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 | 7 |
| | Glycine Biosynthesis | 1 |
| | Glycine and Serine Utilization | 13 |
| | Glycine cleavage system | 5 |
| | Serine Biosynthesis | 5 |
| Amino Acids and Derivatives : Arginine; urea cycle, polyamines | Arginine Biosynthesis extended | 10 |
| | Arginine Deiminase Pathway | 2 |
| | Arginine and Ornithine Degradation | 11 |
| | Cyanophycin Metabolism | 1 |
| | Polyamine Metabolism | 8 |
| | Urea decomposition | 1 |
| Amino Acids and Derivatives : Aromatic amino acids and derivatives | Aromatic amino acid degradation | 1 |
| | Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. | 5 |
| | Chorismate Synthesis | 14 |
| | Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) | 12 |
| | Phenylalanine and Tyrosine Branches from Chorismate | 6 |
| | Tryptophan synthesis | 7 |
| Amino Acids and Derivatives : Branched-chain amino acids | Branched-Chain Amino Acid Biosynthesis | 14 |
| | Isoleucine degradation | 5 |
| | Ketoisovalerate oxidoreductase | 1 |
| | Leucine Biosynthesis | 5 |
| | Leucine Degradation and HMG-CoA Metabolism | 1 |
| | Valine degradation | 5 |
| Amino Acids and Derivatives : Glutamine, glutamate, aspartate, asparagine; ammonia assimilation | Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis | 12 |
| | Glutamine synthetases | 1 |
| Amino Acids and Derivatives : Histidine Metabolism | Histidine Biosynthesis | 8 |
| Amino Acids and Derivatives : Lysine, threonine, methionine, and cysteine | Cysteine Biosynthesis | 20 |
| | Lysine Biosynthesis DAP Pathway | 10 |
| | Lysine degradation | 2 |
| | Methionine Biosynthesis | 25 |
| | Methionine Degradation | 7 |
| | Methionine Salvage | 5 |
| | Threonine anaerobic catabolism gene cluster | 4 |
| | Threonine and Homoserine Biosynthesis | 10 |
| Amino Acids and Derivatives : Proline and 4-hydroxyproline | Proline, 4-hydroxyproline uptake and utilization | 7 |
| | Proline Synthesis | 3 |
| Carbohydrates | Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway | 2 |
| Carbohydrates : Aminosugars | Chitin and N-acetylglucosamine utilization | 10 |
| | N-Acetyl-Galactosamine and Galactosamine Utilization | 2 |
| Carbohydrates : CO2 fixation | Calvin-Benson cycle | 11 |
| | Carboxysome | 5 |
| | Photorespiration (oxidative C2 cycle) | 12 |
| Carbohydrates : Central carbohydrate metabolism | Dihydroxyacetone kinases | 1 |
| | Entner-Doudoroff Pathway | 15 |
| | Glycolate, glyoxylate interconversions | 3 |
| | Glycolysis and Gluconeogenesis | 15 |
| | Glycolysis and Gluconeogenesis, including Archaeal enzymes | 12 |
| | Methylglyoxal Metabolism | 1 |
| | Pentose phosphate pathway | 11 |
| | Pyruvate Alanine Serine Interconversions | 7 |
| | Pyruvate metabolism I: anaplerotic reactions, PEP | 7 |
| | Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate | 9 |
| | TCA Cycle | 17 |
| Carbohydrates : Di- and oligosaccharides | Beta-Glucoside Metabolism | 5 |
| | Fructooligosaccharides(FOS) and Raffinose Utilization | 1 |
| | Lactose and Galactose Uptake and Utilization | 11 |
| | Lactose utilization | 1 |
| | Maltose and Maltodextrin Utilization | 12 |
| | Sucrose utilization | 4 |
| | Sucrose utilization Shewanella | 1 |
| | Trehalose Biosynthesis | 4 |
| | Trehalose Uptake and Utilization | 4 |
| Carbohydrates : Fermentation | Acetoin, butanediol metabolism | 4 |
| | Acetyl-CoA fermentation to Butyrate | 4 |
| | Butanol Biosynthesis | 6 |
| | Fermentations: Lactate | 2 |
| | Fermentations: Mixed acid | 15 |
| Carbohydrates : Glycoside hydrolases | Predicted carbohydrate hydrolases | 3 |
| Carbohydrates : Monosaccharides | 2-Ketogluconate Utilization | 1 |
| | D-Galacturonate and D-Glucuronate Utilization | 9 |
| | D-Tagatose and Galactitol Utilization | 1 |
| | D-galactarate, D-glucarate and D-glycerate catabolism | 8 |
| | D-gluconate and ketogluconates metabolism | 5 |
| | D-ribose utilization | 4 |
| | Deoxyribose and Deoxynucleoside Catabolism | 7 |
| | Fructose utilization | 10 |
| | L-Arabinose utilization | 5 |
| | L-ascorbate utilization (and related gene clusters) | 12 |
| | L-fucose utilization | 1 |
| | L-rhamnose utilization | 9 |
| | Xylose utilization | 2 |
| Carbohydrates : One-carbon Metabolism | One-carbon metabolism by tetrahydropterines | 4 |
| | Serine-glyoxylate cycle | 16 |
| Carbohydrates : Organic acids | Isobutyryl-CoA to Propionyl-CoA Module | 1 |
| | Lactate utilization | 2 |
| | Propionate-CoA to Succinate Module | 1 |
| Carbohydrates : Polysaccharides | Glycogen metabolism | 4 |
| Carbohydrates : Sugar alcohols | Di-Inositol-Phosphate biosynthesis | 1 |
| | Ethanolamine utilization | 2 |
| | Glycerol and Glycerol-3-phosphate Uptake and Utilization | 11 |
| | Glycerol fermenation to 1,3-propanediol | 1 |
| | Inositol catabolism | 13 |
| | Mannitol Utilization | 7 |
| | Propanediol utilization | 1 |
| | Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization | 2 |
| Cell Division and Cell Cycle | Bacterial Cytoskeleton | 22 |
| | Control of cell elongation - division cycle in Bacilli | 1 |
| | Macromolecular synthesis operon | 8 |
| | MukBEF Chromosome Condensation | 5 |
| | Two cell division clusters relating to chromosome partitioning | 6 |
| Cell Wall and Capsule | Peptidoglycan Biosynthesis | 27 |
| | UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis | 8 |
| Cell Wall and Capsule : Capsular and extracellular polysacchrides | CMP-N-acetylneuraminate Biosynthesis | 1 |
| | Capsular heptose biosynthesis | 5 |
| | Colanic acid biosynthesis | 6 |
| | O-Methyl Phosphoramidate Capsule Modification in Campylobacter | 1 |
| | Rhamnose containing glycans | 10 |
| | Sialic Acid Metabolism | 9 |
| | dTDP-rhamnose synthesis | 7 |
| Cell Wall and Capsule : Cell wall of Mycobacteria | linker unit-arabinogalactan synthesis | 8 |
| | mycolic acid synthesis | 6 |
| Cell Wall and Capsule : Gram-Negative cell wall components | KDO2-Lipid A biosynthesis | 15 |
| | LOS core oligosaccharide biosynthesis | 12 |
| | Lipid A-Ara4N pathway ( Polymyxin resistance ) | 8 |
| | Lipid A modifications | 7 |
| | Lipopolysaccharide-related cluster in Alphaproteobacteria | 1 |
| Cell Wall and Capsule : Gram-Positive cell wall components | Teichoic and lipoteichoic acids biosynthesis | 3 |
| | Teichuronic acid biosynthesis | 2 |
| Clustering-based subsystems | Bacterial Cell Division | 25 |
| | Bacterial RNA-metabolizing Zn-dependent hydrolases | 7 |
| | CBSS-214092.1.peg.3450 | 5 |
| | CBSS-562.2.peg.5158 SK3 including | 5 |
| | Conserved gene cluster associated with Met-tRNA formyltransferase | 16 |
| | LMPTP YfkJ cluster | 1 |
| | LMPTP YwlE cluster | 4 |
| | NusA-TFII Cluster | 3 |
| | PA0057 cluster | 1 |
| | Putative hemin transporter | 1 |
| Clustering-based subsystems : Clustering-based subsystems | CBSS-262719.3.peg.410 | 2 |
| Clustering-based subsystems : Lysine, threonine, methionine, and cysteine | YeiH | 2 |
| Clustering-based subsystems : Type III secretion system, extended | Type III secretion systems, extended | 17 |
| Clustering-based subsystems : proteosome related | Cluster-based Subsystem Grouping Hypotheticals - perhaps Proteosome Related | 2 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments | Thiamin biosynthesis | 10 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Biotin | Biotin biosynthesis | 8 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme A | Coenzyme A Biosynthesis | 10 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Folate and pterines | Folate Biosynthesis | 21 |
| | Molybdenum cofactor biosynthesis | 14 |
| | Pterin biosynthesis | 1 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Lipoic acid | Lipoic acid metabolism | 4 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : NAD and NADP | NAD and NADP cofactor biosynthesis global | 13 |
| | NAD regulation | 9 |
| | PnuC-like transporters | 2 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Pyridoxine | Pyridoxin (Vitamin B6) Biosynthesis | 11 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Quinone cofactors | Menaquinone and Phylloquinone Biosynthesis | 4 |
| | Ubiquinone Biosynthesis | 10 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Riboflavin, FMN, FAD | Flavodoxin | 4 |
| | Riboflavin, FMN and FAD metabolism | 3 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Tetrapyrroles | Coenzyme B12 biosynthesis | 1 |
| | Experimental tye | 13 |
| | Heme and Siroheme Biosynthesis | 14 |
| DNA Metabolism | DNA structural proteins, bacterial | 8 |
| | Restriction-Modification System | 7 |
| | YcfH | 3 |
| DNA Metabolism : DNA recombination | RuvABC plus a hypothetical | 3 |
| DNA Metabolism : DNA repair | 2-phosphoglycolate salvage | 4 |
| | DNA Repair Base Excision | 15 |
| | DNA repair, UvrABC system | 3 |
| | DNA repair, bacterial | 43 |
| | DNA repair, bacterial DinG and relatives | 2 |
| | DNA repair, bacterial MutL-MutS system | 2 |
| | DNA repair, bacterial RecFOR pathway | 10 |
| | DNA repair, bacterial UvrD and related helicases | 3 |
| DNA Metabolism : DNA replication | DNA-replication | 46 |
| | DNA replication, archaeal | 1 |
| | DNA topoisomerases, Type I, ATP-independent | 3 |
| | DNA topoisomerases, Type II, ATP-dependent | 5 |
| | Plasmid replication | 2 |
| Fatty Acids, Lipids, and Isoprenoids | Polyhydroxybutyrate metabolism | 3 |
| Fatty Acids, Lipids, and Isoprenoids : Fatty acids | Fatty Acid Biosynthesis FASII | 13 |
| Fatty Acids, Lipids, and Isoprenoids : Isoprenoids | Archaeal lipids | 5 |
| | Carotenoids | 2 |
| | Isoprenoid Biosynthesis | 12 |
| | Polyprenyl Diphosphate Biosynthesis | 2 |
| | polyprenyl synthesis | 7 |
| Fatty Acids, Lipids, and Isoprenoids : Phospholipids | Glycerolipid and Glycerophospholipid Metabolism in Bacteria | 24 |
| Fatty Acids, Lipids, and Isoprenoids : Triacylglycerols | Triacylglycerol metabolism | 1 |
| Iron acquisition and metabolism | Campylobacter Iron Metabolism | 5 |
| | Heme, hemin uptake and utilization systems in GramPositives | 1 |
| | Hemin transport system | 6 |
| | Iron acquisition in Vibrio | 14 |
| | Transport of Iron | 9 |
| Iron acquisition and metabolism : Siderophores | Siderophore Aerobactin | 2 |
| Membrane Transport | Ton and Tol transport systems | 14 |
| | Transport of Manganese | 6 |
| | Transport of Molybdenum | 4 |
| | Transport of Zinc | 8 |
| Membrane Transport : ABC transporters | ABC transporter alkylphosphonate (TC 3.A.1.9.1) | 1 |
| | ABC transporter branched-chain amino acid (TC 3.A.1.4.1) | 5 |
| | ABC transporter dipeptide (TC 3.A.1.5.2) | 9 |
| | ABC transporter oligopeptide (TC 3.A.1.5.1) | 10 |
| | ABC transporter peptide (TC 3.A.1.5.5) | 3 |
| Membrane Transport : Protein and nucleoprotein secretion system, Type IV | Type IV pilus | 11 |
| | pVir Plasmid of Campylobacter | 6 |
| Membrane Transport : Protein secretion system, Type III | Type III secretion system orphans | 2 |
| Membrane Transport : Protein translocation across cytoplasmic membrane | Twin-arginine translocation system | 4 |
| Membrane Transport : Sugar Phosphotransferase Systems, PTS | Fructose and Mannose Inducible PTS | 2 |
| Membrane Transport : Uni- Sym- and Antiporters | Na(+) H(+) antiporter | 2 |
| Metabolism of Aromatic Compounds | Aromatic Amin Catabolism | 1 |
| | Benzoate transport and degradation cluster | 1 |
| | Gentisare degradation | 1 |
| Metabolism of Aromatic Compounds : Metabolism of central aromatic intermediates | Homogentisate pathway of aromatic compound degradation | 3 |
| | Salicylate and gentisate catabolism | 2 |
| Metabolism of Aromatic Compounds : Peripheral pathways for catabolism of aromatic compounds | Benzoate degradation | 1 |
| | Phenylpropanoid compound degradation | 1 |
| | Quinate degradation | 2 |
| | Salicylate ester degradation | 1 |
| | n-Phenylalkanoic acid degradation | 4 |
| | p-Hydroxybenzoate degradation | 1 |
| Miscellaneous | YaaA | 1 |
| | YbbK | 2 |
| | ZZ gjo need homes | 10 |
| Miscellaneous : Plant-Prokaryote DOE project | Conserved gene cluster possibly involved in RNA metabolism | 2 |
| | Synechocystis experimental | 1 |
| Motility and Chemotaxis | Bacterial Chemotaxis | 32 |
| Motility and Chemotaxis : Flagellar motility in Prokaryota | Flagellar motility | 17 |
| | Flagellum | 46 |
| | Flagellum in Campylobacter | 5 |
| Nitrogen Metabolism | Allantoin Utilization | 2 |
| | Ammonia assimilation | 9 |
| | Cyanate hydrolysis | 4 |
| | Dissimilatory nitrite reductase | 1 |
| | Nitrate and nitrite ammonification | 1 |
| | Nitric oxide synthase | 4 |
| Nucleosides and Nucleotides | Adenosyl nucleosidases | 2 |
| | Ribonucleotide reduction | 9 |
| Nucleosides and Nucleotides : Detoxification | Nudix proteins (nucleoside triphosphate hydrolases) | 11 |
| Nucleosides and Nucleotides : Purines | De Novo Purine Biosynthesis | 12 |
| | Purine Utilization | 4 |
| | Purine conversions | 19 |
| | Purine nucleotide synthesis regulator | 1 |
| Nucleosides and Nucleotides : Pyrimidines | De Novo Pyrimidine Synthesis | 11 |
| | Pyrimidine utilization | 4 |
| Phages, Prophages, Transposable elements : Bacteriophage structural proteins | Phage capsid proteins | 12 |
| Phages, Prophages, Transposable elements, Plasmids : Pathogenicity islands | Listeria Pathogenicity Island LIPI-1 extended | 1 |
| | Staphylococcal pathogenicity islands SaPI | 5 |
| | Vibrio pathogenicity island | 1 |
| Phages, Prophages, Transposable elements, Plasmids : Phages, Prophages | Staphylococcal phi-Mu50B-like prophages | 1 |
| Phosphorus Metabolism | Alkylphosphonate utilization | 4 |
| | High affinity phosphate transporter and control of PHO regulon | 8 |
| | Phosphate metabolism | 24 |
| Potassium metabolism | Glutathione-regulated potassium-efflux system and associated functions | 4 |
| | Potassium homeostasis | 14 |
| Protein Metabolism : Protein biosynthesis | Ribosome LSU bacterial | 31 |
| | Ribosome SSU bacterial | 19 |
| | Ribosome activity modulation | 3 |
| | Ribosome biogenesis bacterial | 11 |
| | Trans-translation by stalled ribosomes | 1 |
| | Translation elongation factor G family | 1 |
| | Translation elongation factors eukaryotic and archaeal | 1 |
| | Translation initiation factors eukaryotic and archaeal | 2 |
| | Universal GTPases | 15 |
| | tRNA aminoacylation, Asp and Asn | 2 |
| | tRNA aminoacylation, Glu and Gln | 2 |
| Protein Metabolism : Protein degradation | Proteasome bacterial | 6 |
| | Protein degradation | 2 |
| | Proteolysis in bacteria, ATP-dependent | 17 |
| | Putative TldE-TldD proteolytic complex | 1 |
| Protein Metabolism : Protein folding | GroEL GroES | 2 |
| | Peptidyl-prolyl cis-trans isomerase | 3 |
| | Periplasmic disulfide interchange | 4 |
| | Protein chaperones | 10 |
| Protein Metabolism : Protein processing and modification | N-linked Glycosylation in Bacteria | 2 |
| | Ribosomal protein S12p Asp methylthiotransferase | 3 |
| | Ribosomal protein S5p acylation | 2 |
| | Signal peptidase | 2 |
| Protein Metabolism : Selenoproteins | Glycine reductase, sarcosine reductase and betaine reductase | 2 |
| RNA Metabolism : RNA processing and modification | ATP-dependent RNA helicases, bacterial | 3 |
| | Polyadenylation bacterial | 4 |
| | Queuosine-Archaeosine Biosynthesis | 13 |
| | RNA processing and degradation, bacterial | 8 |
| | Ribonuclease H | 2 |
| | Wyeosine-MimG Biosynthesis | 2 |
| | tRNA nucleotidyltransferase | 1 |
| | tRNA processing | 11 |
| RNA Metabolism : Transcription | RNA polymerase bacterial | 4 |
| | Rrf2 family transcriptional regulators | 2 |
| | Transcription factors bacterial | 9 |
| | Transcription factors cyanobacterial RpoD-like sigma factors | 1 |
| | Transcription initiation, bacterial sigma factors | 11 |
| Regulation and Cell signaling | CytR regulation | 2 |
| | DNA-binding regulatory proteins, strays | 6 |
| | Orphan regulatory proteins | 11 |
| | Pseudomonas quinolone signal PQS | 1 |
| | Sex pheromones in Enterococcus faecalis and other Firmicutes | 7 |
| | Stringent Response, (p)ppGpp metabolism | 3 |
| | Two-component regulatory systems in Campylobacter | 3 |
| | cAMP signaling in bacteria | 7 |
| Regulation and Cell signaling : Programmed Cell Death and Toxin-antitoxin Systems | Murein hydrolase regulation and cell death | 11 |
| Regulation and Cell signaling : Quorum sensing and biofilm formation | Autoinducer 2 (AI-2) transport and processing (lsrACDBFGE operon) | 1 |
| | Quorum Sensing: Autoinducer-2 Synthesis | 1 |
| | Quorum sensing regulation in Pseudomonas | 1 |
| Respiration | Biogenesis of c-type cytochromes | 4 |
| | Biogenesis of cytochrome c oxidases | 1 |
| | Formate hydrogenase | 3 |
| | Soluble cytochromes and functionally related electron carriers | 3 |
| Respiration : ATP synthases | F0F1-type ATP synthase | 6 |
| Respiration : Electron accepting reactions | Anaerobic respiratory reductases | 4 |
| | Terminal cytochrome O ubiquinol oxidase | 4 |
| | Terminal cytochrome d ubiquinol oxidases | 4 |
| | Terminal cytochrome oxidases | 8 |
| Respiration : Electron donating reactions | Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes | 6 |
| | Respiratory Complex I | 13 |
| | Respiratory dehydrogenases 1 | 6 |
| | Succinate dehydrogenase | 14 |
| Secondary Metabolism : Aromatic amino acids and derivatives | Cinnamic Acid Degradation | 1 |
| Secondary Metabolism : Plant Hormones | Auxin biosynthesis | 4 |
| | Auxin degradation | 1 |
| Stress Response | Bacterial hemoglobins | 5 |
| | Flavohaemoglobin | 1 |
| | Hfl operon | 5 |
| | Sugar-phosphate stress regulation | 1 |
| | Universal stress protein family | 2 |
| Stress Response : Acid stress | Acid resistance mechanisms | 1 |
| Stress Response : Detoxification | Glutathione-dependent pathway of formaldehyde detoxification | 2 |
| Stress Response : Heat shock | Heat shock dnaK gene cluster extended | 15 |
| Stress Response : Osmotic stress | Choline and Betaine Uptake and Betaine Biosynthesis | 7 |
| Stress Response : Oxidative stress | Glutaredoxins | 4 |
| | Glutathione: Biosynthesis and gamma-glutamyl cycle | 5 |
| | Glutathione: Non-redox reactions | 8 |
| | Glutathione: Redox cycle | 4 |
| | Glutathionylspermidine and Trypanothione | 1 |
| | Oxidative stress | 20 |
| | Redox-dependent regulation of nucleus processes | 4 |
| | Rubrerythrin | 1 |
| Sulfur Metabolism | Galactosylceramide and Sulfatide metabolism | 1 |
| | Sulfate reduction-associated complexes | 1 |
| | Sulfur oxidation | 1 |
| | Thioredoxin-disulfide reductase | 4 |
| Sulfur Metabolism : Organic sulfur assimilation | Alkanesulfonate assimilation | 1 |
| | Taurine Utilization | 4 |
| | Utilization of glutathione as a sulphur source | 3 |
| Virulence : Type III, Type IV, Type VI, ESAT secretion systems | Type 4 secretion and conjugative transfer | 3 |
| Virulence, Disease and Defense : Detection | MLST | 4 |
| Virulence, Disease and Defense : Invasion and intracellular resistance | Salmonella invasion locus | 1 |
| Virulence, Disease and Defense : Resistance to antibiotics and toxic compounds | Arsenic resistance | 1 |
| | Cobalt-zinc-cadmium resistance | 3 |
| | Copper homeostasis | 3 |
| | Copper homeostasis: copper tolerance | 5 |
| | Methicillin resistance in Staphylococci | 3 |
| | Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria | 8 |
| | Multidrug Resistance Efflux Pumps | 6 |
| | Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) | 1 |
| | Resistance to fluoroquinolones | 5 |