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 | 3 |
| | Glycine and Serine Utilization | 5 |
| | Glycine cleavage system | 1 |
| | Serine Biosynthesis | 3 |
| Amino Acids and Derivatives : Arginine; urea cycle, polyamines | Arginine Biosynthesis extended | 5 |
| | Arginine Deiminase Pathway | 4 |
| | Arginine and Ornithine Degradation | 5 |
| | Polyamine Metabolism | 10 |
| 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. | 6 |
| | Chorismate Synthesis | 8 |
| | Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) | 7 |
| | Phenylalanine and Tyrosine Branches from Chorismate | 1 |
| | Tryptophan synthesis | 4 |
| Amino Acids and Derivatives : Branched-chain amino acids | Branched-Chain Amino Acid Biosynthesis | 1 |
| | Isoleucine degradation | 3 |
| | Valine degradation | 3 |
| Amino Acids and Derivatives : Glutamine, glutamate, aspartate, asparagine; ammonia assimilation | Glutamate dehydrogenases | 1 |
| | Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis | 9 |
| | Glutamine synthetases | 1 |
| Amino Acids and Derivatives : Histidine Metabolism | Histidine Biosynthesis | 1 |
| | Histidine Degradation | 4 |
| Amino Acids and Derivatives : Lysine, threonine, methionine, and cysteine | Cysteine Biosynthesis | 2 |
| | Lysine Biosynthesis DAP Pathway | 1 |
| | Lysine degradation | 4 |
| | Methionine Biosynthesis | 13 |
| | Methionine Degradation | 10 |
| | Threonine anaerobic catabolism gene cluster | 3 |
| | Threonine and Homoserine Biosynthesis | 4 |
| | Threonine degradation | 1 |
| Amino Acids and Derivatives : Proline and 4-hydroxyproline | Proline, 4-hydroxyproline uptake and utilization | 1 |
| Carbohydrates | Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway | 2 |
| Carbohydrates : Aminosugars | Chitin and N-acetylglucosamine utilization | 2 |
| | N-Acetyl-Galactosamine and Galactosamine Utilization | 1 |
| Carbohydrates : CO2 fixation | Calvin-Benson cycle | 9 |
| | Photorespiration (oxidative C2 cycle) | 1 |
| Carbohydrates : Central carbohydrate metabolism | Dihydroxyacetone kinases | 2 |
| | Entner-Doudoroff Pathway | 5 |
| | Glycolysis and Gluconeogenesis | 12 |
| | Glycolysis and Gluconeogenesis, including Archaeal enzymes | 9 |
| | Methylglyoxal Metabolism | 3 |
| | Pentose phosphate pathway | 5 |
| | Pyruvate:ferredoxin oxidoreductase | 2 |
| | Pyruvate Alanine Serine Interconversions | 3 |
| | Pyruvate metabolism I: anaplerotic reactions, PEP | 6 |
| | Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate | 3 |
| | TCA Cycle | 1 |
| Carbohydrates : Di- and oligosaccharides | Lactose and Galactose Uptake and Utilization | 8 |
| | Maltose and Maltodextrin Utilization | 3 |
| | Trehalose Biosynthesis | 2 |
| Carbohydrates : Fermentation | Acetyl-CoA fermentation to Butyrate | 11 |
| | Butanol Biosynthesis | 4 |
| | Fermentations: Lactate | 4 |
| | Fermentations: Mixed acid | 9 |
| Carbohydrates : Glycoside hydrolases | Predicted carbohydrate hydrolases | 3 |
| Carbohydrates : Monosaccharides | D-Sorbitol(D-Glucitol) and L-Sorbose Utilization | 1 |
| | D-Tagatose and Galactitol Utilization | 1 |
| | D-galactarate, D-glucarate and D-glycerate catabolism | 1 |
| | D-gluconate and ketogluconates metabolism | 1 |
| | D-ribose utilization | 2 |
| | Deoxyribose and Deoxynucleoside Catabolism | 1 |
| | Fructose utilization | 3 |
| | L-rhamnose utilization | 1 |
| | Mannose Metabolism | 1 |
| Carbohydrates : One-carbon Metabolism | One-carbon metabolism by tetrahydropterines | 5 |
| | Serine-glyoxylate cycle | 8 |
| Carbohydrates : Organic acids | Isobutyryl-CoA to Propionyl-CoA Module | 3 |
| | Lactate utilization | 2 |
| Carbohydrates : Polysaccharides | Glycogen metabolism | 7 |
| Carbohydrates : Sugar alcohols | Ethanolamine utilization | 19 |
| | Glycerol and Glycerol-3-phosphate Uptake and Utilization | 8 |
| | Glycerol fermenation to 1,3-propanediol | 1 |
| | Inositol catabolism | 1 |
| | Mannitol Utilization | 4 |
| | Propanediol utilization | 8 |
| | Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization | 1 |
| Cell Division and Cell Cycle | Bacterial Cytoskeleton | 15 |
| | Control of cell elongation - division cycle in Bacilli | 2 |
| | Macromolecular synthesis operon | 4 |
| | Two cell division clusters relating to chromosome partitioning | 7 |
| Cell Wall and Capsule | Peptidoglycan Biosynthesis | 20 |
| | UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis | 8 |
| Cell Wall and Capsule : Capsular and extracellular polysacchrides | Alginate metabolism | 1 |
| | Capsular heptose biosynthesis | 2 |
| | Phosphorylcholine incorporation in LPS | 1 |
| | Polysaccharide deacetylases | 2 |
| | Rhamnose containing glycans | 5 |
| | Sialic Acid Metabolism | 7 |
| | dTDP-rhamnose synthesis | 3 |
| Cell Wall and Capsule : Cell wall of Mycobacteria | linker unit-arabinogalactan synthesis | 5 |
| | mycolic acid synthesis | 5 |
| Cell Wall and Capsule : Gram-Negative cell wall components | KDO2-Lipid A biosynthesis | 11 |
| | LOS core oligosaccharide biosynthesis | 9 |
| | Lipid A-Ara4N pathway ( Polymyxin resistance ) | 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 | 23 |
| | Bacterial RNA-metabolizing Zn-dependent hydrolases | 6 |
| | Conserved gene cluster associated with Met-tRNA formyltransferase | 16 |
| | LMPTP YfkJ cluster | 1 |
| | LMPTP YwlE cluster | 4 |
| | NusA-TFII Cluster | 4 |
| | 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 | 1 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments | Thiamin biosynthesis | 13 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Biotin | Biotin biosynthesis | 5 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme A | Coenzyme A Biosynthesis | 5 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Folate and pterines | Folate Biosynthesis | 14 |
| | Molybdenum cofactor biosynthesis | 2 |
| | Pterin biosynthesis | 1 |
| | p-Aminobenzoyl-Glutamate Utilization | 4 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : NAD and NADP | NAD and NADP cofactor biosynthesis global | 10 |
| | NAD regulation | 8 |
| | PnuC-like transporters | 1 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Pyridoxine | Pyridoxin (Vitamin B6) Biosynthesis | 8 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Riboflavin, FMN, FAD | Flavodoxin | 8 |
| | Riboflavin, FMN and FAD metabolism | 2 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Tetrapyrroles | Cobalamin synthesis | 14 |
| | Coenzyme B12 biosynthesis | 23 |
| | Experimental tye | 7 |
| | Heme and Siroheme Biosynthesis | 8 |
| DNA Metabolism | DNA structural proteins, bacterial | 2 |
| | Restriction-Modification System | 5 |
| | YcfH | 1 |
| DNA Metabolism : CRISPs | CRISPRs | 4 |
| DNA Metabolism : DNA recombination | RuvABC plus a hypothetical | 3 |
| DNA Metabolism : DNA repair | DNA Repair Base Excision | 6 |
| | DNA repair, UvrABC system | 4 |
| | DNA repair, bacterial | 18 |
| | DNA repair, bacterial DinG and relatives | 1 |
| | DNA repair, bacterial MutL-MutS system | 4 |
| | DNA repair, bacterial RecFOR pathway | 8 |
| | DNA repair, bacterial UvrD and related helicases | 2 |
| DNA Metabolism : DNA replication | DNA-replication | 23 |
| | DNA replication, archaeal | 1 |
| | DNA topoisomerases, Type I, ATP-independent | 1 |
| | DNA topoisomerases, Type II, ATP-dependent | 2 |
| Fatty Acids, Lipids, and Isoprenoids | Polyhydroxybutyrate metabolism | 4 |
| Fatty Acids, Lipids, and Isoprenoids : Fatty acids | Fatty Acid Biosynthesis FASII | 10 |
| Fatty Acids, Lipids, and Isoprenoids : Isoprenoids | Isoprenoid Biosynthesis | 8 |
| | Polyprenyl Diphosphate Biosynthesis | 1 |
| | polyprenyl synthesis | 5 |
| Fatty Acids, Lipids, and Isoprenoids : Phospholipids | Glycerolipid and Glycerophospholipid Metabolism in Bacteria | 20 |
| Fatty Acids, Lipids, and Isoprenoids : Triacylglycerols | Triacylglycerol metabolism | 1 |
| Iron acquisition and metabolism | Campylobacter Iron Metabolism | 14 |
| | Heme, hemin uptake and utilization systems in GramPositives | 1 |
| | Hemin transport system | 10 |
| | Iron acquisition in Vibrio | 6 |
| | Transport of Iron | 7 |
| Iron acquisition and metabolism : Siderophores | Siderophore Pyoverdine | 3 |
| Membrane Transport | ECF class transporters | 5 |
| | Ton and Tol transport systems | 9 |
| | Transport of Manganese | 4 |
| | Transport of Nickel and Cobalt | 11 |
| Membrane Transport : ABC transporters | ABC transporter alkylphosphonate (TC 3.A.1.9.1) | 3 |
| | ABC transporter branched-chain amino acid (TC 3.A.1.4.1) | 6 |
| | ABC transporter dipeptide (TC 3.A.1.5.2) | 16 |
| | ABC transporter oligopeptide (TC 3.A.1.5.1) | 9 |
| Membrane Transport : Protein and nucleoprotein secretion system, Type IV | Type IV pilus | 5 |
| | pVir Plasmid of Campylobacter | 2 |
| Membrane Transport : Sugar Phosphotransferase Systems, PTS | Fructose and Mannose Inducible PTS | 3 |
| Membrane Transport : Uni- Sym- and Antiporters | Na(+) H(+) antiporter | 2 |
| Metabolism of Aromatic Compounds | Benzoate transport and degradation cluster | 1 |
| Metabolism of Aromatic Compounds : Metabolism of central aromatic intermediates | Protocatechuate branch of beta-ketoadipate pathway | 1 |
| Metabolism of Aromatic Compounds : Peripheral pathways for catabolism of aromatic compounds | Quinate degradation | 1 |
| Miscellaneous | Muconate lactonizing enzyme family | 1 |
| | YbbK | 2 |
| | ZZ gjo need homes | 6 |
| Miscellaneous : Plant-Prokaryote DOE project | Conserved gene cluster possibly involved in RNA metabolism | 1 |
| Motility and Chemotaxis | Bacterial Chemotaxis | 3 |
| Motility and Chemotaxis : Flagellar motility in Prokaryota | Flagellar motility | 5 |
| | Flagellum | 3 |
| | Flagellum in Campylobacter | 2 |
| Nitrogen Metabolism | Ammonia assimilation | 1 |
| | Dissimilatory nitrite reductase | 1 |
| | Nitrosative stress | 2 |
| Nucleosides and Nucleotides | Adenosyl nucleosidases | 1 |
| | Ribonucleotide reduction | 5 |
| Nucleosides and Nucleotides : Detoxification | Nudix proteins (nucleoside triphosphate hydrolases) | 3 |
| Nucleosides and Nucleotides : Purines | De Novo Purine Biosynthesis | 10 |
| | Purine Utilization | 4 |
| | Purine conversions | 11 |
| Nucleosides and Nucleotides : Pyrimidines | De Novo Pyrimidine Synthesis | 11 |
| | Pyrimidine utilization | 1 |
| Phages, Prophages, Transposable elements, Plasmids : Pathogenicity islands | Staphylococcal pathogenicity islands SaPI | 4 |
| Phages, Prophages, Transposable elements, Plasmids : Transposable elements | Tn552 | 1 |
| Phosphorus Metabolism | Alkylphosphonate utilization | 1 |
| | Phosphate metabolism | 6 |
| Potassium metabolism | Glutathione-regulated potassium-efflux system and associated functions | 2 |
| | Potassium homeostasis | 6 |
| Protein Metabolism : Protein biosynthesis | Ribosome LSU bacterial | 28 |
| | Ribosome SSU bacterial | 18 |
| | Ribosome activity modulation | 1 |
| | Ribosome biogenesis bacterial | 12 |
| | Trans-translation by stalled ribosomes | 1 |
| | Translation elongation factor G family | 2 |
| | Translation elongation factors eukaryotic and archaeal | 1 |
| | Translation initiation factors eukaryotic and archaeal | 1 |
| | Universal GTPases | 15 |
| | tRNA aminoacylation, Asp and Asn | 2 |
| Protein Metabolism : Protein degradation | Proteasome bacterial | 4 |
| | Protein degradation | 1 |
| | Proteolysis in bacteria, ATP-dependent | 4 |
| Protein Metabolism : Protein folding | GroEL GroES | 2 |
| | Peptidyl-prolyl cis-trans isomerase | 1 |
| | Protein chaperones | 6 |
| Protein Metabolism : Protein processing and modification | N-linked Glycosylation in Bacteria | 4 |
| | Ribosomal protein S12p Asp methylthiotransferase | 2 |
| | 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 | Polyadenylation bacterial | 2 |
| | Queuosine-Archaeosine Biosynthesis | 12 |
| | RNA processing and degradation, bacterial | 4 |
| | Ribonuclease H | 1 |
| | Wyeosine-MimG Biosynthesis | 3 |
| | tRNA nucleotidyltransferase | 1 |
| | tRNA processing | 5 |
| | tRNA splicing | 1 |
| RNA Metabolism : Transcription | RNA polymerase bacterial | 4 |
| | Rrf2 family transcriptional regulators | 3 |
| | Transcription factors bacterial | 6 |
| | Transcription factors cyanobacterial RpoD-like sigma factors | 1 |
| | Transcription initiation, bacterial sigma factors | 4 |
| Regulation and Cell signaling | Sex pheromones in Enterococcus faecalis and other Firmicutes | 8 |
| | Stringent Response, (p)ppGpp metabolism | 1 |
| | cAMP signaling in bacteria | 3 |
| Regulation and Cell signaling : Programmed Cell Death and Toxin-antitoxin Systems | MazEF toxin-antitoxing (programmed cell death) system | 1 |
| | Murein hydrolase regulation and cell death | 6 |
| 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 |
| Respiration : ATP synthases | F0F1-type ATP synthase | 5 |
| | V-Type ATP synthase | 9 |
| Respiration : Electron accepting reactions | Anaerobic respiratory reductases | 7 |
| Respiration : Electron donating reactions | Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes | 6 |
| | Respiratory dehydrogenases 1 | 1 |
| | Succinate dehydrogenase | 1 |
| Respiration : Sodium Ion-Coupled Energetics | Na+ translocating decarboxylases and related biotin-dependent enzymes | 2 |
| Secondary Metabolism : Bacterial cytostatics, differentiation factors and antibiotics | Phenazine biosynthesis | 1 |
| Stress Response | SigmaB stress responce regulation | 1 |
| Stress Response : Acid stress | Acid resistance mechanisms | 2 |
| Stress Response : Heat shock | Heat shock dnaK gene cluster extended | 14 |
| Stress Response : Osmotic stress | Choline and Betaine Uptake and Betaine Biosynthesis | 1 |
| Stress Response : Oxidative stress | Glutaredoxins | 1 |
| | Glutathione: Non-redox reactions | 2 |
| | Glutathione: Redox cycle | 1 |
| | Oxidative stress | 4 |
| | Redox-dependent regulation of nucleus processes | 3 |
| | Rubrerythrin | 1 |
| Sulfur Metabolism | Galactosylceramide and Sulfatide metabolism | 1 |
| | Thioredoxin-disulfide reductase | 3 |
| Virulence : Type III, Type IV, Type VI, ESAT secretion systems | Type 4 secretion and conjugative transfer | 1 |
| Virulence, Disease and Defense : Adhesion | Adhesion of Campylobacter | 1 |
| | Streptococcus pyogenes recombinatorial zone | 1 |
| Virulence, Disease and Defense : Detection | MLST | 4 |
| Virulence, Disease and Defense : Resistance to antibiotics and toxic compounds | Arsenic resistance | 3 |
| | Beta-lactamase | 1 |
| | Cobalt-zinc-cadmium resistance | 6 |
| | Copper homeostasis: copper tolerance | 2 |
| | Methicillin resistance in Staphylococci | 2 |
| | Multidrug Resistance Efflux Pumps | 7 |
| | Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) | 1 |
| | Resistance to fluoroquinolones | 2 |