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 | 6 |
| | Glycine cleavage system | 1 |
| | Serine Biosynthesis | 4 |
| Amino Acids and Derivatives : Arginine; urea cycle, polyamines | Arginine Biosynthesis extended | 9 |
| | Arginine Deiminase Pathway | 1 |
| | Arginine and Ornithine Degradation | 1 |
| | Polyamine Metabolism | 3 |
| | Urea decomposition | 25 |
| Amino Acids and Derivatives : Aromatic amino acids and derivatives | Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. | 5 |
| | Chorismate Synthesis | 10 |
| | Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) | 8 |
| | Phenylalanine and Tyrosine Branches from Chorismate | 3 |
| | Tryptophan synthesis | 6 |
| Amino Acids and Derivatives : Branched-chain amino acids | Branched-Chain Amino Acid Biosynthesis | 12 |
| | Isoleucine degradation | 1 |
| | Ketoisovalerate oxidoreductase | 2 |
| | Leucine Biosynthesis | 6 |
| | Leucine Degradation and HMG-CoA Metabolism | 1 |
| | Valine degradation | 1 |
| Amino Acids and Derivatives : Glutamine, glutamate, aspartate, asparagine; ammonia assimilation | Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis | 17 |
| | Glutamine synthetases | 2 |
| Amino Acids and Derivatives : Histidine Metabolism | Histidine Biosynthesis | 12 |
| Amino Acids and Derivatives : Lysine, threonine, methionine, and cysteine | Cysteine Biosynthesis | 18 |
| | Lysine Biosynthesis DAP Pathway | 7 |
| | Methionine Biosynthesis | 15 |
| | Methionine Degradation | 3 |
| | Methionine Salvage | 3 |
| | Threonine anaerobic catabolism gene cluster | 1 |
| | Threonine and Homoserine Biosynthesis | 12 |
| Amino Acids and Derivatives : Proline and 4-hydroxyproline | Proline, 4-hydroxyproline uptake and utilization | 1 |
| | Proline Synthesis | 3 |
| Carbohydrates | Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway | 2 |
| Carbohydrates : CO2 fixation | CO2 uptake, carboxysome | 1 |
| | Calvin-Benson cycle | 12 |
| | Carboxysome | 3 |
| | Photorespiration (oxidative C2 cycle) | 7 |
| Carbohydrates : Central carbohydrate metabolism | Dihydroxyacetone kinases | 2 |
| | Entner-Doudoroff Pathway | 12 |
| | Glycolate, glyoxylate interconversions | 2 |
| | Glycolysis and Gluconeogenesis | 13 |
| | Glycolysis and Gluconeogenesis, including Archaeal enzymes | 9 |
| | Methylglyoxal Metabolism | 4 |
| | Pentose phosphate pathway | 10 |
| | Pyruvate Alanine Serine Interconversions | 3 |
| | Pyruvate metabolism I: anaplerotic reactions, PEP | 4 |
| | Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate | 7 |
| | TCA Cycle | 10 |
| Carbohydrates : Di- and oligosaccharides | Fructooligosaccharides(FOS) and Raffinose Utilization | 1 |
| | Lactose and Galactose Uptake and Utilization | 2 |
| | Maltose and Maltodextrin Utilization | 2 |
| | Sucrose utilization | 2 |
| | Sucrose utilization Shewanella | 2 |
| | Trehalose Biosynthesis | 2 |
| Carbohydrates : Fermentation | Acetoin, butanediol metabolism | 2 |
| | Acetyl-CoA fermentation to Butyrate | 8 |
| | Fermentations: Lactate | 1 |
| | Fermentations: Mixed acid | 4 |
| Carbohydrates : Monosaccharides | D-Galacturonate and D-Glucuronate Utilization | 1 |
| | D-gluconate and ketogluconates metabolism | 2 |
| | D-ribose utilization | 2 |
| | Deoxyribose and Deoxynucleoside Catabolism | 1 |
| | Fructose utilization | 3 |
| | L-rhamnose utilization | 1 |
| | Mannose Metabolism | 4 |
| Carbohydrates : One-carbon Metabolism | Formaldehyde assimilation: Ribulose monophosphate pathway | 4 |
| | Methanogenesis | 3 |
| | One-carbon metabolism by tetrahydropterines | 5 |
| | Serine-glyoxylate cycle | 12 |
| Carbohydrates : Organic acids | Lactate utilization | 1 |
| | Methylcitrate cycle | 3 |
| | Propionate-CoA to Succinate Module | 4 |
| Carbohydrates : Polysaccharides | Glycogen metabolism | 5 |
| Carbohydrates : Sugar alcohols | Di-Inositol-Phosphate biosynthesis | 1 |
| | Ethanolamine utilization | 5 |
| | Glycerol and Glycerol-3-phosphate Uptake and Utilization | 2 |
| | Mannitol Utilization | 3 |
| | Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization | 2 |
| Cell Division and Cell Cycle | Bacterial Cytoskeleton | 16 |
| | Control of cell elongation - division cycle in Bacilli | 1 |
| | Macromolecular synthesis operon | 6 |
| | Two cell division clusters relating to chromosome partitioning | 10 |
| Cell Wall and Capsule | Peptidoglycan Biosynthesis | 26 |
| | UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis | 5 |
| | YjeE | 1 |
| Cell Wall and Capsule : Capsular and extracellular polysacchrides | Alginate metabolism | 3 |
| | Capsular heptose biosynthesis | 2 |
| | Rhamnose containing glycans | 10 |
| | Sialic Acid Metabolism | 3 |
| | dTDP-rhamnose synthesis | 7 |
| Cell Wall and Capsule : Cell wall of Mycobacteria | linker unit-arabinogalactan synthesis | 8 |
| | mycolic acid synthesis | 7 |
| Cell Wall and Capsule : Gram-Negative cell wall components | KDO2-Lipid A biosynthesis | 9 |
| | LOS core oligosaccharide biosynthesis | 8 |
| | Lipid A-Ara4N pathway ( Polymyxin resistance ) | 2 |
| | Lipid A modifications | 1 |
| | Lipopolysaccharide-related cluster in Alphaproteobacteria | 1 |
| Cell Wall and Capsule : Gram-Positive cell wall components | Teichoic and lipoteichoic acids biosynthesis | 1 |
| | Teichuronic acid biosynthesis | 1 |
| Clustering-based subsystems | Bacterial Cell Division | 21 |
| | Bacterial RNA-metabolizing Zn-dependent hydrolases | 6 |
| | Conserved gene cluster associated with Met-tRNA formyltransferase | 15 |
| | LMPTP YfkJ cluster | 1 |
| | LMPTP YwlE cluster | 3 |
| | NusA-TFII Cluster | 3 |
| | Putative hemin transporter | 1 |
| Clustering-based subsystems : Clustering-based subsystems | CBSS-262719.3.peg.410 | 2 |
| 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 | 7 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Folate and pterines | Folate Biosynthesis | 18 |
| | Molybdenum cofactor biosynthesis | 14 |
| | Pterin biosynthesis | 3 |
| 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 | 5 |
| | PnuC-like transporters | 1 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Pyridoxine | Pyridoxin (Vitamin B6) Biosynthesis | 7 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Quinone cofactors | Coenzyme PQQ synthesis | 3 |
| | Pyrroloquinoline Quinone biosynthesis | 3 |
| | Ubiquinone Biosynthesis | 7 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Riboflavin, FMN, FAD | Riboflavin, FMN and FAD metabolism | 5 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Tetrapyrroles | Cobalamin synthesis | 7 |
| | Coenzyme B12 biosynthesis | 11 |
| | Experimental tye | 13 |
| | Heme and Siroheme Biosynthesis | 13 |
| DNA Metabolism | DNA structural proteins, bacterial | 4 |
| | Restriction-Modification System | 4 |
| | YcfH | 2 |
| DNA Metabolism : DNA recombination | RuvABC plus a hypothetical | 3 |
| DNA Metabolism : DNA repair | 2-phosphoglycolate salvage | 4 |
| | DNA Repair Base Excision | 6 |
| | DNA repair, UvrABC system | 3 |
| | DNA repair, bacterial | 15 |
| | DNA repair, bacterial DinG and relatives | 1 |
| | DNA repair, bacterial MutL-MutS system | 2 |
| | DNA repair, bacterial RecFOR pathway | 6 |
| | DNA repair, bacterial UvrD and related helicases | 4 |
| DNA Metabolism : DNA replication | DNA-replication | 26 |
| | DNA replication, archaeal | 1 |
| | DNA topoisomerases, Type I, ATP-independent | 1 |
| | DNA topoisomerases, Type II, ATP-dependent | 2 |
| | Plasmid replication | 3 |
| Fatty Acids, Lipids, and Isoprenoids : Fatty acids | Fatty Acid Biosynthesis FASII | 13 |
| Fatty Acids, Lipids, and Isoprenoids : Isoprenoids | Archaeal lipids | 2 |
| | Carotenoids | 5 |
| | Isoprenoid Biosynthesis | 9 |
| | Polyprenyl Diphosphate Biosynthesis | 2 |
| | polyprenyl synthesis | 5 |
| Fatty Acids, Lipids, and Isoprenoids : Phospholipids | Glycerolipid and Glycerophospholipid Metabolism in Bacteria | 16 |
| Iron acquisition and metabolism | Campylobacter Iron Metabolism | 6 |
| | Hemin transport system | 12 |
| | Iron acquisition in Vibrio | 11 |
| | Transport of Iron | 8 |
| Membrane Transport | ECF class transporters | 1 |
| | Ton and Tol transport systems | 29 |
| | Transport of Molybdenum | 5 |
| | Transport of Nickel and Cobalt | 3 |
| | Transport of Zinc | 5 |
| Membrane Transport : ABC transporters | ABC transporter branched-chain amino acid (TC 3.A.1.4.1) | 4 |
| | ABC transporter dipeptide (TC 3.A.1.5.2) | 4 |
| | ABC transporter oligopeptide (TC 3.A.1.5.1) | 4 |
| Membrane Transport : Protein and nucleoprotein secretion system, Type IV | Mannose-sensitive hemagglutinin type 4 pilus | 6 |
| | Type IV pilus | 19 |
| | pVir Plasmid of Campylobacter | 2 |
| Membrane Transport : Protein translocation across cytoplasmic membrane | Twin-arginine translocation system | 3 |
| Membrane Transport : Sugar Phosphotransferase Systems, PTS | Fructose and Mannose Inducible PTS | 1 |
| Membrane Transport : Uni- Sym- and Antiporters | Na(+) H(+) antiporter | 1 |
| Metabolism of Aromatic Compounds | Benzoate transport and degradation cluster | 1 |
| Metabolism of Aromatic Compounds : Metabolism of central aromatic intermediates | Central meta-cleavage pathway of aromatic compound degradation | 2 |
| | N-heterocyclic aromatic compound degradation | 4 |
| | Salicylate and gentisate catabolism | 1 |
| Metabolism of Aromatic Compounds : Peripheral pathways for catabolism of aromatic compounds | Benzoate degradation | 2 |
| | Phenylpropanoid compound degradation | 2 |
| | Quinate degradation | 1 |
| | Salicylate ester degradation | 1 |
| | n-Phenylalkanoic acid degradation | 1 |
| Miscellaneous | YbbK | 2 |
| | ZZ gjo need homes | 9 |
| Miscellaneous : Plant-Prokaryote DOE project | Conserved gene cluster possibly involved in RNA metabolism | 4 |
| Motility and Chemotaxis | Bacterial Chemotaxis | 33 |
| Motility and Chemotaxis : Flagellar motility in Prokaryota | Flagellar motility | 24 |
| | Flagellum | 42 |
| | Flagellum in Campylobacter | 7 |
| Nitrogen Metabolism | Ammonia assimilation | 17 |
| | Cyanate hydrolysis | 4 |
| | Denitrification | 1 |
| | Dissimilatory nitrite reductase | 2 |
| | Nitrate and nitrite ammonification | 12 |
| | Nitrogen fixation | 19 |
| | Nitrosative stress | 1 |
| Nucleosides and Nucleotides | Ribonucleotide reduction | 4 |
| Nucleosides and Nucleotides : Detoxification | Nudix proteins (nucleoside triphosphate hydrolases) | 5 |
| Nucleosides and Nucleotides : Purines | De Novo Purine Biosynthesis | 11 |
| | Purine Utilization | 1 |
| | Purine conversions | 15 |
| Nucleosides and Nucleotides : Pyrimidines | De Novo Pyrimidine Synthesis | 9 |
| Phages, Prophages, Transposable elements, Plasmids : Pathogenicity islands | Staphylococcal pathogenicity islands SaPI | 4 |
| Phosphorus Metabolism | Alkylphosphonate utilization | 1 |
| | High affinity phosphate transporter and control of PHO regulon | 8 |
| | Phosphate metabolism | 27 |
| Potassium metabolism | Glutathione-regulated potassium-efflux system and associated functions | 3 |
| | Potassium homeostasis | 15 |
| Protein Metabolism : Protein biosynthesis | Ribosome LSU bacterial | 30 |
| | Ribosome SSU bacterial | 20 |
| | Ribosome activity modulation | 1 |
| | Ribosome biogenesis bacterial | 9 |
| | 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 | 1 |
| | Universal GTPases | 16 |
| | tRNA aminoacylation, Glu and Gln | 2 |
| Protein Metabolism : Protein degradation | Proteasome bacterial | 4 |
| | Protein degradation | 3 |
| | Proteolysis in bacteria, ATP-dependent | 8 |
| | Putative TldE-TldD proteolytic complex | 1 |
| Protein Metabolism : Protein folding | GroEL GroES | 4 |
| | Peptidyl-prolyl cis-trans isomerase | 2 |
| | Periplasmic disulfide interchange | 4 |
| | Protein chaperones | 8 |
| Protein Metabolism : Protein processing and modification | N-linked Glycosylation in Bacteria | 4 |
| | Ribosomal protein S12p Asp methylthiotransferase | 3 |
| | Ribosomal protein S5p acylation | 1 |
| | Signal peptidase | 2 |
| Protein Metabolism : Selenoproteins | Glycine reductase, sarcosine reductase and betaine reductase | 3 |
| RNA Metabolism : RNA processing and modification | ATP-dependent RNA helicases, bacterial | 3 |
| | Polyadenylation bacterial | 4 |
| | Queuosine-Archaeosine Biosynthesis | 16 |
| | RNA processing and degradation, bacterial | 7 |
| | Ribonuclease H | 2 |
| | Wyeosine-MimG Biosynthesis | 4 |
| | tRNA nucleotidyltransferase | 1 |
| | tRNA processing | 8 |
| RNA Metabolism : Transcription | RNA polymerase bacterial | 4 |
| | Rrf2 family transcriptional regulators | 1 |
| | Transcription factors bacterial | 7 |
| | Transcription factors cyanobacterial RpoD-like sigma factors | 1 |
| | Transcription initiation, bacterial sigma factors | 7 |
| Regulation and Cell signaling | DNA-binding regulatory proteins, strays | 5 |
| | Orphan regulatory proteins | 1 |
| | Oxygen and light sensor PpaA-PpsR | 1 |
| | Sex pheromones in Enterococcus faecalis and other Firmicutes | 3 |
| | Stringent Response, (p)ppGpp metabolism | 2 |
| | Two-component regulatory systems in Campylobacter | 10 |
| | cAMP signaling in bacteria | 3 |
| Regulation and Cell signaling : Programmed Cell Death and Toxin-antitoxin Systems | Murein hydrolase regulation and cell death | 4 |
| Regulation and Cell signaling : Quorum sensing and biofilm formation | Quorum Sensing: Autoinducer-2 Synthesis | 1 |
| Respiration | Biogenesis of c-type cytochromes | 6 |
| | Biogenesis of cbb3-type cytochrome c oxidases | 4 |
| | Biogenesis of cytochrome c oxidases | 6 |
| | Formate hydrogenase | 6 |
| | Soluble cytochromes and functionally related electron carriers | 12 |
| Respiration : ATP synthases | F0F1-type ATP synthase | 5 |
| Respiration : Electron accepting reactions | Anaerobic respiratory reductases | 3 |
| | Terminal cytochrome C oxidases | 9 |
| | Terminal cytochrome O ubiquinol oxidase | 4 |
| | Terminal cytochrome d ubiquinol oxidases | 2 |
| | Terminal cytochrome oxidases | 6 |
| | Ubiquinone Menaquinone-cytochrome c reductase complexes | 3 |
| Respiration : Electron donating reactions | Hydrogenases | 1 |
| | Membrane-bound Ni, Fe-hydrogenase | 1 |
| | Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes | 1 |
| | Respiratory Complex I | 16 |
| | Respiratory dehydrogenases 1 | 8 |
| | Succinate dehydrogenase | 3 |
| Secondary Metabolism : Plant Hormones | Auxin biosynthesis | 4 |
| | Auxin degradation | 1 |
| Stress Response | Bacterial hemoglobins | 41 |
| | Hfl operon | 5 |
| Stress Response : Heat shock | Heat shock dnaK gene cluster extended | 16 |
| Stress Response : Osmotic stress | Choline and Betaine Uptake and Betaine Biosynthesis | 3 |
| Stress Response : Oxidative stress | Glutaredoxins | 2 |
| | Glutathione: Biosynthesis and gamma-glutamyl cycle | 2 |
| | Glutathione: Non-redox reactions | 6 |
| | Glutathione: Redox cycle | 1 |
| | Oxidative stress | 20 |
| | Redox-dependent regulation of nucleus processes | 2 |
| | Rubrerythrin | 1 |
| Sulfur Metabolism | Sulfur oxidation | 2 |
| | Thioredoxin-disulfide reductase | 10 |
| Sulfur Metabolism : Organic sulfur assimilation | Alkanesulfonate assimilation | 2 |
| | Alkanesulfonates Utilization | 2 |
| Virulence, Disease and Defense : Detection | MLST | 4 |
| Virulence, Disease and Defense : Resistance to antibiotics and toxic compounds | Arsenic resistance | 2 |
| | Beta-lactamase | 1 |
| | Cobalt-zinc-cadmium resistance | 14 |
| | Copper homeostasis | 5 |
| | Copper homeostasis: copper tolerance | 4 |
| | Methicillin resistance in Staphylococci | 2 |
| | Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria | 2 |
| | Multidrug Resistance Efflux Pumps | 17 |
| | Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) | 10 |
| | Resistance to fluoroquinolones | 2 |
| | Zinc resistance | 2 |