KEGG Modules

Energy metabolism

 Carbon fixation

 Nitrogen metabolism
M00531 Assimilatory nitrate reduction, nitrate => ammonia [PATH: bam00910]
M00530 Dissimilatory nitrate reduction, nitrate => ammonia [PATH: bam00910]


 Methane metabolism
M00345 Formaldehyde assimilation, ribulose monophosphate pathway [PATH: bam00680]
M00344 Formaldehyde assimilation, xylulose monophosphate pathway [PATH: bam00680]


 Sulfur metabolism
M00176 Sulfur reduction, sulfate => H2S [PATH: bam00920]

Carbohydrate and lipid metabolism

 Central carbohydrate metabolism
M00002 Glycolysis, core module involving three-carbon compounds [PATH: bam00010]
M00003 Gluconeogenesis, oxaloacetate => fructose-6P [PATH: bam00010 bam00020]
M00307 Pyruvate oxidation, pyruvate => acetyl-CoA [PATH: bam00010 bam00020 bam00620]
M00009 Citrate cycle (TCA cycle, Krebs cycle) [PATH: bam00020]
M00010 Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH: bam00020]
M00011 Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH: bam00020]
M00004 Pentose phosphate pathway (Pentose phosphate cycle) [PATH: bam00030]
M00006 Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P [PATH: bam00030]
M00007 Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P [PATH: bam00030]
M00005 PRPP biosynthesis, ribose 5P => PRPP [PATH: bam00030 bam00230]
M00008 Entner-Doudoroff pathway, glucose-6P => glyceraldehyde-3P + pyruvate [PATH: bam00030]


 Other carbohydrate metabolism
M00012 Glyoxylate cycle [PATH: bam00630]


 Fatty acid metabolism
M00083 Fatty acid biosynthesis, elongation [PATH: bam00061]
M00086 beta-Oxidation, acyl-CoA synthesis [PATH: bam00071]
M00087 beta-Oxidation [PATH: bam00071]


 Lipid metabolism
M00093 Phosphatidylethanolamine (PE) biosynthesis, PA => PS => PE [PATH: bam00564]


 Lipopolysaccharide metabolism
M00063 CMP-KDO biosynthesis [PATH: bam00540]


 Sugar metabolism
M00549 Nucleotide sugar biosynthesis, glucose => UDP-glucose [PATH: bam00520]
M00554 Nucleotide sugar biosynthesis, galactose => UDP-galactose [PATH: bam00520 bam00052]


 Glycan metabolism

 Glycosaminoglycan metabolism

 Terpenoid backbone biosynthesis
M00096 C5 isoprenoid biosynthesis, non-mevalonate pathway [PATH: bam00900]
M00364 C10-C20 isoprenoid biosynthesis, bacteria [PATH: bam00900]


 Sterol biosynthesis

 Other terpenoid biosynthesis
Nucleotide and amino acid metabolism

 Purine metabolism
M00048 Inosine monophosphate biosynthesis, PRPP + glutamine => IMP [PATH: bam00230]
M00049 Adenine ribonucleotide biosynthesis, IMP => ADP,ATP [PATH: bam00230]
M00050 Guanine ribonucleotide biosynthesis IMP => GDP,GTP [PATH: bam00230]


 Pyrimidine metabolism
M00052 Pyrimidine ribonucleotide biosynthesis, UMP => UDP/UTP,CDP/CTP [PATH: bam00240]


 Serine and threonine metabolism
M00020 Serine biosynthesis, glycerate-3P => serine [PATH: bam00260]
M00018 Threonine biosynthesis, apartate => homoserine => threonine [PATH: bam00260]
M00555 Betaine biosynthesis, choline => betaine [PATH: bam00260]


 Cysteine and methionine metabolism
M00021 Cysteine biosynthesis, serine => cysteine [PATH: bam00270]
M00034 Methionine salvage pathway [PATH: bam00270]


 Branched-chain amino acid metabolism
M00019 Valine/isoleucine biosynthesis, pyruvate => valine / 2-oxobutanoate => isoleucine [PATH: bam00290]
M00570 Isoleucine biosynthesis, threonine => 2-oxobutanoate => isoleucine [PATH: bam00290]
M00432 Leucine biosynthesis, 2-oxoisovalerate => 2-oxoisocaproate [PATH: bam00290]
M00036 Leucine degradation, leucine => acetoacetate + acetyl-CoA [PATH: bam00280]


 Lysine metabolism
M00016 Lysine biosynthesis, succinyl-DAP pathway, aspartate => lysine [PATH: bam00300]
M00525 Lysine biosynthesis, acetyl-DAP pathway, aspartate => lysine [PATH: bam00300]


 Arginine and proline metabolism
M00015 Proline biosynthesis, glutamate => proline [PATH: bam00330]
M00028 Ornithine biosynthesis, glutamate => ornithine [PATH: bam00330]


 Histidine metabolism
M00026 Histidine biosynthesis, PRPP => histidine [PATH: bam00340]
M00045 Histidine degradation, histidine => N-formiminoglutamate => glutamate [PATH: bam00340]


 Aromatic amino acid metabolism
M00022 Shikimate pathway, phosphoenolpyruvate + erythrose-4P => chorismate [PATH: bam00400]
M00023 Tryptophan biosynthesis, chorismate => tryptophan [PATH: bam00400]
M00024 Phenylalanine biosynthesis, chorismate => phenylalanine [PATH: bam00400]
M00025 Tyrosine biosynthesis, chorismate => tyrosine [PATH: bam00400]
M00533 Homoprotocatechuate degradation, homoprotocatechuate => 2-oxohept-3-enedioate [PATH: bam00350]


 Other amino acid metabolism

 Cofactor and vitamin biosynthesis
M00127 Thiamine biosynthesis, AIR => thiamine-P/thiamine-2P [PATH: bam00730]
M00115 NAD biosynthesis, aspartate => NAD [PATH: bam00760]
M00119 Pantothenate biosynthesis, valine/L-aspartate => pantothenate [PATH: bam00770]
M00120 Coenzyme A biosynthesis, pantothenate => CoA [PATH: bam00770]
M00123 Biotin biosynthesis, pimeloyl-ACP/CoA => biotin [PATH: bam00780]
M00573 Biotin biosynthesis, BioI pathway, long-chain-acyl-ACP => pimeloyl-ACP => biotin [PATH: bam00780]
M00577 Biotin biosynthesis, BioW pathway, pimelate => pimeloyl-CoA => biotin [PATH: bam00780]
M00126 Tetrahydrofolate biosynthesis, GTP => THF [PATH: bam00790 bam00670]
M00118 Glutathione biosynthesis, glutamate => glutathione [PATH: bam00480]


 Polyamine biosynthesis
M00133 Polyamine biosynthesis, arginine => agmatine => putrescine => spermidine [PATH: bam00330]


 Phenylpropanoid and flavonoid biosynthesis

 Alkaloid and other secondary metabolite biosynthesis
Secondary metabolism

 Aromatics degradataion
M00551 Benzoate degradation, benzoate => catechol [PATH: bam00362 bam00622]
M00568 Catechol ortho-cleavage, catechol => 3-oxoadipate [PATH: bam00362]

Energy metabolism

 Photosynthesis

 ATP synthesis
M00144 NADH:quinone oxidoreductase, prokaryotes [PATH: bam00190]
M00149 Succinate dehydrogenase, prokaryotes [PATH: bam00190]
M00151 Cytochrome bc1 complex respiratory unit [PATH: bam00190]
M00155 Cytochrome c oxidase, prokaryotes [PATH: bam00190]
M00153 Cytochrome d ubiquinol oxidase [PATH: bam00190]
M00417 Cytochrome o ubiquinol oxidase [PATH: bam00190]
M00416 Cytochrome aa3-600 menaquinol oxidase [PATH: bam00190]
M00157 F-type ATPase, bacteria [PATH: bam00190]

Carbohydrate and lipid metabolism

 Carbohydrate metabolism
M00313 indolepyruvate:ferredoxin oxidoreductase


 Glycan metabolism
Genetic information processing

 DNA polymerase
M00260 DNA polymerase III complex, bacteria [BR:ko03032 ko03400][PATH: bam03030 bam03430 bam03440]


 Replication system

 Repair system

 RNA polymerase
M00183 RNA polymerase, bacteria [BR:ko03021 ko03400][PATH: bam03020]


 Spliceosome

 RNA processing

 Ribosome
M00178 Ribosome, bacteria [BR:ko03011][PATH: bam03010]


 Proteasome

 Ubiquitin system

 Protein processing
Environmental information processing

 Mineral and organic ion transport system
M00185 Sulfate transport system [BR:ko02000][PATH: bam02010]
M00189 Molybdate transport system [BR:ko02000][PATH: bam02010]
M00188 NitT/TauT family transport system [BR:ko02000]
M00436 Sulfonate transport system [BR:ko02000][PATH: bam02010]
M00190 Iron(III) transport system [BR:ko02000][PATH: bam02010]
M00300 Putrescine transport system [BR:ko02000][PATH: bam02010]
M00193 Putative spermidine/putrescine transport system [BR:ko02000]
M00302 2-Aminoethylphosphonate transport system [BR:ko02000][PATH: bam02010]
M00208 Glycine betaine/proline transport system [BR:ko02000][PATH: bam02010]
M00209 Osmoprotectant transport system [BR:ko02000][PATH: bam02010]


 Saccharide and polyol transport system
M00196 Multiple sugar transport system [BR:ko02000][PATH: bam02010]
M00213 L-Arabinose transport system [BR:ko02000][PATH: bam02010]
M00215 D-Xylose transport system [BR:ko02000][PATH: bam02010]
M00212 Ribose transport system [BR:ko02000][PATH: bam02010]
M00197 Putative fructooligosaccharide transport system [BR:ko02000]
M00198 Putative sn-glycerol-phosphate transport system [BR:ko02000][PATH: bam02010]
M00200 Putative sorbitol/mannitol transport system [BR:ko02000][PATH: bam02010]
M00207 Putative multiple sugar transport system [BR:ko02000]
M00221 Putative simple sugar transport system [BR:ko02000]
M00210 Putative ABC transport system [BR:ko02000]
M00211 Putative ABC transport system [BR:ko02000]


 Phosphate and amino acid transport system
M00222 Phosphate transport system [BR:ko02000][PATH: bam02010]
M00225 Lysine/arginine/ornithine transport system [BR:ko02000][PATH: bam02010]
M00226 Histidine transport system [BR:ko02000][PATH: bam02010]
M00230 Glutamate/aspartate transport system [BR:ko02000][PATH: bam02010]
M00231 Octopine/nopaline transport system [BR:ko02000][PATH: bam02010]
M00234 Cystine transport system [BR:ko02000][PATH: bam02010]
M00585 L-Cystine transport system [BR:ko02000][PATH: bam02010]
M00237 Branched-chain amino acid transport system [BR:ko02000][PATH: bam02010]
M00323 Urea transport system [BR:ko02000][PATH: bam02010]
M00238 D-Methionine transport system [BR:ko02000][PATH: bam02010]
M00228 Putative glutamine transport system [BR:ko02000][PATH: bam02010]
M00586 Putative amino-acid transport system [BR:ko02000][PATH: bam02010]
M00236 Putative polar amino acid transport system [BR:ko02000]


 Peptide and nickel transport system
M00439 Oligopeptide transport system [BR:ko02000][PATH: bam02010]
M00324 Dipeptide transport system [BR:ko02000][PATH: bam02010]
M00566 Dipeptide transport system, Firmicutes [BR:ko02000][PATH: bam02010]
M00348 Glutathione transport system [BR:ko02000][PATH: bam02010]
M00239 Peptides/nickel transport system [BR:ko02000][PATH: bam02010]
M00349 Microcin C transport system [BR:ko02000][PATH: bam02010]


 Metallic cation, iron-siderophore and vitamin B12 transport system
M00240 Iron complex transport system [BR:ko02000][PATH: bam02010]
M00242 Zinc transport system [BR:ko02000][PATH: bam02010]
M00582 Energy-coupling factor transport system [BR:ko02000][PATH: bam02010]
M00244 Putative zinc/manganese transport system [BR:ko02000]


 ABC-2 type and other transport systems
M00298 Multidrug/hemolysin transport system [BR:ko02000][PATH: bam02010]
M00250 Lipopolysaccharide transport system [BR:ko02000][PATH: bam02010]
M00320 Lipopolysaccharide export system [BR:ko02000][PATH: bam02010]
M00251 Teichoic acid transport system [BR:ko02000][PATH: bam02010]
M00252 Lipooligosaccharide transport system [BR:ko02000][PATH: bam02010]
M00314 Bacitracin transport system [BR:ko02000][PATH: bam02010 bam02020]
M00255 Lipoprotein-releasing system [BR:ko02000][PATH: bam02010]
M00584 Acetoin utilization transport system [BR:ko02000][PATH: bam02010]
M00256 Cell division transport system [BR:ko02000][PATH: bam02010]
M00315 Uncharacterized ABC transport system [BR:ko02000][PATH: bam02020]
M00248 Putative antibiotic transport system [BR:ko02000][PATH: bam02010]
M00258 Putative ABC transport system [BR:ko02000]


 Phosphotransferase system (PTS)
M00282 PTS system, D-glucosamine-specific II component [BR:ko02000][PATH: bam00520 bam02060]
M00271 PTS system, beta-glucosides-specific II component [BR:ko02000][PATH: bam02060]
M00270 PTS system, trehalose-specific II component [BR:ko02000][PATH: bam00500 bam02060]
M00268 PTS system, arbutin-like II component [BR:ko02000][PATH: bam00010 bam02060]
M00273 PTS system, fructose-specific II component [BR:ko02000][PATH: bam00051 bam02060]
M00274 PTS system, mannitol-specific II component [BR:ko02000][PATH: bam00051 bam02060]
M00281 PTS system, lactose-specific II component [BR:ko02000][PATH: bam00052 bam02060]
M00275 PTS system, cellobiose-specific II component [BR:ko02000][PATH: bam02060]


 Bacterial secretion system
M00330 Adhesin protein transport system [BR:ko02044]
M00331 Type II general secretion system [BR:ko02044][PATH: bam03070]
M00332 Type III secretion system [BR:ko02044][PATH: bam03070]
M00333 Type IV secretion system [BR:ko02044][PATH: bam03070]
M00334 Type VI secretion system [BR:ko02044][PATH: bam03070]
M00335 Sec (secretion) system [BR:ko02044][PATH: bam03070]
M00336 Twin-arginine translocation (Tat) system [BR:ko02044][PATH: bam03070]
M00429 Competence-related DNA transformation transporter [BR:ko02044]

Metabolism

 Aminoacyl tRNA
M00360 Aminoacyl-tRNA biosynthesis, prokaryotes [PATH: bam00970]


 Nucleotide sugar
Environmental information processing

 Two-component regulatory system
M00434 PhoR-PhoB (phosphate starvation response) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00445 EnvZ-OmpR (osmotic stress response) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00448 CssS-CssR (secretion stress response) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00452 CusS-CusR (copper tolerance) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00454 KdpD-KdpE (potassium transport) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00457 TctE-TctD (tricarboxylic acid transport) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00458 ResE-ResD (aerobic and anaerobic respiration) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00459 VicK-VicR (cell wall metabolism) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00469 BceS-BceR (bacitracin transport) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00476 ComP-ComA (competence) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00478 DegS-DegU (multicellular behavior control) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00479 DesK-DesR (membrane lipid fluidity regulation) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00481 LiaS-LiaR (cell wall stress response) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00485 KinABCDE-Spo0FA (sporulation control) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00490 MalK-MalR (malate transport) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00492 LytS-LytR (autolysis and cell wall metabolism) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00497 GlnL-GlnG (nitrogen regulation) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00504 DctB-DctD (C4-dicarboxylate transport) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00509 WspE-WspRF (chemosensory) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00518 GlnK-GlnL (glutamine utilization) two-component regulatory system [BR:ko02022][PATH: bam02020]
M00523 RegB-RegA (redox response) two-component regulatory system [BR:ko02022][PATH: bam02020]

Genotypic signature

 Pathogenicity