while its negatives would be genomes whose Ndk role is filled by another kinase. Ndk is base-generic and adds no guanylate specificity.riboflavin_biosynthesis and folate_biosynthesis take GTP as an input anchor with no producer GIFT, and gift_graph draws no edge from guanylate_biosynthesis to them.
71DBC-20260818-VITAMIN-UPTAKE-REFUSED2026.15.12026-08-18T19:55ZgiftclarificationnoneCobalamin uptake is refused as a transport GIFT, so the layer reports no cross-feeding outputThe corrinoid importers that matter in host-associated communities are the ones this marker set cannot see. Curating the Proteobacterial system alone would call the dominant gut corrinoid importers negative, which is worse than declining the trait.The btuB, btuC and btuD orthology groups are complete together in 734 bacterial genomes, concentrated in Proteobacteria; Bacteroides thetaiotaomicron carries none of the three, and the Bacteroidetes corrinoid receptors have no KEGG orthology group at all.No anchor in the layer is declared extracellular, so gift_profile reports cross_feeding_output as 0 and resource_strategy as private for all twenty GIFTs. Vitamin sharing remains outside what the model can state.
72DBC-20260818-COSUBSTRATE-ANCHORS2026.15.12026-08-18T20:00ZanchorclarificationnoneA co-substrate is not declared as an anchor merely because the reaction consumes itThe PdxS/PdxT reaction consumes ribose 5-phosphate, glyceraldehyde 3-phosphate and glutamine. Declaring all three would have made every sugar degradation GIFT that ends at glyceraldehyde 3-phosphate an upstream neighbour of vitamin B6 biosynthesis, which says nothing a reader wants: the trait is defined by the pentose and the nitrogen donor, not by the triose.Purine core biosynthesis sets the precedent. It declares PRPP and nothing else, although its route also consumes glycine, L-aspartate, formate and glutamine, three of which are curated anchors. Declaring GAP here produced a catabolic-to-anabolic edge from the uronate degradation GIFTs that no reader would have read as biology.plp_biosynthesis_r5p declares D-ribose 5-phosphate and L-glutamine as inputs. The anchor set of the catabolic layer is unchanged, and its exits remain pyruvate and lactaldehyde.
73DBC-20260818-CENTRAL-CYCLE-LAYER2026.16.12026-08-18T21:30ZgiftadditionbroadensOxidative citric acid cycle chemistry curated as four composable segment GIFTs, reversing the earlier finding that the cycle cannot be anchoredThe earlier assessment refused citric acid cycle anchors because it was testing product claims: whether a genome can be said to form and release citrate, fumarate or succinate. Those refusals stand. This layer asks a different question, the one gifter's other GIFTs already answer, which is what chemistry a genome encodes between two boundaries. Segmented that way the cycle is highly informative: all sixteen configurations of the four segments are occupied across 11783 KEGG organisms, and the branched Helicobacter architecture, the actinobacterial decarboxylase bypass and the Bacteroides reductive arm become separable instead of collapsing into one incomplete class. Two of the four segments are declared interconversion rather than directional, because succinate dehydrogenase and fumarate reductase are one orthology group in most bacteria and fumarase and malate dehydrogenase are at equilibrium; claiming a direction there would exceed the evidence.67 KEGG orthology groups over the 11783 organisms carrying at least one of them, retrieved 2026-08-18; Rhea release 141 for all fourteen reactions and every KEGG reaction and EC cross-reference; ChEBI release 253 for the four anchors. Gene-level checks on sau:SA1518, bth:BT_2070, bth:BT_2071 and bth:BT_2072 for the citrate synthase decision. KEGG modules M00009, M00010 and M00011 for the external boundaries. Full assessment in inst/doc/proposal-central-metabolic-cycles.md.Four new GIFTs, four new anchors, fourteen new reactions and thirty-five new KO markers. A new gift facet, metabolic_cycle, records the curated name of a cycle a GIFT belongs to; whether a genome closes the cycle stays derived. pyruvate_to_acetyl_coa and acetate_interconversion gain outgoing edges through ACETYL_COA, so neither is a terminal node any more. The oxidative citric acid cycle becomes an elementary cycle of the composition graph. No existing GIFT call changes: no existing route, system, component or marker was edited.
74DBC-20260818-SHIKIMATE-AROMATIC-LAYER2026.17.12026-08-18T22:10ZgiftadditionbroadensShikimate-derived aromatic biosynthesis curated as three composable GIFTs: chorismate, salicylate and indole-3-acetateChorismate is the point at which aromatic metabolism leaves central carbon metabolism, and gifter already had two GIFTs consuming it and none producing it. Curating the shikimate pathway closes that gap and turns paba_biosynthesis and menaquinone_biosynthesis from entry points into intermediates. Salicylate and indole-3-acetate are curated separately rather than as one aromatic capability, because a GIFT is a directed capability between declared anchors and aromatic compound biosynthesis is a chemical family, not a capability. Indole-3-acetate is cut at tryptophan, not at chorismate: tryptophan is a branchpoint and a building block, and running the trait through aromatic amino acid biosynthesis would bundle two independently useful capabilities.Scored across the 10151 bacterial and 470 archaeal genomes of the KEGG release of 2026-08-18. chorismate_biosynthesis completes in 7644 bacteria and 90 archaea; salicylate_biosynthesis in 646 bacteria and no archaeon; indole_3_acetate_biosynthesis in 86 bacteria. 4604 bacteria complete both chorismate and pABA, and 598 both chorismate and salicylate. Ten reactions were added, all with Rhea masters; the salicylate route reuses the existing isochorismate synthase reaction RHEA:18985 rather than duplicating it.Three new metabolic GIFTs, four new anchors, ten reactions, twenty-three enzyme systems and twenty-one markers. paba_biosynthesis and menaquinone_biosynthesis gain an upstream neighbour in the composition graph and change from network position entry to intermediate.
75DBC-20260818-SHIKIMATE-SDH-ORPHAN2026.17.12026-08-18T22:12ZrouteclarificationbroadensThe shikimate dehydrogenase step of the shikimate pathway is curated as not requiredThis is a coverage hole in the marker, not a gap in the biology. Every other step of the pathway is annotated in 8461 to 9149 bacteria while K00014 reaches 5585, and the organisms that fall out are ones that demonstrably make aromatic amino acids. It is the orphan-step rule the vitamin layer established, applied to a step that has a KO which does not reach the taxa that need it.Requiring the step drops the route from 7644 to 5420 bacteria. The 2224 lost carry every other step and include 201 of 213 Cyanobacteriota and 1061 of 1642 Actinomycetota. Mycobacterium tuberculosis Rv2552c and Synechocystis slr1559 are annotated shikimate 5-dehydrogenase in RefSeq and are assigned to no KO at all. TIGRFAM TIGR00507 was added alongside K00014 so that a genome annotated against NCBIfam satisfies the step; YdiB K05887 was accepted at ambiguous confidence and moves the route by 180 bacteria.chorismate_biosynthesis completes in 7644 rather than 5420 bacteria. A genome that does carry a shikimate dehydrogenase marker still shows the step as supported in its trace.
76DBC-20260818-SALICYLATE-SYNTHASE-SYSTEMS2026.17.12026-08-18T22:14Zenzyme_systemadditionbroadensPchA and the bifunctional salicylate synthases are curated as enzyme systems of the existing isochorismate synthase reaction, not as a second route to salicylateMbtI, Irp9 and YbtS run the same two chemical transformations as PchA and PchB, isomerisation followed by pyruvate elimination, in one active site instead of two proteins. That is a multifunctional protein, which gifter represents at the system layer, exactly as the bifunctional PabBC is curated as a system of both the 4-amino-4-deoxychorismate synthase and lyase reactions. Materialising it as a separate route would assert a different minimal chemical path where there is none.KEGG assigns K04781 both EC 5.4.4.2 and EC 4.2.99.21, and the isochorismate intermediate of MbtI is enzyme-bound rather than obligately released. 104 of 109 pchA genomes also carry pchB; 359 bacteria carry K04781; 646 complete the route on some combination.Enzyme systems attach to reactions rather than to routes, so accepting PchA and MbtI for RHEA:18985 also makes them available to the menaquinone route. That is chemically correct and measurably small: it adds 7 genomes to menaquinone_biosynthesis.
77DBC-20260818-IAA-ROUTES-REFUSED2026.17.12026-08-18T22:16ZrouteclarificationnoneOnly the indole-3-acetamide route to the auxin is curated; the indole-3-pyruvate, tryptamine, indole-3-acetonitrile and side-chain oxidase routes are refusedEvery one of the refused routes is real chemistry with no marker that discriminates it. Invariant 16 decides the case: a trait named for indole-3-acetate may not be evidenced by markers that cannot distinguish indole-3-acetate formation from ordinary transamination, decarboxylation or aldehyde oxidation.The indole-3-pyruvate route needs an aromatic aminotransferase and an aldehyde dehydrogenase, both generic, plus K04103; KEGG assigns K04103 to proteins annotated only as putative thiamine pyrophosphate enzymes in Salmonella, 417 of its 648 bacterial carriers are Enterobacteria, and one carrier is annotated indolepyruvate/phenylpyruvate decarboxylase. The tryptamine route rests on K01593, which KEGG names aromatic-L-amino-acid/L-tryptophan decarboxylase and which also makes dopamine and serotonin. The nitrile route rests on the broad nitrilase K01501 and has no bacterial marker for the aldoxime step. The side-chain oxidase route has no marker in any namespace.indole_3_acetate_biosynthesis carries one route and completes in 86 bacteria rather than the several hundred a marker-permissive definition would produce.
78DBC-20260818-GALLATE-REFUSED2026.17.12026-08-18T22:18ZgiftclarificationnoneGallate biosynthesis from 3-dehydroshikimate is refused and not curatedThe candidate fails two invariants before the specificity question is even reached. Rhea has no reaction for the dehydrogenation of 3-dehydroshikimate to gallate, so there is no stable reaction identity to curate, and the only enzymes described as performing it are plant shikimate dehydrogenases, whose markers are the AroE markers of the core shikimate pathway. Admitting them would make every genome with a shikimate pathway a gallate producer.Rhea release 141 records gallate in nine reactions, all of them consuming it or releasing it from a conjugate, and none forming it from 3-dehydroshikimate. KEGG has eight gallate KOs and every one is degradative or plant-specific: galA/desB dioxygenase, the lpdBCD decarboxylase, ligM, desZ, galR and the plant glucosyltransferase. No EC number, TIGRFAM or Pfam family describes a gallate-forming dehydrogenase.No GIFT added. The bacterial capability that does have evidence is release of gallate from hydrolysable tannins by tannase, EC 3.1.1.20 and KO K10759, which is different chemistry between different boundaries and is deferred rather than refused.
79DBC-20260818-BIOSYNTHETIC-FAMILY-FACET2026.17.12026-08-18T22:20ZgiftadditionnoneA biosynthetic_family facet is registered and shikimate_derived_aromatic assigned to five GIFTsThe four capabilities of this layer share a biosynthetic origin and nothing else that the existing vocabulary records. substrate_class was deliberately not reused: it answers which chemistry a capability is about, and overloading it to mean the chemical family of the product would break the classes it already partitions and could not be assigned to menaquinone or 4-aminobenzoate without taking their cofactor class away.The five GIFTs carrying the new value hold three different substrate classes between them, cofactor for 4-aminobenzoate and menaquinone and aromatic_compound for the three new ones, which is the demonstration that the two facets are orthogonal rather than redundant.Five GIFTs classified. Facets classify a call and never enter the completeness logic, so no genome's result changes.
80DBC-20260818-NITROGEN-LAYER2026.18.12026-08-18T23:40ZgiftadditionbroadensFourteen nitrogen, methylamine and organosulfonate catabolism GIFTs curatedgifter had no nitrogen boundary at all: ammonium appeared in four curated reactions and in no anchor, so every capability that liberates nitrogen was scored only for its carbon. The twelve compounds of distillR bundle D06 were reassessed against KEGG orthology, Rhea 141 and ChEBI 253 over all 10151 bacterial genomes.Prevalence computed from KEGG link/genes/ko sets intersected with the 10151 bacterial organism codes of BRITE br08601, KEGG release 2026-08-18. Urea hydrolysis 3725, nitrate assimilation 3045, sarcosine demethylation 2041, taurine ABC uptake 1462, urate degradation 1214, taurine desulfonation 1065, carnitine to betaine 944, allantoin degradation 893, betaine demethylation 759, taurine sulfoacetaldehyde route 397, carnitine to trimethylamine 271, methylamine degradation 213, creatinine degradation 194, ammonium assimilation 9482. The assessment is inst/doc/proposal-nitrogen-compound-catabolism.md.5587 of 10151 bacteria complete at least one of the eleven non-transport, non-assimilation capabilities and 4564 complete none. AMMONIUM becomes the most connected anchor in the database, with six incoming GIFTs, and no within-mode cycle arises because nothing in gifter produces urate, allantoin, betaine, creatinine, carnitine, taurine or nitrate.
81DBC-20260818-NITROGEN-ANCHOR-RULE2026.18.12026-08-18T23:41ZanchorclarificationnoneAmmonium is an anchor only where a reaction exists to liberate or assimilate itAmmonium is a common reaction participant, so admitting it as an anchor wherever it appears would make it a boundary of much of the database by accident. The cofactor-anchor rule does not settle this, because it asks whether the molecule is consumed and the ammonia-dependent NAD synthetase genuinely consumes ammonium. The nitrogen rule asks instead what the reaction is for.Applied to the four curated reactions that mention NH4(+): RHEA:12172, the glucosamine-6-phosphate deaminase, is admitted because the reaction is the deamination; RHEA:21868 in riboflavin biosynthesis and RHEA:40075 in menaquinone biosynthesis are rejected because ammonium is a leaving group of chemistry aimed at a ring; RHEA:21188, the ammonia-dependent NAD synthetase, is rejected because ammonium is a co-substrate of an amidation.One admitted, three rejected. Without the rule, riboflavin and menaquinone biosynthesis would become nitrogen sources and NAD biosynthesis would become a nitrogen sink that every ammonium-releasing catabolic GIFT composed into. No call changes.
82DBC-20260818-ELECTRON-ACCEPTOR-SCOPE2026.18.12026-08-18T23:42ZgiftclarificationnoneCapabilities requiring an external terminal electron acceptor are out of scopeThe refusal was already recorded on the FUMARATE anchor for fumarate respiration. The nitrogen layer forces it to become a general rule, because it decides four requested capabilities at once and because the markers for all four are specific, abundant and easy to curate, which is exactly why the boundary needs writing down.Refused: nitrate respiration (NarGHI, 2393 bacteria; NapAB, 1326), denitrification (NirK or NirS, 1512), dissimilatory nitrate reduction to ammonium (NrfAH, 499), and taurine to hydrogen sulfide (DsrAB, 228; AsrAB, 284). Nitrate respiration fails a second, independent test: K00370 is named by KEGG as nitrate reductase / nitrite oxidoreductase, one accession for two opposite reactions, so it cannot license a directed claim.A genome encoding a complete denitrification pathway scores negative on everything in this layer. Curate the part of the chemistry that ends before the acceptor: nitrate assimilation ends at ammonium and both taurine capabilities end at sulfite. Reversing this is an architectural decision needing its own completeness contract.
83DBC-20260818-AMINOSUGAR-AMMONIUM2026.18.12026-08-18T23:43ZanchoradditionnoneGlcNAc and sialic acid degradation now declare the ammonium their deaminase liberatesBoth capabilities end at RHEA:12172, the glucosamine-6-phosphate deaminase, whose entire purpose is to remove the amino group. Under the nitrogen-anchor rule they qualify to declare AMMONIUM as an output boundary, which they previously could not because gifter had no nitrogen anchor.RHEA:12172 is alpha-D-glucosamine 6-phosphate + H2O = beta-D-fructose 6-phosphate + ammonium, and it is the terminal reaction of route GLCNAC_KINASE and of the sialic acid route.Two rows in gift_anchors.tsv and the nitrogen_acquisition role on both GIFTs. No route, reaction, system, component or marker changed, and no call changed. The two host-glycan foraging capabilities are now also nitrogen sources and compose into ammonium assimilation.
84DBC-20260818-CARNITINE-SPLIT2026.18.12026-08-18T23:44ZgiftcorrectionnarrowsThe carnitine dehydrogenase route makes glycine betaine, not trimethylamine, and is a separate GIFTThe curation proposal treated CntAB and the CdhA/CdhC dehydrogenase route as two alternative routes of one carnitine-to-trimethylamine capability, on the strength of KEGG naming CdhC a trimethylamine transferase. Checking the reaction against Rhea before curating showed the product is the betainyl thioester and no free amine is released.RHEA:47044 is 3-dehydrocarnitine + acetyl-CoA = N,N,N-trimethylglycyl-CoA + acetoacetate, and RHEA:45716 is N,N,N-trimethylglycyl-CoA + H2O = glycine betaine + CoA + H(+). Neither releases trimethylamine. CntAB alone completes in 271 bacteria and the dehydrogenase route in 944; they overlap in 32.Two GIFTs instead of one with two routes. carnitine_degradation_trimethylamine claims trimethylamine release from 271 genomes rather than from 972, which is the narrowing. carnitine_to_betaine composes into betaine demethylation through the BETAINE anchor, so carnitine still reaches glycine by composition.
85DBC-20260818-NITROGEN-REFUSALS2026.18.12026-08-18T23:45ZgiftclarificationnonePhenylethylamine and hypotaurine degradation are refused on marker specificityBoth were elements of distillR bundle D06 and both fail the first clause of the evidence test: no marker matches the specificity of the compound the trait is named for.Phenylethylamine: K00276 is by KEGG's own name a primary-amine oxidase (975 bacteria) and K00274 a monoamine oxidase (1704); both act on tyramine, histamine and putrescine, so neither can identify the amine. K00146, phenylacetaldehyde dehydrogenase, is substrate-specific but is the wrong step. Hypotaurine: K00485, the only orthology group naming hypotaurine, has zero bacterial members, and the legacy definition used taurine-pyruvate aminotransferase plus a generic aldehyde dehydrogenase, which cannot distinguish the two compounds. Two further refusals on the same clause: the urea amidolyase route, whose fused orthology group K14541 has zero bacterial members, and the creatinine deiminase route, whose first marker K01485 is a cytosine/creatinine deaminase carried by 2702 genomes mostly for the cytosine activity.No GIFT is created for either compound. Accepting a primary-amine oxidase for phenylethylamine would have damaged every other amine trait the same accession matches, which is invariant 16 exactly.
86DBC-20260819-AROMATIC-LAYER2026.19.12026-08-19T10:05ZgiftadditionbroadensTwelve aerobic aromatic ring catabolism GIFTs, built around the catechol and 3-oxoadipyl-CoA convergence nodesThe requested layer was KEGG's Xenobiotics biodegradation module category. Twenty-four candidates were tested and ten were refused or deferred, so what is curated here is the aromatic core that survived: three peripheral entries into catechol, the two ring-cleavage strategies, the shared lower routes, the aerobic phenylacetate route, and the phenylpropanoid node. Every route has a Rhea master at every step and a KEGG module or pathway boundary to compare against.Prevalence measured against 11 949 KEGG genomes on 2026-08-18: benzoate to catechol complete in 718, catechol ortho-cleavage in 873, catechol meta-cleavage in 312, the phenylacetate core in 950, the phenylpropanoate chain in 91. All 67 EC numbers spanning the layer returned a Rhea master. Full assessment in inst/doc/proposal-aromatic-degradation.md.Twelve new GIFTs, twelve new anchors, thirty new reactions and forty-nine new markers. Broadens only: no existing call changes except through the separate acetaldehyde dehydrogenase entry.
87DBC-20260819-AROMATIC-CUTS2026.19.12026-08-19T10:06ZgiftclarificationnoneFour KEGG module boundaries were cut differently, because a module ORs substrates or duplicates a shared segmentA KEGG module is not a GIFT. M00569 and M00545 both bundle a shared lower route that five modules duplicate, so it is curated once as oxopentenoate_degradation and composed through the 2-oxopent-4-enoate anchor. M00545 ORs two different input substrates into one module, which gifter cannot do because a route must connect the GIFT's own declared boundaries, so it becomes three GIFTs around the dihydroxyphenylpropanoate node. M00878 and M00568 both end in the same thiolysis, curated once as oxoadipyl_coa_thiolysis. M00548 names benzene as its substrate but its marker set is a phenol 2-monooxygenase, so only the phenol reaction is claimed.KEGG module DEFINITION lines and REACTION lists retrieved 2026-08-18; Rhea masters for every step confirm which reaction each marker set catalyses.The relations recorded in gift_xrefs state each difference: subset_of where gifter cuts shorter, overlaps for the phenol case, equivalent only where the boundaries genuinely agree.
88DBC-20260819-META-CLEAVAGE-MARKER2026.19.12026-08-19T10:07ZmarkerclarificationnoneK07104 is refused as evidence of catechol 2,3-dioxygenase; K00446 and NCBIfam TIGR03211 are accepted insteadBoth KEGG orthologues carry the same EC number, but they do not describe the same thing. Accepting the broad one would put a marker in the database that fires in genomes with no aromatic catabolism at all, and it would be available to every future GIFT declaring this activity, not only to this one.K07104 is assigned in 2081 of 11 949 KEGG genomes, led by Bacillus (161), Streptococcus (105), Staphylococcus (100) and Listeria (48); only 276 of those genomes carry any lower meta pathway gene. K00446 is assigned in 335 genomes, led by aromatic degraders.catechol_meta_cleavage calls rest on the specific orthologue. Genomes carrying only K07104 are negative.
89DBC-20260819-RIESKE-COMPONENTS2026.19.12026-08-19T10:08Zenzyme_componentclarificationnoneShared ferredoxin and reductase subunits are deliberately not curated as components of Rieske oxygenase systemsenzyme_component has no required flag, so every curated component is a hard AND. The electron-transfer subunits of ring-hydroxylating oxygenases are interchangeable between systems and systematically under-annotated, so requiring them would report an annotation gap as a missing capability. The substrate-determining subunits are curated instead, and the omission is stated in each system description.Catalytic against electron-transfer annotation in KEGG: anthranilate andAc 281 against andAa 101; phthalate pht3 279 against pht2 99; naphthalene ferredoxin 216 against reductase 86.Affects the benzoate, anthranilate and phenylpropanoate oxygenase systems. The phenol hydroxylase and the phenylacetyl-CoA epoxidase keep all their subunits, because there the components are the enzyme rather than shared carriers.
90DBC-20260819-ACETALDEHYDE-SYSTEMS2026.19.12026-08-19T10:09Zenzyme_systemadditionnoneTwo alternative acylating acetaldehyde dehydrogenase systems added to RHEA:23288The lower meta-cleavage route ends in the same reaction ethanol formation already uses. MhpF and XylQ are standalone counterparts of the AdhE aldehyde domain and genuinely catalyse it, so they are curated as alternative systems of the shared reaction rather than duplicated.KEGG orthology K04073 (1277 genomes) and K18366 (328), both annotated to EC 1.2.1.10, the EC of the existing reaction.Checked rather than assumed, and the answer was no call changes: ethanol formation's second reaction rests on adhE alone, and a genome carrying adhE already satisfied the first, so no genome's ethanol call moves. The systems matter to the aromatic lower route, which has no adhE.
91DBC-20260819-AROMATIC-CLASS2026.19.12026-08-19T10:10ZgiftclarificationnoneThe aromatic_compound substrate class now covers ring-cleavage products as wellThree of the new GIFTs act on compounds that are no longer aromatic: 2-oxopent-4-enoate, 3-oxoadipate and its CoA thioester. They exist only because a ring was opened, and classifying them as organic acids would split one degradation funnel across two substrate classes.The class was registered by the aromatic biosynthesis layer for benzenoid and heteroaromatic compounds and their branchpoint precursors; this extends the same reasoning downstream.No existing classification changes; the definition is widened, not redirected.
92DBC-20260819-AROMATIC-REFUSALS2026.19.12026-08-19T10:11ZgiftclarificationnoneNine ring-hydroxylating dioxygenase traits are refused on marker specificity, and five more on evidence availabilityToluene, benzene, xylene, cumate, p-cymene, biphenyl, carbazole, naphthalene and terephthalate degradation are each named for a substrate recognised in the active site of a Rieske oxygenase, and no marker resolves it. KEGG's own orthologue names admit the promiscuity, and InterPro offers only the family signature. Unlike the butyrate case, no namespace change rescues them. Anaerobic toluene, benzoyl-CoA and cyclohexanecarboxylate degradation are refused on prevalence, caffeine because the reductase its demethylases require has no orthology group at all, and salicylate and phthalate degradation are deferred until the protocatechuate node is curated.KEGG orthology prevalence at the bottleneck step: carbazole 1 genome, caffeine 2, xylene 7, terephthalate 8, cymene 10, cumate 11, biphenyl 13, naphthalene 12, anaerobic toluene 12, benzoyl-CoA 16, cyclohexanecarboxylate 24. InterPro returns IPR001663 and PS00570, both substrate-blind, for every dioxygenase alpha subunit searched.No GIFT is curated for any of them. The register is inst/doc/proposal-aromatic-degradation.md; the benzoate and phenylpropanoate GIFTs carry the specificity statements that follow from it.
93DBC-20260819-AMINO-ACID-BIOSYNTHESIS2026.19.12026-08-19T04:40ZgiftadditionbroadensThe fifteen remaining proteinogenic amino acids curated as eighteen composable biosynthesis GIFTsgifter covered five amino acids and the aspartate trunk; every other family entry point was already an anchor, and four of them -- L-aspartate, chorismate, L-glutamine and 3-methyl-2-oxobutanoate -- were declared as inputs that no GIFT produced. Six boundaries depart from the KEGG modules, each at a branchpoint where genomes measurably differ: meso-diaminopimelate separates the peptidoglycan precursor from lysine and lets the four acylation routes become one capability (75.3 per cent of bacterial genomes against 51.4, 5.6, 6.8 and 17.2 for the modules read separately); 3-methyl-2-oxobutanoate and 2-oxobutanoate separate valine, leucine and isoleucine, which KEGG fuses because the enzymes are shared; and L-glutamine is curated as its own capability although glutamine synthetase also appears inside ammonium assimilation, because the amide nitrogen is consumed by four other GIFTs.KEGG orthology over the 10151 bacterial genomes of KEGG release 2026-08-18 for every route count; KEGG modules M00015, M00016, M00019, M00023 to M00028, M00432, M00525 to M00527, M00535, M00570 and M00844 for pathway organisation; Rhea release 141 for all 66 new reactions, their direction and their KEGG and EC cross-references; ChEBI release 253 for the fourteen new anchors. Full assessment in inst/doc/proposal-amino-acid-metabolism.md.Eighteen new GIFTs, fourteen new anchors, twenty-five routes, 66 reactions and 98 new KO markers. Pantothenate, folate, menaquinone, pyrimidine and pyridoxal phosphate biosynthesis stop being nodes whose inputs nothing produces, and the aspartate family now reaches lysine. No existing GIFT call changes: no existing route, system, component or marker was edited.
94DBC-20260819-AROMATIC-TRANSAMINASE-WIDENED2026.19.12026-08-19T04:40ZmarkeradditionbroadensThe final transamination of phenylalanine and tyrosine biosynthesis accepts the aspartate and branched-chain aminotransferasesKEGG requires TyrB (K00832) or the fungal Aro8 (K00838) for the last step of both aromatic amino acids. Requiring them calls phenylalanine biosynthesis in 2296 bacterial genomes and tyrosine in 1558, while the aryl skeleton that discriminates the traits is present in 7796 and 5893. The aspartate and branched-chain aminotransferases transaminate aromatic 2-oxo acids, and accepting them recovers 7733 and 5852 -- so the step carries almost no information, which is a statement about the transaminase and not about the pathway. It is kept required because it is real chemistry, and the specificity of the claim rests on the skeleton, which is separately evidenced.KEGG orthology counts over 10151 bacterial genomes, 2026-08-18: skeleton alone 7796 and 5893, with the KEGG transaminase 2296 and 1558, with the widened set 7733 and 5852.K00812, K00813, K11358, K00826 and K05821 become accepted evidence for the aromatic transamination components. The same accessions already evidence aspartate biosynthesis and the branched-chain transaminations, which is chemically true of the enzymes and does not equate the traits, because each 2-oxo acid skeleton is separately required.
95DBC-20260819-AMINO-DONOR-RULE2026.19.12026-08-19T04:40ZanchorclarificationnoneThe amino donor of a transamination is never declared as an anchor; the nitrogen source of an assimilation isL-glutamate is a co-substrate of nearly every reaction in the amino acid layer. Declaring it wherever it is consumed would give sixteen new GIFTs an input edge from one node and reduce the composition graph to a star around it. The rule keeps L-glutamate as an anchor only where its carbon skeleton becomes the product -- proline, ornithine and glutamine -- and admits AMMONIUM only under the nitrogen-anchor rule already recorded for the nitrogen layer. It is the nitrogen analogue of the sulfur decision the methionine and cysteine GIFTs encode, and it follows the co-substrate rule recorded as DBC-20260818-COSUBSTRATE-ANCHORS.Applied to the eighteen biosynthesis GIFTs of this release: three declare L-glutamate, and the twelve that merely transaminate do not. Applied in the other direction to the ten catabolic GIFTs, every one that liberates ammonium declares it.No call changes. The rule is what keeps gift_graph() readable at 119 GIFTs, and it is the reason alanine and asparagine biosynthesis declare only their carbon precursor although their routes differ in nitrogen source.
96DBC-20260819-AMINO-ACID-CATABOLISM2026.19.12026-08-19T04:40ZgiftadditionbroadensTen amino acid degradation and transformation capabilities curated, including the first Stickland contentgifter had no amino acid degradation content of any kind. The ten curated here are those whose markers are specific enough for the trait as named: the arginine deiminase pathway, histidine degradation, threonine and serine deamination, glutamate decarboxylation to GABA, tryptophanase, methionine gamma-lyase, cysteine desulfidation, and the two Stickland reductases. Threonine deamination is curated once, as catabolism, and isoleucine biosynthesis composes from the 2-oxobutanoate anchor rather than repeating the reaction; the resulting chain crosses modes, which the composition rule anticipates.KEGG orthology over 10151 bacterial genomes: arginine deiminase pathway 1733, histidine degradation 3688, threonine deaminase 7742, serine dehydratase 6922, glutamate decarboxylase 1684, tryptophanase 741, methionine gamma-lyase 2320, dedicated cysteine desulfidases 2365, complete glycine reductase 128, proline reductase with racemase 90. Rhea release 141 for all fifteen new reactions, including RHEA:12232 and RHEA:12737 for the two selenoprotein reductases.Ten new GIFTs and five new anchors. Hydrogen sulfide gains a producer, so the two sulfide-dependent biosynthesis GIFTs stop being fed by nothing; ammonium gains eight further producers; and the amino acid layer connects to the fermentation layer through pyruvate. No existing GIFT call changes.
97DBC-20260819-CYSTEINE-SULFIDE-UNDERCALLED2026.19.12026-08-19T04:40ZmarkerclarificationnoneCysteine desulfidation is evidenced by dedicated desulfidases only, and is knowingly under-calledMicrobial hydrogen sulfide from cysteine is carried out by many PLP enzymes as a side activity -- cystathionine beta-lyase, cystathionine gamma-lyase, MalY, CyuA. Accepting those markers would raise the count from 2365 to over 4000 genomes and destroy the claim, because K01760 is already curated as evidence for cysteine biosynthesis through transsulfuration: every transsulfuration genome would become a sulfide producer. The trait is therefore curated with the dedicated desulfidase orthology groups only.K20021, K26607 and K28981 in 2365 of 10151 bacterial genomes; K01760 in 4117, already curated as evidence for cysteine_biosynthesis_homocysteine.cysteine_degradation_sulfide is negative in genomes whose only cysteine-lyase evidence is a promiscuous PLP enzyme. What would change the decision is a protein family separating desulfidase-competent sequences from the biosynthetic enzymes.
98DBC-20260819-ACETYL-PHOSPHATE-ANCHOR2026.19.12026-08-19T04:40ZanchoradditionnoneAcetyl phosphate declared as an anchor, because glycine reductase has no other product to declareThe nitrogen layer met this question from the taurine route and left the intermediate internal, recording the missing edge. That resolution is not available here: source validation requires every metabolic GIFT to declare an output anchor, and acetyl phosphate is the sole product of the Stickland glycine reduction. Declaring it is therefore the condition of curating the trait at all.RHEA:12232 releases acetyl phosphate, ammonium and phosphate and nothing else. acetate_interconversion continues to hold the same molecule internally between phosphotransacetylase and acetate kinase.ACETYL_PHOSPHATE becomes an output-only anchor, on the precedent of GLYOXYLATE, TRIMETHYLAMINE and SULFITE. No edge to acetate formation is created, because acetate_interconversion does not declare the molecule; that edge appears only if that GIFT is re-cut.
99DBC-20260819-ASPARTATE-GLUTAMINE-ESSENTIAL2026.19.12026-08-19T05:20ZanchorcorrectionnoneL-aspartate and L-glutamine are marked as biomass building blocksBoth were curated as biomass_essential = no when they existed only as input boundaries: aspartate as the head of the aspartate trunk, glutamine as the amide donor of pyrimidine and pyridoxal phosphate biosynthesis. Both are proteinogenic amino acids, so a growing cell must obtain or synthesise them, which is exactly what the facet says. The oversight only became visible when the amino acid layer gave both a producer, because gift_profile derives auxotrophy_indicator from this facet and the two capabilities were reporting as though nothing depended on them.The facet definition in facet_terms.tsv: a building block a growing cell must obtain or synthesise. The eighteen other proteinogenic amino acid anchors in the database already carry yes.gift_profile.auxotrophy_indicator becomes true for aspartate_biosynthesis and glutamine_biosynthesis, so all twenty proteinogenic amino acids are covered. No Boolean call changes: the facet is read by the derived profile only.
100DBC-20260819-MERCURY-DEFENSE2026.19.12026-08-19T12:40ZgiftadditionbroadensMercury detoxification curated as a defense GIFT, with MerA-dependent reduction the only required functionHg(II) reduction is real chemistry with a Rhea master, but it is not a directed conversion between nutrient anchors, so no mode describes it honestly: catabolic would claim carbon or energy metabolism, interconversion would claim a reversibility the cell never uses, and transport describes only the merT and merP part. Inventing a fifth mode for one trait would put mercury into the anchor graph as edges through metal-ion anchors that mean nothing. The defense contract already covers a chemical challenge, and the machinery model supplies exactly the required and accessory distinction the mer operon needs. Reduction alone is required because a genome carrying merA detoxifies the Hg(II) that reaches its cytoplasm; requiring merT and merP would refuse such genomes on an operon architecture that varies, since merC and merE substitute for the pair in several lineages.MerA K00520 with NCBIfam TIGR02053; MerT K08363 with MerP K08364, MerC K19058, MerE K19059; MerR K08365; MerB K00221. RHEA:23856 for the reduction, run in reverse by MerA, and RHEA:18777 for the organomercurial lyase. The assessment is inst/doc/proposal-aromatic-degradation.md, section 8.8.mercury_detoxification is positive on merA evidence alone, and is the first defense GIFT that is not anti-phage. The three accessory functions are reported as unsupported without changing the call. No metabolic GIFT, anchor, route or reaction is touched, and no existing call changes.
101DBC-20260819-CHEMICAL-DETOXIFICATION-CLASS2026.19.12026-08-19T12:40Zgiftadditionnonedefense_class gains chemical_detoxification, named for the mechanism rather than for the metal or the phenotypedefense_class is single-valued and partitions the defense type, so the value chosen here is the bucket every future defense GIFT falls into exactly once, and the way to choose it is to write out what each candidate name would have to hold. A resistance class was rejected on three grounds: its roster is mostly not defense GIFTs, since metal efflux is transport, MerR and CmtR are regulatory and lipid A modification is structural; resistance is an outcome, which gifter claims of no GIFT and which this GIFT's own description explicitly disclaims; and invariant 18 puts phenotypic descriptions in a derived layer. metal_detoxification was rejected as too narrow to be worth a partition, leaving three curatable members ever. Naming the class for the mechanism instead admits a populated roster whose members are all markable.ArsM has no orthology group; chrR K19784 is defined as a generic NAD(P)H:quinone dehydrogenase and does not resolve chromate; ArsC K00537 produces As(III), which is more toxic than the As(V) it consumes, so the detoxifying step is the ArsB efflux that a detoxification class excludes. The curated vocabulary already carries the precedent: restriction_modification and crispr_cas are both anti-phage and were deliberately not merged into a phage_resistance class. The rosters are in inst/doc/proposal-aromatic-degradation.md, section 10.6.Future candidates in this class include tellurite methylation (TehB), Cu(I) oxidation (CueO), superoxide and peroxide removal, nitrosative defense, and methylglyoxal and formaldehyde disposal. Efflux, sequestration and repair are excluded by the definition, so an arsenite-efflux GIFT would need a different class. If the axis of which challenge a system acts against is ever wanted, it is a separate multi-valued facet, not a re-cut of this one.
102DBC-20260819-MER-EVIDENCE-REFUSALS2026.19.12026-08-19T12:40ZmarkerclarificationnoneNF033555, the InterPro accessions and merD are refused as mer evidenceNF033555 and IPR004927 name MerB, and IPR021179 names MerA, more specifically than any accepted accession does. They are not curated because gifter's evidence layer recognises KO, EC, PFAM, TIGRFAM, CAZY and CUSTOM_HMM only: an NF or IPR accession would be stored and never matched, which is worse than leaving it out, because a curator reading the component would see evidence that can never fire. TIGR02053 carries the same claim for MerA in an accepted namespace and is curated in its place; MerB is left on K00221 alone. merD K19057 is refused on different grounds, which are biological: it modulates MerR-driven transcription as a co-regulator rather than activating the promoter, and evidence rows are alternatives within a component, so accepting it would let a genome carrying no activator claim the induction function.R/evaluation.R infers and normalises those six namespaces and no others. InterPro records TIGR02053 as integrated into IPR021179 and NF033555 as not integrated into any InterPro entry, both retrieved 2026-08-19.The organomercurial lysis function is evidenced by K00221 only, and the induction function by K08365 only. Extending the namespace vocabulary to NCBIfam NF accessions or to InterPro is a code change carrying its own evaluation contract and its own confidence ordering, not a content decision, and it needs a second demonstrated need before it is worth making.
103DBC-20260820-ISOCITRATE-RECUT2026.20.12026-08-20T05:30ZgiftcorrectionmixedThe upper oxidative TCA segment is cut at isocitrate and the glyoxylate bypass is curated without duplicated reactionsIsocitrate is a real branchpoint: oxidative decarboxylation and isocitrate lyase are alternative fates, and keeping it internal forced a bypass GIFT either to repeat citrate synthase and aconitase or to start at an undeclared boundary. The re-cut makes each chemical claim atomic. The bypass ends at succinate and malate and composes back to oxaloacetate through existing segments; glyoxylate remains internal because the complete route both makes and consumes it.Rhea release 141: RHEA:13245 and RHEA:18181, with CHEBI:15562 for D-threo-isocitrate. KEGG module M00012, verified 2026-08-20, defines K01637 followed by K01638 or the two-reaction K19282 implementation. K01639 is N-acetylneuraminate lyase and is refused. Full assessment in inst/doc/proposal-central-metabolic-cycles.md and inst/doc/proposal-next-gift-release.md.acetyl_coa_to_oxoglutarate is replaced by acetyl_coa_to_isocitrate plus isocitrate_to_oxoglutarate. Existing complete upper-TCA marker sets now support two atomic calls instead of one bundled call. glyoxylate_bypass is new on K01637 plus K01638, and a second derived named cycle appears without affecting any member's Boolean call.
104DBC-20260820-NITROGEN-FIXATION2026.20.12026-08-20T05:31ZgiftadditionbroadensNitrogen fixation is curated as dinitrogen-to-ammonium chemistry with complete Mo and V nitrogenase architecturesNitrogen fixation is a bounded metabolic capability, but NifH alone cannot license it. The Mo route therefore requires the catalytic/electron-delivery NifHDK system and nitrogenase-specific NifEN and NifB cofactor assembly. The V route separately requires VnfHDGK, VnfEN and NifB. Fe-S supply and folding factors are excluded where housekeeping pathways can substitute; expression, oxygen protection and electron-donor context are not claimed.RHEA release 141 RHEA:21448 and RHEA:55543; ChEBI release 253 CHEBI:17997 and CHEBI:28938; KEGG M00175 and K02585/K02587/K02592/K02586/K02588/K02591/K22896-K22899/K22903, verified 2026-08-20. Minimum Mo and alternative-nitrogenase assembly evidence is reviewed in inst/doc/proposal-next-gift-release.md.nitrogen_fixation becomes callable through two complete routes. NifH alone, incomplete catalytic complexes and cofactor-assembly-only marker sets remain negative. The Fe-only Anf architecture is documented but deferred because current KO evidence cannot state its minimum native architecture without overclaiming.
105DBC-20260820-SULFATE-ASSIMILATION2026.20.12026-08-20T05:32ZgiftadditionbroadensAssimilatory sulfate reduction is curated as four explicit APS/PAPS and NADPH/ferredoxin routesThe sulfate-to-sulfide boundary is shared by distinct activation and terminal-reductase implementations. Materialising four minimal routes preserves OR across valid pathways and AND within each. K00390 is not accepted for either branch-defining component because KEGG assigns it both EC 1.8.4.8 and 1.8.4.10; using it would silently make APS and PAPS routes equivalent. Reaction-specific EC evidence keeps the claims separable. Dissimilatory AprAB and DsrAB are excluded.Rhea release 141 RHEA:18136, RHEA:24152, RHEA:11724, RHEA:21976, RHEA:13804 and RHEA:23132; ChEBI release 253 CHEBI:16189 and CHEBI:29919; KEGG M00176 and its KO definitions, verified 2026-08-20; the assimilatory APS-reductase literature reviewed in inst/doc/proposal-next-gift-release.md.assimilatory_sulfate_reduction becomes callable on any one complete route and connects sulfate to the existing sulfide-dependent cysteine and methionine GIFTs. Sulfite made by taurine desulfonation does not create an edge because it remains an internal reaction participant here, not an input boundary.
106DBC-20260821-CAZY-AGREEMENT-FLOOR2026.21.12026-08-21T09:00ZmarkercorrectionnarrowsdbCAN-sub clusters whose EC agreement is below half are withdrawn as markersThe marker policy admits a polyspecific CAZy family as ambiguous evidence because the family genuinely carries the activity among others. A dbCAN-sub cluster in which 3 of 96 EC-annotated members carry the claimed EC is a different thing: the quantified support argues against the assignment rather than weakly for it. Forty cluster markers below 50 percent agreement are withdrawn from the xylan, arabinoxylan and starch components. The floor now also governs new CAZy curation.Agreement recomputed from data-raw/reference/cazy-subfamily-ec.tsv, derived from dbCAN db_v5-2-9_5-5-2026 dbCAN_sub.hmm. The withdrawn markers span 3 to 47 percent agreement.Calls resting only on a withdrawn cluster become negative. Genomes evidenced by KEGG orthology or by a cluster above the floor are unaffected.
107DBC-20260821-CHITIN-DEGRADATION2026.21.12026-08-21T09:00ZgiftadditionbroadensChitin saccharification is curated as endo-acting chitinase plus exo-acting hexosaminidaseChitin reaches the gut in dietary arthropod and fungal biomass and is saccharified by the same endo-then-exo logic as xylan and starch, so it takes the same shape: one GIFT per substrate capability, with both activities required and oxidative chain cleavage accessory. GH18, GH19 and GH20 are activity-coherent enough that most of the evidence grades above ambiguous.ChEBI release 253 CHEBI:17029; dbCAN db_v5-2-9_5-5-2026 fam-substrate-mapping and dbCAN-sub clusters for EC 3.2.1.14, 3.2.1.52 and 1.14.99.53; KEGG K01183, K13381 and K01207, verified 2026-08-21.chitin_degradation becomes callable. Chitinase alone or hexosaminidase alone remains negative, and the released GlcNAc composes with glcnac_degradation.
108DBC-20260821-MUCIN-O-GLYCAN2026.21.12026-08-21T09:00ZgiftadditionbroadensMucin O-glycan foraging is curated as three parallel exo-glycosidase capabilitiesMucin O-glycan has no polymer-to-oligomer cut, so the tier model does not apply and the substrate is curated as parallel monosaccharide-release GIFTs from one anchor, as the polysaccharide proposal set out. Sialidase, alpha-L-fucosidase and alpha-N-acetylgalactosaminidase were curated because their linkages are host-glycan-specific. Beta-galactosidase and beta-N-acetylhexosaminidase were assessed and rejected: GH2, GH35 and GH42 cannot separate mucin galactose release from lactose hydrolysis, and NagZ hexosaminidase is primarily peptidoglycan recycling, so either would have called mucin foraging from housekeeping chemistry.ChEBI release 253 CHEBI:28037; dbCAN db_v5-2-9_5-5-2026 clusters for EC 3.2.1.18, 3.2.1.51, 3.2.1.63, 3.2.1.111 and 3.2.1.49; KEGG K01186, K23550, K01206, K15923 and K01204, verified 2026-08-21.Three mucin GIFTs become callable and compose with neuac_degradation, fucose_degradation_isomerase and the sugar tier. Released GalNAc has no downstream capability curated yet, so that chain ends at the anchor.
109DBC-20260821-EXTRACELLULAR-HANDOFF2026.21.12026-08-21T09:05ZschemacorrectionnoneA handoff out of extracellular chemistry through an unsplit anchor is recorded as compartment-inexactThe gift_graph view called an edge exact whenever both GIFTs named the same anchor, without asking where the upstream chemistry happens. A secreted glycosidase releases its sugar outside the cell and a catabolic GIFT consumes it inside, so when no transporter evidence licensed splitting that sugar into compartment variants the two GIFTs name one unsplit anchor and the membrane between them disappeared from the graph. The view now asks whether the upstream GIFT declares an extracellular input, and downgrades the edge when it does. This is the distinction between a public-goods degrader, a selfish forager and a cross-feeder, which is the main thing the compartment model exists to carry. The database held two conventions before this: xylan_degradation and collagen_cleavage declare extracellular products, while starch_degradation declares an unspecified one. The rule covers both, so starch is correct in advance of any glucose catabolism GIFT.Derived from the declared anchor compartments alone; no curated content changed. Three edges are reclassified and 214 are unaffected.No call changes. gift_graph and the community handoff network report chitin_degradation to glcnac_degradation, mucin_sialic_acid_release to neuac_degradation and mucin_fucose_release to fucose_degradation_isomerase as compartment_inexact. Callers filtering on exact edges no longer see them.
110DBC-20260821-PECTIN-DEGRADATION2026.21.22026-08-21T17:30ZgiftadditionbroadensHydrolytic pectin saccharification is curated as endo- plus exo-polygalacturonasePectin is the dominant soluble fibre of a plant-based diet and had no representation at all: unlike starch there is no KEGG-orthology fallback that reaches it, so the capability was invisible by every route. The hydrolytic chemistry takes the same endo-then-exo shape as xylan, starch and chitin, with methyl-ester removal accessory in the same way acetyl removal is accessory to xylan. GH28 is substrate-coherent, carrying seven characterised activities that are all on pectin, so the bare family is recorded as ambiguous because it cannot separate endo from exo action rather than because it might be acting on something else. CE8 is monoactivity. The lyase chemistry is assessed and deferred, not rejected: see the effect column.ChEBI release 253 CHEBI:17309; dbCAN db_v5-2-9_5-5-2026 clusters for EC 3.2.1.15, 3.2.1.67 and 3.1.1.11 across GH28, GH4 and CE8; KEGG K01184, K01213, K22933 and K01051 with map00040, verified 2026-08-21.pectin_degradation becomes callable and hands D-galacturonate to galacturonate_degradation on a compartment-inexact edge. Endo activity alone remains negative. Pectate lyase is NOT curated: PL1, PL2, PL3, PL9 and PL10 markers exist and are well supported, but the lyase route yields unsaturated oligogalacturonides that enter catabolism through 2-dehydro-3-deoxy-D-gluconate, which is an internal intermediate of galacturonate_degradation and not a declared anchor. A lyase GIFT therefore cannot state an output boundary. Promoting that intermediate to an anchor would let both the lyase route and glucuronate catabolism declare it, and is the specific change that would unblock this.
111DBC-20260821-KDG-ANCHOR2026.21.32026-08-21T20:10ZanchorcorrectionmixedThe hexuronate routes are cut at 2-dehydro-3-deoxy-D-gluconate and the shared Entner-Doudoroff tail becomes its own capability2-dehydro-3-deoxy-D-gluconate is a real branchpoint, and the case is the same one the isocitrate re-cut of 2026.20.1 already settled. Galacturonate catabolism, glucuronate catabolism and the pectate lyase route all converge on it, and keeping it internal forced a lyase GIFT either to repeat kdgK and eda a third time or to start at an undeclared boundary. The three-part granularity rule holds. Boundaries are distinct: the heads consume a uronate and produce the branchpoint, the tail consumes the branchpoint and produces pyruvate and glyceraldehyde-3P. Variation is independent, and strongly so: KdgK and Eda are the enzymes of the Entner-Doudoroff pathway proper and of gluconate and alginate catabolism, so genomes carry the tail with no hexuronate head at all, which is the opposite of the noise case the rule is written against. The interpretive consequence is that a negative hexuronate call now says which half is missing, and that the two pectin chemistries become visibly convergent in the graph instead of one of them being inexpressible. The anchor is not an ecological substrate, which is no objection: DHAP, lactaldehyde, isocitrate and glyceraldehyde-3P are anchors on the same grounds, because an anchor marks a branchpoint rather than a traded metabolite. The cost is a change to two shipped GIFTs, and both keep their identifiers and move to version 2.ChEBI release 253 CHEBI:57990, verified as the participant of RHEA:14797 which the database already carries. No new marker evidence: the two reactions moved unchanged, with their enzyme systems, components and KEGG orthology markers K00874, K01625, K17463 and K28887 attached to the reactions rather than to the routes.No genome's marker evidence changes and no reaction leaves the database. galacturonate_degradation and glucuronate_degradation now end at KDG and each declares one output anchor instead of two; a genome carrying only a uronate head, with no kdgK or eda, calls them complete where it did not before, and reaching pyruvate requires kdg_degradation to compose. Callers reading the output anchors of either GIFT see KDG rather than PYRUVATE and GAP. The KEGG M00061 cross-reference on glucuronate_degradation drops from equivalent to subset_of. gift_richness over the hexuronate layer rises by one where the full chemistry is present, because one capability became two.
112DBC-20260821-PECTATE-LYASE2026.21.32026-08-21T20:40ZgiftadditionbroadensPectin degradation by beta-elimination is curated as a capability separate from the hydrolytic routePectate lyases are more common than polygalacturonases in gut Bacteroidetes, so pectin_degradation on its own missed most real pectin degraders and PL was an entirely unused CAZy class. This is a separate GIFT rather than a second route of pectin_degradation because beta-elimination and hydrolysis end at different metabolites, and anchors are declared per GIFT: the same reasoning that made the isomerase and oxidative xylose routes two capabilities. The route runs past the polymer boundary into three intracellular steps because its immediate products are unsaturated oligogalacturonides, which are not promoted to anchors; oligogalacturonide lyase, the ketol isomerase and the 5-dehydrogenase have no other substrate in the database, so folding them in is the granularity rule rather than an exception to it. Pectin lyase is accessory because it is an alternative entry on esterified backbone rather than a required step, and pectinesterase is accessory in the same way it is to the hydrolytic route. PL3 and PL10 are monoactivity. PL2 carries two activities, both pectin. PL1 and PL9 are ambiguous, and for different reasons that the marker notes state separately: PL1 cannot separate endo from exo action or esterified from de-esterified backbone but is otherwise pectin-coherent, while PL9 additionally carries a thiopeptidoglycan lyase, so a PL9 hit may not be acting on pectin at all.dbCAN db_v5-2-9_5-5-2026: 32 eCAMI clusters for EC 4.2.2.2 across PL1, PL2, PL3, PL9 and PL10, of which 10 are curated and 22 high-confidence; 2 clusters for EC 4.2.2.9 across PL2 and PL9; 6 clusters for EC 4.2.2.10 in PL1. Three CBM clusters appearing under EC 4.2.2.2, CBM13_e184, CBM2_e111 and CBM35_e12, are excluded because a binding module catalyses nothing. PL1_e2 is excluded from EC 4.2.2.9 at 5 of 20 annotated members, which is below the 50% agreement floor, although the same cluster is admitted for EC 4.2.2.2 at 15 of 20. Rhea release 141 RHEA:57104, RHEA:20269, RHEA:23896 and RHEA:24232; EC 4.2.2.2 and EC 4.2.2.10 have no Rhea master and carry local reaction identifiers with EC cross-references. KEGG K01728, K19551, K01731, K22994, K01730, K01815, K00065 and K01732 with map00040, verified 2026-08-21.pectate_lyase_degradation becomes callable and hands 2-dehydro-3-deoxy-D-gluconate to kdg_degradation, on a compartment-inexact edge because the depolymerisation is extracellular and the anchor leaves the compartment unresolved. Pectin now has two convergent degradation capabilities that meet at the branchpoint, one through galacturonate and one directly. The call is conservative by construction: the exo-lyase step is required chemistry but rests on two eCAMI clusters, two KEGG orthologues and three bare families, the thinnest support in the route, so a genome with endo-lyase and the full intracellular trio but no recognisable exo-lyase is negative. Unsaturated glucuronyl hydrolase, EC 3.2.1.179, is not curated here: its Rhea reactions are on gellan and glycosaminoglycan substrates, not pectin, and EC 3.2.1.172 is rhamnogalacturonan chemistry, so neither supports a homogalacturonan claim.
113DBC-20260822-ECTOINE-DEGRADATION2026.22.12026-08-22T19:20ZgiftadditionbroadensEctoine degradation is curated as the ectoine-specific pair of ring hydrolysis and deacetylation, ending at L-2,4-diaminobutanoateECTOINE was an output-only anchor: gifter could say a genome makes ectoine and nothing about what happens to it. DoeA and DoeB are the committed, ectoine-specific steps of its catabolism and both carry single-reaction orthologues. The boundary is L-2,4-diaminobutanoate rather than L-aspartate 4-semialdehyde or L-aspartate, and the reason is structural rather than biological: the next step, DoeD, catalyses RHEA:11160, which ectoine_biosynthesis also uses in reverse, and K15785 was refused as an EctB alternative when that GIFT was curated because it does not establish the biosynthetic direction. Enzyme systems attach to reactions rather than to routes, so adding a DoeD system to RHEA:11160 would admit K15785 as evidence for the biosynthetic step as well and would silently reverse that refusal. Cutting where ectoine-specific chemistry ends is also the granularity rule applied normally: everything after the deacetylation is generic amino-acid chemistry.Rhea release 141 RHEA:52304 and RHEA:40951, both forward. KEGG K15783 doeA in 788 organisms and K15784 doeB in 573, verified 2026-08-22. KEGG module M00919 runs on to L-aspartate and is linked subset_of. K15785 doeD and K15786 doeC are deliberately not admitted; the register records what would unblock them.ectoine_degradation becomes callable and ECTOINE becomes a shared anchor, closing a mode-crossing loop with ectoine_biosynthesis through ASA and ECTOINE that the acyclicity check expects and permits. DABA is a new output-only anchor with no consumer yet, which is the honest state of the boundary rather than a gap in the route.
114DBC-20260822-HYDROXYECTOINE2026.22.12026-08-22T19:20ZgiftadditionbroadensEctoine hydroxylation to 5-hydroxyectoine is curated as a capability separate from ectoine biosynthesisThe compatible-solutes release excluded hydroxyectoine chemistry from the ectoine_biosynthesis boundary but did not refuse it as a capability. It earns its own GIFT rather than a fourth step of that route because 5-hydroxyectoine is a distinct compatible solute rather than a modified intermediate, and because only some ectoine producers encode EctD: folding it into the biosynthetic route would make every hydroxyectoine producer the same call as every ectoine producer. One reaction is a small GIFT, but it is the standard cut for this chemistry and the product boundary is a real change of identity, which is what the granularity rule asks for.Rhea release 141 RHEA:45740, forward, EC 1.14.11.55. KEGG K10674 ectD in 903 organisms, verified 2026-08-22. The 2-oxoglutarate co-substrate and its succinate product are internal chemistry and are not declared anchors, following the taurine dioxygenase and the cofactor-anchor rule.hydroxyectoine_biosynthesis becomes callable and consumes the ECTOINE anchor. A genome encoding EctABC without EctD is now distinguishable from one encoding both, which it was not before.
115DBC-20260822-LACTALDEHYDE-OXIDATION2026.22.12026-08-22T19:20ZgiftadditionbroadensLactaldehyde oxidation to (S)-lactate is curated as the second fate of the lactaldehyde branchpointLACTALDEHYDE has been an anchor since the SCFA release, with exactly one fate: reduction to propane-1,2-diol by FucO. That made it a branchpoint with one branch. Oxidation to (S)-lactate is the other, it is what fucose and rhamnose catabolism feed under aerobic conditions, and it connects the sugar layer to the organic acid layer through an anchor both already declare. It is a separate GIFT from lactate_formation rather than a second route of it because the input boundary differs: lactate_formation starts at pyruvate, and a genome can encode either without the other.Rhea release 141 RHEA:14277, forward, EC 1.2.1.22. KEGG K19266 in 59 organisms and K07248 aldA in 995, verified 2026-08-22. K07248 also carries EC 1.2.1.21 for glycolaldehyde; the specificity screen classifies that breadth as a promiscuous enzyme rather than an ambiguous orthologue, and the route input anchor states which substrate the GIFT is about, so it is admitted as an OR alternative on the same component.lactate_formation_lactaldehyde becomes callable, rhamnose_degradation and fucose_degradation_isomerase gain a second downstream capability through LACTALDEHYDE, and lactate_racemisation gains a third feeder beside lactate_formation and malolactic_fermentation.
116DBC-20260823-NCBIFAM-NAMESPACE2026.23.12026-08-23T10:00ZmarkeradditionnoneNCBIFAM is admitted as a marker namespace, and 53 equivalog-grade profiles join 25 enzyme components as OR alternatives beside the KEGG orthologs already thereNCBIfam grades every profile, and the equivalog grades assert that a family's members share one function - the property invariant 16 keeps asking for and the property a KEGG ortholog does not guarantee. Three rules bound the admission. Only equivalog and equivalog_domain profiles are admitted, and the grade is declared in each evidence row's notes and enforced by the compiler, because a subfamily or domain profile is the over-broad evidence invariant 16 refuses. Accessions carry the release version suffix, because the profile behind NF040708 is not necessarily the profile behind NF040708.3. And the release is additive: every profile joins a component that already accepts a marker, so no component became newly satisfiable and no route, system or component was added. Four candidate profiles that passed the grade filter were refused on biology rather than grade - the deferrochelatase TIGR01412.1, the MetX-like esterase NF005262.1, the self-declared uncertain TIGR01392.2, and the alternative-type oxepin-CoA hydrolase NF046063.1.NCBIfam release hmm_PGAP/20.0, retrieved 2026-08-23 from https://ftp.ncbi.nlm.nih.gov/hmm/current/hmm_PGAP.tsv, SHA-256 972f910ac7c54c6373e286c0d96dee71f643f9abd576a019bcb05ec7f5834b7b. The target reaction set is recomputed by data-raw/ncbifam_equivalog_screen.R against Rhea release 141: of 13,888 equivalog-grade profiles, 3,470 reach exactly one Rhea master, covering 1,302 masters, of which 93 are resolved by no single-reaction KO and 25 are reactions gifter curates. Per-profile readings and the four refusals are in inst/doc/proposal-ncbifam-namespace.md.No Boolean call changes for any marker set drawn from the namespaces already in the database, which is asserted by evaluating a battery of marker sets against the shipped database and against a copy with every NCBIFAM evidence row deleted. A genome annotated with NCBIfam accessions can now satisfy 25 components it previously could not, across assimilatory_sulfate_reduction, catechol_meta_cleavage, citrate_fermentation, corrin_ring_biosynthesis, enterobactin_biosynthesis, fucose_degradation_isomerase, glyoxylate_bypass, heme_b_biosynthesis, both methionine routes, oxoglutarate_to_succinate, purine_core_biosynthesis, serine_biosynthesis and thiamine_precursor_salvage.
117DBC-20260823-SIROHEME-TO-HEME-B2026.24.12026-08-23T14:30ZgiftadditionbroadensThe Ahb route from siroheme to heme b is curated as siroheme_to_heme_b, the first capability that depends on the NCBIFAM namespaceDatabase 2026.20.3 refused this GIFT and recorded its retrigger precisely: AhbA and AhbB are jointly required subunits of one decarboxylase and KEGG assigns both to K22225, so one observed gene could have satisfied two distinct required components. NF040708.3 and NF040707.3 separate them, and K22225 is admitted on neither component. The whole route was verified before curation rather than only the heterodimer: AhbC has the specific orthology K22226 and the equivalog TIGR04546.1, AhbD has K22227 and TIGR04545.1, and the terminal step has a second alternative in the peroxide-dependent HemQ reaction that heme_b_biosynthesis already curates, which KEGG M00847 admits as an alternative for the same step. The fused NirDL-like siroheme decarboxylase NF046668.3 is refused because it is domain-graded, so it cannot carry the one-function guarantee that admits this namespace at all. SIROHEME and HEME_B are both existing anchors, so the GIFT composes with siroheme_biosynthesis without a new boundary and 12,18-didecarboxysiroheme and Fe-coproporphyrin III stay internal.Rhea release 141 masters RHEA:19093, RHEA:37431 and RHEA:56520, forward in every route; KEGG module M00847, definition K22225 K22226 (K22227,K25033); MetaCyc PWY-7552 from the reconnaissance in inst/doc/proposal-metacyc-expansion.md; NCBIfam release hmm_PGAP/20.0 for NF040708.3, NF040707.3, TIGR04546.1 and TIGR04545.1, all equivalog-graded.siroheme_to_heme_b becomes callable on AhbA and AhbB together plus AhbC plus either AhbD or HemQ, and composes with siroheme_biosynthesis through the SIROHEME anchor, closing the graph path from UROGEN_III to HEME_B by the siroheme branch. AhbA alone does not complete the first reaction and no route completes without it. No existing GIFT changes: heme_b_biosynthesis keeps its boundaries and its seven routes, and RHEA:56516 gains a second route membership without gaining or losing evidence. The route requires an NCBIfam-emitting annotation, because no KEGG accession separates the two subunits.
118DBC-20260827-HISTIDINE-PHOSPHATASE-MARKERS2026.25.12026-08-27T09:00ZmarkeradditionbroadensNine NCBIfam equivalogs are admitted on the two histidine steps that orthology splits across unrelated familiesRHEA:14465, histidinol-phosphate phosphatase, is solved by at least three unrelated protein families and RHEA:22828 by two protein forms. The curated KO layer already carried five accessions for the first and three for the second and still under-called: over the 11908-genome reference set the best marker on the phosphatase reaches 22.8% of genomes and the best on the diphosphatase 38.7%, against a GIFT prevalence of 57.9%. Histidine is biomass-essential, so a capability curated for it that fires in three fifths of genomes is under-calling something.The phenotype validation layer measured it independently. Against strains observed to grow on chemically defined media supplying no histidine, histidine_biosynthesis scored recall 0.520 over 152 nutrient-level tests, and gifter's own trace named RHEA:14465 in 22 of 30 sampled failures and RHEA:22828 in 15 of 30. Actinomycetota dominate the failures on both halves of the benchmark, and TIGR02067.1 hisN is the actinobacterial solution to the phosphatase step. Every admitted profile is equivalog or equivalog_domain grade and declares the EC its reaction carries: 3.1.3.15 for RHEA:14465 and 3.6.1.31 for RHEA:22828, both verified against reaction_xrefs before curation. TIGR03188.1 was checked twice over: its source identifier names the hisI cyclohydrolase gene while its declared EC is the diphosphatase's, which is the fused HisIE naming and not a chemistry mismatch. Recorded in inst/doc/proposal-phenotype-curation-leads.md.histidine_biosynthesis gains marker coverage on two required reactions and no new route, reaction or system. No genome loses a call: every previously supported genome keeps every marker it matched. Genomes whose phosphatase or diphosphatase is one of the newly admitted families move from unsupported to supported, which is a broadening. The claim the GIFT makes is unchanged.
119DBC-20260827-GLCNAC-PTS-ROUTE2026.26.12026-08-27T13:00ZrouteadditionbroadensA second route into glcnac_degradation enters through the phosphoenolpyruvate-dependent PTS, so the capability no longer requires a cytoplasmic kinase most of its users do not encodeThe single curated route GLCNAC_KINASE required RHEA:17417, an ATP-dependent cytoplasmic N-acetylglucosamine kinase carried by 950 of the 11908 reference genomes, or 8.0 per cent, while the two reactions downstream of it reach 59.5 and 47.3 per cent. The gap is not an annotation gap. Most bacteria import N-acetylglucosamine through a PTS that phosphorylates it in transit, so they arrive at N-acetylglucosamine 6-phosphate having never needed the kinase, and the curated route asked them for an enzyme they genuinely do not encode. The boundaries were never wrong; the route inventory was incomplete. RHEA:49240 is the Rhea master for the group translocation, EC 2.7.1.193, and it is curated as the first reaction of a second route sharing the deacetylase and deaminase steps with the first. This is invariant 6 in its ordinary form: a non-homologous replacement for one step, represented at the route layer because the two entries are different reactions rather than different enzyme systems for one reaction.Prevalence over the 11908-genome reference set, from manuscript/analysis/output/gift-prevalence.tsv and the KO matrix behind it. The kinase orthology groups reach 1837 genomes and the N-acetylglucosamine-specific PTS enzyme II reaches 2929, of which 2180 carry no kinase at all. With the deacetylase and deaminase conjunction at 5090 genomes, the kinase route completes in 1532 and the PTS route in 2362, and their union is 3157. The phenotype validation layer found the same shortfall independently: glcnac_degradation scored recall 0.154 over 119 strains observed to use N-acetylglucosamine as a carbon source, the worst score of any tested capability, with RHEA:17417 named in 30 of 30 sampled failures. It was re-measured after curation, on a BacDive sweep that had meanwhile grown to 229 paired observations over 142 genera. Because both the database and the reference had moved, the before value was recomputed against the same enlarged test set rather than compared across two experiments: recall rises from 0.128 to 0.205, recovering 6 of the 78 observed-positive strains, and the permitted encoded-not-observed cell grows from 6 to 11, which is what a broadening looks like. gifter's own discovery screen had already flagged K02803 and K02804 as reaching an uncurated reaction adjacent to the GLCNAC anchor; the row is in data-raw/reference/discovery-candidates.tsv. Two alternatives were considered and refused, in inst/doc/proposal-phenotype-curation-leads.md: moving the input boundary to an N-acetylglucosamine 6-phosphate anchor, which would mint a boundary molecule for an internal intermediate, break the composition edge from chitin_degradation and leave a one-reaction kinase GIFT; and accepting the narrowed claim by downgrading the phenotype crosswalk rows, which would not have silenced the benchmark because subset_of is recall-usable, and would have required superset_of, discarding the 119 observations that found the problem.glcnac_degradation gains one route, one reaction, one enzyme system and one component. Its declared anchors, mode and name are unchanged, and GLCNAC stays compartment-unspecified because the two entries start on opposite sides of the membrane: the PTS substrate is extracellular, while the kinase also serves N-acetylglucosamine recovered from the cell's own peptidoglycan. No genome loses a call. Genomes whose entry is the PTS move from unsupported to supported, which is a broadening; measured over the 11908-genome reference set after rebuilding, prevalence rises from 1564 to 3189 genomes, 13.1 to 26.8 per cent. The remaining ceiling is the deacetylase and deaminase conjunction at 42.7 per cent, which no boundary choice could have moved and which the marker change released alongside this one is aimed at. No other GIFT is affected: RHEA:49240 belongs to no other route, and the deacetylase and deaminase rows are reused rather than duplicated.
120DBC-20260827-AMINO-SUGAR-NCBIFAM-MARKERS2026.26.12026-08-27T13:30ZmarkeradditionbroadensTen NCBIfam equivalogs are admitted on the three amino sugar steps orthology under-covers, including NF046059.1 nagB-II for a deaminase family K02564 does not nameRHEA:12172, glucosamine-6-phosphate deaminase, carries one curated orthology group reaching 47.3 per cent of the reference genomes, and RHEA:17417 carries three reaching 8.0 per cent at best. The deaminase is the more consequential of the two because it is the last step of both amino sugar capabilities: NagB-II is a structurally distinct deaminase family that K02564 does not cover, so a genome carrying only NagB-II fails a reaction it can perform. Six equivalog profiles reach RHEA:12172 and two reach RHEA:17417. The deacetylase between them, RHEA:22936, gains two more, so that the whole of both amino sugar routes is reachable in a genome annotated only against NCBIfam rather than only most of it.Every profile is equivalog grade, the stricter of the two the compiler admits, and every declared EC was checked against the reaction cross-reference before curating, as database 2026.25.1 did for the histidine markers: 3.5.99.6 for RHEA:12172 and 2.7.1.59 for RHEA:17417, both read from reaction_xrefs.tsv. Where NCBIfam supplies GO terms they agree, GO:0004342 for the deaminase and GO:0045127 for the kinase. The screen listing them is data-raw/reference/ncbifam-curated-reaction-gain.tsv and the admissions are recorded in data-raw/reference/ncbifam-curated-grades.tsv. Two profiles are taxonomically narrow, NF001682.0 for Caryophanales and NF041128.1 for Thermococcaceae, and are admitted on the same reasoning that admitted NF052359.1 in 2026.25.1: the restriction is the profile's own and not a claim gifter makes.glcnac_degradation and neuac_degradation gain marker coverage on shared required reactions, and no new route, reaction or system. No genome loses a call: every previously supported genome keeps every marker it matched. Genomes whose deaminase or kinase belongs to one of the newly admitted families move from unsupported to supported. The gain is not measurable on the KEGG-derived reference set, which reaches no NCBIfam profile, and that is itself worth stating: the benefit falls to users who annotate against NCBIfam.
121DBC-20260827-SERINE-GLYCINE-DIRECTION2026.27.12026-08-27T16:00ZanchorclarificationnoneGLYCINE is not declared as an input anchor of serine_biosynthesis, RHEA:15481 is not curated forward, and glycine_biosynthesis stays anabolic rather than becoming an interconversion GIFTSerine hydroxymethyltransferase is reversible and gifter curates RHEA:15481 reverse inside glycine_biosynthesis, so its forward direction was proposed as a second entry into SERINE. Three shapes were considered and all three are refused. A second route of serine_biosynthesis with GLYCINE as a second input anchor, and a separate directed GLYCINE to SERINE GIFT, both close a two-node cycle in the anabolic mode; that is invariant 8 and not invariant 6, because an alternative route is an alternative between a GIFT's declared boundaries and this one would change the boundary set, and because gift_anchors declares inputs per GIFT rather than per route the GIFT would claim to require glycine on the phosphorylated route and 3-phosphoglycerate on the glycine route. The interconversion exemption does not reach it: that exemption exists because an interconversion GIFT must declare every anchor in both roles and two adjacent ones therefore cycle by arithmetic, whereas both GIFTs here are anabolic and each asserts one direction, so the loop is a claim rather than an artefact. Making glycine_biosynthesis an interconversion GIFT is the third shape, it validates cleanly, and it is declined because it delivers no route into SERINE while trading away a directed claim that the phenotype layer scores at recall 0.974. The weakest boundary is not SERINE or GLYCINE but the one that is missing: RHEA:15481 forward consumes 5,10-methylenetetrahydrofolate, and gifter has no one-carbon anchor layer, which is the same obstacle that already defers the glycine cleavage system and refuses reductive glycine carbon fixation.Measured over the 11908-genome reference set of manuscript/analysis, through the KO layer that set can reach. Complete SER_PHOSPHORYLATED reaches 6716 genomes; K00600 reaches 11493, or 96.5 per cent, so the glycine entry would take the GIFT to 11569, a gain of 4853. Of that gain 3471 carry no complete glycine cleavage system, and gifter's only anabolic producer of GLYCINE is glycine_biosynthesis, whose input is SERINE. Of the 1288 genomes carrying no marker of any of the three phosphorylated steps, 1092 carry K00600, among them 118 of 118 Chlamydia, 55 Rickettsia and 43 Wolbachia, whose serine auxotrophy is the reason they are obligate. Against the phenotype benchmark, 84 of the 86 organisms observed to grow without serine and called unsupported carry K00600, so 84 would flip to supported - but only 9 of them carry a complete glycine cleavage system and only 3 carry it with formate-tetrahydrofolate ligase, so at most 9 would flip for a reason. The other 75 would flip on the near-universality of one marker, which is not the benchmark being satisfied but the trait ceasing to discriminate. Both refused shapes were run through validate_gifter_sources before this entry was written and both were rejected as Circular anabolic GIFT composition. The full record, including the mode change that validates, is inst/doc/proposal-phenotype-curation-leads.md section 2.No call changes. RHEA:15481 stays in exactly one route, GLY_SHMT, oriented reverse; GLYCINE stays an output of glycine_biosynthesis and sarcosine_demethylation and an input of glycine_reduction_stickland, and of nothing else; serine_biosynthesis keeps PG3 as its only input. Anyone promoting GLYCINE to an input of serine_biosynthesis, curating RHEA:15481 forward in an anabolic route, or converting glycine_biosynthesis to interconversion will find the database fails to build or a test failing, which is the point. The retrigger is the one-carbon anchor layer, not a direction decision: when methylenetetrahydrofolate and formate become boundaries this row is re-read together with the glycine cleavage system and reductive glycine fixation.
122DBC-20260827-PHOSPHOSERINE-TRANSAMINASE-ARCHAEAL2026.27.12026-08-27T16:30ZmarkeradditionbroadensK28205 is admitted as a second orthology group for RHEA:14329 with confidence ambiguous, the only marker the serine investigation found for the step that carries the shortfallRHEA:14329, phosphoserine aminotransferase, is named by gifter's own trace in 62 of the 86 organisms observed to grow on a defined medium supplying no serine and called unsupported. The NCBIfam screen offers no profile on it at any grade, so the namespace that closed the histidine steps cannot close this one. K28205 is the only other orthology group KEGG assigns to the reaction, and it is narrower than the curated K00831 rather than broader: KEGG gives it EC 2.6.1.52, GO:0004648 and the single reaction R04173, while K00831 also carries R05085, the pyridoxal phosphate transamination that plp_biosynthesis_dxp curates as RHEA:16573. It is admitted on COMP_14329_CATALYTIC only, so it evidences the serine reaction and not the vitamin B6 one. Confidence is ambiguous rather than curated because the evidence is genuinely contested: UniProt names the characterised member, Q5JDI4 TK1548, a probable serine--glyoxylate aminotransferase and gives it no EC, and the publication that founded the group is about phosphoglycolate removal in hyperthermophilic archaea. Both readings are class V aminotransferases. Under the weakest-confidence rule a genome whose only evidence for the step is K28205 gets an ambiguous call, which is the honest report of that state.KEGG orthology retrieved 2026-08-27; EC 2.6.1.52 checked against reaction_xrefs.tsv for RHEA:14329 before curating, as database 2026.25.1 did for the histidine markers. Prevalence over the 11908-genome reference set: K28205 reaches 50 genomes, all Thermococcales or Desulfurococcales. None of the 50 carries K00831 and 49 carry both serA and a curated phosphatase, so the step is the only one they appear to lack; adding the marker completes SER_PHOSPHORYLATED in 48 of them and takes the GIFT from 6716 to 6764 genomes. That co-occurrence argues for the admission and is deliberately not the basis of it, because gene neighbourhood and co-occurrence are the axis the deferral register records gifter as not having. One of the 86 benchmark failures is rescued. Two further KEGG orthology groups reaching RHEA:21208 were examined and refused in the same pass: K05518 rsbX and K07315 rsbU_P carry EC 3.1.3.3 because they dephosphorylate a phosphoserine residue on an anti-anti-sigma factor, not the free metabolite, and accepting them would have added 90 genomes, rescued none of the 86, and equated a stress-response protein phosphatase with metabolic phosphoserine phosphatase.serine_biosynthesis gains one marker on one existing required component, and no new route, reaction, system or component. No genome loses a call. Genomes whose phosphoserine aminotransferase is the archaeal group move from unsupported to supported at ambiguous confidence, which is a broadening; over the KO-reachable reference set that is 48 genomes, from 6716 to 6764. plp_biosynthesis_dxp is untouched: K28205 is not admitted on COMP_16573_CATALYTIC, and the two transamination reactions stay separately evidenced. The admission is reversible on one row if the archaeal enzyme's activity on O-phospho-L-serine is characterised the other way.
123DBC-20261002-LPT-APPARATUS2026.28.12026-10-02T11:29ZgiftadditionbroadensA structural GIFT now reports a complete canonical LptA--G lipopolysaccharide export apparatus as three jointly required machine functionsThe boundary follows the experimentally reconstituted machine: LptB/C/F/G extract lipopolysaccharide from the inner membrane, LptA forms the soluble bridge and LptD/E form the outer-membrane translocon. All seven proteins plus ATP were necessary and sufficient for membrane-to-membrane transport in the reconstituted system (PMID 29449493), so the Boolean architecture is a biological completeness claim rather than a co-occurrence checklist. It deliberately excludes precursor synthesis, MsbA, BAM, LptM, YedD and any inference of expression, transport in a sampled condition, permeability, viability or a generic diderm envelope. LptC remains required because the reported bypass uses particular LptF suppressor substitutions (PMID 36541759), which component-presence markers cannot resolve. LptE remains required in this canonical architecture; the LptE-independent Neisseria meningitidis result (PMID 21705335) cannot safely become a generic LptD-only system without evidence that distinguishes that context.KEGG REST records checked 2026-10-02 identify separate orthologies for LptA K09774, LptB K06861, LptC K11719, LptD K04744, LptE K03643, LptF K07091 and LptG K11720. In the 11,949-organism reference frame, 3,426 organisms carry all seven; all-but-one counts show that no single component is redundant evidence. Seventeen KEGG gene records carry both the LptF and LptG orthologies, so the ordinary component logic intentionally permits one gene to satisfy both roles. Eleven additional NCBIfam hmm_PGAP/20.0 profiles are admitted only where their grade is equivalog and their label is component-specific; combined LptF/LptG, broad LptA/LptD_N and Pfam-equivalent profiles are refused. Primary work supports LptM as a lineage-restricted maturation factor (PMID 37821449) and YedD as conditionally important for optimal transport (PMID 40127101), not as universal required components.The catalogue gains lpt_lipopolysaccharide_export_apparatus, one canonical architecture, three required functions, three systems and seven components. A genome completes it only when every LptA--G role is supported; deletion of any role makes the call incomplete, while a fused gene carrying both component-specific LptF and LptG evidence can support both permease roles. Existing GIFT calls do not change. The known LptE-independent Neisseria implementation is deliberately under-called and remains registered for a future context-resolving architecture.
124DBC-20261002-RIBITOL-WTA2026.29.12026-10-02T17:22ZgiftadditionbroadensPoly(ribitol-phosphate) wall teichoic acid becomes a structural GIFT with separate Staphylococcus-type and W23-type complete architecturesThe chemistry-specific public boundary avoids a generic wall-teichoic-acid claim and keeps the 168-type glycerol-phosphate polymer separate. Both ribitol architectures require the conserved undecaprenyl-linked linkage unit, UDP-ManNAc, CDP-glycerol and CDP-ribitol supply, TagG/TagH export and LCP-family attachment. The Staphylococcus architecture requires equivalog-resolved TarF plus TarL; the W23 architecture instead requires TarK plus TarL. TarL alone, donor synthesis alone, an exporter or a generic TagF-like profile cannot complete the GIFT. The two architectures are admitted through the standing biological-importance exception despite measured prevalence below 50 genomes; rarity changes curation priority, not the biological completeness contract.KEGG pathway map00552 and REST records K02851, K05946, K01791, K00980, K21285, K09692, K09693, K01005, K21030, K05352, K21592 and K18704 checked 2026-10-02; NCBIfam hmm_PGAP/20.0 equivalogs NF041712.1 and NF041713.1 at their curated gathering thresholds; exact reference-frame screen in data-raw/reference/wta-ncbifam-prevalence.tsv resolves 48 Staphylococcus-type and 22 W23-type complete architectures. Primary biochemistry supports bifunctional Staphylococcus TarL (PMID 18281399), separate W23 TarK priming and TarL elongation (PMID 21035733), TagB linkage priming (PMID 16150696), and substitutable LCP-family attachment (PMID 23935043). The boundary and refusals are recorded in inst/doc/proposal-structural-gifts.md section 5.4.The catalogue gains ribitol_phosphate_wall_teichoic_acid with two alternative architectures, eight distinct required functions, eight systems and fourteen component roles. The Staphylococcus architecture is callable only with NF041712.1 and NF041713.1 plus every shared role; its broader KO proxies are deliberately insufficient. The W23 architecture is callable only with both K21592 and K18704 plus every shared role. Existing GIFT calls do not change. K09809, NF016357.7 and NF041712.1 as evidence for the 168-type TagF polymerase remain refused, so poly(glycerol-phosphate) WTA remains deferred.
125DBC-20261002-GLC2DAG-LTA2026.30.12026-10-02T19:44ZgiftadditionbroadensDiglucosyldiacylglycerol-anchored poly(glycerol-phosphate) lipoteichoic acid becomes a structural GIFT with one three-function architectureA broad lipoteichoic-acid or type-I-LTA claim would exceed the audited evidence: LTA anchor chemistry varies, Listeria requires an LtaP primase before LtaS elongation, Bacillus carries several LtaS-family paralogues and other LTA types use different chemistry. The admitted boundary instead names the structure established by the Staphylococcus-type pathway. YpfP/UgtP-family processive glycosylation makes the diglucosyldiacylglycerol anchor, LtaA flips that anchor and LtaS polymerizes the glycerol-phosphate chain. All three functions are required. Residual diacylglycerol-anchored polymer after ypfP loss is outside the named structure rather than an alternative that weakens anchor synthesis. Dlt-dependent D-alanylation, glycosylation, regulation and phenotype are excluded.Primary evidence: the Staphylococcus glycolipid-anchor pathway (PMID 17209021), residual diacylglycerol-anchored LTA after ypfP loss (PMID 17640274), LtaS polymer synthesis (PMID 17483484) and LtaA anchor transport (PMID 32367070). NCBIfam hmm_PGAP/20.0 equivalogs NF010134.0, NF047396.1 and NF053595.1 were checked at their gathering thresholds. A targeted screen found 127 complete profile sets among 128 downloadable proteomes from the K03429/K19005 proxy intersection; the unexpected Sulfitobacter donghicola match was retained because all three profiles pass and taxonomy cannot negate marker evidence. K03429 and K19005 remain uncurated proxies. The Listeria LtaP/LtaS architecture (PMID 19682249; PMID 25128528) remains deferred because no admitted profile separates its complete primase-dependent design and anchor inventory. Full audit in inst/doc/proposal-structural-gifts.md section 5.4 and data-raw/reference/lta-peptidoglycan-marker-audit.tsv.The catalogue gains diglucosyl_diacylglycerol_anchored_lipoteichoic_acid with one architecture, three required functions, three one-component systems and three equivalog-grade NCBIfam markers. A genome completes the GIFT only with NF010134.0, NF047396.1 and NF053595.1; removing any role makes the call incomplete. No KO alone can fire it, no existing GIFT changes, and the result neither claims all LTA nor calls expression, assembly in a condition, envelope integrity, susceptibility, virulence or phenotype. Broad LTA, Listeria-type LTA, Bacillus alternatives, non-type-I LTA and the peptidoglycan sacculus remain deferred.
126DBC-20261003-SECRETION-SYSTEMS2026.31.12026-10-03T05:40ZgiftadditionbroadensType VI secretion and the non-flagellar type III secretion injectisome become structural GIFTs with one curated architecture eachBoth candidates had been deferred on the argument that an unordered marker set cannot distinguish one secretion machine from its homologues, and that system identity therefore requires gene-cluster context. The 2026-10-03 screen tests that argument instead of assuming it, and it does not hold for these two architectures. KEGG and NCBIfam both carry system-specific accessions for every required role, so the injectisome export apparatus is identified by injectisome-specific accessions rather than by flagellar FliP/Q/R, FlhA, FlhB and FliI; the three flagellated controls that encode neither machine support no role of either architecture, and 4,399 genomes complete the flagellar export apparatus without supporting any injectisome role. Completeness remains an unordered Boolean over the required functions: no row asserts that the components lie in one locus, and the curated architecture is what makes a role set a machine. Two roles are deliberately accessory or excluded because their markers do not reach systems that demonstrably build the machine: TssJ, absent from the Agrobacterium and Acinetobacter reference genomes, and the SctL stator, which no accepted accession reaches in the Inv-Mxi-Spa and Esc families. The Francisella-type and Bacteroidota-type type VI apparatuses, chlamydial and rhizobial injectisomes and Ralstonia-type HrpY pili are explicit under-calls rather than negatives.KEGG REST records for 38 orthologies checked 2026-10-03; NCBIfam hmm_PGAP/20.0 equivalog and equivalog_domain profiles at their curated gathering thresholds. Primary evidence: the contractile sheath and its dynamics (PMID 22367545), ClpV-dependent sheath remodelling as crucial for secretion (PMID 19131969), TssA priming and coordination of tube and sheath polymerisation (PMID 26909579), an active Acinetobacter apparatus whose secretion depends on TssM (PMID 23365692), injectisome assembly and composition (PMID 24484471), the in situ Salmonella machine and its sorting platform (PMID 28283062), and the shared ancestry that makes marker specificity the whole question (PMID 23028376). The frame screen, role inventory, KO-versus-equivalog audit and 17 named reference-strain controls are retained in data-raw/reference/secretion-system-prevalence.tsv, secretion-system-roles.tsv, secretion-system-marker-audit.tsv and secretion-system-controls.tsv, reproducible through data-raw/secretion_system_prevalence.R. The boundary, refusals and under-calls are recorded in inst/doc/proposal-structural-gifts.md section 7.The catalogue gains type_vi_secretion_apparatus with eight functions, seven of them required, and type_iii_secretion_injectisome with seven required functions. In the 11,908-genome reference frame 1,701 genomes complete the type VI architecture and 344 the injectisome. No existing GIFT changes: flagellar_apparatus keeps its own accessions, and no injectisome accession is accepted for it. K11918 is refused as TssJ evidence, no marker alone fires either GIFT, and a positive call claims encoded machinery only, never expression, firing, an effector, a target, antagonism, virulence or any other phenotype.
127DBC-20261003-ARCHAELLUM2026.32.12026-10-03T05:45ZgiftadditionbroadensThe archaellum becomes a structural GIFT with one core architecture of five required functions and two lineage-restricted accessory functionsThe archaellum is the motility machine of most motile archaea and is unrelated to the bacterial flagellum, so flagellar_apparatus cannot report it. The required inventory is the one the Methanococcus maripaludis and Sulfolobus acidocaldarius deletion series share: archaellin, a class III signal peptidase, the FlaF/FlaG stator, the FlaI/FlaH motor and the FlaJ platform. The homology with archaeal type IV pili was measured, not assumed: the FlaI and FlaJ orthologies also collect pilus and bindosome ATPases and platforms, so they are accepted only inside the conjunction and at putative confidence, and the call rests on the machine-specific archaellin, FlaF, FlaG and FlaH. The euryarchaeal FlaC/D/E switch complex is required for archaellation in M. maripaludis but absent from Methanomicrobiales, most Methanosarcinales and every crenarchaeal and thaumarchaeal locus, and the crenarchaeal FlaX ring has no KEGG orthology; requiring either would measure lineage or annotation, so both are accessory. The peptidase is a shared component: PibD also processes type IV pilins, so the function is required for assembly and contributes no specificity.KEGG REST definitions for 13 orthologies re-checked 2026-10-03 and unchanged since 2026-08-22. Every one of 5,093 KO-assigned proteins in the frame was searched with the NCBIfam hmm_PGAP/20.0 archaellum equivalogs and with pilus, bindosome and Pfam contrast profiles at their gathering thresholds: 268 of 885 K07332 proteins in archaellum-encoding archaea pass the FlaI equivalog, 252 of those 256 genomes carry one, and only 33 of 192 archaea lacking the core carry one, 20 of them missing only the FlaF orthology. K07325 proteins match the archaeal-type flagellin family and never the bacterial FlgA chaperone family. K07991 collects the pilin-specific EppA beside FlaK in all 22 archaellum-encoding Methanococcales. Primary evidence: M. maripaludis fla deletions (PMID 17887963), the S. acidocaldarius fla deletions (PMID 22081969), FlaK essential for flagellation (PMID 14622420), PibD substrate breadth (PMID 12813086), FlaK versus EppA substrates (PMID 17114255), the ArlF/ArlG stator (PMID 34912317), the ArlCDE switch complex (PMID 32416640), the archaellum name (PMID 22613456), the arl gene names (PMID 29912330) and a functional archaellum in Chloroflexota with PibD or PilD as its peptidase (PMID 40962902, PMID 42388304). Aggregates are in data-raw/reference/archaellum-*.tsv, reproducible through data-raw/archaellum_ncbifam_prevalence.R; the decision is in inst/doc/proposal-structural-gifts.md section 6.1.The catalogue gains archaellum. In the KEGG reference frame 253 of 470 archaea and 2 of 10,143 bacteria, both Chloroflexota, complete it; 25 archaea are one function short, 17 of them on the stator. KO-only calls report putative evidence confidence because FlaI and FlaJ rest on putative orthologies, and NCBIfam equivalogs raise it to high-confidence. No combination of FlaI, FlaJ and a peptidase fires the GIFT, archaellum markers support no flagellar_apparatus or type_iva_pilus function, and K02654 is now shared between the type IVa pilus and the bacterial archaellum peptidase without changing any type IVa call. A positive call claims encoded assembly machinery only, never swimming, taxis, rotation direction or expression.
128DBC-20261003-T2SS2026.33.12026-10-03T06:58ZgiftadditionbroadensThe type II secretion system becomes a structural GIFT, and the shared-component rule it waited on is settledThe candidate was deferred because its class III prepilin peptidase is not a homologue of the type IVa pilus peptidase but the same enzyme, and KEGG files most of them under PilD rather than GspO. That is a shared component, not an ambiguous marker: the protein genuinely performs both jobs, so no genome is called positive for machinery it does not encode. The accession is therefore accepted on this GIFT and on type_iva_pilus, the function it supports contributes no specificity to either, and the apparatus is identified by its other four functions. The curated architecture follows the four real subassemblies plus maturation: GspD secretin, GspC/F/L/M inner-membrane platform, GspE ATPase, GspG/H/I/J/K pseudopilus and the peptidase. GspC is retained as required despite being the weakest marker in the inventory, because it is biologically required and its misses are spread across 108 genera rather than blinding a clade; making it accessory would use required=0 for inconvenient evidence. The GspS pilotin, GspN, GspAB and every secreted substrate are outside the claim.KEGG REST records K02452-K02462, K02464 and K02654 checked 2026-10-03; eleven equivalog-grade NCBIfam hmm_PGAP/20.0 profiles at their curated gathering thresholds. Primary evidence: the apparatus architecture and subassemblies (PMID 22466878), one peptidase processing both pilins and pseudopilins (PMID 1309616), minor pseudopilin priming of pseudopilus elongation (PMID 22157749) and platform interactions in the pullulanase secreton (PMID 10735856). Screen in data-raw/t2ss_prevalence.R with results in data-raw/reference/t2ss-prevalence.tsv, t2ss-roles.tsv and t2ss-controls.tsv: 1,536 of 11,908 prokaryotic frame genomes complete the architecture across 319 genera; 703 complete it without completing the type IVa pilus and 674 complete the pilus without it, so the two machines separate. Of twelve named control strains, five expected systems complete, three expected negatives are correctly incomplete, and the two remaining expected positives are explained -- Legionella pneumophila lacks a GspC marker, and Vibrio cholerae N16961 lacks a GspD marker because its epsD region carries an authentic frameshift, so the incomplete call reports a disrupted secretin. The boundary and the rule are recorded in inst/doc/proposal-structural-gifts.md section 8 and inst/doc/architecture.md.The catalogue gains type_ii_secretion_system with one architecture, five required functions, five systems and twelve component roles. K02654 now serves components of three GIFTs and is the only accession that crosses structural GIFTs; a test requires any two GIFTs sharing a component accession to each require a function the other does not. No existing GIFT changes: type_iva_pilus and archaellum keep their inventories and their calls. No marker alone fires the GIFT, and a positive call claims encoded machinery only, never expression, assembly, secretion, a substrate, polymer degradation, host colonisation or virulence.
129DBC-20261003-FRAME-LABEL2026.33.22026-10-03T09:20ZschemaclarificationnoneThe biomass_essential_anabolism preset label is capitalised as Biomass-essential anabolic GIFTsEvery other named reference frame carries a sentence-case display label; this one alone began in lower case, which made it read as a fragment in the atlas and in any preset-labelled output.reference_frames.tsv labels of the nineteen presets in database release 2026.33.1.Display label only. No frame membership, boundedness, filter, metric, GIFT or Boolean call changes. The default frame set built by the package keeps its own lower-case label, so default trait outputs are unchanged; reference_frame(preset = biomass_essential_anabolism) now reports the capitalised label.
130DBC-20261003-GIFT-EVIDENCE2026.34.12026-10-03T12:10ZschemaadditionnoneEvery GIFT now records the curation documents, analysis scripts and result tables behind its definition, linked to the source repositoryThe atlas showed what a GIFT is but not where it was worked out, so a reader could not open the proposal that defends a boundary, the R code run to decide it, or the table that code wrote. That trail existed only in the catalogue-expansion attempt log, outside the database. Recording it in the database keeps it versioned with the definitions it explains and lets the atlas and the R API link each file at the release commit.inst/doc/catalogue-expansion-attempts.tsv implemented_gifts and source columns; data-raw/reference/README.md for which script regenerates each result table; SOURCES.md for the five initial nucleotide GIFTs.No GIFT, route, architecture, circuit, mechanism, marker or Boolean call changes. Schema version 8 adds gift_evidence (188 rows covering all 160 GIFTs: 162 curation documents, 5 analysis scripts, 21 result tables) and database_release.source_repository. get_gift_evidence() reads it, and each atlas GIFT page lists it with links.
131DBC-20261004-SERINE-CHEMORECEPTION2026.35.12026-10-04T02:09ZgiftadditionbroadensTsr-equivalog serine chemoreception becomes a regulatory GIFTA receptor with ligand-resolving evidence can be combined with the existing complete chemotaxis circuit without claiming taxis as a phenotype. KO K05874 names Tsr but collects paralogues and is retained only for the broad receptor function.NCBIfam hmm_PGAP/20.0 equivalogs NF011615.0 and NF011622.0; UniProt P02942 for characterised Tsr; KEGG K05874 receptor assignments; inst/doc/proposal-regulatory-defense-expansion.md.Adds one circuit with a Tsr-specific reception role and three reused downstream functions. Only NF011615.0 plus the full circuit supports serine_chemoreception; K05874, a generic MCP or Tar alone does not. NF011615.0 now also supports the core receptor function, so an NCBIfam-only Tsr annotation with the remaining chemotaxis functions completes both core and serine calls. Existing KO-based chemotaxis and aspartate calls do not change.
132DBC-20261004-ANTIMICROBIAL-DETOX2026.35.12026-10-04T02:09ZgiftadditionbroadensBeta-lactam hydrolysis and chloramphenicol acetylation become defense GIFTsBoth convert the challenge chemical and fit chemical_detoxification. The beta-lactam mechanism has four Ambler-class alternative systems; the chloramphenicol mechanism has type A and type B CAT alternatives. Neither claims susceptibility, drug spectrum or enzyme activity in a particular environment.Rhea masters RHEA:20401 and RHEA:18421; KEGG EC 3.5.2.6 and EC 2.3.1.28 orthologies; the 66 plus two accessions in data-raw/reference/ko-reaction-specificity.tsv; inst/doc/proposal-antimicrobial-detoxification.md and inst/doc/proposal-regulatory-defense-expansion.md.Adds two defense GIFTs with 68 enzyme-specific KO markers. A class-specific beta-lactamase or either CAT suffices for its own hydrolysis or acetylation mechanism. Generic metallo-beta-lactamase fold, target alteration, drug efflux and antimicrobial-resistance outcome remain refused. Existing calls do not change.
133DBC-20261004-CHALLENGE-CLASS2026.35.12026-10-04T02:09ZgiftadditionnoneChallenge class separates the target of a defense mechanism from how it worksChemical detoxification now spans metals, reactive oxygen, electrophiles and antimicrobial compounds. The existing defense_class names conversion; a separate facet names the challenge without changing the mechanism or creating an outcome claim.inst/doc/proposal-antimicrobial-detoxification.md section 11.2; inst/doc/proposal-regulatory-defense-expansion.md.Five defense GIFTs carry challenge_class metadata: the two new antimicrobial GIFTs and existing mercury, superoxide and methylglyoxal detoxification. No Boolean calls change because of the facet.
134DBC-20261004-CRISPR-CLASS-DEFINITION2026.35.22026-10-04T03:51ZgiftclarificationnoneCRISPR-Cas defense class definition matches the machinery-only claimThe prior defense_class definition described recognition through stored spacers, which could imply an array and guide RNA that the curated type I-E protein-marker GIFT cannot evidence. The class identifies the CRISPR-Cas mechanism family, while the GIFT claims only encoded machinery.inst/doc/proposal-defense-gifts.md, Curated, narrowed: type I-E CRISPR-Cas machinery; inst/extdata/database-source/SOURCES.md, Regulatory and defense content; Brouns et al. 2008, Science 321:960-964, doi:10.1126/science.1159689.The crispr_cas facet term now states that classification alone does not establish an array, guide RNA or interference. Its assignment to type_i_e_crispr_cas_machinery, all marker evidence, completeness logic and Boolean calls are unchanged.
135DBC-20261004-ACYL-CARRIER-COMPARTMENT2026.36.12026-10-04T04:33ZanchorclarificationnoneFour CoA and acyl-carrier thioester boundaries are declared cytoplasmicThe curated routes use acetyl-CoA, pimeloyl-CoA or pimeloyl-ACP, 3-oxoadipyl-CoA and succinyl-CoA as activated intracellular carriers. CoA is highly charged, and experimental supplementation of E. coli CoA-biosynthesis mutants did not deliver extracellular CoA or dephospho-CoA across the membrane. ACP was localized to the E. coli cytoplasm. This supports the location of these curated boundaries without reading localisation from KO or EC markers. The claim is confined to the attached routes; it does not assert that these molecules can never occur outside a cell or that every charged metabolite is cytoplasmic.Balibar et al. 2011, J Bacteriol 193:3304-3312, PMID 21551303; Jackowski et al. 1985, J Bacteriol 162:5-8, PMID 3884600; inst/extdata/database-source/SOURCES.md, Intracellular activated-carrier boundaries.ACETYL_COA, PIMELOYL_COA, OXOADIPYL_COA and SUCCINYL_COA change from unspecified to cytoplasmic. Eleven existing metabolic GIFTs use these anchors; their Boolean calls, reaction routes and same-anchor composition edges do not change. These anchors remain unable to license a cross-genome handoff. No extracellular variant or transport GIFT is created.
136DBC-20261004-SERINE-DEAMINATION-SYSTEMS2026.37.12026-10-04T11:41Zenzyme_systemcorrectionmixedSerine deamination requires a complete single-chain enzyme or both split SdaAA and SdaAB subunitsKEGG K01752 is assigned both to complete E. coli single-chain serine dehydratases and to each of the B. subtilis split subunits; one K01752 marker therefore cannot prove the whole enzyme. NCBIfam equivalogs TIGR00718.1, TIGR00719.1 and TIGR00720.1 distinguish alpha, beta and single-chain architectures at published gathering thresholds. A stratified 122-genome audit of 257 K01752-assigned proteins retained 120 genomes on the audited proteins or K17989 and exposed two with incomplete profile evidence. K17989 remains a separate single-protein alternative. The reaction and SERINE to PYRUVATE boundaries do not change.inst/doc/assessment-serine-deamination-revision.md; data-raw/serine_deamination_marker_audit.py; data-raw/reference/serine-deamination-gene-audit.tsv; data-raw/reference/serine-deamination-genome-audit.tsv; KEGG K01752 and NCBIfam hmm_PGAP/20.0, retrieved 2026-10-04.Retires K01752 as completing evidence, adds a TIGR00720.1 single-chain system and an AND-of-TIGR00718.1-and-TIGR00719.1 split system, and keeps K17989 as its own system. KO-only K01752 calls are lost unless K17989 is present; NCBIfam-annotated single-chain or complete split enzymes can now make calls. The full-frame mixed-input call delta was not measured; no activity or phenotype is inferred.
137DBC-20261004-REFERENCE-VERIFICATION2026.38.12026-10-04T16:32ZschemaadditionnoneSchema 9 pins Rhea, ChEBI and KEGG records and checks the source tables against themThe validator proved that the tables agreed with each other and nothing more, so a plausible but wrong accession, a Rhea identifier that was not a master, or an anchor on the wrong side of its route compiled as curated content. An audit of the shipped tables against the live resources found no invented identifier but did find wrong identifiers of exactly that kind.inst/extdata/reference-snapshot/MANIFEST.tsv; data-raw/reference_snapshot.R; Rhea release 142 and ChEBI release 254, retrieved 2026-10-04. inst/doc/architecture.md.Adds reactions.equation and anchors.chebi_name, imported from the snapshot; reaction_xrefs.notes; basis and reference on the four marker-evidence tables; route_chemistry_exceptions; and gift_reviews, which is written by a human reviewer and starts empty. Closes the confidence and evidence_type vocabularies. Moves the pins to Rhea 142 and ChEBI 254. No call changes.
138DBC-20261004-RHEA-MASTER-IDS2026.38.12026-10-04T16:32ZreactioncorrectionnoneThree reactions keyed by a bidirectional Rhea identifier now use the masterRHEA:55543, RHEA:18136 and RHEA:13804 are the bidirectional forms of masters RHEA:55540, RHEA:18133 and RHEA:13801. Invariant 4 identifies a reaction by its master and stores direction in the route. The repair was deferred until a release that could move the foreign keys, and the reference check now refuses a non-master.inst/extdata/reference-snapshot/rhea-reactions.tsv; inst/doc/proposal-ncbifam-discovery.md section 4.6.reaction_id and rhea_master change in reactions.tsv and the keys follow in reaction_xrefs, route_reactions and enzyme_systems. A bidirectional identifier reads the same way as its master, so no orientation changes. System and component identifiers keep the old number because they are stable public keys. No call changes.
139DBC-20261004-ROUTE-ORIENTATION2026.38.12026-10-04T16:32ZroutecorrectionnoneFour route steps were oriented against the direction the route runsThe reference check reads each step on the side of the Rhea master equation its orientation selects. RHEA:17845 in RIBOFLAVIN_GTP, RHEA:16233 in PANTOTHENATE_PANBCDE, RHEA:15009 in FOLATE_THF and RHEA:12733 in NAMN_NADC were curated forward although the master is written in the opposite direction, so each route consumed its own product at that step.inst/extdata/reference-snapshot/rhea-participants.tsv.The four steps are now reverse. Orientation is descriptive and does not enter evaluation, so no call changes; the atlas and get_gift_reactions() now show the correct direction.
140DBC-20261004-ANCHOR-CHEBI-FORMS2026.38.12026-10-04T16:32ZanchorcorrectionnoneSixteen anchors now carry the ChEBI entity Rhea writes at pH 7.3An anchor is a boundary claim about a route, and the claim is checkable only if the anchor names the entity the route reactions name. Thirteen anchors used a neutral or differently protonated entity that Rhea maps to another identifier, and three more, QUINOLINATE, COBYRINATE_DIAMIDE and TMP, used an entity Rhea does not write at all. For thirteen ChEBI relates the old and new entity directly by protonation. For GTP, TMP and QUINOLINATE it records no single identity step between them, and the new entity is chosen because it is the one the route reactions name.inst/extdata/reference-snapshot/chebi-compounds.tsv; Rhea chebi_pH7_3_mapping.tsv.chebi_id changes for AIR, BIOTIN, CHORISMATE, COBYRINATE_DIAMIDE, DXP, E4P, FMNH2, GTP, NAD, PLP, QUINOLINATE, RIBOFLAVIN, RIBULOSE_5P, THF, TMP, UROGEN_III. anchor_id, molecule and name are unchanged, so composition and every call are unchanged. data-raw/reference/chebi-anchor-aliases.tsv is regenerated: thirteen previous identifiers are now derived aliases of their anchor, and those of GTP, TMP and QUINOLINATE are not.
141DBC-20261004-REACTION-XREFS2026.38.12026-10-04T16:32ZreactioncorrectionnoneReaction cross-references that Rhea does not record are corrected, removed or explainedThirty cross-references on Rhea-mastered reactions were absent from the mapping Rhea publishes for the master. Seven named a different or partial KEGG reaction, among them R01818, mannose-6-phosphate phosphomutase, on 4-amino-4-deoxychorismate lyase. Five EC numbers were neither in Rhea nor assigned by KEGG to any accepted orthologue, so nothing checkable supported them. The remaining eighteen are assigned by KEGG to an accepted orthologue and are kept with that reason recorded.inst/extdata/reference-snapshot/rhea-xrefs.tsv; KEGG reaction and orthology links retrieved 2026-10-04.R00006, R01818, R00428, R10712, R05681, R00277 and R07302 are replaced by the KEGG reaction Rhea maps. EC 4.2.1.55 on RHEA:26558, 2.8.3.8 on RHEA:30071, 1.7.99.- on RHEA:21068, 1.1.1.35 on RHEA:34851 and 2.6.1.- on RHEA:25315 are removed. Eighteen kept cross-references carry a note. Cross-references do not enter evaluation, so no call changes.
142DBC-20261004-UNSUPPORTED-MARKER-CONFIDENCE2026.38.12026-10-04T16:32ZmarkercorrectionnoneThirty KO assignments with no checkable support are reported as putativeFor a KO on an enzyme component, support is derived rather than asserted: KEGG links the orthologue to the reaction, or assigns it an EC number the reaction carries, or places it in a module the GIFT cross-references. Thirty rows have none of these and cite no publication or result table, yet were recorded as curated or high-confidence with the same provenance string as rows KEGG does support. They include transporter subunits and maturation proteins that KEGG does not link to reactions, and assignments KEGG does not make, such as K16838 on 5-hydroxyisourate hydrolase and K00826 on the tyrosine and phenylalanine aminotransferase reactions.inst/extdata/database-source/component_markers.tsv basis column; KEGG orthology links retrieved 2026-10-04.Confidence becomes putative on the thirty rows. Markers are neither added nor removed, so no Boolean call changes; evidence_confidence falls to putative where one of these rows is the best evidence for a component. A row regains its confidence when a PMID, DOI or result table is recorded in reference.
143DBC-20261004-ROUTE-CHEMISTRY-EXCEPTIONS2026.38.12026-10-04T16:32ZrouteclarificationnoneTwenty-five places where a route does not literally reach its anchors or chain in Rhea are recordedRhea writes some reactions on an anomer, a tautomer, a stereo-unspecified parent or the reduced member of a redox couple, some routes rely on a non-enzymatic step, and some leave a conversion out. Each was implicit in the choice of reactions. Two are not form differences and need curation: MK_FUTALOSINE joins 1,4-dihydroxy-6-naphthoate to a prenyltransferase written on 1,4-dihydroxy-2-naphthoate, and CORRIN_ANAEROBIC joins cobalt-factor and cobalt-precorrin reactions that differ in oxidation state.inst/extdata/database-source/route_chemistry_exceptions.tsv; inst/extdata/reference-snapshot/rhea-participants.tsv.Adds route_chemistry_exceptions rows for twenty-two routes. The rationales were written during this change and have not been reviewed by a curator. No call changes.
144DBC-20261004-FAMILY-MARKER-BASIS2026.39.12026-10-04T17:39ZmarkercorrectionnoneNCBIfam and CAZy assignments are checked against their own releases, and eight with no matching EC number are reported as putativeThe basis derivation covered KO markers only. The pinned NCBIfam release and the committed dbCAN tables state which EC numbers a profile, a family or a subfamily carries, so the same comparison with the reaction is available for 604 further assignments. 594 match. Nine dbCAN subfamilies on the fucosidase component carry the linkage-specific EC 3.2.1.63 or 3.2.1.111 while RXN_MUCIN_FUCOSE_RELEASE records only the general EC 3.2.1.51, and the AhbC profile TIGR04546.1 has no EC number in the release.data-raw/reference/marker-links.tsv; data-raw/reference/cazy-subfamily-ec.tsv; data-raw/reference/fam-substrate-mapping.tsv; inst/extdata/reference-snapshot/marker-accessions.tsv; NCBIfam hmm_PGAP/20.0.Seven GH29 and GH95 subfamily rows and TIGR04546.1 fall from high-confidence to putative; two fucosidase rows were already ambiguous. All 145 declared NCBIfam grades match the release. Markers are neither added nor removed, so no Boolean call changes; evidence_confidence can fall to putative for mucin_fucose_release, and for siroheme_to_heme_b only where the profile is the sole evidence for AhbC.
change_gift474 rows · 2 columns
change_pkgift_pk
2135
2141
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8136
637
91
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database_release1 rows · 9 columns
release_pkgifter_db_versionschema_versionbuild_daterhea_releasechebi_releasekegg_releasesource_commitsource_repository
12026.39.192026-10-041422542026-10-04unreleasedhttps://github.com/alberdilab/gifter
gift_evidence203 rows · 4 columns
gift_pkevidence_kindlocationdescription
38curation_documentinst/doc/proposal-scfa-biosynthesis.mdCuration proposal: short-chain fatty acid formation GIFTs
48curation_documentinst/doc/proposal-organic-acid-formation.mdCuration proposal: organic acid formation GIFTs
69curation_documentinst/doc/proposal-central-metabolic-cycles.mdDesign proposal: circular central metabolism and higher-order metabolic topology
2curation_documentinst/extdata/database-source/SOURCES.mdReference database provenance: the KEGG modules and Rhea reactions the initial nucleotide GIFTs were curated from, and the boundary choices against them
103curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
77curation_documentinst/doc/proposal-nitrogen-compound-catabolism.mdCuration proposal: nitrogen compound catabolism GIFTs
89curation_documentinst/doc/proposal-nitrogen-compound-catabolism.mdCuration proposal: nitrogen compound catabolism GIFTs
91curation_documentinst/doc/proposal-aromatic-degradation.mdCuration proposal: aromatic compound degradation and mercury detoxification GIFTs
16curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
25curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
27curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
159curation_documentinst/doc/deferral-register.mdDeferral register entry recording the earlier blocker and what lifted it
159curation_documentinst/doc/proposal-structural-gifts.mdStructural GIFTs: curated content, refusals, and open questions
159analysis_scriptdata-raw/archaellum_ncbifam_prevalence.RExact KO/NCBIfam screen for the archaellum structural GIFT
159result_tabledata-raw/reference/archaellum-accessory.tsvSupport for the lineage-restricted accessory functions among complete archaellum genomes
159result_tabledata-raw/reference/archaellum-controls.tsvNamed reference genomes evaluated with evaluate_gifts() against what each is established to encode
159result_tabledata-raw/reference/archaellum-ko-ncbifam-agreement.tsvKO-assigned proteins and genomes by orthology and best-scoring archaellum or contrast profile
159result_tabledata-raw/reference/archaellum-ncbifam-profiles.tsvCandidate NCBIfam equivalogs and contrast profiles, with grade and taxonomic range
159result_tabledata-raw/reference/archaellum-one-short.tsvGenomes exactly one function short of a complete archaellum, by missing function and lineage
159result_tabledata-raw/reference/archaellum-prevalence.tsvComplete archaellum architectures over the archaeal and bacterial genomes of the KEGG frame
159result_tabledata-raw/reference/archaellum-role-agreement.tsvGenomes in which a KO-assigned protein passes each archaellum role equivalog
119curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
120curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
105curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
104curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
33curation_documentinst/doc/proposal-regulatory-gifts.mdRegulatory GIFTs: curated content, refusals, and open questions
8curation_documentinst/doc/proposal-amino-acid-biosynthesis.mdCuration proposal: serine, threonine, cysteine and methionine GIFTs
134curation_documentinst/doc/proposal-next-gift-release.mdCuration proposal: next coherent GIFT release
90curation_documentinst/doc/proposal-aromatic-degradation.mdCuration proposal: aromatic compound degradation and mercury detoxification GIFTs
80curation_documentinst/doc/proposal-nitrogen-compound-catabolism.mdCuration proposal: nitrogen compound catabolism GIFTs
59curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
39curation_documentinst/doc/proposal-scfa-biosynthesis.mdCuration proposal: short-chain fatty acid formation GIFTs
83curation_documentinst/doc/proposal-nitrogen-compound-catabolism.mdCuration proposal: nitrogen compound catabolism GIFTs
84curation_documentinst/doc/proposal-nitrogen-compound-catabolism.mdCuration proposal: nitrogen compound catabolism GIFTs
96curation_documentinst/doc/proposal-aromatic-degradation.mdCuration proposal: aromatic compound degradation and mercury detoxification GIFTs
93curation_documentinst/doc/proposal-aromatic-degradation.mdCuration proposal: aromatic compound degradation and mercury detoxification GIFTs
32curation_documentinst/doc/proposal-regulatory-gifts.mdRegulatory GIFTs: curated content, refusals, and open questions
143curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
141curation_documentinst/doc/proposal-compatible-solutes-heme-enterobactin-detoxification.mdProposal: compatible-solute and heme biosynthesis, enterobactin assembly
73curation_documentinst/doc/proposal-shikimate-aromatics.mdCuration proposal: shikimate-derived aromatic biosynthesis
46curation_documentinst/doc/proposal-organic-acid-formation.mdCuration proposal: organic acid formation GIFTs
66curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
65curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
29curation_documentinst/doc/proposal-protein-degradation.mdCuration proposal: protein degradation GIFTs
64curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
82curation_documentinst/doc/proposal-nitrogen-compound-catabolism.mdCuration proposal: nitrogen compound catabolism GIFTs
14curation_documentinst/doc/proposal-amino-acid-biosynthesis.mdCuration proposal: serine, threonine, cysteine and methionine GIFTs
13curation_documentinst/doc/proposal-amino-acid-biosynthesis.mdCuration proposal: serine, threonine, cysteine and methionine GIFTs
127curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
5curation_documentinst/extdata/database-source/SOURCES.mdReference database provenance: the KEGG modules and Rhea reactions the initial nucleotide GIFTs were curated from, and the boundary choices against them
106curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
156curation_documentinst/doc/proposal-structural-gifts.mdStructural GIFTs: curated content, refusals, and open questions
156result_tabledata-raw/reference/lta-peptidoglycan-marker-audit.tsvAudit of the candidate lipoteichoic acid and peptidoglycan marker profiles
156result_tabledata-raw/reference/lta-peptidoglycan-prevalence.tsvPrevalence of the narrow lipoteichoic acid architecture and peptidoglycan proxy sets over the KEGG frame
137curation_documentinst/doc/proposal-compatible-solutes-heme-enterobactin-detoxification.mdProposal: compatible-solute and heme biosynthesis, enterobactin assembly
101curation_documentinst/doc/proposal-aromatic-degradation.mdCuration proposal: aromatic compound degradation and mercury detoxification GIFTs
67curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
135curation_documentinst/doc/proposal-compatible-solutes-heme-enterobactin-detoxification.mdProposal: compatible-solute and heme biosynthesis, enterobactin assembly
150curation_documentinst/doc/proposal-anchor-fates.mdCuration proposal: fates for anchors that had only one
138curation_documentinst/doc/proposal-compatible-solutes-heme-enterobactin-detoxification.mdProposal: compatible-solute and heme biosynthesis, enterobactin assembly
47curation_documentinst/doc/proposal-organic-acid-formation.mdCuration proposal: organic acid formation GIFTs
30curation_documentinst/doc/proposal-structural-gifts.mdStructural GIFTs: curated content, refusals, and open questions
51curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
17curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
72curation_documentinst/doc/proposal-central-metabolic-cycles.mdDesign proposal: circular central metabolism and higher-order metabolic topology
19curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
22curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
20curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
23curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
124curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
102curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
7curation_documentinst/doc/proposal-amino-acid-biosynthesis.mdCuration proposal: serine, threonine, cysteine and methionine GIFTs
128curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
132curation_documentinst/doc/proposal-next-gift-release.mdCuration proposal: next coherent GIFT release
3curation_documentinst/extdata/database-source/SOURCES.mdReference database provenance: the KEGG modules and Rhea reactions the initial nucleotide GIFTs were curated from, and the boundary choices against them
136curation_documentinst/doc/proposal-compatible-solutes-heme-enterobactin-detoxification.mdProposal: compatible-solute and heme biosynthesis, enterobactin assembly
116curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
121curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
52curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
9curation_documentinst/doc/proposal-amino-acid-biosynthesis.mdCuration proposal: serine, threonine, cysteine and methionine GIFTs
151curation_documentinst/doc/proposal-anchor-fates.mdCuration proposal: fates for anchors that had only one
100curation_documentinst/doc/proposal-aromatic-degradation.mdCuration proposal: aromatic compound degradation and mercury detoxification GIFTs
75curation_documentinst/doc/proposal-shikimate-aromatics.mdCuration proposal: shikimate-derived aromatic biosynthesis
131curation_documentinst/doc/proposal-central-metabolic-cycles.mdDesign proposal: circular central metabolism and higher-order metabolic topology
112curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
148curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
43curation_documentinst/doc/proposal-organic-acid-formation.mdCuration proposal: organic acid formation GIFTs
152curation_documentinst/doc/proposal-anchor-fates.mdCuration proposal: fates for anchors that had only one
44curation_documentinst/doc/proposal-organic-acid-formation.mdCuration proposal: organic acid formation GIFTs
110curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
154curation_documentinst/doc/proposal-structural-gifts.mdStructural GIFTs: curated content, refusals, and open questions
107curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
45curation_documentinst/doc/proposal-organic-acid-formation.mdCuration proposal: organic acid formation GIFTs
68curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
130curation_documentinst/doc/proposal-aromatic-degradation.mdCuration proposal: aromatic compound degradation and mercury detoxification GIFTs
12curation_documentinst/doc/proposal-amino-acid-biosynthesis.mdCuration proposal: serine, threonine, cysteine and methionine GIFTs
11curation_documentinst/doc/proposal-amino-acid-biosynthesis.mdCuration proposal: serine, threonine, cysteine and methionine GIFTs
126curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
85curation_documentinst/doc/proposal-nitrogen-compound-catabolism.mdCuration proposal: nitrogen compound catabolism GIFTs
139curation_documentinst/doc/proposal-compatible-solutes-heme-enterobactin-detoxification.mdProposal: compatible-solute and heme biosynthesis, enterobactin assembly
145curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
146curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
144curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
62curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
61curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
63curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
21curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
79curation_documentinst/doc/proposal-nitrogen-compound-catabolism.mdCuration proposal: nitrogen compound catabolism GIFTs
133curation_documentinst/doc/proposal-next-gift-release.mdCuration proposal: next coherent GIFT release
118curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
94curation_documentinst/doc/proposal-aromatic-degradation.mdCuration proposal: aromatic compound degradation and mercury detoxification GIFTs
95curation_documentinst/doc/proposal-aromatic-degradation.mdCuration proposal: aromatic compound degradation and mercury detoxification GIFTs
111curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
70curation_documentinst/doc/proposal-central-metabolic-cycles.mdDesign proposal: circular central metabolism and higher-order metabolic topology
108curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
97curation_documentinst/doc/proposal-aromatic-degradation.mdCuration proposal: aromatic compound degradation and mercury detoxification GIFTs
50curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
56curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
149curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
147curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
92curation_documentinst/doc/proposal-aromatic-degradation.mdCuration proposal: aromatic compound degradation and mercury detoxification GIFTs
98curation_documentinst/doc/proposal-aromatic-degradation.mdCuration proposal: aromatic compound degradation and mercury detoxification GIFTs
113curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
99curation_documentinst/doc/proposal-aromatic-degradation.mdCuration proposal: aromatic compound degradation and mercury detoxification GIFTs
34curation_documentinst/doc/proposal-regulatory-gifts.mdRegulatory GIFTs: curated content, refusals, and open questions
58curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
57curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
117curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
129curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
40curation_documentinst/doc/proposal-scfa-biosynthesis.mdCuration proposal: short-chain fatty acid formation GIFTs
42curation_documentinst/doc/proposal-scfa-biosynthesis.mdCuration proposal: short-chain fatty acid formation GIFTs
41curation_documentinst/doc/proposal-scfa-biosynthesis.mdCuration proposal: short-chain fatty acid formation GIFTs
1curation_documentinst/extdata/database-source/SOURCES.mdReference database provenance: the KEGG modules and Rhea reactions the initial nucleotide GIFTs were curated from, and the boundary choices against them
4curation_documentinst/extdata/database-source/SOURCES.mdReference database provenance: the KEGG modules and Rhea reactions the initial nucleotide GIFTs were curated from, and the boundary choices against them
37curation_documentinst/doc/proposal-scfa-biosynthesis.mdCuration proposal: short-chain fatty acid formation GIFTs
60curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
18curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
155curation_documentinst/doc/proposal-structural-gifts.mdStructural GIFTs: curated content, refusals, and open questions
155analysis_scriptdata-raw/wta_ncbifam_prevalence.RExact candidate-specific NCBIfam prevalence screen for wall teichoic acid
155result_tabledata-raw/reference/wta-ncbifam-prevalence.tsvExact NCBIfam prevalence of the wall teichoic acid architectures within the KO-complete candidate set
49curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
74curation_documentinst/doc/proposal-shikimate-aromatics.mdCuration proposal: shikimate-derived aromatic biosynthesis
81curation_documentinst/doc/proposal-nitrogen-compound-catabolism.mdCuration proposal: nitrogen compound catabolism GIFTs
6curation_documentinst/doc/proposal-amino-acid-biosynthesis.mdCuration proposal: serine, threonine, cysteine and methionine GIFTs
123curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
123curation_documentinst/doc/assessment-serine-deamination-revision.mdArchitecture-specific reassessment of serine ammonia-lyase evidence
123analysis_scriptdata-raw/serine_deamination_marker_audit.pyStratified KEGG protein and NCBIfam profile audit
123result_tabledata-raw/reference/serine-deamination-gene-audit.tsvGene-level alpha, beta and single-chain profile calls
123result_tabledata-raw/reference/serine-deamination-genome-audit.tsvGenome-level architecture support in the fixed sample
142curation_documentinst/doc/proposal-compatible-solutes-heme-enterobactin-detoxification.mdProposal: compatible-solute and heme biosynthesis, enterobactin assembly
153curation_documentinst/doc/proposal-ncbifam-namespace.mdAssessment: NCBIfam as a marker namespace, read against the deferral register
28curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
71curation_documentinst/doc/proposal-central-metabolic-cycles.mdDesign proposal: circular central metabolism and higher-order metabolic topology
140curation_documentinst/doc/proposal-compatible-solutes-heme-enterobactin-detoxification.mdProposal: compatible-solute and heme biosynthesis, enterobactin assembly
87curation_documentinst/doc/proposal-nitrogen-compound-catabolism.mdCuration proposal: nitrogen compound catabolism GIFTs
86curation_documentinst/doc/proposal-nitrogen-compound-catabolism.mdCuration proposal: nitrogen compound catabolism GIFTs
88curation_documentinst/doc/proposal-nitrogen-compound-catabolism.mdCuration proposal: nitrogen compound catabolism GIFTs
54curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
55curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
53curation_documentinst/doc/proposal-vitamin-biosynthesis.mdCuration proposal: vitamin biosynthesis GIFTs
10curation_documentinst/doc/proposal-amino-acid-biosynthesis.mdCuration proposal: serine, threonine, cysteine and methionine GIFTs
122curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
115curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
125curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
36curation_documentinst/doc/proposal-defense-gifts.mdDefense GIFTs: curated content, refusals, and open questions
35curation_documentinst/doc/proposal-defense-gifts.mdDefense GIFTs: curated content, refusals, and open questions
160curation_documentinst/doc/architecture.mdDevelopment and architecture guide; states the shared-component rule this curation depends on
160curation_documentinst/doc/proposal-structural-gifts.mdStructural GIFTs: curated content, refusals, and open questions
160analysis_scriptdata-raw/t2ss_prevalence.RPrevalence and specificity screen for the type II secretion system
160result_tabledata-raw/reference/t2ss-controls.tsvNamed strains with what each is established to encode beside the marker result
160result_tabledata-raw/reference/t2ss-prevalence.tsvCounts testing whether the Gsp inventory identifies a machine distinct from the type IVa pilus
160result_tabledata-raw/reference/t2ss-roles.tsvEach Gsp role with its KO, its equivalog and the frame genomes carrying it, plus the shared peptidase
158curation_documentinst/doc/proposal-structural-gifts.mdStructural GIFTs: curated content, refusals, and open questions
158analysis_scriptdata-raw/secretion_system_prevalence.RMarker and prevalence screen for type III and type VI secretion as structural GIFTs
158result_tabledata-raw/reference/secretion-system-controls.tsvNamed reference strains with their established secretion systems beside the marker result
158result_tabledata-raw/reference/secretion-system-marker-audit.tsvAccessions tested against a role equivalog before acceptance, including the one refused
158result_tabledata-raw/reference/secretion-system-prevalence.tsvComplete and near-complete type III and type VI architectures, and overlap with the flagellar export apparatus
158result_tabledata-raw/reference/secretion-system-roles.tsvRole inventory of both secretion architectures with accepted KOs and equivalogs and genome counts
31curation_documentinst/doc/proposal-structural-gifts.mdStructural GIFTs: curated content, refusals, and open questions
157curation_documentinst/doc/proposal-structural-gifts.mdStructural GIFTs: curated content, refusals, and open questions
157analysis_scriptdata-raw/secretion_system_prevalence.RMarker and prevalence screen for type III and type VI secretion as structural GIFTs
157result_tabledata-raw/reference/secretion-system-controls.tsvNamed reference strains with their established secretion systems beside the marker result
157result_tabledata-raw/reference/secretion-system-marker-audit.tsvAccessions tested against a role equivalog before acceptance, including the one refused
157result_tabledata-raw/reference/secretion-system-prevalence.tsvComplete and near-complete type III and type VI architectures, and overlap with the flagellar export apparatus
157result_tabledata-raw/reference/secretion-system-roles.tsvRole inventory of both secretion architectures with accepted KOs and equivalogs and genome counts
114curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
76curation_documentinst/doc/proposal-nitrogen-compound-catabolism.mdCuration proposal: nitrogen compound catabolism GIFTs
78curation_documentinst/doc/proposal-nitrogen-compound-catabolism.mdCuration proposal: nitrogen compound catabolism GIFTs
109curation_documentinst/doc/proposal-amino-acid-metabolism.mdCuration proposal: the rest of amino acid metabolism
26curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
15curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
24curation_documentinst/doc/proposal-polysaccharide-degradation.mdCuration proposal: complex polysaccharide and sugar degradation GIFTs
161curation_documentinst/doc/proposal-regulatory-defense-expansion.mdRegulatory and defense GIFT expansion: October 2026 assessment
162curation_documentinst/doc/proposal-antimicrobial-detoxification.mdCuration proposal: antimicrobial detoxification, and CARD as a gifter source
162curation_documentinst/doc/proposal-regulatory-defense-expansion.mdRegulatory and defense GIFT expansion: October 2026 assessment
163curation_documentinst/doc/proposal-antimicrobial-detoxification.mdCuration proposal: antimicrobial detoxification, and CARD as a gifter source
163curation_documentinst/doc/proposal-regulatory-defense-expansion.mdRegulatory and defense GIFT expansion: October 2026 assessment
162analysis_scriptdata-raw/marker_specificity_screen.RKO to Rhea marker-specificity screen
162result_tabledata-raw/reference/ko-reaction-specificity.tsvKO to Rhea marker-specificity results
161curation_documentinst/doc/proposal-ncbifam-namespace.mdNCBIfam namespace and equivalog admission assessment
163analysis_scriptdata-raw/marker_specificity_screen.RKO to Rhea marker-specificity screen
163result_tabledata-raw/reference/ko-reaction-specificity.tsvKO to Rhea marker-specificity results
32curation_documentinst/doc/proposal-regulatory-defense-expansion.mdRegulatory and defense GIFT expansion: October 2026 assessment
No matching table rows.