Subsystems are shown if they have at least one gene assigned to them. Because many roles are assigned to more than one subsystem, the subsystem may not be present even if the gene annotation(s) are correct.
| Category | Subsystem | #Genes |
|---|
| Amino Acids and Derivatives : Alanine, serine, and glycine | Alanine biosynthesis | 4 |
| | Glycine Biosynthesis | 4 |
| | Glycine and Serine Utilization | 23 |
| | Glycine cleavage system | 5 |
| | Serine Biosynthesis | 11 |
| Amino Acids and Derivatives : Arginine; urea cycle, polyamines | Arginine Biosynthesis extended | 7 |
| | Arginine Deiminase Pathway | 1 |
| | Arginine and Ornithine Degradation | 7 |
| | Cyanophycin Metabolism | 1 |
| | Polyamine Metabolism | 4 |
| | Urea decomposition | 2 |
| Amino Acids and Derivatives : Aromatic amino acids and derivatives | Aromatic amino acid degradation | 2 |
| | Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. | 3 |
| | Chorismate Synthesis | 8 |
| | Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) | 7 |
| | Phenylalanine and Tyrosine Branches from Chorismate | 1 |
| | Tryptophan synthesis | 5 |
| Amino Acids and Derivatives : Branched-chain amino acids | Branched-Chain Amino Acid Biosynthesis | 17 |
| | HMG CoA Synthesis | 4 |
| | Isoleucine degradation | 16 |
| | Ketoisovalerate oxidoreductase | 4 |
| | Leucine Biosynthesis | 8 |
| | Leucine Degradation and HMG-CoA Metabolism | 11 |
| | Valine degradation | 18 |
| Amino Acids and Derivatives : Glutamine, glutamate, aspartate, asparagine; ammonia assimilation | Glutamate dehydrogenases | 2 |
| | Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis | 15 |
| | Glutamine synthetases | 2 |
| Amino Acids and Derivatives : Histidine Metabolism | Histidine Biosynthesis | 7 |
| Amino Acids and Derivatives : Lysine, threonine, methionine, and cysteine | Cysteine Biosynthesis | 12 |
| | Lysine Biosynthesis DAP Pathway | 3 |
| | Lysine degradation | 3 |
| | Methionine Biosynthesis | 18 |
| | Methionine Degradation | 10 |
| | Methionine Salvage | 4 |
| | Threonine anaerobic catabolism gene cluster | 2 |
| | Threonine and Homoserine Biosynthesis | 11 |
| | Threonine degradation | 4 |
| Amino Acids and Derivatives : Proline and 4-hydroxyproline | Proline, 4-hydroxyproline uptake and utilization | 3 |
| | Proline Synthesis | 4 |
| Carbohydrates | Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway | 1 |
| Carbohydrates : Aminosugars | Chitin and N-acetylglucosamine utilization | 2 |
| | N-Acetyl-Galactosamine and Galactosamine Utilization | 1 |
| Carbohydrates : CO2 fixation | CO2 uptake, carboxysome | 36 |
| | Calvin-Benson cycle | 12 |
| | Carboxysome | 41 |
| | Photorespiration (oxidative C2 cycle) | 16 |
| Carbohydrates : Central carbohydrate metabolism | Dihydroxyacetone kinases | 1 |
| | Entner-Doudoroff Pathway | 26 |
| | Glycolate, glyoxylate interconversions | 2 |
| | Glycolysis and Gluconeogenesis | 20 |
| | Glycolysis and Gluconeogenesis, including Archaeal enzymes | 17 |
| | Methylglyoxal Metabolism | 15 |
| | Pentose phosphate pathway | 9 |
| | Pyruvate Alanine Serine Interconversions | 4 |
| | Pyruvate metabolism I: anaplerotic reactions, PEP | 5 |
| | Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate | 27 |
| | TCA Cycle | 19 |
| Carbohydrates : Di- and oligosaccharides | Beta-Glucoside Metabolism | 5 |
| | Fructooligosaccharides(FOS) and Raffinose Utilization | 7 |
| | Lactose and Galactose Uptake and Utilization | 7 |
| | Lactose utilization | 2 |
| | Maltose and Maltodextrin Utilization | 6 |
| | Melibiose Utilization | 1 |
| | Trehalose Biosynthesis | 4 |
| | Trehalose Uptake and Utilization | 1 |
| Carbohydrates : Fermentation | Acetoin, butanediol metabolism | 3 |
| | Acetyl-CoA fermentation to Butyrate | 14 |
| | Butanol Biosynthesis | 11 |
| | Fermentations: Lactate | 1 |
| | Fermentations: Mixed acid | 16 |
| Carbohydrates : Monosaccharides | D-Galacturonate and D-Glucuronate Utilization | 1 |
| | D-Tagatose and Galactitol Utilization | 1 |
| | D-gluconate and ketogluconates metabolism | 1 |
| | D-ribose utilization | 1 |
| | Deoxyribose and Deoxynucleoside Catabolism | 1 |
| | Fructose utilization | 1 |
| | L-Arabinose utilization | 1 |
| | L-fucose utilization temp | 1 |
| | L-rhamnose utilization | 5 |
| | Mannose Metabolism | 8 |
| Carbohydrates : One-carbon Metabolism | One-carbon metabolism by tetrahydropterines | 5 |
| | Serine-glyoxylate cycle | 29 |
| Carbohydrates : Organic acids | Isobutyryl-CoA to Propionyl-CoA Module | 10 |
| | Lactate utilization | 5 |
| | Methylcitrate cycle | 1 |
| | Propionate-CoA to Succinate Module | 3 |
| Carbohydrates : Polysaccharides | Glycogen metabolism | 2 |
| Carbohydrates : Sugar alcohols | Di-Inositol-Phosphate biosynthesis | 2 |
| | Ethanolamine utilization | 1 |
| | Glycerol and Glycerol-3-phosphate Uptake and Utilization | 7 |
| | Glycerol fermenation to 1,3-propanediol | 1 |
| | Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization | 2 |
| Cell Division and Cell Cycle | Bacterial Cytoskeleton | 2 |
| | Control of cell elongation - division cycle in Bacilli | 1 |
| | Macromolecular synthesis operon | 4 |
| | Two cell division clusters relating to chromosome partitioning | 5 |
| | YgjD and YeaZ | 1 |
| Cell Wall and Capsule | Peptidoglycan Biosynthesis | 5 |
| | UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis | 3 |
| Cell Wall and Capsule : Capsular and extracellular polysacchrides | Alginate metabolism | 3 |
| | Capsular heptose biosynthesis | 3 |
| | Colanic acid biosynthesis | 3 |
| | O-Methyl Phosphoramidate Capsule Modification in Campylobacter | 2 |
| | Rhamnose containing glycans | 3 |
| | Sialic Acid Metabolism | 2 |
| | dTDP-rhamnose synthesis | 2 |
| Cell Wall and Capsule : Cell wall of Mycobacteria | linker unit-arabinogalactan synthesis | 3 |
| | mycolic acid synthesis | 11 |
| Cell Wall and Capsule : Gram-Negative cell wall components | KDO2-Lipid A biosynthesis | 1 |
| | Lipid A-Ara4N pathway ( Polymyxin resistance ) | 1 |
| Cell Wall and Capsule : Gram-Positive cell wall components | Teichuronic acid biosynthesis | 1 |
| Clustering-based subsystems | Bacterial Cell Division | 18 |
| | Bacterial RNA-metabolizing Zn-dependent hydrolases | 1 |
| | Conserved gene cluster associated with Met-tRNA formyltransferase | 8 |
| | LMPTP YfkJ cluster | 1 |
| | LMPTP YwlE cluster | 8 |
| | NusA-TFII Cluster | 6 |
| Clustering-based subsystems : Clustering-based subsystems | CBSS-262719.3.peg.410 | 1 |
| Clustering-based subsystems : Lysine, threonine, methionine, and cysteine | YeiH | 4 |
| Clustering-based subsystems : proteosome related | Cluster-based Subsystem Grouping Hypotheticals - perhaps Proteosome Related | 2 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments | Thiamin biosynthesis | 6 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Biotin | Biotin biosynthesis | 5 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme A | Coenzyme A Biosynthesis | 8 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Folate and pterines | Folate Biosynthesis | 13 |
| | Molybdenum cofactor biosynthesis | 5 |
| | Pterin biosynthesis | 2 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Lipoic acid | Lipoic acid metabolism | 3 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : NAD and NADP | NAD and NADP cofactor biosynthesis global | 8 |
| | NAD regulation | 4 |
| | PnuC-like transporters | 1 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Pyridoxine | Pyridoxin (Vitamin B6) Biosynthesis | 13 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Quinone cofactors | Ubiquinone Biosynthesis | 5 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Riboflavin, FMN, FAD | Riboflavin, FMN and FAD metabolism | 3 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Tetrapyrroles | Experimental tye | 6 |
| | Heme and Siroheme Biosynthesis | 7 |
| DNA Metabolism | YcfH | 2 |
| DNA Metabolism : DNA repair | DNA Repair Base Excision | 4 |
| | DNA repair, bacterial | 11 |
| | DNA repair, bacterial MutL-MutS system | 8 |
| | DNA repair, bacterial RecFOR pathway | 6 |
| | DNA repair, bacterial UvrD and related helicases | 1 |
| | DNA repair and recombination eukaryotic | 2 |
| DNA Metabolism : DNA replication | DNA-replication | 3 |
| | DNA replication, archaeal | 13 |
| | DNA topoisomerases, Type I, ATP-independent | 2 |
| | DNA topoisomerases, Type II, ATP-dependent | 1 |
| Fatty Acids, Lipids, and Isoprenoids | Polyhydroxybutyrate metabolism | 6 |
| Fatty Acids, Lipids, and Isoprenoids : Fatty acids | Fatty Acid Biosynthesis FASII | 13 |
| Fatty Acids, Lipids, and Isoprenoids : Isoprenoids | Archaeal lipids | 6 |
| | Carotenoids | 7 |
| | Isoprenoid Biosynthesis | 6 |
| | polyprenyl synthesis | 1 |
| Fatty Acids, Lipids, and Isoprenoids : Phospholipids | Glycerolipid and Glycerophospholipid Metabolism in Bacteria | 43 |
| Iron acquisition and metabolism | Campylobacter Iron Metabolism | 1 |
| Membrane Transport | Choline Transport | 1 |
| | Ton and Tol transport systems | 2 |
| | Transport of Manganese | 2 |
| | Transport of Nickel and Cobalt | 1 |
| Membrane Transport : Protein and nucleoprotein secretion system, Type IV | Type IV pilus | 1 |
| | pVir Plasmid of Campylobacter | 4 |
| Membrane Transport : Protein translocation across cytoplasmic membrane | Twin-arginine translocation system | 1 |
| Metabolism of Aromatic Compounds | Aromatic Amin Catabolism | 2 |
| | Benzoate transport and degradation cluster | 1 |
| | Cresol degradation | 1 |
| | Gentisare degradation | 5 |
| Metabolism of Aromatic Compounds : Metabolism of central aromatic intermediates | Catechol branch of beta-ketoadipate pathway | 4 |
| | Homogentisate pathway of aromatic compound degradation | 2 |
| | Protocatechuate branch of beta-ketoadipate pathway | 1 |
| | Salicylate and gentisate catabolism | 7 |
| Metabolism of Aromatic Compounds : Peripheral pathways for catabolism of aromatic compounds | Phenylpropanoid compound degradation | 1 |
| | Quinate degradation | 4 |
| | Salicylate ester degradation | 1 |
| | n-Phenylalkanoic acid degradation | 6 |
| Miscellaneous | ZZ gjo need homes | 12 |
| Miscellaneous : Plant-Prokaryote DOE project | Synechocystis experimental | 1 |
| Motility and Chemotaxis : Flagellar motility in Prokaryota | Flagellum | 1 |
| Nitrogen Metabolism | Allantoin Utilization | 1 |
| | Ammonia assimilation | 6 |
| | Cyanate hydrolysis | 3 |
| | Nitrate and nitrite ammonification | 5 |
| | Nitrogen fixation | 1 |
| Nucleosides and Nucleotides | Adenosyl nucleosidases | 1 |
| | Hydantoin metabolism | 3 |
| | Ribonucleotide reduction | 3 |
| Nucleosides and Nucleotides : Detoxification | Nudix proteins (nucleoside triphosphate hydrolases) | 2 |
| Nucleosides and Nucleotides : Purines | De Novo Purine Biosynthesis | 9 |
| | Purine Utilization | 5 |
| | Purine conversions | 23 |
| Nucleosides and Nucleotides : Pyrimidines | De Novo Pyrimidine Synthesis | 8 |
| Phages, Prophages, Transposable elements, Plasmids : Pathogenicity islands | Staphylococcal pathogenicity islands SaPI | 10 |
| Phosphorus Metabolism | Phosphate metabolism | 6 |
| Potassium metabolism | Potassium homeostasis | 2 |
| Protein Metabolism : Protein biosynthesis | Ribosome LSU bacterial | 9 |
| | Ribosome LSU eukaryotic and archaeal | 38 |
| | Ribosome SSU bacterial | 2 |
| | Ribosome SSU eukaryotic and archaeal | 29 |
| | Ribosome SSU mitochondrial | 1 |
| | Ribosome biogenesis bacterial | 1 |
| | Translation elongation factor G family | 5 |
| | Translation elongation factors eukaryotic and archaeal | 12 |
| | Translation initiation factors eukaryotic and archaeal | 13 |
| | Universal GTPases | 20 |
| | tRNA aminoacylation, Asp and Asn | 2 |
| | tRNA aminoacylation, Glu and Gln | 2 |
| Protein Metabolism : Protein degradation | Proteasome bacterial | 4 |
| | Proteasome eukaryotic | 33 |
| | Protein degradation | 4 |
| | Proteolysis in bacteria, ATP-dependent | 9 |
| Protein Metabolism : Protein folding | GroEL GroES | 9 |
| | Peptidyl-prolyl cis-trans isomerase | 1 |
| | Protein chaperones | 18 |
| | Thermosome, archaeal | 8 |
| Protein Metabolism : Protein processing and modification | N-linked Glycosylation in Bacteria | 1 |
| Protein Metabolism : Selenoproteins | Glycine reductase, sarcosine reductase and betaine reductase | 4 |
| RNA Metabolism : RNA processing and modification | Polyadenylation bacterial | 2 |
| | Queuosine-Archaeosine Biosynthesis | 12 |
| | RNA processing and degradation, bacterial | 3 |
| | Ribonuclease H | 2 |
| | Ribosome biogenesis archaeal | 1 |
| | Wyeosine-MimG Biosynthesis | 4 |
| | tRNA nucleotidyltransferase | 2 |
| | tRNA processing | 7 |
| RNA Metabolism : Transcription | RNA polymerase I | 7 |
| | RNA polymerase II | 10 |
| | RNA polymerase III | 9 |
| | RNA polymerase III initiation factors | 2 |
| | RNA polymerase II initiation factors | 12 |
| | RNA polymerase archaeal initiation factors | 1 |
| | Transcription factors cyanobacterial RpoD-like sigma factors | 1 |
| | Transcription initiation, bacterial sigma factors | 1 |
| Regulation and Cell signaling | Oxygen and light sensor PpaA-PpsR | 1 |
| | cAMP signaling in bacteria | 5 |
| Regulation and Cell signaling : Programmed Cell Death and Toxin-antitoxin Systems | Murein hydrolase regulation and cell death | 1 |
| Regulation and Cell signaling : Quorum sensing and biofilm formation | Quorum Sensing: Autoinducer-2 Synthesis | 1 |
| Respiration | Biogenesis of cytochrome c oxidases | 5 |
| | Formate hydrogenase | 1 |
| | Soluble cytochromes and functionally related electron carriers | 5 |
| Respiration : ATP synthases | F0F1-type ATP synthase | 3 |
| | V-Type ATP synthase | 2 |
| Respiration : Electron accepting reactions | Anaerobic respiratory reductases | 11 |
| | Terminal cytochrome C oxidases | 1 |
| | Ubiquinone Menaquinone-cytochrome c reductase complexes | 3 |
| Respiration : Electron donating reactions | Respiratory Complex I | 6 |
| | Respiratory dehydrogenases 1 | 9 |
| | Succinate dehydrogenase | 2 |
| Secondary Metabolism : Biologically active compounds in metazoan cell defence and differentiation | Quinolinic acid and its derivatives | 1 |
| Secondary Metabolism : Plant Hormones | Auxin biosynthesis | 7 |
| Stress Response | Bacterial hemoglobins | 1 |
| | Dimethylarginine metabolism | 4 |
| Stress Response : Acid stress | Acid resistance mechanisms | 3 |
| Stress Response : Detoxification | Glutathione-dependent pathway of formaldehyde detoxification | 3 |
| Stress Response : Heat shock | Heat shock dnaK gene cluster extended | 15 |
| Stress Response : Osmotic stress | Choline and Betaine Uptake and Betaine Biosynthesis | 6 |
| Stress Response : Oxidative stress | Glutaredoxins | 2 |
| | Glutathione: Biosynthesis and gamma-glutamyl cycle | 7 |
| | Glutathione: Non-redox reactions | 8 |
| | Glutathione: Redox cycle | 1 |
| | Oxidative stress | 6 |
| | Redox-dependent regulation of nucleus processes | 9 |
| | Rubrerythrin | 2 |
| Sulfur Metabolism | Galactosylceramide and Sulfatide metabolism | 3 |
| | Thioredoxin-disulfide reductase | 4 |
| Sulfur Metabolism : Organic sulfur assimilation | Alkanesulfonate assimilation | 3 |
| | Taurine Utilization | 3 |
| | Utilization of glutathione as a sulphur source | 2 |
| Virulence, Disease and Defense : Detection | MLST | 6 |
| Virulence, Disease and Defense : Invasion and intracellular resistance | Listeria surface proteins: Internalin-like proteins | 1 |
| Virulence, Disease and Defense : Resistance to antibiotics and toxic compounds | Arsenic resistance | 3 |
| | Beta-lactamase | 1 |
| | Cobalt-zinc-cadmium resistance | 2 |
| | Copper homeostasis | 4 |
| | Copper homeostasis: copper tolerance | 2 |
| | Multidrug Resistance Efflux Pumps | 1 |