SEED Subsystems in Variovorax sp. OAS795

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 L-2-amino-thiazoline-4-carboxylic acid-Lcysteine conversion 1
Amino Acids and Derivatives : Alanine, serine, and glycine Alanine biosynthesis 4
  Glycine Biosynthesis 3
  Glycine and Serine Utilization 18
  Glycine cleavage system 2
  Serine Biosynthesis 14
Amino Acids and Derivatives : Arginine; urea cycle, polyamines Arginine Biosynthesis extended 13
  Arginine Deiminase Pathway 3
  Arginine and Ornithine Degradation 12
  Cyanophycin Metabolism 2
  Polyamine Metabolism 10
  Urea decomposition 22
Amino Acids and Derivatives : Aromatic amino acids and derivatives Aromatic amino acid degradation 16
  Aromatic amino acid interconversions with aryl acids 9
  Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. 7
  Chorismate Synthesis 14
  Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 12
  Phenylalanine and Tyrosine Branches from Chorismate 3
  Tryptophan synthesis 7
Amino Acids and Derivatives : Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis 30
  HMG CoA Synthesis 15
  Isoleucine degradation 58
  Ketoisovalerate oxidoreductase 6
  Leucine Biosynthesis 11
  Leucine Degradation and HMG-CoA Metabolism 22
  Valine degradation 54
Amino Acids and Derivatives : Glutamine, glutamate, aspartate, asparagine; ammonia assimilation Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 34
  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 7
  Lysine degradation 2
  Methionine Biosynthesis 29
  Methionine Degradation 10
  Methionine Salvage 1
  Threonine anaerobic catabolism gene cluster 3
  Threonine and Homoserine Biosynthesis 22
  Threonine degradation 10
Amino Acids and Derivatives : Proline and 4-hydroxyproline Proline, 4-hydroxyproline uptake and utilization 8
  Proline Synthesis 2
Carbohydrates Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway 7
Carbohydrates : Aminosugars Chitin and N-acetylglucosamine utilization 3
  N-Acetyl-Galactosamine and Galactosamine Utilization 3
Carbohydrates : CO2 fixation CO2 uptake, carboxysome 5
  Calvin-Benson cycle 19
  Carboxysome 5
  Photorespiration (oxidative C2 cycle) 21
Carbohydrates : Central carbohydrate metabolism Entner-Doudoroff Pathway 35
  Glycolate, glyoxylate interconversions 10
  Glycolysis and Gluconeogenesis 22
  Glycolysis and Gluconeogenesis, including Archaeal enzymes 18
  Methylglyoxal Metabolism 18
  Pentose phosphate pathway 12
  Pyruvate Alanine Serine Interconversions 11
  Pyruvate metabolism I: anaplerotic reactions, PEP 14
  Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 24
  TCA Cycle 26
Carbohydrates : Di- and oligosaccharides Beta-Glucoside Metabolism 2
  Fructooligosaccharides(FOS) and Raffinose Utilization 2
  Lactose and Galactose Uptake and Utilization 8
  Maltose and Maltodextrin Utilization 11
  Sucrose utilization 1
  Sucrose utilization Shewanella 1
  Trehalose Biosynthesis 12
  Trehalose Uptake and Utilization 1
Carbohydrates : Fermentation Acetoin, butanediol metabolism 5
  Acetyl-CoA fermentation to Butyrate 53
  Butanol Biosynthesis 41
  Fermentations: Lactate 2
  Fermentations: Mixed acid 11
Carbohydrates : Glycoside hydrolases Predicted carbohydrate hydrolases 1
Carbohydrates : Monosaccharides 2-Ketogluconate Utilization 3
  D-Galacturonate and D-Glucuronate Utilization 7
  D-Tagatose and Galactitol Utilization 1
  D-galactarate, D-glucarate and D-glycerate catabolism 8
  D-galactonate catabolism 3
  D-gluconate and ketogluconates metabolism 7
  D-ribose utilization 17
  Deoxyribose and Deoxynucleoside Catabolism 4
  Fructose utilization 8
  L-Arabinose utilization 15
  L-fucose utilization temp 1
  L-rhamnose utilization 4
  Mannose Metabolism 3
  Xylose utilization 11
Carbohydrates : One-carbon Metabolism Formaldehyde assimilation: Ribulose monophosphate pathway 2
  Methanogenesis 5
  One-carbon metabolism by tetrahydropterines 6
  Serine-glyoxylate cycle 47
Carbohydrates : Organic acids Isobutyryl-CoA to Propionyl-CoA Module 16
  Lactate utilization 4
  Malonate decarboxylase 8
  Methylcitrate cycle 5
  Propionate-CoA to Succinate Module 6
  Propionyl-CoA to Succinyl-CoA Module 4
  Tricarballylate Utilization 2
Carbohydrates : Polysaccharides Glycogen metabolism 7
Carbohydrates : Sugar alcohols Di-Inositol-Phosphate biosynthesis 2
  Ethanolamine utilization 5
  Glycerol and Glycerol-3-phosphate Uptake and Utilization 15
  Inositol catabolism 1
  Mannitol Utilization 4
  Propanediol utilization 1
  Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 15
Cell Division and Cell Cycle Bacterial Cytoskeleton 24
  Control of cell elongation - division cycle in Bacilli 1
  Cyanobacterial Circadian Clock 1
  Macromolecular synthesis operon 6
  Two cell division clusters relating to chromosome partitioning 11
Cell Wall and Capsule Peptidoglycan Biosynthesis 33
  UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis 6
Cell Wall and Capsule : Capsular and extracellular polysacchrides Alginate metabolism 4
  CMP-N-acetylneuraminate Biosynthesis 1
  Capsular heptose biosynthesis 4
  Colanic acid biosynthesis 8
  O-Methyl Phosphoramidate Capsule Modification in Campylobacter 1
  Polysaccharide deacetylases 1
  Rhamnose containing glycans 16
  Sialic Acid Metabolism 11
  dTDP-rhamnose synthesis 7
Cell Wall and Capsule : Cell wall of Mycobacteria linker unit-arabinogalactan synthesis 13
  mycolic acid synthesis 33
Cell Wall and Capsule : Gram-Negative cell wall components KDO2-Lipid A biosynthesis 12
  LOS core oligosaccharide biosynthesis 2
  Lipid A-Ara4N pathway ( Polymyxin resistance ) 2
  Lipid A modifications 4
  Lipopolysaccharide-related cluster in Alphaproteobacteria 1
Cell Wall and Capsule : Gram-Positive cell wall components Teichoic and lipoteichoic acids biosynthesis 2
  Teichuronic acid biosynthesis 2
Clustering-based subsystems Bacterial Cell Division 28
  Bacterial RNA-metabolizing Zn-dependent hydrolases 7
  Conserved gene cluster associated with Met-tRNA formyltransferase 17
  LMPTP YfkJ cluster 4
  LMPTP YwlE cluster 4
  NusA-TFII Cluster 7
  PA0057 cluster 5
  Putative sulfate assimilation cluster 4
Clustering-based subsystems : Clustering-based subsystems CBSS-262719.3.peg.410 3
Clustering-based subsystems : Lysine, threonine, methionine, and cysteine YeiH 1
Clustering-based subsystems : proteosome related Cluster-based Subsystem Grouping Hypotheticals - perhaps Proteosome Related 2
Cofactors, Vitamins, Prosthetic Groups, Pigments Thiamin biosynthesis 23
Cofactors, Vitamins, Prosthetic Groups, Pigments : Biotin Biotin biosynthesis 17
Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme A Coenzyme A Biosynthesis 16
Cofactors, Vitamins, Prosthetic Groups, Pigments : Folate and pterines Folate Biosynthesis 24
  Molybdenum cofactor biosynthesis 15
  Pterin biosynthesis 3
  p-Aminobenzoyl-Glutamate Utilization 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 18
  NAD regulation 11
  PnuC-like transporters 1
Cofactors, Vitamins, Prosthetic Groups, Pigments : Pyridoxine Pyridoxin (Vitamin B6) Biosynthesis 19
Cofactors, Vitamins, Prosthetic Groups, Pigments : Quinone cofactors Coenzyme PQQ synthesis 4
  Menaquinone and Phylloquinone Biosynthesis 1
  Plastoquinone Biosynthesis 2
  Pyrroloquinoline Quinone biosynthesis 4
  Tocopherol Biosynthesis 2
  Ubiquinone Biosynthesis 4
Cofactors, Vitamins, Prosthetic Groups, Pigments : Riboflavin, FMN, FAD Riboflavin, FMN and FAD metabolism 3
Cofactors, Vitamins, Prosthetic Groups, Pigments : Tetrapyrroles Cobalamin synthesis 6
  Coenzyme B12 biosynthesis 11
  Experimental tye 14
  Heme and Siroheme Biosynthesis 14
DNA Metabolism DNA structural proteins, bacterial 6
  Restriction-Modification System 1
  YcfH 2
DNA Metabolism : DNA recombination RuvABC plus a hypothetical 3
DNA Metabolism : DNA repair 2-phosphoglycolate salvage 7
  DNA Repair Base Excision 13
  DNA repair, UvrABC system 4
  DNA repair, bacterial 23
  DNA repair, bacterial DinG and relatives 2
  DNA repair, bacterial MutL-MutS system 2
  DNA repair, bacterial RecFOR pathway 7
  DNA repair, bacterial UvrD and related helicases 3
DNA Metabolism : DNA replication DNA-replication 25
  DNA replication, archaeal 1
  DNA topoisomerases, Type I, ATP-independent 3
  DNA topoisomerases, Type II, ATP-dependent 4
  Plasmid replication 4
Fatty Acids, Lipids, and Isoprenoids Polyhydroxybutyrate metabolism 53
Fatty Acids, Lipids, and Isoprenoids : Fatty acids Fatty Acid Biosynthesis FASII 46
Fatty Acids, Lipids, and Isoprenoids : Isoprenoids Archaeal lipids 1
  Carotenoids 4
  Isoprenoid Biosynthesis 8
  polyprenyl synthesis 5
Fatty Acids, Lipids, and Isoprenoids : Phospholipids Glycerolipid and Glycerophospholipid Metabolism in Bacteria 54
Fatty Acids, Lipids, and Isoprenoids : Triacylglycerols Triacylglycerol metabolism 1
Iron acquisition and metabolism Campylobacter Iron Metabolism 11
  Heme, hemin uptake and utilization systems in GramPositives 1
  Hemin transport system 3
  Iron acquisition in Vibrio 14
  Transport of Iron 13
Iron acquisition and metabolism : Siderophores Siderophore Pyoverdine 9
Membrane Transport Choline Transport 1
  ECF class transporters 2
  Ton and Tol transport systems 22
  Transport of Manganese 1
  Transport of Molybdenum 4
  Transport of Nickel and Cobalt 3
  Transport of Zinc 4
Membrane Transport : ABC transporters ABC transporter alkylphosphonate (TC 3.A.1.9.1) 6
  ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 114
  ABC transporter dipeptide (TC 3.A.1.5.2) 16
  ABC transporter oligopeptide (TC 3.A.1.5.1) 14
  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 1
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
Membrane Transport : Uni- Sym- and Antiporters Sodium Hydrogen Antiporter 5
Metabolism of Aromatic Compounds Aromatic Amin Catabolism 3
  Benzoate transport and degradation cluster 21
  Gentisare degradation 15
  carbazol degradation cluster 2
Metabolism of Aromatic Compounds : Metabolism of central aromatic intermediates 4-Hydroxyphenylacetic acid catabolic pathway 8
  Catechol branch of beta-ketoadipate pathway 17
  Central meta-cleavage pathway of aromatic compound degradation 12
  Homogentisate pathway of aromatic compound degradation 28
  N-heterocyclic aromatic compound degradation 6
  Protocatechuate branch of beta-ketoadipate pathway 19
  Salicylate and gentisate catabolism 32
Metabolism of Aromatic Compounds : Peripheral pathways for catabolism of aromatic compounds Benzoate degradation 9
  Biphenyl Degradation 4
  Chloroaromatic degradation pathway 10
  Naphtalene and antracene degradation 2
  Phenylpropanoid compound degradation 13
  Quinate degradation 2
  Salicylate ester degradation 10
  Toluene degradation 1
  n-Phenylalkanoic acid degradation 39
  p-Hydroxybenzoate degradation 3
Miscellaneous YaaA 1
  YbbK 2
  ZZ gjo need homes 23
Miscellaneous : Plant-Prokaryote DOE project Conserved gene cluster possibly involved in RNA metabolism 3
Motility and Chemotaxis Bacterial Chemotaxis 11
Motility and Chemotaxis : Flagellar motility in Prokaryota Flagellar motility 5
  Flagellum 5
  Flagellum in Campylobacter 2
Nitrogen Metabolism Allantoin Utilization 3
  Ammonia assimilation 19
  Cyanate hydrolysis 6
  Denitrification 2
  Dissimilatory nitrite reductase 2
  Nitrate and nitrite ammonification 13
  Nitric oxide synthase 3
  Nitrosative stress 1
Nucleosides and Nucleotides Hydantoin metabolism 7
  Ribonucleotide reduction 2
Nucleosides and Nucleotides : Detoxification Nudix proteins (nucleoside triphosphate hydrolases) 7
Nucleosides and Nucleotides : Purines De Novo Purine Biosynthesis 13
  Purine Utilization 9
  Purine conversions 22
Nucleosides and Nucleotides : Pyrimidines De Novo Pyrimidine Synthesis 12
  Pyrimidine utilization 3
Phages, Prophages, Transposable elements : Bacteriophage structural proteins Phage capsid proteins 2
Phages, Prophages, Transposable elements, Plasmids : Pathogenicity islands Staphylococcal pathogenicity islands SaPI 6
Phages, Prophages, Transposable elements, Plasmids : Transposable elements Tn552 2
Phosphorus Metabolism Alkylphosphonate utilization 4
  High affinity phosphate transporter and control of PHO regulon 9
  Phosphate metabolism 31
Potassium metabolism Glutathione-regulated potassium-efflux system and associated functions 3
  Potassium homeostasis 14
Protein Metabolism : Protein biosynthesis Ribosome LSU bacterial 28
  Ribosome SSU bacterial 20
  Ribosome activity modulation 1
  Ribosome biogenesis bacterial 10
  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 6
  Universal GTPases 20
  tRNA aminoacylation, Glu and Gln 2
Protein Metabolism : Protein degradation Proteasome bacterial 7
  Protein degradation 3
  Proteolysis in bacteria, ATP-dependent 15
  Putative TldE-TldD proteolytic complex 1
Protein Metabolism : Protein folding GroEL GroES 2
  Peptidyl-prolyl cis-trans isomerase 4
  Periplasmic disulfide interchange 4
  Protein chaperones 11
Protein Metabolism : Protein processing and modification N-linked Glycosylation in Bacteria 9
  Ribosomal protein S12p Asp methylthiotransferase 3
  Ribosomal protein S5p acylation 2
  Signal peptidase 2
Protein Metabolism : Secretion Protein secretion by ABC-type exporters 1
Protein Metabolism : Selenoproteins Glycine reductase, sarcosine reductase and betaine reductase 6
  Selenocysteine metabolism 2
RNA Metabolism : RNA processing and modification ATP-dependent RNA helicases, bacterial 4
  Polyadenylation bacterial 4
  Queuosine-Archaeosine Biosynthesis 21
  RNA 3'-terminal phosphate cyclase 4
  RNA processing and degradation, bacterial 5
  Ribonuclease H 3
  Wyeosine-MimG Biosynthesis 6
  tRNA nucleotidyltransferase 1
  tRNA processing 12
RNA Metabolism : Transcription RNA polymerase bacterial 4
  Rrf2 family transcriptional regulators 1
  Transcription factors bacterial 8
  Transcription factors cyanobacterial RpoD-like sigma factors 1
  Transcription initiation, bacterial sigma factors 10
Regulation and Cell signaling DNA-binding regulatory proteins, strays 12
  Orphan regulatory proteins 15
  Sex pheromones in Enterococcus faecalis and other Firmicutes 5
  Stringent Response, (p)ppGpp metabolism 1
  Two-component regulatory systems in Campylobacter 1
  cAMP signaling in bacteria 17
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 7
  Biogenesis of cbb3-type cytochrome c oxidases 3
  Biogenesis of cytochrome c oxidases 8
  Carbon monoxide dehydrogenase maturation factors 5
  Formate hydrogenase 6
  Soluble cytochromes and functionally related electron carriers 20
Respiration : ATP synthases F0F1-type ATP synthase 6
Respiration : Electron accepting reactions Anaerobic respiratory reductases 23
  Terminal cytochrome C oxidases 16
  Terminal cytochrome O ubiquinol oxidase 4
  Terminal cytochrome d ubiquinol oxidases 3
  Terminal cytochrome oxidases 7
  Ubiquinone Menaquinone-cytochrome c reductase complexes 3
Respiration : Electron donating reactions CO Dehydrogenase 10
  Hydrogenases 7
  Membrane-bound Ni, Fe-hydrogenase 7
  Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes 1
  NiFe hydrogenase maturation 6
  Respiratory Complex I 14
  Respiratory dehydrogenases 1 17
  Succinate dehydrogenase 6
Secondary Metabolism : Aromatic amino acids and derivatives Cinnamic Acid Degradation 1
Secondary Metabolism : Plant Alkaloids Alkaloid biosynthesis from L-lysine 1
Secondary Metabolism : Plant Hormones Auxin biosynthesis 4
Stress Response Bacterial hemoglobins 7
  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 15
Stress Response : Osmotic stress Choline and Betaine Uptake and Betaine Biosynthesis 14
Stress Response : Oxidative stress Glutaredoxins 3
  Glutathione: Biosynthesis and gamma-glutamyl cycle 8
  Glutathione: Non-redox reactions 19
  Glutathione: Redox cycle 2
  Oxidative stress 31
  Redox-dependent regulation of nucleus processes 4
  Rubrerythrin 5
Sulfur Metabolism Sulfur oxidation 1
  Thioredoxin-disulfide reductase 11
Sulfur Metabolism : Organic sulfur assimilation Alkanesulfonate assimilation 32
  Alkanesulfonates Utilization 15
  Taurine Utilization 3
  Utilization of glutathione as a sulphur source 4
Virulence : Type III, Type IV, Type VI, ESAT secretion systems Type 4 secretion and conjugative transfer 2
Virulence, Disease and Defense : Adhesion Streptococcus pyogenes recombinatorial zone 1
Virulence, Disease and Defense : Detection MLST 4
Virulence, Disease and Defense : Resistance to antibiotics and toxic compounds Arsenic resistance 4
  Beta-lactamase 6
  Cobalt-zinc-cadmium resistance 15
  Copper homeostasis 7
  Copper homeostasis: copper tolerance 3
  Methicillin resistance in Staphylococci 4
  Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 7
  Multidrug Resistance Efflux Pumps 11
  Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) 4
  Resistance to fluoroquinolones 4