The BaFF web server allows to automatically detect the biological features that characterize a set of prokaryotic organisms given as input by the user. The core of the system is a searchable database of tens of diverse features compiled for more than 20.000 prokaryotic organisms.
You can locate qualitative or quantitative features differentially associated to an input set of organisms respect to a custom background or resulting from a database search.

Bacterial Features

Get a list of bacteria matching one or more of the following criteria. You can use it as input for an overrepresentation analysis.

Taxonomy ID

Name

Disease

Taxonomy (Term name)

Gram staining - Gram - Gram + Unknown

Biosystems - (5R)-carbapenem biosynthesis (5Z)-dodec-5-enoate biosynthesis (deoxy)ribose phosphate degradation (Kdo)2-lipid A biosynthesis I (R)-acetoin biosynthesis I (R)-acetoin biosynthesis II (R,R)-butanediol biosynthesis (R,R)-butanediol degradation 1,2-Dichloroethane degradation 1,4-Dichlorobenzene degradation 1,4-dihydroxy-2-naphthoate biosynthesis 1,4-dihydroxy-2-naphthoate biosynthesis I 1,4-dihydroxy-6-naphthoate biosynthesis II 1,6-anhydro-N-acetylmuramic acid recycling 1- and 2-Methylnaphthalene degradation 2'-(5'-phosphoribosyl)-3'-dephospho-CoA biosynthesis I (citrate lyase) 2'-(5'-phosphoribosyl)-3'-dephospho-CoA biosynthesis II (malonate decarboxylase) 2'-deoxy-alpha-D-ribose 1-phosphate degradation 2,3-dihydroxybenzoate biosynthesis 2,4-Dichlorobenzoate degradation 2-amino-3-carboxymuconate semialdehyde degradation to 2-oxopentenoate 2-aminoethylphosphonate degradation I 2-Aminoethylphosphonate transport system 2-keto-L-gulonate biosynthesis 2-ketoglutarate dehydrogenase complex 2-methylcitrate cycle I 2-methylcitrate cycle II 2-nitrobenzoate degradation I 2-nitrobenzoate degradation II 2-nitropropane degradation 2-O-alpha-mannosyl-D-glycerate degradation 2-oxobutanoate degradation I 2-Oxocarboxylic acid chain extension, 2-oxoglutarate => 2-oxoadipate => 2-oxopimelate => 2-oxosuberate 2-Oxocarboxylic acid metabolism 2-oxoglutarate decarboxylation to succinyl-CoA 2-oxoisovalerate decarboxylation to isobutanoyl-CoA 2-oxopentenoate degradation 3,4,6-trichlorocatechol degradation 3,4-dichlorocatechol degradation 3,5-dichlorocatechol degradation 3-Chloroacrylic acid degradation 3-chlorocatechol degradation 3-chlorotoluene degradation II 3-dehydroquinate biosynthesis I 3-Hydroxypropionate bi-cycle 3-methylthiopropanoate biosynthesis 3-oxoadipate degradation 3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation 3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation to 2-oxopent-4-enoate 3-phenylpropionate and 3-(3-hydroxyphenyl)propionate degradation 3-phenylpropionate degradation 4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis 4-aminobenzoate biosynthesis 4-aminobutanoate degradation I 4-aminobutanoate degradation II 4-aminobutanoate degradation III 4-aminobutanoate degradation V 4-aminobutyrate degradation 4-aminobutyrate degradation I 4-aminobutyrate degradation II 4-aminobutyrate degradation III 4-aminobutyrate degradation V 4-chlorocatechol degradation 4-deoxy-L-threo-hex-4-enopyranuronate degradation 4-hydroxybenzoate biosynthesis II (bacteria and fungi) 4-hydroxybenzoate biosynthesis II (microbes) 4-hydroxymandelate degradation 4-hydroxyphenylacetate degradation 4-hydroxyphenylpyruvate biosynthesis 4-hydroxyproline degradation II 4-methyl-5(beta-hydroxyethyl)thiazole salvage (yeast) 5,6-dimethylbenzimidazole biosynthesis 5,6-dimethylbenzimidazole biosynthesis I (aerobic) 5-(carboxymethoxy)uridine biosynthesis 5-aminoimidazole ribonucleotide biosynthesis I 5-aminoimidazole ribonucleotide biosynthesis II 5-dehydro-4-deoxy-D-glucuronate degradation 6-hydroxymethyl-dihydropterin diphosphate biosynthesis 6-hydroxymethyl-dihydropterin diphosphate biosynthesis I 7-keto-8-aminopelargonate biosynthesis I 7-keto-8-aminopelargonate biosynthesis II 8-amino-7-oxononanoate biosynthesis I 8-amino-7-oxononanoate biosynthesis II 8-amino-7-oxononanoate biosynthesis III AauS-AauR (acidic amino acids utilization) two-component regulatory system ABC transporters ABC-2 type transport system acetate conversion to acetyl-CoA acetate formation from acetyl-CoA I acetate formation from acetyl-CoA II acetate formation from acetyl-CoA III (succinate) acetoacetate degradation (to acetyl CoA) Acetogen acetoin biosynthesis I acetoin biosynthesis II acetoin degradation Acetoin utilization transport system acetyl-CoA biosynthesis (from pyruvate) acetyl-CoA biosynthesis III (from citrate) acetyl-CoA fermentation to butanoate II acetyl-CoA fermentation to butyrate I acetyl-CoA fermentation to butyrate II Acetyl-CoA pathway, CO2 => acetyl-CoA acrylonitrile degradation acrylonitrile degradation I actinorhodin biosynthesis acyl carrier protein activation acyl carrier protein metabolism acyl carrier protein metabolism I acyl-ACP thioesterase pathway acyl-CoA hydrolysis adenine and adenosine salvage I adenine and adenosine salvage II adenine and adenosine salvage III adenine and adenosine salvage IV adenine and adenosine salvage V Adenine ribonucleotide biosynthesis, IMP => ADP,ATP adenosine deoxyribonucleotides de novo biosynthesis adenosine deoxyribonucleotides de novo biosynthesis I adenosine deoxyribonucleotides de novo biosynthesis II adenosine nucleotides de novo biosynthesis adenosine nucleotides degradation II adenosine nucleotides degradation III adenosine ribonucleotides de novo biosynthesis adenosylcobalamin biosynthesis from cobyrinate a,c-diamide I adenosylcobalamin biosynthesis from cobyrinate a,c-diamide II adenosylcobalamin biosynthesis I (early cobalt insertion) adenosylcobalamin biosynthesis II (late cobalt incorporation) adenosylcobalamin salvage from cobalamin adenosylcobalamin salvage from cobinamide and cobalamin adenosylcobalamin salvage from cobinamide I AdeS-AdeR two-component regulatory system Adhesin protein transport system ADP-L-glycero-beta-D-manno-heptose biosynthesis ADP-L-glycero-D-manno-heptose biosynthesis aerobactin biosynthesis aerobic respiration (cytochrome c) aerobic respiration -- electron donor II aerobic respiration -- electron donor III aerobic respiration I (cytochrome c) Aerotactic Two-Component Signal Transduction System AGE-RAGE signaling pathway in diabetic complications AgrC-AgrA (exoprotein synthesis) two-component regulatory system AI-2 transport system alanine biosynthesis I alanine biosynthesis II alanine biosynthesis III alanine degradation I alanine degradation IV Alanine, aspartate and glutamate metabolism aldoxime degradation AlgE-type Mannuronan C-5-Epimerase transport system AlgZ-AlgR (alginate production) two-component regulatory system alkylnitronates degradation allantoin degradation IV (anaerobic) allantoin degradation to glyoxylate II allantoin degradation to glyoxylate III allantoin degradation to ureidoglycolate II (ammonia producing) alpha-1,4-Digalacturonate transport system alpha-Glucoside transport system alpha-Hemolysin/cyclolysin transport system alpha-Linolenic acid metabolism Amino sugar and nucleotide sugar metabolism Aminoacyl-tRNA biosynthesis Aminoacyl-tRNA biosynthesis, prokaryotes Aminobenzoate degradation Aminoglycoside resistance, protease FtsH Aminoglycoside resistance, protease HtpX aminopropanol biosynthesis aminopropanol phosphate biosynthesis I aminopropylcadaverine biosynthesis ammonia assimilation cycle II ammonia assimilation cycle III ammonium transport anandamide degradation androstenedione degradation anhydromuropeptides recycling Anoxygenic photosynthesis in green nonsulfur bacteria Anoxygenic photosynthesis in green sulfur bacteria Anoxygenic photosynthesis in purple bacteria Anoxygenic photosystem I Anoxygenic photosystem II anthranilate degradation I (aerobic) Anthranilate degradation, anthranilate => catechol arabinogalactan oligomer/maltooligosaccharide transport system Arabinosaccharide transport system Arachidonic acid metabolism ArcAB Two-Component Signal Transduction System, quinone dependent ArcB-ArcA (anoxic redox control) two-component regulatory system Archaeal proteasome Arginine and proline metabolism Arginine biosynthesis arginine biosynthesis I arginine biosynthesis I (via L-ornithine) arginine biosynthesis II (acetyl cycle) arginine biosynthesis IV (archaebacteria) arginine degradation I (arginase pathway) arginine degradation II (AST pathway) arginine degradation III (arginine decarboxylase/agmatinase pathway) arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway) arginine degradation V (arginine deiminase pathway) arginine degradation VI (arginase 2 pathway) arginine degradation XI arginine dependent acid resistance Arginine transport system arginine, ornithine and proline interconversion Arginine/lysine/histidine/glutamine transport system Arginine/ornithine transport system ArlS-ArlR (virulence regulation) two-component regulatory system aromatic compounds degradation via beta-ketoadipate arsenate detoxification II arsenate detoxification II (glutaredoxin) Ascorbate and aldarate metabolism Ascorbate degradation, ascorbate => D-xylulose-5P asparagine biosynthesis I asparagine biosynthesis II asparagine degradation I aspartate biosynthesis aspartate biosynthesis II aspartate degradation I aspartate degradation II aspartate superpathway Assimilatory nitrate reduction, nitrate => ammonia Assimilatory sulfate reduction, sulfate => H2S AtoS-AtoC (cPHB biosynthesis) two-component regulatory system AtoSC Two-Component Signal Transduction System Atrazine degradation atrazine degradation I (aerobic) autoinducer AI-2 biosynthesis I autoinducer AI-2 degradation Avermectin biosynthesis, 2-methylbutanoyl-CoA/isobutyryl-CoA => 6,8a-Seco-6,8a-deoxy-5-oxoavermectin 1a/1b aglycone => avermectin A1a/B1a/A1b/B1b bacillibactin biosynthesis bacillithiol biosynthesis bacilysin biosynthesis Bacilysin biosynthesis, prephenate => bacilysin Bacitracin resistance, BceAB transporter Bacitracin resistance, VraDE transporter Bacitracin transport system Bacterial chemotaxis Bacterial invasion of epithelial cells Bacterial proteasome Bacterial secretion system BaeS-BaeR (envelope stress response) two-component regulatory system BaeSR Two-Component Signal Transduction System BarA UvrY Two-Component Signal Transduction System BarA-UvrY (central carbon metabolism) two-component regulatory system Basal transcription factors Base excision repair base-degraded thiamin salvage BasS-BasR (antimicrobial peptide resistance) two-component regulatory system BasSR Two-Component Signal Transduction System BceS-BceR (bacitracin transport) two-component regulatory system BceSR two-component signal transduction system Benzene degradation, benzene => catechol Benzene/toluene degradation, benzene => catechol / toluene => 3-methylcatechol Benzoate degradation benzoate degradation I (aerobic) Benzoate degradation via CoA ligation Benzoate degradation via hydroxylation Benzoate degradation, benzoate => catechol / methylbenzoate => methylcatechol Benzoate degradation, cyclohexanecarboxylic acid =>pimeloyl-CoA Benzoyl-CoA degradation, benzoyl-CoA => 3-hydroxypimeloyl-CoA beta-alanine biosynthesis II beta-alanine biosynthesis III beta-alanine biosynthesis IV beta-alanine degradation II beta-Alanine metabolism beta-carotene biosynthesis beta-D-glucuronide and D-glucuronate degradation beta-Lactam resistance beta-Lactam resistance, AmpC system beta-Lactam resistance, Bla system beta-Oxidation beta-Oxidation, acyl-CoA synthesis Betaine biosynthesis, choline => betaine betanidin degradation Bicarbonate transport system Biofilm formation - Vibrio cholerae Biosynthesis of 12-, 14- and 16-membered macrolides Biosynthesis of amino acids Biosynthesis of ansamycins Biosynthesis of antibiotics Biosynthesis of secondary metabolites Biosynthesis of siderophore group nonribosomal peptides Biosynthesis of type II polyketide backbone Biosynthesis of type II polyketide products Biosynthesis of unsaturated fatty acids Biosynthesis of vancomycin group antibiotics biotin biosynthesis from 7-keto-8-aminopelargonate biotin biosynthesis from 8-amino-7-oxononanoate biotin biosynthesis from 8-amino-7-oxononanoate I biotin biosynthesis from 8-amino-7-oxononanoate II biotin biosynthesis I biotin biosynthesis II Biotin biosynthesis, BioI pathway, long-chain-acyl-ACP => pimeloyl-ACP => biotin Biotin biosynthesis, BioW pathway, pimelate => pimeloyl-CoA => biotin Biotin biosynthesis, pimeloyl-ACP/CoA => biotin Biotin metabolism Biotin transport system biotin-carboxyl carrier protein biotin-carboxyl carrier protein assembly biphenyl degradation Biphenyl degradation, biphenyl => 2-oxopent-4-enoate + benzoate Bisphenol A degradation Branched-chain amino acid transport system BraS-BraR (bacitracin transport) two-component regulatory system butanediol biosynthesis butanediol degradation Butanoate metabolism C1-unit interconversion, prokaryotes C10-C20 isoprenoid biosynthesis, archaea C10-C20 isoprenoid biosynthesis, bacteria C4 photosynthetic carbon assimilation cycle C5 isoprenoid biosynthesis, mevalonate pathway C5 isoprenoid biosynthesis, non-mevalonate pathway C5-Branched dibasic acid metabolism Caffeine metabolism Calvin-Benson-Bassham cycle CAM (Crassulacean acid metabolism), dark CAM (Crassulacean acid metabolism), light canavanine biosynthesis Caprolactam degradation Capsular polysaccharide transport system Carbapenem biosynthesis Carbapenem-3-carboxylate biosynthesis, pyrroline-5-carboxylate + malonyl-CoA => carbapenem-3-carboxylate Carbazole degradation, carbazole => 2-oxopent-4-enoate + anthranilate Carbon fixation in photosynthetic organisms Carbon fixation pathways in prokaryotes Carbon metabolism cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas) cardiolipin biosynthesis I cardiolipin biosynthesis II cardiolipin biosynthesis III carnitine degradation I Carotenoid biosynthesis catechol degradation II (meta-cleavage pathway) catechol degradation III (ortho-cleavage pathway) catechol degradation to 2-oxopent-4-enoate I catechol degradation to 2-oxopent-4-enoate II catechol degradation to beta-ketoadipate Catechol meta-cleavage, catechol => acetyl-CoA / 4-methylcatechol => propanoyl-CoA Catechol ortho-cleavage, catechol => 3-oxoadipate Cationic antimicrobial peptide (CAMP) resistance Cationic antimicrobial peptide (CAMP) resistance, ethanolaminephosphotransferase EptB Cationic antimicrobial peptide (CAMP) resistance, N-acetylmuramoyl-L-alanine amidase AmiA and AmiC Cationic antimicrobial peptide (CAMP) resistance, arnBCADTEF operon Cationic antimicrobial peptide (CAMP) resistance, dltABCD operon Cationic antimicrobial peptide (CAMP) resistance, envelope protein folding and degrading factors DegP and DsbA Cationic antimicrobial peptide (CAMP) resistance, ethanolaminephosphotransferase EptA Cationic antimicrobial peptide (CAMP) resistance, lysyl-phosphatidylglycerol (L-PG) synthase MprF Cationic antimicrobial peptide (CAMP) resistance, palmitoyl transferase PagP Cationic antimicrobial peptide (CAMP) resistance, protease PgtE Cationic antimicrobial peptide (CAMP) resistance, VraFG transporter Cationic antimicrobial peptide transport system Cationic peptide transport system CckA-CtrA/CpdR (cell cycle control) two-component regulatory system CDP-diacylglycerol biosynthesis I CDP-diacylglycerol biosynthesis II CDP-diacylglycerol biosynthesis III Cell cycle - Caulobacter Cell division transport system Cellobiose transport system cellulose biosynthesis Cephamycin C biosynthesis, aminoadipate + cycteine + valine => cephamycin C CheA-CheYBV (chemotaxis) two-component regulatory system Chemotactic Two-Component Signal Transduction chitobiose degradation Chloroalkane and chloroalkene degradation Chlorocyclohexane and chlorobenzene degradation chlorophyllide a biosynthesis I chlorophyllide a biosynthesis I (aerobic, light-dependent) chlorophyllide a biosynthesis III (aerobic, light independent) chlorosalicylate degradation cholesterol degradation to androstenedione I (cholesterol oxidase) cholesterol degradation to androstenedione II (cholesterol dehydrogenase) choline degradation I chorismate biosynthesis chorismate biosynthesis from 3-dehydroquinate chorismate biosynthesis I ChpA-ChpB/PilGH (chemosensory) two-component regulatory system ChvG-ChvI (acidity sensing) two-component regulatory system CiaH-CiaR two-component regulatory system cinnamate and 3-hydroxycinnamate degradation to 2-oxopent-4-enoate cis-dodecenoate biosynthesis cis-dodecenoyl biosynthesis cis-vaccenate biosynthesis CitA-CitB (citrate fermentation) two-component regulatory system Citrate cycle (TCA cycle) Citrate cycle (TCA cycle, Krebs cycle) Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate citrate degradation citrate fermentation to diacetyl citrate lyase activation citrulline degradation CitS-CitT (magnesium-citrate transport) two-component regulatory system CitST two-component signal transduction system Clavaminate biosynthesis, arginine + glyceraldehyde-3P => clavaminate Clavulanic acid biosynthesis CMP phosphorylation CMP-3-deoxy-D-manno-octulosonate biosynthesis CMP-KDO biosynthesis CMP-KDO biosynthesis I CMP-KDO biosynthesis II (from D-arabinose 5-phosphate) CMP-N-acetylneuraminate biosynthesis II (bacteria) CMP-pseudaminate biosynthesis CO2 fixation into oxaloacetate (anapleurotic) cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion) cob(II)yrinate a,c-diamide biosynthesis II (late cobalt incorporation) Cobalamin biosynthesis, cobinamide => cobalamin Cobalt/nickel transport system coenzyme A biosynthesis coenzyme A biosynthesis I coenzyme A biosynthesis II (mammalian) Coenzyme A biosynthesis, pantothenate => CoA Coenzyme M biosynthesis colanic acid building blocks biosynthesis ComD-ComE (competence) two-component regulatory system ComP-ComA (competence) two-component regulatory system ComPA two-component signal transduction system Competence-related DNA transformation transporter conversion of succinate to propanoate conversion of succinate to propionate copper transport II Copper-processing system Cph1-Rcp1 (light response) two-component regulatory system CpxA-CpxR (envelope stress response) two-component regulatory system CpxAR Two-Component Signal Transduction System creatinine degradation I creatinine degradation II CreC-CreB (phosphate regulation) two-component regulatory system CreCB Two-Component Signal Transduction System crotonate fermentation (to acetate and cyclohexane carboxylate) CssS-CssR (secretion stress response) two-component regulatory system CssSR two-component signal transduction system Cumate degradation, p-cumate => 2-oxopent-4-enoate + 2-methylpropanoate curcumin degradation CusS-CusR (copper tolerance) two-component regulatory system CusSR Two-Component Signal Transduction System Cutin, suberine and wax biosynthesis cyanate degradation Cyanoamino acid metabolism cyanurate degradation cyclohexanol degradation cyclopropane fatty acid (CFA) biosynthesis Cymene degradation, p-cymene => p-cumate Cysteine and methionine metabolism cysteine biosynthesis I cysteine biosynthesis II Cysteine biosynthesis, homocysteine + serine => cysteine Cysteine biosynthesis, methionine => cysteine Cysteine biosynthesis, serine => cysteine cysteine biosynthesis/homocysteine degradation Cystine transport system cytidylyl molybdenum cofactor biosynthesis Cytochrome aa3-600 menaquinol oxidase Cytochrome b6f complex Cytochrome bc1 complex respiratory unit Cytochrome c oxidase, cbb3-type Cytochrome c oxidase, prokaryotes Cytochrome d ubiquinol oxidase Cytochrome o ubiquinol oxidase D-Alanine metabolism D-allose degradation D-Allose transport system D-arabinose degradation I D-arabinose degradation II D-arabitol degradation D-Arginine and D-ornithine metabolism D-camphor degradation D-chiro-inositol degradation D-fructuronate degradation D-galactarate degradation I D-galactarate degradation II D-galactonate degradation D-galactonate degradation, De Ley-Doudoroff pathway, D-galactonate => glycerate-3P D-galactosamine and N-acetyl-D-galactosamine degradation D-galactose degradation I (Leloir pathway) D-galactose degradation III D-galacturonate degradation D-Galacturonate degradation (bacteria), D-galacturonate => pyruvate + D-glyceraldehyde 3P D-galacturonate degradation I D-glucarate degradation I D-glucarate degradation II D-gluconate degradation D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P D-Glutamine and D-glutamate metabolism D-lactate to cytochrome bo oxidase electron transport D-malate degradation D-mannose degradation D-Methionine transport system D-serine degradation D-sorbitol degradation I D-sorbitol degradation II D-Xylose transport system DctB-DctD (C4-dicarboxylate transport) two-component regulatory system DctS-DctR (C4-dicarboxylate transport) two-component regulatory system DctSR two-component signal transduction system DcuS-DcuR (C4-dicarboxylate metabolism) two-component regulatory system DcuSR Two-Component Signal Transduction System, dicarboxylate-dependent deacetylcephalosporin C biosynthesis Degradation of aromatic compounds degradation of purine ribonucleosides degradation of pyrimidine ribonucleosides DegS-DegU (multicellular behavior control) two-component regulatory system DegSU two-component signal transduction system dehydrodiconiferyl alcohol degradation demethylmenaquinol-6 biosynthesis II demethylmenaquinol-8 biosynthesis I demethylmenaquinol-9 biosynthesis demethylmenaquinone-8 biosynthesis Denitrification, nitrate => nitrogen DesK-DesR (membrane lipid fluidity regulation) two-component regulatory system DesKR two-component signal transduction system DevS-DevR (redox response) two-component regulatory system di-trans,poly-cis-undecaprenyl diphosphate biosynthesis di-trans,poly-cis-undecaprenyl phosphate biosynthesis diacylglycerol and triacylglycerol biosynthesis Dicarboxylate-hydroxybutyrate cycle diethylphosphate degradation Dihydrokalafungin biosynthesis, octaketide => dihydrokalafungin DIMBOA-glucoside activation DIMBOA-glucoside degradation dimethyl sulfoxide degradation Dioxin degradation Dipeptide transport system Dipeptide transport system, Firmicutes Dissimilatory nitrate reduction, nitrate => ammonia Dissimilatory sulfate reduction, sulfate => H2S DNA polymerase II complex, archaea DNA polymerase III complex, bacteria DNA replication DpiBA Two-Component Signal Transduction System dTDP-6-deoxy-D-allose biosynthesis dTDP-D-desosamine biosynthesis dTDP-L-megosamine biosynthesis dTDP-L-mycarose biosynthesis dTDP-L-oleandrose biosynthesis dTDP-L-rhamnose biosynthesis dTDP-L-rhamnose biosynthesis I dTDP-N-acetylthomosamine biosynthesis dTDP-N-acetylviosamine biosynthesis ectoine biosynthesis Ectoine biosynthesis, aspartate => ectoine EHEC pathogenicity signature, Shiga toxin EHEC/EPEC pathogenicity signature, T3SS and effectors Energy-coupling factor transport system enterobacterial common antigen biosynthesis enterobactin biosynthesis Entner-Doudoroff pathway I Entner-Doudoroff pathway, glucose-6P => glyceraldehyde-3P + pyruvate EnvZ Two-Component Signal Transduction System, osmotic responsive EnvZ-OmpR (osmotic stress response) two-component regulatory system Epithelial cell signaling in Helicobacter pylori infection Erythritol transport system Erythromycin biosynthesis, propanoyl-CoA + methylmalonyl-CoA => deoxyerythronolide B => erythromycin A/B Erythromycin resistance, macrolide 2'-phosphotransferase I MphA ethanol degradation ethanol degradation I ethanol degradation II ethanol degradation IV ethanolamine utilization Ether lipid metabolism Ethylbenzene degradation ethylene glycol degradation Ethylmalonyl pathway EvgS-EvgA (acid and drug tolerance) two-component regulatory system EvgSA Two-Component Signal Transduction System Exosome, archaea F-type ATPase, prokaryotes and chloroplasts F420 biosynthesis factor 420 biosynthesis factor 420 polyglutamylation fatty acid activation fatty acid beta-oxidation I fatty acid beta-oxidation II (core pathway) fatty acid beta-oxidation III (unsaturated, odd number) fatty acid beta-oxidation IV (unsaturated, even number) Fatty acid biosynthesis fatty acid biosynthesis initiation I fatty acid biosynthesis initiation II fatty acid biosynthesis initiation III Fatty acid biosynthesis, elongation Fatty acid biosynthesis, initiation Fatty acid degradation Fatty acid elongation fatty acid elongation -- saturated fatty acid elongation -- unsaturated fatty acid elongation -- unsaturated I Fatty acid metabolism ferulate degradation FitF-FitH (insecticidal toxin regulation) two-component regulatory system FixL-FixJ (nitrogen fixation) two-component regulatory system Flagellar assembly flavin biosynthesis flavin biosynthesis I (bacteria and plants) flavonoid biosynthesis FlrB-FlrC (polar flagellar synthesis) two-component regulatory system Fluorene degradation Fluorobenzoate degradation Fluoroquinolone resistance, efflux pump LfrA Fluoroquinolone resistance, gyrase-protecting protein Qnr Fluoroquinolone transport system Folate biosynthesis folate polyglutamylation folate polyglutamylation I folate polyglutamylation II folate transformations folate transformations I folate transformations II formaldehyde assimilation I (serine pathway) formaldehyde assimilation II (RuMP Cycle) Formaldehyde assimilation, ribulose monophosphate pathway Formaldehyde assimilation, serine pathway formaldehyde oxidation I formaldehyde oxidation II (glutathione-dependent) formaldehyde oxidation V (tetrahydrofolate pathway) formate assimilation into 5,10-methylenetetrahydrofolate formate oxidation to CO2 formate reduction to 5,10-methylenetetrahydrofolate formate to dimethyl sulfoxide electron transfer formate to nitrate electron transfer formate to nitrite electron transfer formate to trimethylamine N-oxide electron transfer formylTHF biosynthesis formylTHF biosynthesis I formylTHF biosynthesis II fructan biosynthesis Fructose and mannose metabolism fructose degradation Fructose transport system fructoselysine and psicoselysine degradation fucose degradation Fumarate reductase, prokaryotes Furfural degradation GABA (gamma-Aminobutyrate) shunt GABA biosynthesis, eukaryotes, putrescine => GABA GABA biosynthesis, prokaryotes, putrescine => GABA GABA shunt galactitol degradation galactosamine degradation galactose degradation I galactose degradation I (Leloir pathway) galactose degradation II Galactose degradation, Leloir pathway, galactose => alpha-D-glucose-1P Galactose metabolism gallate degradation I gallate degradation II gallate degradation III (anaerobic) gamma-glutamyl cycle gamma-Hexachlorocyclohexane degradation gamma-Hexachlorocyclohexane transport system gamma-linolenate biosynthesis II (animals) GDP-6-deoxy-D-talose biosynthesis GDP-alpha-D-perosamine biosynthesis GDP-D-perosamine biosynthesis GDP-D-rhamnose biosynthesis GDP-glucose biosynthesis GDP-L-fucose biosynthesis I (from GDP-D-mannose) GDP-mannose biosynthesis GDP-mannose biosynthesis I GDP-mannose biosynthesis II GDP-mannose metabolism General L-amino acid transport system Geraniol degradation geranyl diphosphate biosynthesis geranyldiphosphate biosynthesis geranylgeranyldiphosphate biosynthesis GlnK-GlnL (glutamine utilization) two-component regulatory system GlnKL two-component signal transduction system GlnL-GlnG (nitrogen regulation) two-component regulatory system GlrK-GlrR (amino sugar metabolism) two-component regulatory system GlrKR Two-Component Signal Transduction System gluconeogenesis gluconeogenesis I Gluconeogenesis, oxaloacetate => fructose-6P glucose and glucose-1-phosphate degradation glucose and xylose degradation Glucose/arabinose transport system Glucose/mannose transport system glucosylglycerate biosynthesis I glutamate and glutamine biosynthesis glutamate biosynthesis I glutamate biosynthesis II glutamate biosynthesis III glutamate biosynthesis IV glutamate biosynthesis V glutamate degradation I glutamate degradation II glutamate degradation III glutamate degradation III (via 4-aminobutyrate) glutamate degradation IV glutamate degradation IX (via 4-aminobutyrate) glutamate degradation VI (to pyruvate) glutamate degradation VII glutamate degradation VII (to butanoate) glutamate degradation VII (to butyrate) glutamate degradation X glutamate dependent acid resistance Glutamate transport system Glutamate/aspartate transport system glutamine biosynthesis glutamine biosynthesis I glutamine degradation I glutamine degradation II Glutamine transport system glutaryl-CoA degradation glutathione biosynthesis Glutathione biosynthesis, glutamate => glutathione Glutathione metabolism glutathione redox reactions I glutathione redox reactions II Glutathione transport system glutathione-glutaredoxin redox reactions glutathionylspermidine biosynthesis glyceraldehyde 3-phosphate degradation glycerol and glycerophosphodiester degradation glycerol degradation I glycerol degradation II glycerol degradation to butanol glycerol degradation V Glycerol transport system glycerol-3-phosphate to cytochrome bo oxidase electron transfer glycerol-3-phosphate to fumarate electron transfer Glycerolipid metabolism glycerophosphodiester degradation Glycerophospholipid metabolism glycine betaine biosynthesis I (Gram-negative bacteria) glycine betaine biosynthesis II (Gram-positive bacteria) glycine betaine degradation Glycine betaine/proline transport system glycine biosynthesis I glycine biosynthesis II glycine biosynthesis III glycine biosynthesis IV glycine cleavage glycine cleavage complex glycine degradation I Glycine, serine and threonine metabolism glycocholate metabolism (bacteria) glycogen biosynthesis I (from ADP-D-Glucose) glycogen degradation I glycolate and glyoxylate degradation I glycolate and glyoxylate degradation II Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate Glycolysis / Gluconeogenesis glycolysis I glycolysis I (from glucose 6-phosphate) glycolysis I (from glucose-6P) glycolysis II (from fructose 6-phosphate) glycolysis II (from fructose-6P) glycolysis III glycolysis III (from glucose) glycolysis III (glucokinase) glycolysis IV (plant cytosol) glycolysis V Glycolysis, core module involving three-carbon compounds Glycosphingolipid biosynthesis - lacto and neolacto series Glyoxylate and dicarboxylate metabolism glyoxylate cycle GraS-GraR (cationic antimicrobial peptide transport) two-component regulatory system guanine and guanosine salvage guanine and guanosine salvage I guanine and guanosine salvage II guanine and guanosine salvage III Guanine ribonucleotide biosynthesis IMP => GDP,GTP guanosine deoxyribonucleotides de novo biosynthesis I guanosine deoxyribonucleotides de novo biosynthesis II guanosine nucleotides de novo biosynthesis guanosine nucleotides degradation II guanosine nucleotides degradation III guanosine ribonucleotides de novo biosynthesis guanylyl molybdenum cofactor biosynthesis Helicobacter pylori pathogenicity signature, cagA pathogenicity island heme biosynthesis from uroporphyrinogen II heme biosynthesis from uroporphyrinogen-III I heme biosynthesis from uroporphyrinogen-III I (aerobic) heme biosynthesis from uroporphyrinogen-III II heme biosynthesis from uroporphyrinogen-III II (anaerobic) heme biosynthesis I (aerobic) heme biosynthesis II (anaerobic) Heme biosynthesis, glutamate => protoheme/siroheme Heme transport system Hemin transport system Hemophore/metalloprotease transport system heptaprenyl diphosphate biosynthesis heterolactic fermentation hexaprenyl diphosphate biosynthesis hexitol fermentation to lactate, formate, ethanol and acetate histidine biosynthesis Histidine biosynthesis, PRPP => histidine histidine degradation I histidine degradation II histidine degradation IV Histidine degradation, histidine => N-formiminoglutamate => glutamate Histidine metabolism Histidine transport system Hk1-Rrp1 (glycerol uptake and utilization) two-component regulatory system homocysteine and cysteine interconversion homocysteine biosynthesis homolactic fermentation Homologous recombination Homoprotocatechuate degradation, homoprotocatechuate => 2-oxohept-3-enedioate homoserine and methionine biosynthesis homoserine biosynthesis homospermidine biosynthesis hopanoid biosynthesis (bacteria) HupT-HupR (hydrogenase synthesis regulation) two-component regulatory system HydH-HydG (metal tolerance) two-component regulatory system hydrogen oxidation I (aerobic) hydrogen production I hydrogen production III hydrogen production V hydrogen production VI hydrogen sulfide biosynthesis hydrogen sulfide biosynthesis I hydrogen to dimethyl sulfoxide electron transfer hydrogen to fumarate electron transfer hydrogen to trimethylamine N-oxide electron transfer hydroxymethylpyrimidine salvage Hydroxypropionate-hydroxybutylate cycle IAA biosynthesis IV IAA biosynthesis VI (via indole-3-acetamide) Ihk-Irr (virulence regulation) two-component regulatory system Imipenem resistance, repression of porin OprD Incomplete reductive citrate cycle, acetyl-CoA => oxoglutarate Inosine monophosphate biosynthesis, PRPP + glutamine => IMP inosine-5'-phosphate biosynthesis I inosine-5'-phosphate biosynthesis I inosine-5'-phosphate biosynthesis II Inositol phosphate metabolism Inositol transport system Inositol-phosphate transport system Iron complex transport system Iron(III) transport system Iron/zinc/manganese/copper transport system isoleucine biosynthesis I isoleucine biosynthesis I (from threonine) isoleucine biosynthesis III isoleucine biosynthesis IV Isoleucine biosynthesis, pyruvate => 2-oxobutanoate Isoleucine biosynthesis, threonine => 2-oxobutanoate => isoleucine isoleucine degradation I isoleucine degradation II kanosamine biosynthesis II KDO transfer to lipid IVA Kdo transfer to lipid IVA I KDO2-lipid A biosynthesis I KdpD-KdpE (potassium transport) two-component regulatory system KdpDE Two-Component Signal Transduction System, potassium-dependent ketogluconate metabolism ketolysis Ketone body biosynthesis, acetyl-CoA => acetoacetate/3-hydroxybutyrate/acetone KinABCDE-Spo0FA (sporulation control) two-component regulatory system KinB-AlgB (alginate production) two-component regulatory system L-1,2-propanediol degradation L-alanine biosynthesis I L-alanine biosynthesis II L-alanine biosynthesis III L-alanine degradation I L-alanine degradation II (to D-lactate) L-alanine degradation III L-alanine degradation IV L-alanine fermentation to propanoate and acetate L-arabinan degradation L-arabinose degradation I L-arabinose degradation III L-Arabinose transport system L-Arabinose/lactose transport system L-arginine biosynthesis I (via L-ornithine) L-arginine biosynthesis II (acetyl cycle) L-arginine biosynthesis IV (archaebacteria) L-arginine degradation I (arginase pathway) L-arginine degradation II (AST pathway) L-arginine degradation III (arginine decarboxylase/agmatinase pathway) L-arginine degradation V (arginine deiminase pathway) L-arginine degradation VI (arginase 2 pathway) L-arginine degradation X (arginine monooxygenase pathway) L-ascorbate biosynthesis III L-ascorbate biosynthesis IV L-ascorbate biosynthesis V L-ascorbate degradation I (bacterial, anaerobic) L-ascorbate degradation II (bacterial, aerobic) L-asparagine biosynthesis I L-asparagine biosynthesis II L-asparagine degradation I L-asparagine degradation III (mammalian) L-aspartate biosynthesis L-aspartate degradation I L-aspartate degradation II L-carnitine degradation I L-citrulline biosynthesis L-citrulline degradation L-citrulline-nitric oxide cycle L-cysteine biosynthesis I L-cysteine biosynthesis III (from L-homocysteine) L-cysteine degradation I L-cysteine degradation II L-Cystine transport system L-galactonate degradation L-glutamate biosynthesis I L-glutamate biosynthesis II L-glutamate biosynthesis III L-glutamate biosynthesis V L-glutamate degradation I L-glutamate degradation II L-glutamate degradation IX (via 4-aminobutanoate) L-glutamate degradation VI (to pyruvate) L-glutamate degradation VII (to butanoate) L-glutamate degradation X L-glutamine biosynthesis I L-glutamine degradation I L-glutamine degradation II L-histidine biosynthesis L-histidine degradation I L-homocysteine and L-cysteine interconversion L-homocysteine biosynthesis L-homoserine and L-methionine biosynthesis L-homoserine biosynthesis L-idonate degradation L-isoleucine biosynthesis I (from threonine) L-isoleucine degradation I L-lactaldehyde degradation (aerobic) L-lactaldehyde degradation (anaerobic) L-leucine biosynthesis L-lysine biosynthesis I L-lysine biosynthesis II L-lysine biosynthesis VI L-lysine degradation I L-lysine degradation VI L-lysine fermentation to acetate and butanoate L-lyxose degradation L-methionine biosynthesis I L-methionine biosynthesis II L-methionine biosynthesis III L-methionine degradation I (to L-homocysteine) L-methionine degradation II L-methionine salvage from L-homocysteine L-ornithine biosynthesis L-ornithine biosynthesis I L-ornithine degradation I (L-proline biosynthesis) L-ornithine degradation II (Stickland reaction) L-phenylalanine biosynthesis I L-phenylalanine degradation I (aerobic) L-proline biosynthesis I L-proline degradation L-rhamnose degradation I L-serine biosynthesis L-serine degradation L-sorbose degradation L-threonine biosynthesis L-threonine degradation I L-threonine degradation II L-threonine degradation III (to methylglyoxal) L-threonine degradation IV L-tryptophan biosynthesis L-tryptophan degradation I (via anthranilate) L-tryptophan degradation II (via pyruvate) L-tryptophan degradation VII (via indole-3-pyruvate) L-tyrosine biosynthesis I L-tyrosine degradation IV (to 4-methylphenol) L-valine biosynthesis L-valine degradation I L-valine degradation II lactate oxidation lactose and galactose degradation I lactose degradation II lactose degradation III Legionellosis leucine biosynthesis Leucine biosynthesis, 2-oxoisovalerate => 2-oxoisocaproate leucine degradation I leucine degradation III Leucine degradation, leucine => acetoacetate + acetyl-CoA LiaS-LiaR (cell wall stress response) two-component regulatory system LiaSR two-component signal transduction system Limonene and pinene degradation Lincosamide resistance, efflux pump LmrB Linoleic acid metabolism Lipid A-core biosynthesis lipid IVA biosynthesis lipid-A-precursor biosynthesis lipoate biosynthesis and incorporation (glycine cleavage system, yeast) lipoate biosynthesis and incorporation I lipoate biosynthesis and incorporation II lipoate biosynthesis and incorporation III (Bacillus) lipoate salvage and modification lipoate salvage I lipoate salvage II Lipoic acid metabolism Lipooligosaccharide transport system Lipopolysaccharide biosynthesis Lipopolysaccharide biosynthesis, inner core => outer core => O-antigen Lipopolysaccharide biosynthesis, KDO2-lipid A Lipopolysaccharide export system Lipopolysaccharide transport system Lipoprotein-releasing system long-chain fatty acid activation LuxQN/CqsS-LuxU-LuxO (quorum sensing) two-component regulatory system Lysine biosynthesis lysine biosynthesis I lysine biosynthesis II lysine biosynthesis VI Lysine biosynthesis, 2-oxoglutarate => 2-oxoadipate Lysine biosynthesis, acetyl-DAP pathway, aspartate => lysine Lysine biosynthesis, DAP aminotransferase pathway, aspartate => lysine Lysine biosynthesis, DAP dehydrogenase pathway, aspartate => lysine Lysine biosynthesis, mediated by LysW, 2-aminoadipate => lysine Lysine biosynthesis, succinyl-DAP pathway, aspartate => lysine Lysine degradation lysine degradation I lysine degradation VI lysine fermentation to acetate and butyrate Lysine/arginine/ornithine transport system LytS-LytR two-component regulatory system LytST two-component signal transduction system m-cresol degradation m-xylene degradation to m-toluate Macrolide resistance, MacAB-TolC transporter MalK-MalR (malate transport) two-component regulatory system malonate degradation I (biotin-independent) maltose degradation Maltose/maltodextrin transport system mandelate degradation I Manganese transport system Manganese/iron transport system Manganese/zinc transport system Manganese/zinc/iron transport system mannitol degradation I Mannopine transport system mannosylglucosylglycerate biosynthesis I ManS-ManR (manganese homeostasis) two-component regulatory system Mce transport system melibiose degradation menaquinol-6 biosynthesis menaquinol-7 biosynthesis menaquinol-8 biosynthesis menaquinol-9 biosynthesis Menaquinone biosynthesis, chorismate => menaquinone menaquinone-7 biosynthesis menaquinone-8 biosynthesis menaquinone-9 biosynthesis Metabolic pathways Methane metabolism Methane oxidation, methanotroph, methane => formaldehyde methanesulfonate degradation Methanogen Methanogenesis, acetate => methane Methanogenesis, CO2 => methane Methanogenesis, methanol => methane Methanogenesis, methylamine/dimethylamine/trimethylamine => methane methanol oxidation to formaldehyde II Methicillin resistance methionine and methyl-donor-molecule biosynthesis methionine and S-adenosylmethionine synthesis methionine biosynthesis I methionine biosynthesis II methionine biosynthesis III Methionine biosynthesis, apartate => homoserine => methionine Methionine degradation methionine degradation I (to homocysteine) methionine degradation II Methionine salvage pathway methyl parathion degradation Methyl-galactoside transport system Methylaspartate cycle methylerythritol phosphate pathway methylerythritol phosphate pathway I methylglyoxal degradation I methylglyoxal degradation II methylglyoxal degradation III methylglyoxal degradation IV methylglyoxal degradation IX methylmalonyl pathway methylphosphonate degradation I mevalonate degradation mevalonate pathway mevalonate pathway I Microbial metabolism in diverse environments Microcin C transport system Mismatch repair mixed acid fermentation Molybdate transport system Molybdate/tungstate transport system molybdenum cofactor biosynthesis molybdopterin guanine dinucleotide biosynthesis mono-trans, poly-cis decaprenyl phosphate biosynthesis Monobactam biosynthesis MprB-MprA (maintenance of persistent infection) two-component regulatory system mRNA surveillance pathway MtrB-MtrA (osmotic stress response) two-component regulatory system Multidrug resistance, efflux pump AbcA Multidrug resistance, efflux pump AcrAB-TolC/SmeDEF Multidrug resistance, efflux pump AcrAD-TolC Multidrug resistance, efflux pump AcrEF-TolC Multidrug resistance, efflux pump AdeABC Multidrug resistance, efflux pump AmeABC Multidrug resistance, efflux pump Bmr Multidrug resistance, efflux pump BpeEF-OprC Multidrug resistance, efflux pump EbrAB Multidrug resistance, efflux pump EmrAB Multidrug resistance, efflux pump GesABC Multidrug resistance, efflux pump MdtABC Multidrug resistance, efflux pump MdtEF-TolC Multidrug resistance, efflux pump MdtIJ Multidrug resistance, efflux pump MepA Multidrug resistance, efflux pump MexAB-OprM Multidrug resistance, efflux pump MexCD-OprJ Multidrug resistance, efflux pump MexEF-OprN Multidrug resistance, efflux pump MexJK-OprM Multidrug resistance, efflux pump MexPQ-OpmE Multidrug resistance, efflux pump MexXY-OprM Multidrug resistance, efflux pump NorA Multidrug resistance, efflux pump NorB Multidrug resistance, efflux pump OqxAB Multidrug resistance, efflux pump QacA Multidrug resistance, efflux pump SmeABC Multidrug resistance, efflux pump VexEF-TolC Multidrug resistance, efflux pump YkkCD Multidrug resistance, EfrAB transporter Multidrug resistance, MdlAB/SmdAB transporter Multidrug resistance, PatAB transporter Multidrug resistance, repression of porin OmpF Multidrug/hemolysin transport system Multiple protein transport system Multiple sugar transport system muropeptide degradation mycolate biosynthesis mycolyl-arabinogalactan-peptidoglycan complex biosynthesis mycothiol biosynthesis mycothiol oxidation mycothiol-mediated detoxification myo-, chiro- and scillo-inositol degradation myo-inositol biosynthesis myo-inositol degradation myo-inositol degradation I N,N'-Diacetylchitobiose transport system N-acetyl-galactosamine degradation N-acetylglucosamine degradation N-acetylglucosamine degradation I N-acetylglucosamine degradation II N-Acetylglucosamine transport system N-acetylglutaminylglutamine amide biosynthesis N-acetylneuraminate and N-acetylmannosamine degradation N-acetylneuraminate and N-acetylmannosamine degradation I N-acetylneuraminate biosynthesis II (bacteria) N10-formyl-tetrahydrofolate biosynthesis N6-L-threonylcarbamoyladenosine37-modified tRNA biosynthesis NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde NAD biosynthesis I (from aspartate) NAD biosynthesis, aspartate => NAD NAD phosphorylation and dephosphorylation NAD phosphorylation and dephosphorylation I NAD salvage pathway I NAD salvage pathway II NAD salvage pathway III NAD(P)H:quinone oxidoreductase, chloroplasts and cyanobacteria NADH to cytochrome bd oxidase electron transfer NADH to cytochrome bd oxidase electron transfer I NADH to cytochrome bd oxidase electron transport II NADH to cytochrome bo oxidase electron transfer NADH to cytochrome bo oxidase electron transfer I NADH to cytochrome bo oxidase electron transfer II NADH to dimethyl sulfoxide electron transfer NADH to fumarate electron transfer NADH to trimethylamine N-oxide electron transfer NADH:quinone oxidoreductase, prokaryotes Naphthalene and anthracene degradation Naphthalene degradation Naphthalene degradation, naphthalene => salicylate NarQ Two-Component Signal Transduction System, nitrate dependent NarQ-NarP (nitrate respiration) two-component regulatory system NarX Two-Component Signal Transduction System, nitrate dependent NarX-NarL (nitrate respiration) two-component regulatory system NatK-NatR (sodium extrusion) two-component regulatory system NatKR two-component signal transduction system NblS-NblR (photosynthesis) two-component regulatory system Neomycin, kanamycin and gentamicin biosynthesis neurosporene biosynthesis Neutral amino acid transport system Nickel transport system nicotinamide cycling Nicotinate and nicotinamide metabolism Nicotinate degradation, nicotinate => fumarate Nisin resistance, phage shock protein homolog LiaH Nitrate assimilation nitrate reduction III (dissimilatory) nitrate reduction IV (dissimilatory) nitrate reduction IX (dissimilatory) nitrate reduction V (assimilatory) nitrate reduction VIII (dissimilatory) nitrate reduction VIIIb (dissimilatory) nitrate reduction X (periplasmic, dissimilatory) Nitrate/nitrite transport system Nitrification, ammonia => nitrite nitrilotriacetate degradation nitrobenzene degradation I Nitrogen fixation, nitrogen => ammonia Nitrogen metabolism Nitrogen Regulation Two-Component System Nitrotoluene degradation NitT/TauT family transport system Nocardicin A biosynthesis, L-pHPG + arginine + serine => nocardicin A NOD-like receptor signaling pathway Nodulation Nogalavinone/aklavinone biosynthesis, deoxynogalonate/deoxyaklanonate => nogalavinone/aklavinone Non-homologous end-joining Non-phosphorylative Entner-Doudoroff pathway, gluconate/galactonate => glycerate nonaprenyl diphosphate biosynthesis nonaprenyl diphosphate biosynthesis I Nonribosomal peptide structures Novobiocin biosynthesis NreB-NreC (dissimilatory nitrate/nitrite reduction) two-component regulatory system NrsS-NrsR (nickel tolerance) two-component regulatory system NtrBC Two-Component Signal Transduction System, nitrogen-dependent NtrY-NtrX (nitrogen regulation) two-component regulatory system Nucleotide excision repair Nucleotide sugar biosynthesis, galactose => UDP-galactose Nucleotide sugar biosynthesis, glucose => UDP-glucose Nucleotide sugar biosynthesis, prokaryotes nylon-6 oligomer degradation O-antigen biosynthesis (E. coli) O-antigen building blocks biosynthesis (E. coli) octane oxidation octaprenyl diphosphate biosynthesis Octopine/nopaline transport system Oleandomycin transport system oleate beta-oxidation Oligogalacturonide transport system Oligopeptide transport system One carbon pool by folate ornithine biosynthesis Ornithine biosynthesis, glutamate => ornithine Ornithine biosynthesis, mediated by LysW, glutamate => ornithine ornithine degradation I (proline biosynthesis) ornithine degradation II (Stickland reaction) orthanilate degradation Osmoprotectant transport system Other glycan degradation oxalate degradation III oxalate degradation V oxidative ethanol degradation I oxidative ethanol degradation III Oxidative phosphorylation oxidized GTP and dGTP detoxification Oxygenic photosynthesis in plants and cyanobacteria p-cymene degradation to p-cumate p-xylene degradation to p-toluate palmitate biosynthesis II (bacteria and plants) palmitoleate biosynthesis I palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate) Pantothenate and CoA biosynthesis pantothenate and coenzyme A biosynthesis I pantothenate and coenzyme A biosynthesis II pantothenate biosynthesis I Pantothenate biosynthesis, valine/L-aspartate => pantothenate paraoxon degradation parathion degradation ParS-ParR (polymyxin-adaptive resistance) two-component regulatory system Pathogenic Escherichia coli infection Penicillin and cephalosporin biosynthesis Pentose and glucuronate interconversions pentose phosphate pathway pentose phosphate pathway (non-oxidative branch) pentose phosphate pathway (oxidative branch) pentose phosphate pathway (oxidative branch) I pentose phosphate pathway (partial) Pentose phosphate pathway (Pentose phosphate cycle) Pentose phosphate pathway, archaea, fructose 6P => ribose 5P Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P Peptides/nickel transport system Peptidoglycan biosynthesis peptidoglycan biosynthesis I peptidoglycan biosynthesis I (meso-diaminopimelate containing) peptidoglycan biosynthesis III (mycobacteria) peptidoglycan biosynthesis V (beta-lactam resistance) peptidoglycan maturation (meso-diaminopimelate containing) Pertussis Pertussis pathogenicity signature 1, pertussis toxin Pertussis pathogenicity signature 2, T1SS PfeS-PfeR (enterobactin-dependent iron acquisition) two-component regulatory system PgtB-PgtA (phosphoglycerate transport) two-component regulatory system phenylacetate degradation I (aerobic) phenylalanine biosynthesis I phenylalanine biosynthesis II Phenylalanine biosynthesis, chorismate => phenylalanine phenylalanine degradation I (aerobic) Phenylalanine metabolism Phenylalanine, tyrosine and tryptophan biosynthesis phenylethanol biosynthesis phenylethylamine degradation I PhoPR two-component signal transduction pathway PhoQ-PhoP (magnesium transport) two-component regulatory system PhoQP Two-Component Signal Transduction System, magnesium-dependent PhoR-PhoB (phosphate starvation response) two-component regulatory system PhoRB Two-Component Signal Transduction System, phosphate-dependent Phosphate acetyltransferase-acetate kinase pathway, acetyl-CoA => acetate phosphate acquisition Phosphate transport system phosphate utilization in cell wall regeneration Phosphatidylcholine (PC) biosynthesis, PE => PC phosphatidylcholine biosynthesis I phosphatidylcholine resynthesis via glycerophosphocholine Phosphatidylethanolamine (PE) biosynthesis, PA => PS => PE phosphatidylethanolamine biosynthesis I phosphatidylglycerol biosynthesis I (plastid) phosphatidylglycerol biosynthesis I (plastidic) phosphatidylglycerol biosynthesis II phosphatidylglycerol biosynthesis II (non-plastidic) phospholipases phospholipid biosynthesis I phospholipid biosynthesis II Phospholipid transport system Phosphonate and phosphinate metabolism phosphonate degradation Phosphonate transport system phosphopantothenate biosynthesis I Phosphotransferase system (PTS) photorespiration Photosynthesis Photosynthesis - antenna proteins Photosystem I Photosystem II Phthalate degradation, phthalate => protocatechuate Phthalate transport system PilS-PilR (type 4 fimbriae synthesis) two-component regulatory system Pimeloyl-ACP biosynthesis, BioC-BioH pathway, malonyl-ACP => pimeloyl-ACP PixL-PixGH (positive phototaxis) two-component regulatory system Plant-pathogen interaction PleC-PleD (cell fate control) two-component regulatory system Polyamine biosynthesis, arginine => agmatine => putrescine => spermidine Polyamine biosynthesis, arginine => ornithine => putrescine Polycyclic aromatic hydrocarbon degradation polyhydroxybutyrate biosynthesis polyisoprenoid biosynthesis (E. coli) Polyketide sugar unit biosynthesis polymyxin resistance Porphyrin and chlorophyll metabolism ppGpp biosynthesis preQ0 biosynthesis proline biosynthesis I proline biosynthesis III Proline biosynthesis, glutamate => proline proline degradation proline degradation I proline degradation II proline to cytochrome bo oxidase electron transfer Propanoate metabolism propanoyl CoA degradation I Propanoyl-CoA metabolism, propanoyl-CoA => succinyl-CoA propionyl CoA degradation Proteasome protein citrullination Protein export protocatechuate degradation II (ortho-cleavage pathway) protocatechuate degradation III (para-cleavage pathway) PRPP biosynthesis I PRPP biosynthesis II PRPP biosynthesis, ribose 5P => PRPP PrrB-PrrA (intracellular multiplication) two-component regulatory system pseudouridine degradation PTS system, 2-O-A-mannosyl-D-glycerate-specific II component PTS system, alpha-glucoside-specific II component PTS system, arbutin-like II component PTS system, ascorbate-specific II component PTS system, beta-glucoside (arbutin/salicin/cellobiose)-specific II component PTS system, beta-glucoside-specific II component PTS system, beta-glucosides-specific II component PTS system, cellobiose-specific II component PTS system, D-glucosaminate-specific II component PTS system, D-glucosamine-specific II component PTS system, fructose-specific II component PTS system, fructose-specific II-like component PTS system, fructoselysine/glucoselysine-specific II component PTS system, galactitol-specific II component PTS system, galactosamine-specific II component PTS system, glucitol/sorbitol-specific II component PTS system, glucose-specific II component PTS system, lactose-specific II component PTS system, maltose/glucose-specific II component PTS system, mannitol-specific II component PTS system, mannose-specific II component PTS system, N-acetylgalactosamine-specific II component PTS system, N-acetylglucosamine-specific II component PTS system, N-acetylmuramic acid-specific II component PTS system, sorbose-specific II component PTS system, sucrose-specific II component PTS system, trehalose-specific II component purine and pyrimidine metabolism purine degradation II (anaerobic) purine degradation III (anaerobic) Purine degradation, xanthine => urea purine deoxyribonucleosides degradation purine deoxyribonucleosides degradation I purine deoxyribonucleosides salvage Purine metabolism purine nucleobases degradation I (anaerobic) purine nucleotides de novo biosynthesis I purine nucleotides de novo biosynthesis II purine nucleotides degradation II (aerobic) purine nucleotides degradation IV (anaerobic) purine ribonucleosides degradation purine ribonucleosides degradation to ribose-1-phosphate puromycin biosynthesis Putative ABC transport system Putative aldouronate transport system Putative amino-acid transport system Putative chitobiose transport system Putative fructooligosaccharide transport system Putative glutamine transport system Putative hydroxymethylpyrimidine transport system Putative lysine transport system Putative multiple sugar transport system Putative peptide transport system Putative polar amino acid transport system Putative simple sugar transport system Putative sn-glycerol-phosphate transport system Putative sorbitol/mannitol transport system Putative spermidine/putrescine transport system Putative thiamine transport system Putative xylitol transport system Putative zinc/manganese transport system putrescine biosynthesis I putrescine biosynthesis II putrescine biosynthesis III putrescine degradation I putrescine degradation II putrescine degradation III Putrescine transport system pyridine nucleotide cycling pyridoxal 5'-phosphate biosynthesis pyridoxal 5'-phosphate biosynthesis I pyridoxal 5'-phosphate biosynthesis II pyridoxal 5'-phosphate salvage I pyridoxal 5'-phosphate salvage pathway Pyridoxal biosynthesis, erythrose-4P => pyridoxal-5P Pyrimidine degradation, uracil => beta-alanine, thymine => 3-aminoisobutanoate pyrimidine deoxyribonucleosides degradation pyrimidine deoxyribonucleosides salvage pyrimidine deoxyribonucleotide phosphorylation pyrimidine deoxyribonucleotides biosynthesis from CTP pyrimidine deoxyribonucleotides de novo biosynthesis pyrimidine deoxyribonucleotides de novo biosynthesis I pyrimidine deoxyribonucleotides de novo biosynthesis II pyrimidine deoxyribonucleotides de novo biosynthesis III pyrimidine deoxyribonucleotides dephosphorylation Pyrimidine deoxyribonuleotide biosynthesis, CDP/CTP => dCDP/dCTP,dTDP/dTTP Pyrimidine metabolism pyrimidine nucleobases salvage I pyrimidine nucleobases salvage II pyrimidine ribonucleosides degradation pyrimidine ribonucleosides degradation I pyrimidine ribonucleosides degradation II pyrimidine ribonucleosides salvage I pyrimidine ribonucleosides salvage II pyrimidine ribonucleosides salvage III Pyrimidine ribonucleotide biosynthesis, UMP => UDP/UTP,CDP/CTP pyrimidine ribonucleotides de novo biosynthesis pyrimidine ribonucleotides interconversion Pyrrolnitrin biosynthesis, tryptophan => pyrrolnitrin pyruvate decarboxylation to acetyl CoA pyruvate fermentation to acetate and lactate I pyruvate fermentation to acetate and lactate II pyruvate fermentation to acetate I pyruvate fermentation to acetate II pyruvate fermentation to acetate III pyruvate fermentation to acetate IV pyruvate fermentation to acetate V pyruvate fermentation to acetate VI pyruvate fermentation to acetate VII pyruvate fermentation to butanoate pyruvate fermentation to butanol I pyruvate fermentation to ethanol I pyruvate fermentation to ethanol II pyruvate fermentation to ethanol III pyruvate fermentation to lactate pyruvate fermentation to propanoate II (acrylate pathway) pyruvate fermentation to propionate I Pyruvate metabolism pyruvate oxidation pathway Pyruvate oxidation, pyruvate => acetyl-CoA pyruvate to cytochrome bd terminal oxidase electron transfer pyruvate to cytochrome bo oxidase electron transfer QseBC Two-Component Signal Transduction System, quorum sensing related QseC-QseB (quorum sensing) two-component regulatory system queuosine biosynthesis quinate degradation I Raffinose/stachyose/melibiose transport system RaxAB-RaxC type I secretion system RcsC-RcsD-RcsB (capsule synthesis) two-component regulatory system RcsCDB Two-Component Signal Transduction System reductive acetyl coenzyme A pathway Reductive acetyl-CoA pathway (Wood-Ljungdahl pathway) Reductive citrate cycle (Arnon-Buchanan cycle) reductive monocarboxylic acid cycle Reductive pentose phosphate cycle (Calvin cycle) Reductive pentose phosphate cycle, glyceraldehyde-3P => ribulose-5P Reductive pentose phosphate cycle, ribulose-5P => glyceraldehyde-3P RegB-RegA (redox response) two-component regulatory system removal of superoxide radicals ResE-ResD (aerobic and anaerobic respiration) two-component regulatory system ResED two-component signal transduction system respiration (anaerobic) rhamnogalacturonan type I degradation II (bacteria) Rhamnose transport system Riboflavin biosynthesis, GTP => riboflavin/FMN/FAD Riboflavin metabolism ribose degradation Ribose transport system Ribosome Ribosome, archaea Ribosome, bacteria RNA degradation RNA degradosome RNA polymerase RNA polymerase, archaea RNA polymerase, bacteria RpfC-RpfG (cell-to-cell signaling) two-component regulatory system RstB-RstA two-component regulatory system RstBA Two-Component Signal Transduction System RTX toxin transport system S-adenosyl-L-methionine biosynthesis S-adenosyl-L-methionine cycle S-adenosyl-L-methionine cycle I S-adenosyl-L-methionine cycle II S-adenosylmethionine biosynthesis S-Layer protein transport system S-methyl-5'-thioadenosine degradation I S-methyl-5'-thioadenosine degradation II S-methyl-5'-thioadenosine degradation IV S-methyl-5-thio-alpha-D-ribose 1-phosphate degradation S-methyl-5-thio-alpha-D-ribose 1-phosphate degradation I SaeS-SaeR (staphylococcal virulence regulation) two-component regulatory system Salicylate degradation, salicylate => gentisate salinosporamide A biosynthesis SalK-SalR two-component regulatory system Salmonella infection salvage pathways of adenine, hypoxanthine, and their nucleosides salvage pathways of guanine, xanthine, and their nucleosides salvage pathways of purine and pyrimidine nucleotides salvage pathways of pyrimidine deoxyribonucleotides salvage pathways of pyrimidine ribonucleotides SasA-RpaAB (circadian timing mediating) two-component regulatory system Sec (secretion) system Secondary bile acid biosynthesis sedoheptulose bisphosphate bypass seed germination protein turnover selenate reduction Selenoamino acid metabolism Selenocompound metabolism Semi-phosphorylative Entner-Doudoroff pathway, gluconate => glycerate-3P Semi-phosphorylative Entner-Doudoroff pathway, gluconate/galactonate => glycerate-3P SenX3-RegX3 (phosphate starvation response) two-component regulatory system serine and glycine biosynthesis II serine biosynthesis Serine biosynthesis, glycerate-3P => serine serine-isocitrate lyase pathway Sesquiterpenoid and triterpenoid biosynthesis Shigellosis shikimate degradation I Shikimate pathway, phosphoenolpyruvate + erythrose-4P => chorismate siroheme biosynthesis sitosterol degradation to androstenedione Sodium transport system sophorolipid degradation sophorosyloxydocosanoate degradation sorbitol biosynthesis II sorbitol degradation sorbitol degradation II spermidine biosynthesis I Spermidine/putrescine transport system spermine biosynthesis spermine biosynthesis II Sphingolipid metabolism sphingomyelin metabolism SsrA-SsrB two-component regulatory system Staphylococcus aureus infection Starch and sucrose metabolism starch degradation V Staurosporine biosynthesis stearate biosynthesis II (bacteria and plants) stearate biosynthesis II (plants) Steroid biosynthesis Steroid degradation Streptomycin biosynthesis Streptomycin resistance, deactivating enzyme StrAB Styrene degradation Succinate dehydrogenase, prokaryotes succinate fermentation to butanoate succinate to cytochrome bd oxidase electron transfer succinate to cytochrome bo oxidase electron transfer sucrose biosynthesis I (from photosynthesis) sucrose degradation I (sucrose phosphotransferase) sucrose degradation II (sucrose synthase) sucrose degradation IV sucrose degradation to ethanol and lactate (anaerobic) sulfate activation for sulfonation sulfate assimilation II sulfate reduction I (assimilatory) sulfate reduction II (assimilatory) sulfate reduction III (assimilatory) sulfate reduction III (dissimilatory) Sulfate transport system Sulfate-sulfur assimilation sulfide oxidation I (sulfide-quinone reductase) sulfide oxidation III (siroheme sulfite reductase) sulfite oxidation II sulfite oxidation III sulfite oxidation IV Sulfonate transport system sulfoquinovose degradation I Sulfur metabolism Sulfur relay system superoxide radicals degradation superpathway of (Kdo)2-lipid A biosynthesis superpathway of (R,R)-butanediol biosynthesis superpathway of 4-aminobutanoate degradation superpathway of 4-aminobutyrate degradation superpathway of 5-aminoimidazole ribonucleotide biosynthesis superpathway of acetate utilization and formation superpathway of acetyl-CoA biosynthesis superpathway of adenosine nucleotides de novo biosynthesis I superpathway of adenosine nucleotides de novo biosynthesis II superpathway of alanine biosynthesis superpathway of arginine and ornithine degradation superpathway of arginine and polyamine biosynthesis superpathway of arginine, putrescine, and 4-aminobutyrate degradation superpathway of aromatic amino acid biosynthesis superpathway of aromatic compound degradation via 3-oxoadipate superpathway of asparagine biosynthesis superpathway of aspartate and asparagine biosynthesis; interconversion of aspartate and asparagine superpathway of atrazine degradation superpathway of beta-D-glucuronide and D-glucuronate degradation superpathway of branched amino acid biosynthesis superpathway of butanediol biosynthesis superpathway of cholesterol degradation II (cholesterol dehydrogenase) superpathway of chorismate superpathway of chorismate metabolism superpathway of Clostridium acetobutylicum acidogenic fermentation superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle superpathway of D-glucarate and D-galactarate degradation superpathway of demethylmenaquinol-6 biosynthesis II superpathway of demethylmenaquinol-8 biosynthesis superpathway of demethylmenaquinol-9 biosynthesis superpathway of demethylmenaquinone-8 biosynthesis superpathway of fatty acid biosynthesis I (E. coli) superpathway of fatty acid biosynthesis II (plant) superpathway of fatty acid biosynthesis initiation (E. coli) superpathway of fucose and rhamnose degradation superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) superpathway of geranylgeranyldiphosphate biosynthesis II (via MEP) superpathway of gluconate degradation superpathway of glucose and xylose degradation superpathway of glutamate biosynthesis superpathway of glycol metabolism and degradation superpathway of glycolysis and Entner-Doudoroff superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass superpathway of glyoxylate bypass and TCA superpathway of glyoxylate cycle superpathway of guanine and guanosine salvage superpathway of guanosine nucleotides de novo biosynthesis I superpathway of guanosine nucleotides de novo biosynthesis II superpathway of heme biosynthesis from glycine superpathway of heme biosynthesis from uroporphyrinogen-III superpathway of hexitol degradation superpathway of hexitol degradation (bacteria) superpathway of hexuronide and hexuronate degradation superpathway of histidine, purine, and pyrimidine biosynthesis superpathway of KDO2-lipid A biosynthesis superpathway of L-alanine biosynthesis superpathway of L-arginine and L-ornithine degradation superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation superpathway of L-asparagine biosynthesis superpathway of L-aspartate and L-asparagine biosynthesis superpathway of L-citrulline metabolism superpathway of L-cysteine biosynthesis (mammalian) superpathway of L-isoleucine biosynthesis I superpathway of L-lysine, L-threonine and L-methionine biosynthesis I superpathway of L-lysine, L-threonine and L-methionine biosynthesis II superpathway of L-methionine biosynthesis (by sulfhydrylation) superpathway of L-methionine biosynthesis (transsulfuration) superpathway of L-methionine salvage and degradation superpathway of L-serine and glycine biosynthesis I superpathway of L-threonine biosynthesis superpathway of L-threonine metabolism superpathway of L-tryptophan biosynthesis superpathway of L-tyrosine biosynthesis superpathway of leucine, valine, and isoleucine biosynthesis superpathway of linalool biosynthesis superpathway of lipopolysaccharide biosynthesis superpathway of lysine, threonine and methionine biosynthesis I superpathway of lysine, threonine and methionine biosynthesis II superpathway of menaquinol-7 biosynthesis superpathway of menaquinol-8 biosynthesis I superpathway of menaquinol-9 biosynthesis superpathway of menaquinone-7 biosynthesis superpathway of menaquinone-8 biosynthesis superpathway of menaquinone-9 biosynthesis superpathway of methionine biosynthesis (by sulfhydrylation) superpathway of methionine biosynthesis (transsulfuration) superpathway of methylglyoxal degradation superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation superpathway of N-acetylneuraminate degradation superpathway of ornithine degradation superpathway of parathion degradation superpathway of phenylalanine biosynthesis superpathway of phenylalanine, tyrosine, and tryptophan biosynthesis superpathway of phenylalanine, tyrosine, and tryptophan biosynthesis from chorismate superpathway of phenylethylamine degradation superpathway of phosphatidate biosynthesis (yeast) superpathway of phospholipid biosynthesis I (bacteria) superpathway of polyamine biosynthesis I superpathway of polyamine biosynthesis II superpathway of purine deoxyribonucleosides degradation superpathway of purine nucleotides de novo biosynthesis I superpathway of purine nucleotides de novo biosynthesis II superpathway of pyridoxal 5'-phosphate biosynthesis and salvage superpathway of pyrimidine deoxyribonucleoside salvage superpathway of pyrimidine deoxyribonucleosides degradation superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli) superpathway of pyrimidine nucleobases salvage superpathway of pyrimidine ribonucleosides degradation superpathway of pyrimidine ribonucleosides salvage superpathway of pyrimidine ribonucleotides de novo biosynthesis superpathway of S-adenosyl-L-methionine biosynthesis superpathway of saturated and unsaturated fatty acid elongation superpathway of serine and glycine biosynthesis I superpathway of sulfate assimilation and cysteine biosynthesis superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) superpathway of testosterone and androsterone degradation superpathway of tetrahydrofolate biosynthesis superpathway of tetrahydrofolate biosynthesis and salvage superpathway of tetrathionate reduction (Salmonella typhimurium) superpathway of thiamin diphosphate biosynthesis I superpathway of thiamin diphosphate biosynthesis II superpathway of thiamine diphosphate biosynthesis I superpathway of thiamine diphosphate biosynthesis II superpathway of thiosulfate metabolism (Desulfovibrio sulfodismutans) superpathway of threonine metabolism superpathway of tryptophan biosynthesis superpathway of tyrosine biosynthesis superpathway of ubiquinol-8 biosynthesis (prokaryotic) superpathway of unsaturated fatty acids biosynthesis (E. coli) superpathway phosphatidate biosynthesis (yeast) Synthesis and degradation of ketone bodies Taurine and hypotaurine metabolism taurine degradation IV Taurine transport system TCA cycle TCA cycle I (prokaryotic) TCA cycle II (plants and fungi) TCA cycle III (helicobacter) TCA cycle IV (2-oxoglutarate decarboxylase) TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase) TCA cycle variation II TCA cycle variation III (eukaryotic) TCA cycle variation IV TCA cycle VII (acetate-producers) TCA cycle VIII (helicobacter) TctE-TctD (tricarboxylic acid transport) two-component regulatory system teichoic acid (poly-glycerol) biosynthesis Teichoic acid transport system Terephthalate degradation, terephthalate => 3,4-dihydroxybenzoate Terpenoid backbone biosynthesis testosterone and androsterone degradation to androstendione Tetracenomycin C/8-demethyltetracenomycin C biosynthesis, tetracenomycin F2 => tetracenomycin C/8-demethyltetracenomycin C Tetracycline biosynthesis Tetracycline resistance, efflux pump Tetracycline resistance, efflux pump Tet38 Tetracycline resistance, TetA transporter Tetracycline resistance, TetAB(46) transporter tetrahydrobioprein biosynthesis I tetrahydrofolate biosynthesis tetrahydrofolate biosynthesis II Tetrahydrofolate biosynthesis, GTP => THF tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate tetrahydromonapterin biosynthesis tetrahydrotyrosine biosynthesis tetrapyrrole biosynthesis II tetrapyrrole biosynthesis II (from glycine) thiamin biosynthesis I thiamin diphosphate biosynthesis I (E. coli) thiamin diphosphate biosynthesis II (Bacillus) thiamin diphosphate biosynthesis III (Staphylococcus) thiamin salvage I thiamin salvage II thiamin salvage III Thiamine biosynthesis, AIR => thiamine-P/thiamine-2P thiamine diphosphate biosynthesis I (E. coli) thiamine diphosphate biosynthesis II (Bacillus) thiamine diphosphate biosynthesis III (Staphylococcus) Thiamine metabolism thiamine salvage II thiamine salvage III Thiamine transport system thiazole biosynthesis I (E. coli) thiazole biosynthesis I (facultative anaerobic bacteria) thiazole biosynthesis II (aerobic bacteria) thiazole biosynthesis II (Bacillus) thio-molybdenum cofactor biosynthesis thioredoxin pathway thiosulfate disproportionation III (rhodanese) Thiosulfate oxidation by SOX complex, thiosulfate => sulfate threonine biosynthesis threonine biosynthesis from homoserine Threonine biosynthesis, aspartate => homoserine => threonine threonine degradation I threonine degradation II threonine degradation III (to methylglyoxal) threonine degradation IV thymine degradation Tocopherol/tocotorienol biosynthesis Toluene and xylene degradation Toluene degradation toluene degradation to benzoate toluene degradation to protocatechuate (via p-cresol) Toluene degradation, anaerobic, toluene => benzoyl-CoA Toluene degradation, toluene => benzoate TorS-TorR (TMAO respiration) two-component regulatory system TorSR Two-Component Signal Transduction System, TMAO dependent trans, trans-farnesyl diphosphate biosynthesis trans,trans-farnesyl diphosphate biosynthesis trans-4-hydroxy-L-proline degradation I Trans-cinnamate degradation, trans-cinnamate => acetyl-CoA trans-lycopene biosynthesis I (bacteria) TrcS-TrcR two-component regulatory system trehalose biosynthesis I trehalose biosynthesis II trehalose biosynthesis III Trehalose biosynthesis, D-glucose 1P => trehalose trehalose degradation I (low osmolarity) trehalose degradation II (trehalase) trehalose degradation IV trehalose degradation VI (periplasmic) Trehalose transport system Trehalose/maltose transport system triacylglycerol degradation triclosan resistance Trinitrotoluene degradation tryptophan biosynthesis Tryptophan biosynthesis, chorismate => tryptophan tryptophan degradation I (via anthranilate) tryptophan degradation II (via pyruvate) tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde Tryptophan metabolism Tryptophan metabolism, tryptophan => kynurenine => 2-aminomuconate TtrS-TtrR (tetrathionate respiration) two-component regulatory system Tuberculosis Tungstate transport system Twin-arginine translocation (Tat) system two-component alkanesulfonate monooxygenase Two-component system Type I polyketide structures Type II general secretion pathway Type II polyketide backbone biosynthesis, acyl-CoA + malonyl-CoA => polyketide Type III secretion system Type IV secretion system Type VI secretion system tyrosine biosynthesis I tyrosine biosynthesis II tyrosine biosynthesis III tyrosine biosynthesis IV Tyrosine biosynthesis, chorismate => tyrosine Tyrosine biosynthesis, prephanate => pretyrosine => tyrosine tyrosine degradation I tyrosine degradation IV (to 4-methylphenol) Tyrosine metabolism ubiquinol-8 biosynthesis (prokaryotic) Ubiquinone and other terpenoid-quinone biosynthesis Ubiquinone biosynthesis, prokaryotes, chorismate => ubiquinone ubiquinone-10 biosynthesis (prokaryotic) ubiquinone-7 biosynthesis (prokaryotic) ubiquinone-8 biosynthesis (prokaryotic) ubiquinone-9 biosynthesis (prokaryotic) UDP-alpha-D-glucuronate biosynthesis (from myo-inositol) UDP-alpha-D-glucuronate biosynthesis (from UDP-glucose) UDP-D-apiose biosynthesis (from UDP-D-glucuronate) UDP-D-galactose biosynthesis UDP-D-galacturonate biosynthesis I (from UDP-D-glucuronate) UDP-D-galacturonate biosynthesis II (from D-galacturonate) UDP-D-xylose biosynthesis UDP-galactofuranose biosynthesis UDP-galactose biosynthesis (salvage pathway from galactose using UDP-glucose) UDP-glucose biosynthesis UDP-glucose conversion UDP-L-arabinose biosynthesis II (from L-arabinose) UDP-L-rhamnose biosynthesis UDP-N-acetyl-alpha-D-fucosamine biosynthesis UDP-N-acetyl-alpha-D-mannosaminouronate biosynthesis UDP-N-acetyl-alpha-D-quinovosamine biosynthesis UDP-N-acetyl-D-galactosamine biosynthesis I UDP-N-acetyl-D-glucosamine biosynthesis I UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (generic) UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-DAP-containing) UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-diaminopimelate containing) UDP-N-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing) UDP-N-acetylmuramoyl-pentapeptide biosynthesis III (meso-DAP-containing) UDP-sugars interconversion UhpB-UhpA (hexose phosphates uptake) two-component regulatory system UhpBA Two Component Signal Transduction System UMP biosynthesis UMP biosynthesis II Uncharacterized ABC transport system Undecaprenylphosphate alpha-L-Ara4N biosynthesis, UDP-GlcA => undecaprenyl phosphate alpha-L-Ara4N uracil degradation I (reductive) uracil degradation II (reductive) uracil degradation III urate biosynthesis/inosine 5'-phosphate degradation urate degradation to allantoin urate degradation to allantoin I urea cycle urea degradation I urea degradation II Urea transport system ureide biosynthesis Uridine monophosphate biosynthesis, glutamine (+ PRPP) => UMP uridine-5'-phosphate biosynthesis UTP and CTP de novo biosynthesis UTP and CTP dephosphorylation I UTP and CTP dephosphorylation II V/A-type ATPase, prokaryotes valine biosynthesis valine degradation I valine degradation II Valine, leucine and isoleucine biosynthesis Valine, leucine and isoleucine degradation Valine/isoleucine biosynthesis, pyruvate => valine / 2-oxobutanoate => isoleucine Vanadium resistance, efflux pump MexGHI-OpmD Vancomycin resistance Vancomycin resistance, D-Ala-D-Lac type Vancomycin resistance, D-Ala-D-Ser type vanillin and vanillate degradation I vanillin and vanillate degradation II VanS-VanR (actinomycete type vancomycin resistance) two-component regulatory system VanS-VanR (VanB type vancomycin resistance) two-component regulatory system VanS-VanR (VanE type vancomycin resistance) two-component regulatory system Vibrio cholerae infection vibriobactin biosynthesis VicK-VicR (cell wall metabolism) two-component regulatory system Vitamin B12 transport system Vitamin B6 metabolism VraS-VraR (cell-wall peptidoglycan synthesis) two-component regulatory system WalKR two-component signal transduction system wound-induced proteolysis I WspE-WspRF (chemosensory) two-component regulatory system xanthine and xanthosine salvage Xanthomonas spp. pathogenicity signature, T3SS and effectors Xylene degradation Xylene degradation, xylene => methylbenzoate Xylobiose transport system xylose degradation I YdfH-YdfI two-component regulatory system YdfHI two-component signal transduction system YehUT Two-Component Signal Transduction System YesM-YesN two-component regulatory system YpdAB Two-Component Signal Transduction System YufLM two-component signal transduction system, malate-dependent YxdK-YxdJ (antimicrobial peptide response) two-component regulatory system YxdKJ two-component signal transduction system Zinc transport system ZraSR Two-Component Signal Transduction System [2Fe-2S] iron-sulfur cluster biosynthesis Unknown

Phenotype - Unknown Acetic-acid Acidophile African Algicidal Alkaliphile Alkalitolerant Alkalophile Alpha-hemolytic Amylase production Anoxygenic Anti-rotaviral Antibiotic resistant Antimicrobial activities Arsenic metabolizer Bacteriolytic Beta-hemolytic Biodegradation Biofertilizer Biofilm Bioluminescent Blackleg Bloom forming Budding Capnophilic Carbon sequestration Catalase negative Catalase positive Chitinase producer Chondroitinases producer Ciprofloxacin resistant Commensal Detoxification EBPR Ectoparasite Endemic Enteroaggregative Enterohemorrhagic Enteropathogenic Enterotoxigenic Epiphytic Facultative intracellular Fast growing Fastidious Flesh eating bacteria Food poisoning Fungicide Gliding Green non-sulfur Green sulfur Heparinases producer High-light adapted Highly Virulent Insect Parasite Intracellular Intracellular pathogen Keratin degradation L-Lysine containing Lacks Mycolic acids Lipid accumulating Lipophilic Low light adapted Luminescent Magnetotactic MDR (Multi-drug resistant) Metal resistant Metal-mobilizing Methylglucuronoxylan utilization Meticillin resistant Moxifloxacin resistant Multicellular Neutrophilic Nitrogen cycle Non-Biofilm forming Non-filamentous Non-Haemolytic Non-Pathogen Nonfermentative Nonmethanotrophic Nonprobiotic Nontyphoidal Nonvirulent Obligate intracellular Obligate intracellular parasite Obligate intracellular Pathogen Obligate parasite Opportunistic Pathogen Orange-colored Organic fertilizer Parasite Pathogen Photosynthetic Piezophile Pink-colored Plant-growth-promoting rhizobacteria Polar flagella Polyphosphate-accumulating Potential Pathogen Predatory Probiotic Protease production Proteolytic Radiation resistant Saline Salinosporamide producer Saprophyte Small Streptomycin resistant Subtilisin production Sulfur cycle Supports electricity generation Symbiont Symbiotic Synthesizes magnetosomes Thermoacidophile Toxic Ultramicro size Vancomycin resistant Vector of Pathogens Very low light adapted Virulent

Sporulation - Nonsporulating Sporulating Unknown

Motility - Motile Nonmotile Unknown

Temperature range - Hyperthermophile Mesophile Psychrophile Psychrotolerant Psychrotrophic Thermophile Thermotolerant Unknown

Oxygen requirement - Aerobe Anaerobe Facultative Facultative anaerobe Microaerophilic Obligate aerobe Obligate anaerobe Unknown

Biotic relationships - Endophytic Free-living Symbiotic Unknown

Cell Shape - Unknown Bean Coccoid Coccus Crescent Curved Disc Filament Flask Fusiform Helical Irregular Lancet Open-ring Oval Ovoid Pleomorphic Rod Sphere Spindle Spiral Spore Square Triangular Vibrio

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