| Category | Subsystem | #Genes |
|---|
| Amino Acids and Derivatives | L-2-amino-thiazoline-4-carboxylic acid-Lcysteine conversion | 2 |
| Amino Acids and Derivatives : Alanine, serine, and glycine | Alanine biosynthesis | 5 |
| | Glycine Biosynthesis | 3 |
| | Glycine and Serine Utilization | 20 |
| | Glycine cleavage system | 6 |
| | Serine Biosynthesis | 12 |
| Amino Acids and Derivatives : Arginine; urea cycle, polyamines | Arginine Biosynthesis extended | 15 |
| | Arginine Deiminase Pathway | 1 |
| | Arginine and Ornithine Degradation | 5 |
| | Cyanophycin Metabolism | 2 |
| | Polyamine Metabolism | 9 |
| | Urea decomposition | 20 |
| Amino Acids and Derivatives : Aromatic amino acids and derivatives | Aromatic amino acid degradation | 16 |
| | Aromatic amino acid interconversions with aryl acids | 2 |
| | Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. | 3 |
| | Chorismate Synthesis | 14 |
| | Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) | 11 |
| | Phenylalanine and Tyrosine Branches from Chorismate | 5 |
| | Tryptophan synthesis | 6 |
| Amino Acids and Derivatives : Branched-chain amino acids | Branched-Chain Amino Acid Biosynthesis | 25 |
| | HMG CoA Synthesis | 10 |
| | Isoleucine degradation | 23 |
| | Ketoisovalerate oxidoreductase | 5 |
| | Leucine Biosynthesis | 8 |
| | Leucine Degradation and HMG-CoA Metabolism | 13 |
| | Valine degradation | 25 |
| Amino Acids and Derivatives : Glutamine, glutamate, aspartate, asparagine; ammonia assimilation | Glutamate dehydrogenases | 1 |
| | Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis | 28 |
| | Glutamine synthetases | 1 |
| Amino Acids and Derivatives : Histidine Metabolism | Histidine Biosynthesis | 12 |
| | Histidine Degradation | 8 |
| Amino Acids and Derivatives : Lysine, threonine, methionine, and cysteine | Cysteine Biosynthesis | 17 |
| | Lysine Biosynthesis DAP Pathway | 11 |
| | Lysine degradation | 3 |
| | Methionine Biosynthesis | 31 |
| | Methionine Degradation | 14 |
| | Threonine anaerobic catabolism gene cluster | 3 |
| | Threonine and Homoserine Biosynthesis | 20 |
| | Threonine degradation | 9 |
| Amino Acids and Derivatives : Proline and 4-hydroxyproline | Proline, 4-hydroxyproline uptake and utilization | 6 |
| | Proline Synthesis | 3 |
| Carbohydrates | Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway | 3 |
| Carbohydrates : CO2 fixation | Calvin-Benson cycle | 8 |
| | Carboxysome | 4 |
| | Photorespiration (oxidative C2 cycle) | 15 |
| Carbohydrates : Central carbohydrate metabolism | Entner-Doudoroff Pathway | 22 |
| | Glycolate, glyoxylate interconversions | 6 |
| | Glycolysis and Gluconeogenesis | 13 |
| | Glycolysis and Gluconeogenesis, including Archaeal enzymes | 10 |
| | Methylglyoxal Metabolism | 11 |
| | Pentose phosphate pathway | 8 |
| | Pyruvate Alanine Serine Interconversions | 11 |
| | Pyruvate metabolism I: anaplerotic reactions, PEP | 10 |
| | Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate | 23 |
| | TCA Cycle | 17 |
| Carbohydrates : Di- and oligosaccharides | Beta-Glucoside Metabolism | 1 |
| | Lactose and Galactose Uptake and Utilization | 3 |
| | Maltose and Maltodextrin Utilization | 5 |
| | Sucrose utilization | 1 |
| | Sucrose utilization Shewanella | 1 |
| | Trehalose Biosynthesis | 9 |
| Carbohydrates : Fermentation | Acetoin, butanediol metabolism | 4 |
| | Acetyl-CoA fermentation to Butyrate | 26 |
| | Butanol Biosynthesis | 18 |
| | Fermentations: Lactate | 3 |
| | Fermentations: Mixed acid | 8 |
| Carbohydrates : Glycoside hydrolases | Predicted carbohydrate hydrolases | 2 |
| Carbohydrates : Monosaccharides | 2-Ketogluconate Utilization | 5 |
| | D-Galacturonate and D-Glucuronate Utilization | 14 |
| | D-galactarate, D-glucarate and D-glycerate catabolism | 11 |
| | D-galactonate catabolism | 3 |
| | D-gluconate and ketogluconates metabolism | 11 |
| | D-ribose utilization | 7 |
| | Deoxyribose and Deoxynucleoside Catabolism | 4 |
| | Fructose utilization | 7 |
| | L-Arabinose utilization | 9 |
| | L-fucose utilization temp | 5 |
| | L-rhamnose utilization | 1 |
| | Mannose Metabolism | 5 |
| | Xylose utilization | 12 |
| Carbohydrates : One-carbon Metabolism | One-carbon metabolism by tetrahydropterines | 5 |
| | Serine-glyoxylate cycle | 28 |
| Carbohydrates : Organic acids | Isobutyryl-CoA to Propionyl-CoA Module | 12 |
| | Lactate utilization | 5 |
| | Malonate decarboxylase | 10 |
| | Methylcitrate cycle | 6 |
| | Propionate-CoA to Succinate Module | 6 |
| | Propionyl-CoA to Succinyl-CoA Module | 1 |
| Carbohydrates : Polysaccharides | Glycogen metabolism | 4 |
| Carbohydrates : Sugar alcohols | Di-Inositol-Phosphate biosynthesis | 1 |
| | Ethanolamine utilization | 4 |
| | Glycerol and Glycerol-3-phosphate Uptake and Utilization | 16 |
| | Mannitol Utilization | 5 |
| | Propanediol utilization | 1 |
| | Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization | 9 |
| Cell Division and Cell Cycle | Bacterial Cytoskeleton | 23 |
| | 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 | 21 |
| | UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis | 5 |
| | YjeE | 1 |
| Cell Wall and Capsule : Capsular and extracellular polysacchrides | Alginate metabolism | 6 |
| | CMP-N-acetylneuraminate Biosynthesis | 3 |
| | Capsular heptose biosynthesis | 3 |
| | O-Methyl Phosphoramidate Capsule Modification in Campylobacter | 1 |
| | Phosphorylcholine incorporation in LPS | 1 |
| | Polysaccharide deacetylases | 2 |
| | Rhamnose containing glycans | 9 |
| | Sialic Acid Metabolism | 8 |
| | dTDP-rhamnose synthesis | 7 |
| Cell Wall and Capsule : Cell wall of Mycobacteria | linker unit-arabinogalactan synthesis | 9 |
| | mycolic acid synthesis | 15 |
| Cell Wall and Capsule : Gram-Negative cell wall components | KDO2-Lipid A biosynthesis | 13 |
| | LOS core oligosaccharide biosynthesis | 10 |
| | Lipid A-Ara4N pathway ( Polymyxin resistance ) | 5 |
| | Lipid A modifications | 4 |
| | Lipopolysaccharide-related cluster in Alphaproteobacteria | 1 |
| Cell Wall and Capsule : Gram-Positive cell wall components | Teichoic and lipoteichoic acids biosynthesis | 1 |
| | Teichuronic acid biosynthesis | 2 |
| Clustering-based subsystems | Bacterial Cell Division | 27 |
| | Bacterial RNA-metabolizing Zn-dependent hydrolases | 10 |
| | CBSS-562.2.peg.5158 SK3 including | 1 |
| | Conserved gene cluster associated with Met-tRNA formyltransferase | 13 |
| | LMPTP YfkJ cluster | 1 |
| | LMPTP YwlE cluster | 4 |
| | NusA-TFII Cluster | 3 |
| | PA0057 cluster | 3 |
| | Putative sulfate assimilation cluster | 4 |
| Clustering-based subsystems : Clustering-based subsystems | CBSS-262719.3.peg.410 | 2 |
| Clustering-based subsystems : Lysine, threonine, methionine, and cysteine | YeiH | 4 |
| Clustering-based subsystems : Type III secretion system, extended | Type III secretion systems, extended | 6 |
| 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 | 13 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme A | Coenzyme A Biosynthesis | 13 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Folate and pterines | Folate Biosynthesis | 20 |
| | Molybdenum cofactor biosynthesis | 17 |
| | Pterin biosynthesis | 3 |
| | p-Aminobenzoyl-Glutamate Utilization | 1 |
| 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 | 16 |
| | NAD regulation | 8 |
| | PnuC-like transporters | 1 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Pyridoxine | Pyridoxin (Vitamin B6) Biosynthesis | 17 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Quinone cofactors | Coenzyme PQQ synthesis | 4 |
| | Menaquinone and Phylloquinone Biosynthesis | 1 |
| | Plastoquinone Biosynthesis | 4 |
| | Pyrroloquinoline Quinone biosynthesis | 4 |
| | Tocopherol Biosynthesis | 4 |
| | Ubiquinone Biosynthesis | 11 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Riboflavin, FMN, FAD | Riboflavin, FMN and FAD metabolism | 3 |
| Cofactors, Vitamins, Prosthetic Groups, Pigments : Tetrapyrroles | Cobalamin synthesis | 5 |
| | Coenzyme B12 biosynthesis | 9 |
| | Experimental tye | 14 |
| | Heme and Siroheme Biosynthesis | 12 |
| DNA Metabolism | DNA structural proteins, bacterial | 6 |
| | Restriction-Modification System | 1 |
| | YcfH | 3 |
| DNA Metabolism : DNA recombination | RuvABC plus a hypothetical | 3 |
| DNA Metabolism : DNA repair | 2-phosphoglycolate salvage | 4 |
| | DNA Repair Base Excision | 13 |
| | DNA repair, UvrABC system | 4 |
| | DNA repair, bacterial | 23 |
| | DNA repair, bacterial DinG and relatives | 1 |
| | DNA repair, bacterial MutL-MutS system | 2 |
| | DNA repair, bacterial RecFOR pathway | 7 |
| | DNA repair, bacterial UvrD and related helicases | 5 |
| DNA Metabolism : DNA replication | DNA-replication | 24 |
| | DNA replication, archaeal | 1 |
| | DNA topoisomerases, Type I, ATP-independent | 2 |
| | DNA topoisomerases, Type II, ATP-dependent | 4 |
| | Plasmid replication | 3 |
| Fatty Acids, Lipids, and Isoprenoids | Polyhydroxybutyrate metabolism | 29 |
| Fatty Acids, Lipids, and Isoprenoids : Fatty acids | Fatty Acid Biosynthesis FASII | 22 |
| Fatty Acids, Lipids, and Isoprenoids : Isoprenoids | Carotenoids | 1 |
| | Isoprenoid Biosynthesis | 7 |
| | polyprenyl synthesis | 5 |
| Fatty Acids, Lipids, and Isoprenoids : Phospholipids | Glycerolipid and Glycerophospholipid Metabolism in Bacteria | 30 |
| Iron acquisition and metabolism | Campylobacter Iron Metabolism | 8 |
| | Hemin transport system | 4 |
| | Iron acquisition in Vibrio | 16 |
| | Transport of Iron | 15 |
| Membrane Transport | Choline Transport | 1 |
| | ECF class transporters | 2 |
| | Ton and Tol transport systems | 18 |
| | Transport of Manganese | 5 |
| | Transport of Molybdenum | 5 |
| | Transport of Nickel and Cobalt | 1 |
| | Transport of Zinc | 3 |
| Membrane Transport : ABC transporters | ABC transporter alkylphosphonate (TC 3.A.1.9.1) | 2 |
| | ABC transporter branched-chain amino acid (TC 3.A.1.4.1) | 36 |
| | ABC transporter dipeptide (TC 3.A.1.5.2) | 6 |
| | ABC transporter oligopeptide (TC 3.A.1.5.1) | 7 |
| | ABC transporter tungstate (TC 3.A.1.6.2) | 3 |
| Membrane Transport : Protein and nucleoprotein secretion system, Type IV | Type IV pilus | 30 |
| | pVir Plasmid of Campylobacter | 2 |
| Membrane Transport : Protein secretion system, Type II | Widespread colonization island | 17 |
| Membrane Transport : Protein translocation across cytoplasmic membrane | Twin-arginine translocation system | 3 |
| Membrane Transport : Sugar Phosphotransferase Systems, PTS | Fructose and Mannose Inducible PTS | 2 |
| Metabolism of Aromatic Compounds | Aromatic Amin Catabolism | 2 |
| | Benzoate transport and degradation cluster | 3 |
| | Gentisare degradation | 4 |
| | carbazol degradation cluster | 1 |
| Metabolism of Aromatic Compounds : Metabolism of central aromatic intermediates | 4-Hydroxyphenylacetic acid catabolic pathway | 8 |
| | Catechol branch of beta-ketoadipate pathway | 11 |
| | Central meta-cleavage pathway of aromatic compound degradation | 6 |
| | Homogentisate pathway of aromatic compound degradation | 21 |
| | N-heterocyclic aromatic compound degradation | 6 |
| | Protocatechuate branch of beta-ketoadipate pathway | 17 |
| | Salicylate and gentisate catabolism | 9 |
| Metabolism of Aromatic Compounds : Peripheral pathways for catabolism of aromatic compounds | Benzoate degradation | 4 |
| | Biphenyl Degradation | 1 |
| | Chloroaromatic degradation pathway | 5 |
| | Naphtalene and antracene degradation | 1 |
| | Phenylpropanoid compound degradation | 11 |
| | Quinate degradation | 2 |
| | Salicylate ester degradation | 3 |
| | Toluene degradation | 1 |
| | n-Phenylalkanoic acid degradation | 18 |
| | p-Hydroxybenzoate degradation | 4 |
| Miscellaneous | Muconate lactonizing enzyme family | 1 |
| | YaaA | 1 |
| | YbbK | 5 |
| | ZZ gjo need homes | 16 |
| Miscellaneous : Plant-Prokaryote DOE project | Conserved gene cluster possibly involved in RNA metabolism | 3 |
| Motility and Chemotaxis | Bacterial Chemotaxis | 39 |
| Motility and Chemotaxis : Flagellar motility in Prokaryota | Flagellar motility | 28 |
| | Flagellum | 51 |
| | Flagellum in Campylobacter | 6 |
| Nitrogen Metabolism | Allantoin Utilization | 5 |
| | Ammonia assimilation | 17 |
| | Cyanate hydrolysis | 7 |
| | Denitrification | 1 |
| | Dissimilatory nitrite reductase | 1 |
| | Nitrate and nitrite ammonification | 15 |
| | Nitrosative stress | 2 |
| Nucleosides and Nucleotides | Adenosyl nucleosidases | 1 |
| | Hydantoin metabolism | 7 |
| | Ribonucleotide reduction | 3 |
| Nucleosides and Nucleotides : Detoxification | Nudix proteins (nucleoside triphosphate hydrolases) | 5 |
| Nucleosides and Nucleotides : Purines | De Novo Purine Biosynthesis | 12 |
| | Purine Utilization | 10 |
| | Purine conversions | 20 |
| Nucleosides and Nucleotides : Pyrimidines | De Novo Pyrimidine Synthesis | 10 |
| | Pyrimidine utilization | 2 |
| Phages, Prophages, Transposable elements : Bacteriophage structural proteins | Phage capsid proteins | 2 |
| Phages, Prophages, Transposable elements, Plasmids : Pathogenicity islands | Staphylococcal pathogenicity islands SaPI | 8 |
| Phages, Prophages, Transposable elements, Plasmids : Transposable elements | Tn552 | 1 |
| Phosphorus Metabolism | Alkylphosphonate utilization | 6 |
| | High affinity phosphate transporter and control of PHO regulon | 10 |
| | Phosphate metabolism | 30 |
| | Phosphonate metabolism | 1 |
| 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 | 1 |
| | Ribosome biogenesis bacterial | 9 |
| | 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 | 16 |
| | tRNA aminoacylation, Glu and Gln | 2 |
| Protein Metabolism : Protein degradation | Proteasome bacterial | 6 |
| | Protein degradation | 3 |
| | Proteolysis in bacteria, ATP-dependent | 13 |
| | Putative TldE-TldD proteolytic complex | 1 |
| Protein Metabolism : Protein folding | GroEL GroES | 4 |
| | Peptidyl-prolyl cis-trans isomerase | 3 |
| | Periplasmic disulfide interchange | 5 |
| | Protein chaperones | 9 |
| Protein Metabolism : Protein processing and modification | N-linked Glycosylation in Bacteria | 5 |
| | 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 | 4 |
| | Queuosine-Archaeosine Biosynthesis | 28 |
| | RNA 3'-terminal phosphate cyclase | 4 |
| | RNA processing and degradation, bacterial | 8 |
| | Ribonuclease H | 2 |
| | Wyeosine-MimG Biosynthesis | 5 |
| | tRNA nucleotidyltransferase | 1 |
| | tRNA processing | 8 |
| RNA Metabolism : Transcription | RNA polymerase bacterial | 4 |
| | Rrf2 family transcriptional regulators | 3 |
| | Transcription factors bacterial | 8 |
| | Transcription factors cyanobacterial RpoD-like sigma factors | 1 |
| | Transcription initiation, bacterial sigma factors | 9 |
| Regulation and Cell signaling | DNA-binding regulatory proteins, strays | 13 |
| | Orphan regulatory proteins | 11 |
| | Oxygen and light sensor PpaA-PpsR | 1 |
| | Sex pheromones in Enterococcus faecalis and other Firmicutes | 6 |
| | Stringent Response, (p)ppGpp metabolism | 2 |
| | Two-component regulatory systems in Campylobacter | 9 |
| | cAMP signaling in bacteria | 12 |
| Regulation and Cell signaling : Programmed Cell Death and Toxin-antitoxin Systems | Murein hydrolase regulation and cell death | 5 |
| 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 | 3 |
| | Biogenesis of cytochrome c oxidases | 7 |
| | Carbon monoxide dehydrogenase maturation factors | 4 |
| | Formate hydrogenase | 6 |
| | Soluble cytochromes and functionally related electron carriers | 11 |
| Respiration : ATP synthases | F0F1-type ATP synthase | 7 |
| Respiration : Electron accepting reactions | Anaerobic respiratory reductases | 11 |
| | Terminal cytochrome C oxidases | 13 |
| | Terminal cytochrome O ubiquinol oxidase | 8 |
| | Terminal cytochrome d ubiquinol oxidases | 2 |
| | Terminal cytochrome oxidases | 10 |
| | Ubiquinone Menaquinone-cytochrome c reductase complexes | 3 |
| Respiration : Electron donating reactions | CO Dehydrogenase | 7 |
| | Formate dehydrogenase | 1 |
| | Respiratory Complex I | 14 |
| | Respiratory dehydrogenases 1 | 9 |
| | Succinate dehydrogenase | 4 |
| Secondary Metabolism : Aromatic amino acids and derivatives | Cinnamic Acid Degradation | 3 |
| Secondary Metabolism : Bacterial cytostatics, differentiation factors and antibiotics | Phenazine biosynthesis | 1 |
| Secondary Metabolism : Biosynthesis of phenylpropanoids | Phenylpropionate Degradation | 1 |
| Secondary Metabolism : Plant Hormones | Auxin biosynthesis | 4 |
| | Auxin degradation | 1 |
| Stress Response | Bacterial hemoglobins | 10 |
| | Dimethylarginine metabolism | 1 |
| | Flavohaemoglobin | 1 |
| | Hfl operon | 5 |
| | Universal stress protein family | 3 |
| Stress Response : Detoxification | Glutathione-dependent pathway of formaldehyde detoxification | 2 |
| Stress Response : Heat shock | Heat shock dnaK gene cluster extended | 16 |
| Stress Response : Osmotic stress | Choline and Betaine Uptake and Betaine Biosynthesis | 7 |
| Stress Response : Oxidative stress | Glutaredoxins | 3 |
| | Glutathione: Biosynthesis and gamma-glutamyl cycle | 4 |
| | Glutathione: Non-redox reactions | 13 |
| | Glutathione: Redox cycle | 2 |
| | Oxidative stress | 30 |
| | Redox-dependent regulation of nucleus processes | 4 |
| | Rubrerythrin | 2 |
| Sulfur Metabolism | Sulfur oxidation | 13 |
| | Thioredoxin-disulfide reductase | 13 |
| Sulfur Metabolism : Organic sulfur assimilation | Alkanesulfonate assimilation | 27 |
| | Alkanesulfonates Utilization | 12 |
| | Taurine Utilization | 7 |
| | Utilization of glutathione as a sulphur source | 2 |
| Virulence, Disease and Defense : Detection | MLST | 4 |
| Virulence, Disease and Defense : Resistance to antibiotics and toxic compounds | Arsenic resistance | 1 |
| | Beta-lactamase | 5 |
| | Cobalt-zinc-cadmium resistance | 21 |
| | Copper homeostasis | 9 |
| | Copper homeostasis: copper tolerance | 5 |
| | Mercuric reductase | 1 |
| | Mercury resistance operon | 1 |
| | Methicillin resistance in Staphylococci | 2 |
| | Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria | 5 |
| | Multidrug Resistance Efflux Pumps | 15 |
| | Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) | 9 |
| | Resistance to fluoroquinolones | 4 |