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 | 2 |
| | Glycine and Serine Utilization | 4 |
| | Glycine cleavage system | 1 |
| | Serine Biosynthesis | 4 |
| Amino Acids and Derivatives : Arginine; urea cycle, polyamines | Arginine Biosynthesis extended | 8 |
| | Arginine Deiminase Pathway | 2 |
| | Arginine and Ornithine Degradation | 3 |
| | Cyanophycin Metabolism | 1 |
| | Polyamine Metabolism | 4 |
| Amino Acids and Derivatives : Aromatic amino acids and derivatives | Aromatic amino acid interconversions with aryl acids | 8 |
| | Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. | 2 |
| | Chorismate Synthesis | 10 |
| | Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) | 7 |
| | Phenylalanine and Tyrosine Branches from Chorismate | 3 |
| | Tryptophan synthesis | 7 |
| Amino Acids and Derivatives : Branched-chain amino acids | Branched-Chain Amino Acid Biosynthesis | 9 |
| | HMG CoA Synthesis | 1 |
| | Isoleucine degradation | 1 |
| | Ketoisovalerate oxidoreductase | 10 |
| | Leucine Biosynthesis | 4 |
| | Leucine Degradation and HMG-CoA Metabolism | 5 |
| | Valine degradation | 1 |
| Amino Acids and Derivatives : Glutamine, glutamate, aspartate, asparagine; ammonia assimilation | Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis | 7 |
| | Glutamine synthetases | 1 |
| Amino Acids and Derivatives : Histidine Metabolism | Histidine Biosynthesis | 10 |
| Amino Acids and Derivatives : Lysine, threonine, methionine, and cysteine | Cysteine Biosynthesis | 2 |
| | Lysine Biosynthesis DAP Pathway | 4 |
| | Lysine degradation | 2 |
| | Methionine Biosynthesis | 6 |
| | Methionine Degradation | 1 |
| | Methionine Salvage | 2 |
| | Threonine and Homoserine Biosynthesis | 6 |
| Carbohydrates | Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway | 1 |
| Carbohydrates : CO2 fixation | Calvin-Benson cycle | 9 |
| | Carboxysome | 1 |
| | Photorespiration (oxidative C2 cycle) | 2 |
| Carbohydrates : Central carbohydrate metabolism | Entner-Doudoroff Pathway | 6 |
| | Glycolysis and Gluconeogenesis | 6 |
| | Glycolysis and Gluconeogenesis, including Archaeal enzymes | 12 |
| | Pentose phosphate pathway | 6 |
| | Pyruvate:ferredoxin oxidoreductase | 6 |
| | Pyruvate Alanine Serine Interconversions | 3 |
| | Pyruvate metabolism I: anaplerotic reactions, PEP | 5 |
| | Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate | 2 |
| | TCA Cycle | 7 |
| Carbohydrates : Di- and oligosaccharides | Lactose and Galactose Uptake and Utilization | 1 |
| | Maltose and Maltodextrin Utilization | 3 |
| | Trehalose Biosynthesis | 2 |
| Carbohydrates : Fermentation | Acetoin, butanediol metabolism | 3 |
| | Fermentations: Mixed acid | 2 |
| Carbohydrates : Monosaccharides | D-ribose utilization | 1 |
| | Fructose utilization | 1 |
| | Mannose Metabolism | 2 |
| Carbohydrates : One-carbon Metabolism | Formaldehyde assimilation: Ribulose monophosphate pathway | 1 |
| | Methanogenesis | 35 |
| | One-carbon metabolism by tetrahydropterines | 2 |
| | Serine-glyoxylate cycle | 8 |
| Carbohydrates : Organic acids | Alpha-acetolactate operon | 1 |
| Carbohydrates : Polysaccharides | Glycogen metabolism | 2 |
| Carbohydrates : Sugar alcohols | Glycerol and Glycerol-3-phosphate Uptake and Utilization | 1 |
| | Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization | 1 |
| Cell Division and Cell Cycle | Bacterial Cytoskeleton | 5 |
| | Control of cell elongation - division cycle in Bacilli | 2 |
| | Cyanobacterial Circadian Clock | 1 |
| | Macromolecular synthesis operon | 3 |
| | Two cell division clusters relating to chromosome partitioning | 7 |
| | YgjD and YeaZ | 1 |
| Cell Wall and Capsule | Peptidoglycan Biosynthesis | 2 |
| | UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis | 3 |
| | YjeE | 1 |
| Cell Wall and Capsule : Capsular and extracellular polysacchrides | Alginate metabolism | 2 |
| | CMP-N-acetylneuraminate Biosynthesis | 2 |
| | Rhamnose containing glycans | 1 |
| | Sialic Acid Metabolism | 5 |
| Cell Wall and Capsule : Cell wall of Mycobacteria | linker unit-arabinogalactan synthesis | 1 |
| Cell Wall and Capsule : Gram-Negative cell wall components | Lipid A-Ara4N pathway ( Polymyxin resistance ) | 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 | 14 |
| | Bacterial RNA-metabolizing Zn-dependent hydrolases | 3 |
| | Conserved gene cluster associated with Met-tRNA formyltransferase | 7 |
| | LMPTP YwlE cluster | 1 |
| | NusA-TFII Cluster | 1 |
| Clustering-based subsystems : Clustering-based subsystems | CBSS-262719.3.peg.410 | 1 |
| Clustering-based subsystems : Lysine, threonine, methionine, and cysteine | YeiH | 1 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments | Thiamin biosynthesis | 9 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Biotin | Biotin biosynthesis | 7 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme A | Coenzyme A Biosynthesis | 9 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme B | Coenzyme B synthesis | 4 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme F420 | Coenzyme F420 synthesis | 5 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Folate and pterines | Folate Biosynthesis | 7 |
| | Molybdenum cofactor biosynthesis | 28 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : NAD and NADP | NAD and NADP cofactor biosynthesis global | 7 |
| | NAD regulation | 4 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Pyridoxine | Pyridoxin (Vitamin B6) Biosynthesis | 4 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Riboflavin, FMN, FAD | Flavodoxin | 2 |
| | Riboflavin, FMN and FAD metabolism | 5 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Tetrapyrroles | Cobalamin synthesis | 10 |
| | Coenzyme B12 biosynthesis | 22 |
| | Experimental tye | 9 |
| | Heme and Siroheme Biosynthesis | 7 |
| DNA Metabolism | Restriction-Modification System | 1 |
| | YcfH | 1 |
| DNA Metabolism : DNA repair | DNA Repair Base Excision | 7 |
| | DNA repair, UvrABC system | 3 |
| | DNA repair, bacterial | 5 |
| | DNA repair, bacterial DinG and relatives | 1 |
| | DNA repair, bacterial RecFOR pathway | 3 |
| DNA Metabolism : DNA replication | DNA-replication | 5 |
| | DNA replication, archaeal | 17 |
| | DNA topoisomerases, Type I, ATP-independent | 1 |
| | DNA topoisomerases, Type II, ATP-dependent | 2 |
| Fatty Acids, Lipids, and Isoprenoids | Polyhydroxybutyrate metabolism | 1 |
| Fatty Acids, Lipids, and Isoprenoids : Isoprenoids | Archaeal lipids | 10 |
| | Carotenoids | 2 |
| | Isoprenoid Biosynthesis | 5 |
| Fatty Acids, Lipids, and Isoprenoids : Phospholipids | Glycerolipid and Glycerophospholipid Metabolism in Bacteria | 5 |
| Iron acquisition and metabolism | Campylobacter Iron Metabolism | 5 |
| | Heme, hemin uptake and utilization systems in GramPositives | 1 |
| | Iron acquisition in Vibrio | 3 |
| | Transport of Iron | 4 |
| Membrane Transport | ECF class transporters | 11 |
| | Ton and Tol transport systems | 3 |
| | Transport of Molybdenum | 17 |
| | Transport of Nickel and Cobalt | 9 |
| Membrane Transport : Protein and nucleoprotein secretion system, Type IV | pVir Plasmid of Campylobacter | 1 |
| Membrane Transport : Protein secretion system, Type II | Widespread colonization island | 1 |
| Metabolism of Aromatic Compounds | Benzoate transport and degradation cluster | 1 |
| | Gentisare degradation | 1 |
| Metabolism of Aromatic Compounds : Metabolism of central aromatic intermediates | Central meta-cleavage pathway of aromatic compound degradation | 1 |
| | Homogentisate pathway of aromatic compound degradation | 1 |
| | Protocatechuate branch of beta-ketoadipate pathway | 2 |
| | Salicylate and gentisate catabolism | 1 |
| Metabolism of Aromatic Compounds : Peripheral pathways for catabolism of aromatic compounds | Quinate degradation | 1 |
| | n-Phenylalkanoic acid degradation | 1 |
| Miscellaneous | Archease | 1 |
| | YbbK | 2 |
| | ZZ gjo need homes | 8 |
| Miscellaneous : Plant-Prokaryote DOE project | Conserved gene cluster possibly involved in RNA metabolism | 1 |
| Motility and Chemotaxis | Bacterial Chemotaxis | 8 |
| Motility and Chemotaxis : Flagellar motility in Prokaryota | Archaeal Flagellum | 12 |
| | Flagellar motility | 2 |
| | Flagellum | 1 |
| Nitrogen Metabolism | Ammonia assimilation | 10 |
| | Cyanate hydrolysis | 1 |
| | Dissimilatory nitrite reductase | 1 |
| | Nitrogen fixation | 9 |
| | Nitrosative stress | 2 |
| Nucleosides and Nucleotides | AMP to 3-phosphoglycerate | 1 |
| | Ribonucleotide reduction | 2 |
| Nucleosides and Nucleotides : Detoxification | Nudix proteins (nucleoside triphosphate hydrolases) | 2 |
| Nucleosides and Nucleotides : Purines | De Novo Purine Biosynthesis | 13 |
| | Purine Utilization | 1 |
| | Purine conversions | 6 |
| Nucleosides and Nucleotides : Pyrimidines | De Novo Pyrimidine Synthesis | 12 |
| | Pyrimidine utilization | 1 |
| Phages, Prophages, Transposable elements, Plasmids : Pathogenicity islands | Staphylococcal pathogenicity islands SaPI | 1 |
| Phages, Prophages, Transposable elements, Plasmids : Phages, Prophages | Staphylococcal phi-Mu50B-like prophages | 1 |
| Phosphorus Metabolism | High affinity phosphate transporter and control of PHO regulon | 7 |
| | Phosphate metabolism | 9 |
| Potassium metabolism | Glutathione-regulated potassium-efflux system and associated functions | 1 |
| | Potassium homeostasis | 6 |
| Protein Metabolism : Protein biosynthesis | Ribosome LSU eukaryotic and archaeal | 36 |
| | Ribosome SSU eukaryotic and archaeal | 25 |
| | Ribosome biogenesis bacterial | 8 |
| | Translation elongation factor G family | 1 |
| | Translation elongation factors eukaryotic and archaeal | 5 |
| | Translation initiation factors eukaryotic and archaeal | 8 |
| | Universal GTPases | 9 |
| | tRNA aminoacylation, Glu and Gln | 2 |
| Protein Metabolism : Protein degradation | Proteasome archaeal | 3 |
| | Protein degradation | 1 |
| Protein Metabolism : Protein folding | GroEL GroES | 1 |
| | Peptidyl-prolyl cis-trans isomerase | 1 |
| | Periplasmic disulfide interchange | 1 |
| | Thermosome, archaeal | 1 |
| Protein Metabolism : Protein processing and modification | N-linked Glycosylation in Bacteria | 2 |
| | Signal peptidase | 2 |
| Protein Metabolism : Selenoproteins | Glycine reductase, sarcosine reductase and betaine reductase | 3 |
| | Selenocysteine metabolism | 6 |
| RNA Metabolism : RNA processing and modification | Queuosine-Archaeosine Biosynthesis | 17 |
| | RNA 3'-terminal phosphate cyclase | 1 |
| | RNA processing and degradation, bacterial | 1 |
| | Ribonuclease H | 2 |
| | Ribonuclease P archaeal and eukaryal | 4 |
| | Ribosome biogenesis archaeal | 2 |
| | Wyeosine-MimG Biosynthesis | 5 |
| | tRNA nucleotidyltransferase | 2 |
| | tRNA processing | 5 |
| | tRNA splicing | 1 |
| RNA Metabolism : Transcription | RNA polymerase III initiation factors | 1 |
| | RNA polymerase II initiation factors | 1 |
| | RNA polymerase archaeal | 13 |
| | RNA polymerase archaeal initiation factors | 3 |
| | Transcription initiation, bacterial sigma factors | 1 |
| Regulation and Cell signaling | Two-component regulatory systems in Campylobacter | 3 |
| | cAMP signaling in bacteria | 4 |
| Respiration | Biogenesis of c-type cytochromes | 1 |
| | Carbon monoxide induced hydrogenase | 8 |
| | Formate hydrogenase | 1 |
| | Soluble cytochromes and functionally related electron carriers | 7 |
| Respiration : ATP synthases | V-Type ATP synthase | 9 |
| Respiration : Electron accepting reactions | Anaerobic respiratory reductases | 9 |
| Respiration : Electron donating reactions | Coenzyme F420 hydrogenase | 8 |
| | Formate dehydrogenase | 2 |
| | H2:CoM-S-S-HTP oxidoreductase | 12 |
| | Hydrogenases | 3 |
| | Membrane-bound Ni, Fe-hydrogenase | 1 |
| | NiFe hydrogenase maturation | 7 |
| | Respiratory dehydrogenases 1 | 1 |
| | Succinate dehydrogenase | 2 |
| Secondary Metabolism : Plant Hormones | Auxin biosynthesis | 4 |
| Stress Response : Heat shock | Heat shock dnaK gene cluster extended | 2 |
| Stress Response : Osmotic stress | Choline and Betaine Uptake and Betaine Biosynthesis | 3 |
| Stress Response : Oxidative stress | Oxidative stress | 2 |
| | Rubrerythrin | 3 |
| Sulfur Metabolism | Sulfur oxidation | 1 |
| | Thioredoxin-disulfide reductase | 1 |
| Sulfur Metabolism : Organic sulfur assimilation | Alkanesulfonate assimilation | 2 |
| Virulence, Disease and Defense : Adhesion | Adhesins in Staphylococcus | 1 |
| Virulence, Disease and Defense : Detection | MLST | 1 |
| Virulence, Disease and Defense : Resistance to antibiotics and toxic compounds | Arsenic resistance | 2 |
| | Cobalt-zinc-cadmium resistance | 4 |
| | Copper homeostasis | 1 |
| | Methicillin resistance in Staphylococci | 1 |
| | Multidrug Resistance Efflux Pumps | 3 |