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 | 5 |
| | Glycine Biosynthesis | 5 |
| | Glycine and Serine Utilization | 18 |
| | Glycine cleavage system | 4 |
| | Serine Biosynthesis | 6 |
| Amino Acids and Derivatives : Arginine; urea cycle, polyamines | Arginine Biosynthesis extended | 7 |
| | Arginine Deiminase Pathway | 3 |
| | Arginine and Ornithine Degradation | 7 |
| | Cyanophycin Metabolism | 3 |
| | Polyamine Metabolism | 4 |
| 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) | 6 |
| | Phenylalanine and Tyrosine Branches from Chorismate | 3 |
| | Tryptophan synthesis | 6 |
| Amino Acids and Derivatives : Branched-chain amino acids | Branched-Chain Amino Acid Biosynthesis | 12 |
| | HMG CoA Synthesis | 3 |
| | Isoleucine degradation | 10 |
| | Ketoisovalerate oxidoreductase | 1 |
| | Leucine Biosynthesis | 6 |
| | Leucine Degradation and HMG-CoA Metabolism | 12 |
| | Valine degradation | 10 |
| 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 | 8 |
| | Histidine Degradation | 1 |
| Amino Acids and Derivatives : Lysine, threonine, methionine, and cysteine | Cysteine Biosynthesis | 15 |
| | Lysine Biosynthesis DAP Pathway | 9 |
| | Methionine Biosynthesis | 24 |
| | Methionine Degradation | 10 |
| | Threonine and Homoserine Biosynthesis | 12 |
| | Threonine degradation | 2 |
| Amino Acids and Derivatives : Proline and 4-hydroxyproline | Proline, 4-hydroxyproline uptake and utilization | 2 |
| | Proline Synthesis | 3 |
| Carbohydrates | Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway | 3 |
| | Unknown sugar utilization (cluster yphABCDEFG) | 2 |
| Carbohydrates : Aminosugars | Chitin and N-acetylglucosamine utilization | 16 |
| | N-Acetyl-Galactosamine and Galactosamine Utilization | 8 |
| Carbohydrates : CO2 fixation | CO2 uptake, carboxysome | 1 |
| | Calvin-Benson cycle | 19 |
| | Carboxysome | 5 |
| | Photorespiration (oxidative C2 cycle) | 9 |
| Carbohydrates : Central carbohydrate metabolism | Entner-Doudoroff Pathway | 14 |
| | Glycolate, glyoxylate interconversions | 2 |
| | Glycolysis and Gluconeogenesis | 18 |
| | Glycolysis and Gluconeogenesis, including Archaeal enzymes | 12 |
| | Methylglyoxal Metabolism | 2 |
| | Pentose phosphate pathway | 18 |
| | Pyruvate Alanine Serine Interconversions | 5 |
| | Pyruvate metabolism I: anaplerotic reactions, PEP | 5 |
| | Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate | 7 |
| | TCA Cycle | 15 |
| Carbohydrates : Di- and oligosaccharides | Beta-Glucoside Metabolism | 13 |
| | Fructooligosaccharides(FOS) and Raffinose Utilization | 16 |
| | Lactose and Galactose Uptake and Utilization | 35 |
| | Lactose utilization | 26 |
| | Maltose and Maltodextrin Utilization | 17 |
| | Melibiose Utilization | 4 |
| | Sucrose utilization | 1 |
| | Sucrose utilization Shewanella | 1 |
| | Trehalose Biosynthesis | 7 |
| | Trehalose Uptake and Utilization | 4 |
| Carbohydrates : Fermentation | Acetoin, butanediol metabolism | 2 |
| | Acetyl-CoA fermentation to Butyrate | 8 |
| | Butanol Biosynthesis | 5 |
| | Fermentations: Lactate | 1 |
| | Fermentations: Mixed acid | 5 |
| Carbohydrates : Glycoside hydrolases | Predicted carbohydrate hydrolases | 6 |
| Carbohydrates : Monosaccharides | D-Galacturonate and D-Glucuronate Utilization | 52 |
| | D-Tagatose and Galactitol Utilization | 2 |
| | D-galactarate, D-glucarate and D-glycerate catabolism | 1 |
| | D-gluconate and ketogluconates metabolism | 2 |
| | D-ribose utilization | 8 |
| | Deoxyribose and Deoxynucleoside Catabolism | 4 |
| | Fructose utilization | 4 |
| | L-Arabinose utilization | 13 |
| | L-ascorbate utilization (and related gene clusters) | 2 |
| | L-fucose utilization | 11 |
| | L-fucose utilization temp | 13 |
| | L-rhamnose utilization | 39 |
| | Mannose Metabolism | 10 |
| | Xylose utilization | 17 |
| Carbohydrates : One-carbon Metabolism | One-carbon metabolism by tetrahydropterines | 5 |
| | Serine-glyoxylate cycle | 22 |
| Carbohydrates : Organic acids | Isobutyryl-CoA to Propionyl-CoA Module | 3 |
| | Lactate utilization | 6 |
| | Propionate-CoA to Succinate Module | 1 |
| | Propionyl-CoA to Succinyl-CoA Module | 3 |
| Carbohydrates : Polysaccharides | Glycogen metabolism | 6 |
| Carbohydrates : Sugar alcohols | Di-Inositol-Phosphate biosynthesis | 2 |
| | Glycerol and Glycerol-3-phosphate Uptake and Utilization | 4 |
| | Inositol catabolism | 3 |
| | Mannitol Utilization | 1 |
| | Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization | 5 |
| Cell Division and Cell Cycle | Bacterial Cytoskeleton | 15 |
| | Control of cell elongation - division cycle in Bacilli | 1 |
| | Macromolecular synthesis operon | 9 |
| | Two cell division clusters relating to chromosome partitioning | 10 |
| Cell Wall and Capsule | Peptidoglycan Biosynthesis | 23 |
| | UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis | 11 |
| Cell Wall and Capsule : Capsular and extracellular polysacchrides | Alginate metabolism | 11 |
| | CMP-N-acetylneuraminate Biosynthesis | 3 |
| | Capsular heptose biosynthesis | 5 |
| | Colanic acid biosynthesis | 6 |
| | O-Methyl Phosphoramidate Capsule Modification in Campylobacter | 2 |
| | Polysaccharide deacetylases | 2 |
| | Rhamnose containing glycans | 20 |
| | Sialic Acid Metabolism | 14 |
| | dTDP-rhamnose synthesis | 13 |
| Cell Wall and Capsule : Cell wall of Mycobacteria | linker unit-arabinogalactan synthesis | 15 |
| | mycolic acid synthesis | 24 |
| Cell Wall and Capsule : Gram-Negative cell wall components | KDO2-Lipid A biosynthesis | 10 |
| | LOS core oligosaccharide biosynthesis | 7 |
| | Lipid A-Ara4N pathway ( Polymyxin resistance ) | 5 |
| | Lipid A modifications | 1 |
| | Lipopolysaccharide-related cluster in Alphaproteobacteria | 1 |
| Cell Wall and Capsule : Gram-Positive cell wall components | Teichoic and lipoteichoic acids biosynthesis | 3 |
| | Teichuronic acid biosynthesis | 4 |
| Clustering-based subsystems | Bacterial Cell Division | 21 |
| | Bacterial RNA-metabolizing Zn-dependent hydrolases | 7 |
| | Conserved gene cluster associated with Met-tRNA formyltransferase | 9 |
| | LMPTP YfkJ cluster | 3 |
| | LMPTP YwlE cluster | 6 |
| | NusA-TFII Cluster | 3 |
| Clustering-based subsystems : Clustering-based subsystems | CBSS-262719.3.peg.410 | 2 |
| Clustering-based subsystems : Lysine, threonine, methionine, and cysteine | YeiH | 3 |
| Clustering-based subsystems : Type III secretion system related | CBSS-343509.6.peg.2644 | 1 |
| Clustering-based subsystems : Type III secretion system, extended | Type III secretion systems, extended | 1 |
| Clustering-based subsystems : proteosome related | Cluster-based Subsystem Grouping Hypotheticals - perhaps Proteosome Related | 2 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments | Thiamin biosynthesis | 12 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Biotin | Biotin biosynthesis | 5 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme A | Coenzyme A Biosynthesis | 9 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Folate and pterines | Folate Biosynthesis | 23 |
| | Molybdenum cofactor biosynthesis | 9 |
| | Pterin biosynthesis | 4 |
| | p-Aminobenzoyl-Glutamate Utilization | 1 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Lipoic acid | Lipoic acid metabolism | 2 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : NAD and NADP | NAD and NADP cofactor biosynthesis global | 15 |
| | NAD regulation | 10 |
| | PnuC-like transporters | 4 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Pyridoxine | Pyridoxin (Vitamin B6) Biosynthesis | 12 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Quinone cofactors | Menaquinone Biosynthesis via Futalosine | 5 |
| | Plastoquinone Biosynthesis | 1 |
| | Tocopherol Biosynthesis | 1 |
| | Ubiquinone Biosynthesis | 1 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Riboflavin, FMN, FAD | Riboflavin, FMN and FAD metabolism | 3 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Tetrapyrroles | Coenzyme B12 biosynthesis | 2 |
| | Experimental tye | 12 |
| | Heme and Siroheme Biosynthesis | 13 |
| DNA Metabolism | DNA structural proteins, bacterial | 1 |
| | Restriction-Modification System | 1 |
| | YcfH | 1 |
| DNA Metabolism : DNA recombination | RuvABC plus a hypothetical | 3 |
| DNA Metabolism : DNA repair | 2-phosphoglycolate salvage | 1 |
| | DNA Repair Base Excision | 11 |
| | DNA repair, UvrABC system | 4 |
| | DNA repair, bacterial | 17 |
| | DNA repair, bacterial MutL-MutS system | 4 |
| | DNA repair, bacterial RecFOR pathway | 10 |
| | DNA repair, bacterial UvrD and related helicases | 2 |
| DNA Metabolism : DNA replication | DNA-replication | 27 |
| | DNA replication, archaeal | 1 |
| | DNA topoisomerases, Type I, ATP-independent | 3 |
| | DNA topoisomerases, Type II, ATP-dependent | 4 |
| | Plasmid replication | 2 |
| Fatty Acids, Lipids, and Isoprenoids | Polyhydroxybutyrate metabolism | 5 |
| Fatty Acids, Lipids, and Isoprenoids : Fatty acids | Fatty Acid Biosynthesis FASII | 34 |
| Fatty Acids, Lipids, and Isoprenoids : Isoprenoids | Archaeal lipids | 3 |
| | Carotenoids | 10 |
| | Isoprenoid Biosynthesis | 10 |
| | Polyprenyl Diphosphate Biosynthesis | 2 |
| | polyprenyl synthesis | 5 |
| Fatty Acids, Lipids, and Isoprenoids : Phospholipids | Glycerolipid and Glycerophospholipid Metabolism in Bacteria | 17 |
| Iron acquisition and metabolism | Campylobacter Iron Metabolism | 8 |
| | Heme, hemin uptake and utilization systems in GramPositives | 1 |
| | Hemin transport system | 6 |
| | Iron acquisition in Vibrio | 35 |
| | Transport of Iron | 5 |
| Membrane Transport | Choline Transport | 3 |
| | ECF class transporters | 1 |
| | Ton and Tol transport systems | 47 |
| | Transport of Manganese | 2 |
| | Transport of Molybdenum | 2 |
| | Transport of Zinc | 1 |
| Membrane Transport : ABC transporters | ABC transporter alkylphosphonate (TC 3.A.1.9.1) | 3 |
| | ABC transporter dipeptide (TC 3.A.1.5.2) | 3 |
| | ABC transporter oligopeptide (TC 3.A.1.5.1) | 1 |
| Membrane Transport : Protein and nucleoprotein secretion system, Type IV | Type IV pilus | 7 |
| | pVir Plasmid of Campylobacter | 3 |
| Membrane Transport : Protein translocation across cytoplasmic membrane | Twin-arginine translocation system | 2 |
| Metabolism of Aromatic Compounds | Benzoate transport and degradation cluster | 1 |
| | Gentisare degradation | 2 |
| | carbazol degradation cluster | 1 |
| Metabolism of Aromatic Compounds : Metabolism of central aromatic intermediates | Catechol branch of beta-ketoadipate pathway | 4 |
| | Central meta-cleavage pathway of aromatic compound degradation | 2 |
| | Homogentisate pathway of aromatic compound degradation | 3 |
| | N-heterocyclic aromatic compound degradation | 2 |
| | Protocatechuate branch of beta-ketoadipate pathway | 2 |
| | Salicylate and gentisate catabolism | 4 |
| Metabolism of Aromatic Compounds : Peripheral pathways for catabolism of aromatic compounds | Biphenyl Degradation | 1 |
| | Quinate degradation | 1 |
| | Salicylate ester degradation | 1 |
| | n-Phenylalkanoic acid degradation | 2 |
| Miscellaneous | Muconate lactonizing enzyme family | 1 |
| | YbbK | 1 |
| | ZZ gjo need homes | 11 |
| Miscellaneous : Plant-Prokaryote DOE project | Conserved gene cluster possibly involved in RNA metabolism | 5 |
| Motility and Chemotaxis | Bacterial Chemotaxis | 9 |
| Motility and Chemotaxis : Flagellar motility in Prokaryota | Flagellar motility | 4 |
| | Flagellum | 5 |
| | Flagellum in Campylobacter | 1 |
| Nitrogen Metabolism | Allantoin Utilization | 1 |
| | Ammonia assimilation | 9 |
| | Cyanate hydrolysis | 2 |
| | Dissimilatory nitrite reductase | 1 |
| | Nitrate and nitrite ammonification | 5 |
| | Nitric oxide synthase | 1 |
| Nucleosides and Nucleotides | Adenosyl nucleosidases | 2 |
| | Hydantoin metabolism | 1 |
| | Ribonucleotide reduction | 3 |
| Nucleosides and Nucleotides : Detoxification | Nudix proteins (nucleoside triphosphate hydrolases) | 3 |
| Nucleosides and Nucleotides : Purines | De Novo Purine Biosynthesis | 13 |
| | Purine Utilization | 2 |
| | Purine conversions | 21 |
| Nucleosides and Nucleotides : Pyrimidines | De Novo Pyrimidine Synthesis | 10 |
| Phages, Prophages, Transposable elements, Plasmids : Pathogenicity islands | Staphylococcal pathogenicity islands SaPI | 3 |
| Phages, Prophages, Transposable elements, Plasmids : Transposable elements | Conjugative transposon, Bacteroidales | 3 |
| Phosphorus Metabolism | Alkylphosphonate utilization | 6 |
| | High affinity phosphate transporter and control of PHO regulon | 5 |
| | Phosphate metabolism | 19 |
| Potassium metabolism | Glutathione-regulated potassium-efflux system and associated functions | 1 |
| | Potassium homeostasis | 9 |
| Protein Metabolism : Protein biosynthesis | Ribosome LSU bacterial | 29 |
| | Ribosome SSU bacterial | 19 |
| | Ribosome activity modulation | 1 |
| | Ribosome biogenesis bacterial | 7 |
| | 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 | 3 |
| | Protein degradation | 2 |
| | Proteolysis in bacteria, ATP-dependent | 5 |
| Protein Metabolism : Protein folding | GroEL GroES | 2 |
| | Peptidyl-prolyl cis-trans isomerase | 2 |
| | Periplasmic disulfide interchange | 2 |
| | Protein chaperones | 8 |
| Protein Metabolism : Protein processing and modification | N-linked Glycosylation in Bacteria | 7 |
| | Ribosomal protein S12p Asp methylthiotransferase | 3 |
| | Ribosomal protein S5p acylation | 1 |
| | Signal peptidase | 3 |
| Protein Metabolism : Selenoproteins | Glycine reductase, sarcosine reductase and betaine reductase | 5 |
| RNA Metabolism : RNA processing and modification | ATP-dependent RNA helicases, bacterial | 3 |
| | Polyadenylation bacterial | 2 |
| | Queuosine-Archaeosine Biosynthesis | 7 |
| | RNA 3'-terminal phosphate cyclase | 2 |
| | RNA processing and degradation, bacterial | 4 |
| | Ribonuclease H | 2 |
| | Wyeosine-MimG Biosynthesis | 5 |
| | tRNA nucleotidyltransferase | 1 |
| | tRNA processing | 8 |
| RNA Metabolism : Transcription | RNA polymerase bacterial | 3 |
| | Rrf2 family transcriptional regulators | 3 |
| | Transcription factors bacterial | 7 |
| | Transcription factors cyanobacterial RpoD-like sigma factors | 2 |
| | Transcription initiation, bacterial sigma factors | 5 |
| Regulation and Cell signaling | DNA-binding regulatory proteins, strays | 1 |
| | Oxygen and light sensor PpaA-PpsR | 1 |
| | Sex pheromones in Enterococcus faecalis and other Firmicutes | 2 |
| | Stringent Response, (p)ppGpp metabolism | 1 |
| | Two-component regulatory systems in Campylobacter | 8 |
| | cAMP signaling in bacteria | 14 |
| Regulation and Cell signaling : Programmed Cell Death and Toxin-antitoxin Systems | Murein hydrolase regulation and cell death | 2 |
| Regulation and Cell signaling : Quorum sensing and biofilm formation | Quorum Sensing: Autoinducer-2 Synthesis | 1 |
| Regulation and Cell signaling : Regulation of virulence | Streptococcal Mga Regulon | 8 |
| Respiration | Biogenesis of c-type cytochromes | 7 |
| | Biogenesis of cbb3-type cytochrome c oxidases | 2 |
| | Biogenesis of cytochrome c oxidases | 1 |
| | Formate hydrogenase | 2 |
| | Soluble cytochromes and functionally related electron carriers | 6 |
| Respiration : ATP synthases | F0F1-type ATP synthase | 5 |
| Respiration : Electron accepting reactions | Anaerobic respiratory reductases | 7 |
| | Terminal cytochrome C oxidases | 7 |
| | Terminal cytochrome d ubiquinol oxidases | 2 |
| | Terminal cytochrome oxidases | 2 |
| Respiration : Electron donating reactions | Respiratory Complex I | 24 |
| | Respiratory dehydrogenases 1 | 3 |
| | Succinate dehydrogenase | 3 |
| Secondary Metabolism : Biosynthesis of phenylpropanoids | Biflavanoid biosynthesis | 2 |
| | Flavanone biosynthesis | 1 |
| | Tannin biosynthesis | 2 |
| Secondary Metabolism : Plant Hormones | Auxin biosynthesis | 4 |
| | Auxin degradation | 1 |
| Stress Response | Bacterial hemoglobins | 6 |
| | Flavohaemoglobin | 1 |
| | Hfl operon | 1 |
| | SigmaB stress responce regulation | 1 |
| Stress Response : Acid stress | Acid resistance mechanisms | 1 |
| Stress Response : Heat shock | Heat shock dnaK gene cluster extended | 13 |
| Stress Response : Osmotic stress | Choline and Betaine Uptake and Betaine Biosynthesis | 5 |
| Stress Response : Oxidative stress | Glutaredoxins | 1 |
| | Glutathione: Non-redox reactions | 1 |
| | Oxidative stress | 14 |
| | Redox-dependent regulation of nucleus processes | 3 |
| | Rubrerythrin | 4 |
| Sulfur Metabolism | Galactosylceramide and Sulfatide metabolism | 31 |
| | Sulfur oxidation | 2 |
| | Thioredoxin-disulfide reductase | 10 |
| Virulence, Disease and Defense : Detection | MLST | 4 |
| Virulence, Disease and Defense : Invasion and intracellular resistance | Listeria surface proteins: Internalin-like proteins | 2 |
| Virulence, Disease and Defense : Resistance to antibiotics and toxic compounds | Arsenic resistance | 1 |
| | Beta-lactamase | 2 |
| | Cobalt-zinc-cadmium resistance | 14 |
| | Copper homeostasis | 3 |
| | Copper homeostasis: copper tolerance | 2 |
| | Mercuric reductase | 1 |
| | Methicillin resistance in Staphylococci | 4 |
| | Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria | 6 |
| | Multidrug Resistance Efflux Pumps | 4 |
| | Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) | 1 |
| | Resistance to fluoroquinolones | 4 |
| | Zinc resistance | 3 |