SEED Subsystems in Pseudomonas fluorescens GW456-L13

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 7
  Glycine Biosynthesis 4
  Glycine and Serine Utilization 35
  Glycine cleavage system 11
  Serine Biosynthesis 15
Amino Acids and Derivatives : Arginine; urea cycle, polyamines Arginine Biosynthesis extended 13
  Arginine Deiminase Pathway 7
  Arginine and Ornithine Degradation 51
  Cyanophycin Metabolism 2
  Polyamine Metabolism 57
  Urea decomposition 14
Amino Acids and Derivatives : Aromatic amino acids and derivatives Aromatic amino acid degradation 10
  Aromatic amino acid interconversions with aryl acids 1
  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) 12
  Phenylalanine and Tyrosine Branches from Chorismate 5
  Tryptophan synthesis 7
Amino Acids and Derivatives : Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis 23
  HMG CoA Synthesis 9
  Isoleucine degradation 35
  Ketoisovalerate oxidoreductase 2
  Leucine Biosynthesis 8
  Leucine Degradation and HMG-CoA Metabolism 16
  Valine degradation 36
Amino Acids and Derivatives : Glutamine, glutamate, aspartate, asparagine; ammonia assimilation Glutamate dehydrogenases 2
  Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 47
  Glutamine synthetases 1
Amino Acids and Derivatives : Histidine Metabolism Histidine Biosynthesis 10
  Histidine Degradation 9
Amino Acids and Derivatives : Lysine, threonine, methionine, and cysteine Cysteine Biosynthesis 27
  Lysine Biosynthesis DAP Pathway 10
  Lysine degradation 22
  Methionine Biosynthesis 27
  Methionine Degradation 13
  Methionine Salvage 5
  Threonine anaerobic catabolism gene cluster 2
  Threonine and Homoserine Biosynthesis 26
  Threonine degradation 4
Amino Acids and Derivatives : Proline and 4-hydroxyproline Proline, 4-hydroxyproline uptake and utilization 14
  Proline Synthesis 5
Carbohydrates Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway 2
Carbohydrates : Aminosugars Chitin and N-acetylglucosamine utilization 5
Carbohydrates : CO2 fixation Calvin-Benson cycle 9
  Carboxysome 5
  Photorespiration (oxidative C2 cycle) 23
Carbohydrates : Central carbohydrate metabolism Entner-Doudoroff Pathway 30
  Glycolate, glyoxylate interconversions 3
  Glycolysis and Gluconeogenesis 13
  Glycolysis and Gluconeogenesis, including Archaeal enzymes 9
  Methylglyoxal Metabolism 18
  Pentose phosphate pathway 9
  Pyruvate Alanine Serine Interconversions 18
  Pyruvate metabolism I: anaplerotic reactions, PEP 6
  Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 23
  TCA Cycle 16
Carbohydrates : Di- and oligosaccharides Beta-Glucoside Metabolism 1
  Lactose and Galactose Uptake and Utilization 2
  Maltose and Maltodextrin Utilization 4
  Sucrose utilization 1
  Sucrose utilization Shewanella 1
  Trehalose Biosynthesis 6
Carbohydrates : Fermentation Acetoin, butanediol metabolism 3
  Acetyl-CoA fermentation to Butyrate 28
  Butanol Biosynthesis 22
  Fermentations: Lactate 2
  Fermentations: Mixed acid 8
Carbohydrates : Glycoside hydrolases Predicted carbohydrate hydrolases 1
Carbohydrates : Monosaccharides 2-Ketogluconate Utilization 5
  D-Galacturonate and D-Glucuronate Utilization 10
  D-Sorbitol(D-Glucitol) and L-Sorbose Utilization 1
  D-galactarate, D-glucarate and D-glycerate catabolism 14
  D-galactonate catabolism 4
  D-gluconate and ketogluconates metabolism 8
  D-ribose utilization 8
  Deoxyribose and Deoxynucleoside Catabolism 3
  Fructose utilization 7
  L-Arabinose utilization 7
  L-rhamnose utilization 4
  Mannose Metabolism 5
  Xylose utilization 2
Carbohydrates : One-carbon Metabolism One-carbon metabolism by tetrahydropterines 5
  Serine-glyoxylate cycle 28
Carbohydrates : Organic acids Isobutyryl-CoA to Propionyl-CoA Module 16
  Lactate utilization 7
  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 17
  Glycerol fermenation to 1,3-propanediol 1
  Mannitol Utilization 5
  Propanediol utilization 1
  Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 20
Cell Division and Cell Cycle Bacterial Cytoskeleton 25
  Control of cell elongation - division cycle in Bacilli 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 7
  YjeE 1
Cell Wall and Capsule : Capsular and extracellular polysacchrides Alginate metabolism 21
  CMP-N-acetylneuraminate Biosynthesis 5
  Capsular heptose biosynthesis 4
  Colanic acid biosynthesis 4
  O-Methyl Phosphoramidate Capsule Modification in Campylobacter 3
  Polysaccharide deacetylases 1
  Rhamnose containing glycans 10
  Sialic Acid Metabolism 12
  dTDP-rhamnose synthesis 8
Cell Wall and Capsule : Cell wall of Mycobacteria linker unit-arabinogalactan synthesis 9
  mycolic acid synthesis 23
Cell Wall and Capsule : Gram-Negative cell wall components KDO2-Lipid A biosynthesis 12
  LOS core oligosaccharide biosynthesis 6
  Lipid A-Ara4N pathway ( Polymyxin resistance ) 2
  Lipid A modifications 7
  Lipopolysaccharide-related cluster in Alphaproteobacteria 1
Cell Wall and Capsule : Gram-Positive cell wall components Teichoic and lipoteichoic acids biosynthesis 4
  Teichuronic acid biosynthesis 2
Clustering-based subsystems Bacterial Cell Division 26
  Bacterial RNA-metabolizing Zn-dependent hydrolases 7
  CBSS-562.2.peg.5158 SK3 including 1
  Conserved gene cluster associated with Met-tRNA formyltransferase 13
  LMPTP YfkJ cluster 2
  LMPTP YwlE cluster 8
  NusA-TFII Cluster 3
  PA0057 cluster 3
  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 11
Cofactors, Vitamins, Prosthetic Groups, Pigments : Biotin Biotin biosynthesis 13
Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme A Coenzyme A Biosynthesis 11
Cofactors, Vitamins, Prosthetic Groups, Pigments : Folate and pterines Folate Biosynthesis 27
  Molybdenum cofactor biosynthesis 18
  Pterin biosynthesis 5
Cofactors, Vitamins, Prosthetic Groups, Pigments : Lipoic acid Lipoic acid metabolism 5
Cofactors, Vitamins, Prosthetic Groups, Pigments : NAD and NADP NAD and NADP cofactor biosynthesis global 17
  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 7
  Menaquinone Biosynthesis via Futalosine 1
  Menaquinone and Phylloquinone Biosynthesis 1
  Plastoquinone Biosynthesis 2
  Pyrroloquinoline Quinone biosynthesis 8
  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 25
  Experimental tye 15
  Heme and Siroheme Biosynthesis 14
DNA Metabolism DNA structural proteins, bacterial 5
  Restriction-Modification System 4
  YcfH 3
DNA Metabolism : DNA recombination RuvABC plus a hypothetical 3
DNA Metabolism : DNA repair 2-phosphoglycolate salvage 4
  DNA Repair Base Excision 16
  DNA repair, UvrABC system 3
  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 2
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 5
Fatty Acids, Lipids, and Isoprenoids Polyhydroxybutyrate metabolism 28
Fatty Acids, Lipids, and Isoprenoids : Fatty acids Fatty Acid Biosynthesis FASII 31
Fatty Acids, Lipids, and Isoprenoids : Isoprenoids Archaeal lipids 2
  Carotenoids 2
  Isoprenoid Biosynthesis 9
  Polyprenyl Diphosphate Biosynthesis 1
  polyprenyl synthesis 5
Fatty Acids, Lipids, and Isoprenoids : Phospholipids Glycerolipid and Glycerophospholipid Metabolism in Bacteria 44
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 2
  Hemin transport system 11
  Iron acquisition in Vibrio 21
  Transport of Iron 19
Iron acquisition and metabolism : Siderophores Siderophore Enterobactin 2
  Siderophore Pyoverdine 20
Membrane Transport Choline Transport 4
  ECF class transporters 1
  Ton and Tol transport systems 25
  Transport of Molybdenum 4
  Transport of Nickel and Cobalt 2
  Transport of Zinc 7
Membrane Transport : ABC transporters ABC transporter alkylphosphonate (TC 3.A.1.9.1) 20
  ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 10
  ABC transporter dipeptide (TC 3.A.1.5.2) 8
  ABC transporter oligopeptide (TC 3.A.1.5.1) 7
Membrane Transport : Protein and nucleoprotein secretion system, Type IV Type 4 conjugative transfer system, IncI1 type 1
  Type IV pilus 19
  pVir Plasmid of Campylobacter 2
Membrane Transport : Protein secretion system, Type II Widespread colonization island 10
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 2
Membrane Transport : Uni- Sym- and Antiporters Na(+) H(+) antiporter 1
Metabolism of Aromatic Compounds Aromatic Amin Catabolism 8
  Benzoate transport and degradation cluster 3
  Gentisare degradation 6
  carbazol degradation cluster 1
Metabolism of Aromatic Compounds : Metabolism of central aromatic intermediates 4-Hydroxyphenylacetic acid catabolic pathway 2
  Catechol branch of beta-ketoadipate pathway 6
  Central meta-cleavage pathway of aromatic compound degradation 5
  Homogentisate pathway of aromatic compound degradation 9
  N-heterocyclic aromatic compound degradation 5
  Protocatechuate branch of beta-ketoadipate pathway 12
  Salicylate and gentisate catabolism 6
Metabolism of Aromatic Compounds : Peripheral pathways for catabolism of aromatic compounds Benzoate degradation 14
  Biphenyl Degradation 5
  Chloroaromatic degradation pathway 4
  Phenylpropanoid compound degradation 6
  Quinate degradation 3
  n-Phenylalkanoic acid degradation 21
  p-Hydroxybenzoate degradation 2
Miscellaneous Muconate lactonizing enzyme family 1
  YaaA 1
  YbbK 4
  ZZ gjo need homes 23
Miscellaneous : Plant-Prokaryote DOE project Conserved gene cluster possibly involved in RNA metabolism 3
Motility and Chemotaxis Bacterial Chemotaxis 31
Motility and Chemotaxis : Flagellar motility in Prokaryota Flagellar motility 30
  Flagellum 49
  Flagellum in Campylobacter 6
Motility and Chemotaxis : Social motility and nonflagellar swimming in bacteria Rhamnolipids in Pseudomonas 2
Nitrogen Metabolism Allantoin Utilization 7
  Ammonia assimilation 23
  Cyanate hydrolysis 6
  Denitrification 1
  Dissimilatory nitrite reductase 2
  Nitrate and nitrite ammonification 14
  Nitric oxide synthase 2
  Nitrosative stress 3
Nucleosides and Nucleotides Adenosyl nucleosidases 1
  Hydantoin metabolism 7
  Ribonucleotide reduction 3
Nucleosides and Nucleotides : Detoxification Nudix proteins (nucleoside triphosphate hydrolases) 12
Nucleosides and Nucleotides : Purines De Novo Purine Biosynthesis 12
  Purine Utilization 19
  Purine conversions 19
Nucleosides and Nucleotides : Pyrimidines De Novo Pyrimidine Synthesis 11
  Pyrimidine utilization 8
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 2
  High affinity phosphate transporter and control of PHO regulon 11
  Phosphate metabolism 33
  Phosphonate metabolism 4
Potassium metabolism Glutathione-regulated potassium-efflux system and associated functions 4
  Potassium homeostasis 16
Protein Metabolism : Protein biosynthesis Ribosome LSU bacterial 29
  Ribosome SSU bacterial 19
  Ribosome activity modulation 1
  Ribosome biogenesis bacterial 13
  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 14
  tRNA aminoacylation, Glu and Gln 1
Protein Metabolism : Protein degradation Proteasome bacterial 8
  Protein degradation 3
  Proteolysis in bacteria, ATP-dependent 12
  Putative TldE-TldD proteolytic complex 3
Protein Metabolism : Protein folding GroEL GroES 2
  Peptidyl-prolyl cis-trans isomerase 2
  Periplasmic disulfide interchange 9
  Protein chaperones 9
Protein Metabolism : Protein processing and modification N-linked Glycosylation in Bacteria 3
  Ribosomal protein S12p Asp methylthiotransferase 3
  Ribosomal protein S5p acylation 1
  Signal peptidase 2
Protein Metabolism : Secretion Protein secretion by ABC-type exporters 7
Protein Metabolism : Selenoproteins Glycine reductase, sarcosine reductase and betaine reductase 6
  Selenocysteine metabolism 4
RNA Metabolism : RNA processing and modification ATP-dependent RNA helicases, bacterial 4
  Polyadenylation bacterial 4
  Queuosine-Archaeosine Biosynthesis 25
  RNA processing and degradation, bacterial 6
  Ribonuclease H 2
  Wyeosine-MimG Biosynthesis 5
  tRNA nucleotidyltransferase 1
  tRNA processing 11
RNA Metabolism : Transcription RNA polymerase bacterial 4
  Rrf2 family transcriptional regulators 2
  Transcription factors bacterial 9
  Transcription factors cyanobacterial RpoD-like sigma factors 1
  Transcription initiation, bacterial sigma factors 10
Regulation and Cell signaling CytR regulation 1
  DNA-binding regulatory proteins, strays 20
  Orphan regulatory proteins 22
  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 6
  cAMP signaling in bacteria 14
Regulation and Cell signaling : Programmed Cell Death and Toxin-antitoxin Systems Murein hydrolase regulation and cell death 4
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 17
  Biogenesis of cbb3-type cytochrome c oxidases 3
  Biogenesis of cytochrome c oxidases 13
  Formate hydrogenase 10
  Soluble cytochromes and functionally related electron carriers 12
Respiration : ATP synthases F0F1-type ATP synthase 5
Respiration : Electron accepting reactions Anaerobic respiratory reductases 21
  Terminal cytochrome C oxidases 18
  Terminal cytochrome O ubiquinol oxidase 4
  Terminal cytochrome d ubiquinol oxidases 2
  Terminal cytochrome oxidases 6
  Ubiquinone Menaquinone-cytochrome c reductase complexes 3
  trimethylamine N-oxide (TMAO) reductase 1
Respiration : Electron donating reactions Formate dehydrogenase 2
  Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes 5
  Respiratory Complex I 12
  Respiratory dehydrogenases 1 12
  Succinate dehydrogenase 5
Secondary Metabolism : Aromatic amino acids and derivatives Cinnamic Acid Degradation 1
Secondary Metabolism : Biosynthesis of phenylpropanoids Phenylpropionate Degradation 1
Secondary Metabolism : Plant Hormones Auxin biosynthesis 5
Stress Response Bacterial hemoglobins 10
  Flavohaemoglobin 3
  Hfl operon 6
  SigmaB stress responce regulation 3
  Universal stress protein family 3
Stress Response : Acid stress Acid resistance mechanisms 3
Stress Response : Detoxification Glutathione-dependent pathway of formaldehyde detoxification 5
Stress Response : Heat shock Heat shock dnaK gene cluster extended 16
Stress Response : Osmotic stress Choline and Betaine Uptake and Betaine Biosynthesis 37
Stress Response : Oxidative stress Glutaredoxins 6
  Glutathione: Biosynthesis and gamma-glutamyl cycle 4
  Glutathione: Non-redox reactions 17
  Glutathione: Redox cycle 3
  Oxidative stress 33
  Redox-dependent regulation of nucleus processes 5
  Rubrerythrin 4
Sulfur Metabolism Sulfate reduction-associated complexes 1
  Sulfur oxidation 2
  Thioredoxin-disulfide reductase 12
Sulfur Metabolism : Organic sulfur assimilation Alkanesulfonate assimilation 14
  Alkanesulfonates Utilization 10
  Taurine Utilization 10
  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 6
  Beta-lactamase 4
  Cobalt-zinc-cadmium resistance 18
  Copper homeostasis 14
  Copper homeostasis: copper tolerance 3
  Mercury resistance operon 1
  Methicillin resistance in Staphylococci 3
  Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 18
  Multidrug Resistance Efflux Pumps 8
  Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) 4
  Resistance to fluoroquinolones 4
  Streptothricin resistance 1