SEED Subsystems in Pseudomonas sp. DMC3

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 5
  Glycine Biosynthesis 2
  Glycine and Serine Utilization 30
  Glycine cleavage system 10
  Serine Biosynthesis 13
Amino Acids and Derivatives : Arginine; urea cycle, polyamines Arginine Biosynthesis extended 14
  Arginine Deiminase Pathway 8
  Arginine and Ornithine Degradation 40
  Cyanophycin Metabolism 2
  Polyamine Metabolism 34
  Urea decomposition 20
Amino Acids and Derivatives : Aromatic amino acids and derivatives Aromatic amino acid degradation 6
  Aromatic amino acid interconversions with aryl acids 2
  Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. 9
  Chorismate Synthesis 15
  Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 11
  Phenylalanine and Tyrosine Branches from Chorismate 6
  Tryptophan synthesis 7
Amino Acids and Derivatives : Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis 14
  HMG CoA Synthesis 10
  Isoleucine degradation 20
  Ketoisovalerate oxidoreductase 2
  Leucine Biosynthesis 5
  Leucine Degradation and HMG-CoA Metabolism 18
  Valine degradation 24
Amino Acids and Derivatives : Glutamine, glutamate, aspartate, asparagine; ammonia assimilation Glutamate dehydrogenases 2
  Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 45
  Glutamine synthetases 1
Amino Acids and Derivatives : Histidine Metabolism Histidine Biosynthesis 10
  Histidine Degradation 8
Amino Acids and Derivatives : Lysine, threonine, methionine, and cysteine Cysteine Biosynthesis 22
  Lysine Biosynthesis DAP Pathway 10
  Lysine degradation 17
  Methionine Biosynthesis 29
  Methionine Degradation 14
  Methionine Salvage 6
  Threonine anaerobic catabolism gene cluster 2
  Threonine and Homoserine Biosynthesis 22
  Threonine degradation 3
Amino Acids and Derivatives : Proline and 4-hydroxyproline Proline, 4-hydroxyproline uptake and utilization 13
  Proline Synthesis 5
Carbohydrates Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway 9
Carbohydrates : Aminosugars Chitin and N-acetylglucosamine utilization 5
Carbohydrates : CO2 fixation CO2 uptake, carboxysome 1
  Calvin-Benson cycle 12
  Carboxysome 6
  Photorespiration (oxidative C2 cycle) 30
Carbohydrates : Central carbohydrate metabolism Entner-Doudoroff Pathway 22
  Glycolate, glyoxylate interconversions 8
  Glycolysis and Gluconeogenesis 14
  Glycolysis and Gluconeogenesis, including Archaeal enzymes 9
  Methylglyoxal Metabolism 6
  Pentose phosphate pathway 11
  Pyruvate Alanine Serine Interconversions 10
  Pyruvate metabolism I: anaplerotic reactions, PEP 7
  Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 14
  TCA Cycle 17
Carbohydrates : Di- and oligosaccharides Beta-Glucoside Metabolism 2
  Lactose and Galactose Uptake and Utilization 10
  Maltose and Maltodextrin Utilization 7
  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 16
  Butanol Biosynthesis 10
  Fermentations: Lactate 2
  Fermentations: Mixed acid 10
Carbohydrates : Monosaccharides 2-Ketogluconate Utilization 5
  D-Galacturonate and D-Glucuronate Utilization 8
  D-Tagatose and Galactitol Utilization 1
  D-galactarate, D-glucarate and D-glycerate catabolism 17
  D-galactonate catabolism 4
  D-gluconate and ketogluconates metabolism 11
  D-ribose utilization 7
  Deoxyribose and Deoxynucleoside Catabolism 4
  Fructose utilization 8
  L-Arabinose utilization 7
  L-rhamnose utilization 2
  Mannose Metabolism 5
  Xylose utilization 7
Carbohydrates : One-carbon Metabolism One-carbon metabolism by tetrahydropterines 5
  Serine-glyoxylate cycle 29
Carbohydrates : Organic acids Isobutyryl-CoA to Propionyl-CoA Module 12
  Lactate utilization 9
  Malonate decarboxylase 10
  Methylcitrate cycle 5
  Propionate-CoA to Succinate Module 6
Carbohydrates : Polysaccharides Glycogen metabolism 5
Carbohydrates : Sugar alcohols Di-Inositol-Phosphate biosynthesis 1
  Ethanolamine utilization 6
  Glycerol and Glycerol-3-phosphate Uptake and Utilization 16
  Glycerol fermenation to 1,3-propanediol 1
  Inositol catabolism 2
  Mannitol Utilization 6
  Propanediol utilization 1
  Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 22
Cell Division and Cell Cycle Bacterial Cytoskeleton 25
  Control of cell elongation - division cycle in Bacilli 1
  Cyanobacterial Circadian Clock 1
  Macromolecular synthesis operon 5
  Two cell division clusters relating to chromosome partitioning 12
Cell Wall and Capsule Peptidoglycan Biosynthesis 26
  UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis 8
  YjeE 1
Cell Wall and Capsule : Capsular and extracellular polysacchrides Alginate metabolism 19
  CMP-N-acetylneuraminate Biosynthesis 3
  Capsular heptose biosynthesis 4
  Colanic acid biosynthesis 6
  O-Methyl Phosphoramidate Capsule Modification in Campylobacter 2
  Rhamnose containing glycans 21
  Sialic Acid Metabolism 12
  dTDP-rhamnose synthesis 9
Cell Wall and Capsule : Cell wall of Mycobacteria linker unit-arabinogalactan synthesis 18
  mycolic acid synthesis 14
Cell Wall and Capsule : Gram-Negative cell wall components KDO2-Lipid A biosynthesis 12
  LOS core oligosaccharide biosynthesis 8
  Lipid A-Ara4N pathway ( Polymyxin resistance ) 4
  Lipid A modifications 7
  Lipopolysaccharide-related cluster in Alphaproteobacteria 1
Cell Wall and Capsule : Gram-Positive cell wall components Teichoic and lipoteichoic acids biosynthesis 5
  Teichuronic acid biosynthesis 3
Clustering-based subsystems Bacterial Cell Division 28
  Bacterial RNA-metabolizing Zn-dependent hydrolases 8
  CBSS-562.2.peg.5158 SK3 including 1
  Conserved gene cluster associated with Met-tRNA formyltransferase 14
  LMPTP YfkJ cluster 2
  LMPTP YwlE cluster 6
  NusA-TFII Cluster 3
  PA0057 cluster 2
  Putative hemin transporter 1
  Putative sulfate assimilation cluster 3
Clustering-based subsystems : Clustering-based subsystems CBSS-262719.3.peg.410 3
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 12
Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme A Coenzyme A Biosynthesis 9
Cofactors, Vitamins, Prosthetic Groups, Pigments : Folate and pterines Folate Biosynthesis 22
  Molybdenum cofactor biosynthesis 18
  Pterin biosynthesis 4
  p-Aminobenzoyl-Glutamate Utilization 1
Cofactors, Vitamins, Prosthetic Groups, Pigments : Lipoic acid Lipoic acid metabolism 4
Cofactors, Vitamins, Prosthetic Groups, Pigments : NAD and NADP NAD and NADP cofactor biosynthesis global 14
  NAD regulation 8
  PnuC-like transporters 2
Cofactors, Vitamins, Prosthetic Groups, Pigments : Pyridoxine Pyridoxin (Vitamin B6) Biosynthesis 14
Cofactors, Vitamins, Prosthetic Groups, Pigments : Quinone cofactors Coenzyme PQQ synthesis 5
  Menaquinone Biosynthesis via Futalosine 1
  Menaquinone and Phylloquinone Biosynthesis 1
  Plastoquinone Biosynthesis 2
  Pyrroloquinoline Quinone biosynthesis 6
  Tocopherol Biosynthesis 2
  Ubiquinone Biosynthesis 11
Cofactors, Vitamins, Prosthetic Groups, Pigments : Riboflavin, FMN, FAD Flavodoxin 1
  Riboflavin, FMN and FAD metabolism 5
Cofactors, Vitamins, Prosthetic Groups, Pigments : Tetrapyrroles Cobalamin synthesis 14
  Coenzyme B12 biosynthesis 26
  Experimental tye 14
  Heme and Siroheme Biosynthesis 13
DNA Metabolism DNA structural proteins, bacterial 5
  Restriction-Modification System 1
  YcfH 3
DNA Metabolism : DNA recombination RuvABC plus a hypothetical 3
DNA Metabolism : DNA repair 2-phosphoglycolate salvage 5
  DNA Repair Base Excision 16
  DNA repair, UvrABC system 4
  DNA repair, bacterial 24
  DNA repair, bacterial DinG and relatives 2
  DNA repair, bacterial MutL-MutS system 2
  DNA repair, bacterial RecFOR pathway 8
  DNA repair, bacterial UvrD and related helicases 3
DNA Metabolism : DNA replication DNA-replication 32
  DNA replication, archaeal 1
  DNA topoisomerases, Type I, ATP-independent 2
  DNA topoisomerases, Type II, ATP-dependent 4
  Plasmid replication 4
Fatty Acids, Lipids, and Isoprenoids Polyhydroxybutyrate metabolism 19
Fatty Acids, Lipids, and Isoprenoids : Fatty acids Fatty Acid Biosynthesis FASII 22
Fatty Acids, Lipids, and Isoprenoids : Isoprenoids Archaeal lipids 2
  Carotenoids 2
  Isoprenoid Biosynthesis 9
  Polyprenyl Diphosphate Biosynthesis 2
  polyprenyl synthesis 5
Fatty Acids, Lipids, and Isoprenoids : Phospholipids Glycerolipid and Glycerophospholipid Metabolism in Bacteria 38
Fatty Acids, Lipids, and Isoprenoids : Triacylglycerols Triacylglycerol metabolism 1
Iron acquisition and metabolism Campylobacter Iron Metabolism 15
  Heme, hemin uptake and utilization systems in GramPositives 2
  Hemin transport system 17
  Iron acquisition in Vibrio 23
  Transport of Iron 20
Iron acquisition and metabolism : Siderophores Siderophore Enterobactin 2
  Siderophore Pyoverdine 20
Membrane Transport Choline Transport 3
  ECF class transporters 1
  Ton and Tol transport systems 27
  Transport of Manganese 2
  Transport of Molybdenum 4
  Transport of Nickel and Cobalt 3
  Transport of Zinc 7
Membrane Transport : ABC transporters ABC transporter alkylphosphonate (TC 3.A.1.9.1) 25
  ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 13
  ABC transporter dipeptide (TC 3.A.1.5.2) 8
  ABC transporter oligopeptide (TC 3.A.1.5.1) 10
Membrane Transport : Protein and nucleoprotein secretion system, Type IV Type IV pilus 22
  pVir Plasmid of Campylobacter 2
Membrane Transport : Protein secretion system, Type II Widespread colonization island 5
Membrane Transport : Protein secretion system, Type III Type III secretion system orphans 2
Membrane Transport : Protein translocation across cytoplasmic membrane Twin-arginine translocation system 5
Membrane Transport : Sugar Phosphotransferase Systems, PTS Fructose and Mannose Inducible PTS 3
Membrane Transport : Uni- Sym- and Antiporters Na(+) H(+) antiporter 1
  Sodium Hydrogen Antiporter 5
Metabolism of Aromatic Compounds Aromatic Amin Catabolism 3
  Benzoate transport and degradation cluster 2
  Gentisare degradation 4
Metabolism of Aromatic Compounds : Metabolism of central aromatic intermediates Catechol branch of beta-ketoadipate pathway 8
  Central meta-cleavage pathway of aromatic compound degradation 3
  Homogentisate pathway of aromatic compound degradation 6
  N-heterocyclic aromatic compound degradation 7
  Protocatechuate branch of beta-ketoadipate pathway 19
  Salicylate and gentisate catabolism 4
Metabolism of Aromatic Compounds : Peripheral pathways for catabolism of aromatic compounds Benzoate degradation 2
  Chloroaromatic degradation pathway 6
  Phenylpropanoid compound degradation 2
  Quinate degradation 3
  n-Phenylalkanoic acid degradation 13
  p-Hydroxybenzoate degradation 2
Miscellaneous YaaA 1
  ZZ gjo need homes 21
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 30
  Flagellum 47
  Flagellum in Campylobacter 6
Motility and Chemotaxis : Social motility and nonflagellar swimming in bacteria Rhamnolipids in Pseudomonas 2
Nitrogen Metabolism Allantoin Utilization 9
  Ammonia assimilation 27
  Cyanate hydrolysis 11
  Dissimilatory nitrite reductase 2
  Nitrate and nitrite ammonification 8
  Nitric oxide synthase 1
  Nitrosative stress 2
Nucleosides and Nucleotides Adenosyl nucleosidases 1
  Hydantoin metabolism 6
  Ribonucleotide reduction 3
Nucleosides and Nucleotides : Detoxification Nudix proteins (nucleoside triphosphate hydrolases) 11
Nucleosides and Nucleotides : Purines De Novo Purine Biosynthesis 12
  Purine Utilization 17
  Purine conversions 18
Nucleosides and Nucleotides : Pyrimidines De Novo Pyrimidine Synthesis 11
  Pyrimidine utilization 8
Phages, Prophages, Transposable elements : Bacteriophage structural proteins Phage capsid proteins 1
Phages, Prophages, Transposable elements, Plasmids : Pathogenicity islands Staphylococcal pathogenicity islands SaPI 6
Phages, Prophages, Transposable elements, Plasmids : Transposable elements Tn552 1
Phosphorus Metabolism Alkylphosphonate utilization 1
  High affinity phosphate transporter and control of PHO regulon 14
  Phosphate metabolism 33
  Phosphonate metabolism 4
Potassium metabolism Glutathione-regulated potassium-efflux system and associated functions 5
  Potassium homeostasis 15
Protein Metabolism : Protein biosynthesis Ribosome LSU bacterial 29
  Ribosome SSU bacterial 19
  Ribosome activity modulation 2
  Ribosome biogenesis bacterial 14
  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 16
  tRNA aminoacylation, Glu and Gln 1
Protein Metabolism : Protein degradation Proteasome bacterial 8
  Protein degradation 4
  Proteolysis in bacteria, ATP-dependent 13
  Putative TldE-TldD proteolytic complex 3
Protein Metabolism : Protein folding GroEL GroES 2
  Peptidyl-prolyl cis-trans isomerase 2
  Periplasmic disulfide interchange 8
  Protein chaperones 11
Protein Metabolism : Protein processing and modification N-linked Glycosylation in Bacteria 10
  Ribosomal protein S12p Asp methylthiotransferase 3
  Ribosomal protein S5p acylation 2
  Signal peptidase 2
Protein Metabolism : Secretion Protein secretion by ABC-type exporters 5
Protein Metabolism : Selenoproteins Glycine reductase, sarcosine reductase and betaine reductase 5
  Selenocysteine metabolism 4
RNA Metabolism : RNA processing and modification ATP-dependent RNA helicases, bacterial 4
  Polyadenylation bacterial 4
  Queuosine-Archaeosine Biosynthesis 20
  RNA 3'-terminal phosphate cyclase 3
  RNA processing and degradation, bacterial 6
  Ribonuclease H 2
  Wyeosine-MimG Biosynthesis 4
  tRNA nucleotidyltransferase 1
  tRNA processing 12
RNA Metabolism : Transcription RNA polymerase bacterial 4
  Rrf2 family transcriptional regulators 1
  Transcription factors bacterial 10
  Transcription factors cyanobacterial RpoD-like sigma factors 1
  Transcription initiation, bacterial sigma factors 9
Regulation and Cell signaling CytR regulation 1
  DNA-binding regulatory proteins, strays 19
  Orphan regulatory proteins 21
  Oxygen and light sensor PpaA-PpsR 1
  Pseudomonas quinolone signal PQS 1
  Sex pheromones in Enterococcus faecalis and other Firmicutes 3
  Stringent Response, (p)ppGpp metabolism 2
  Two-component regulatory systems in Campylobacter 7
  cAMP signaling in bacteria 15
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 4
  Toxin-antitoxin replicon stabilization systems 1
Regulation and Cell signaling : Quorum sensing and biofilm formation Quorum Sensing: Autoinducer-2 Synthesis 1
  Quorum sensing regulation in Pseudomonas 2
Respiration Biogenesis of c-type cytochromes 16
  Biogenesis of cbb3-type cytochrome c oxidases 3
  Biogenesis of cytochrome c oxidases 11
  Formate hydrogenase 6
  Soluble cytochromes and functionally related electron carriers 6
Respiration : ATP synthases F0F1-type ATP synthase 5
Respiration : Electron accepting reactions Anaerobic respiratory reductases 13
  Terminal cytochrome C oxidases 13
  Terminal cytochrome O ubiquinol oxidase 8
  Terminal cytochrome d ubiquinol oxidases 5
  Terminal cytochrome oxidases 13
  Ubiquinone Menaquinone-cytochrome c reductase complexes 3
Respiration : Electron donating reactions Formate dehydrogenase 2
  Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes 6
  Respiratory Complex I 13
  Respiratory dehydrogenases 1 9
  Succinate dehydrogenase 5
Secondary Metabolism : Aromatic amino acids and derivatives Cinnamic Acid Degradation 1
Secondary Metabolism : Plant Hormones Auxin biosynthesis 4
  Auxin degradation 1
Stress Response Bacterial hemoglobins 7
  Flavohaemoglobin 2
  Hfl operon 6
  SigmaB stress responce regulation 6
  Universal stress protein family 8
Stress Response : Acid stress Acid resistance mechanisms 2
Stress Response : Detoxification Glutathione-dependent pathway of formaldehyde detoxification 3
Stress Response : Heat shock Heat shock dnaK gene cluster extended 17
Stress Response : Osmotic stress Choline and Betaine Uptake and Betaine Biosynthesis 27
Stress Response : Oxidative stress Glutaredoxins 5
  Glutathione: Biosynthesis and gamma-glutamyl cycle 4
  Glutathione: Non-redox reactions 17
  Glutathione: Redox cycle 3
  Glutathionylspermidine and Trypanothione 1
  Oxidative stress 35
  Redox-dependent regulation of nucleus processes 4
  Rubrerythrin 4
Sulfur Metabolism Sulfate reduction-associated complexes 1
  Sulfur oxidation 1
  Thioredoxin-disulfide reductase 11
Sulfur Metabolism : Organic sulfur assimilation Alkanesulfonate assimilation 16
  Alkanesulfonates Utilization 10
  Taurine Utilization 9
  Utilization of glutathione as a sulphur source 2
Virulence, Disease and Defense : Detection MLST 6
Virulence, Disease and Defense : Invasion and intracellular resistance Cytolysin and Lipase operon in Vibrio 2
Virulence, Disease and Defense : Resistance to antibiotics and toxic compounds Arsenic resistance 11
  Beta-lactamase 3
  Cobalt-zinc-cadmium resistance 23
  Copper homeostasis 20
  Copper homeostasis: copper tolerance 3
  Methicillin resistance in Staphylococci 3
  Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 12
  Multidrug Resistance Efflux Pumps 9
  Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) 2
  Resistance to fluoroquinolones 4
  Streptothricin resistance 1