SEED Subsystems in Paraburkholderia graminis OAS925

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 2
Amino Acids and Derivatives : Alanine, serine, and glycine Alanine biosynthesis 5
  Glycine Biosynthesis 5
  Glycine and Serine Utilization 24
  Glycine cleavage system 8
  Serine Biosynthesis 13
Amino Acids and Derivatives : Arginine; urea cycle, polyamines Arginine Biosynthesis extended 13
  Arginine Deiminase Pathway 2
  Arginine and Ornithine Degradation 33
  Polyamine Metabolism 28
  Urea decomposition 24
Amino Acids and Derivatives : Aromatic amino acids and derivatives Aromatic amino acid degradation 17
  Aromatic amino acid interconversions with aryl acids 3
  Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. 4
  Chorismate Synthesis 14
  Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 11
  Phenylalanine and Tyrosine Branches from Chorismate 5
  Tryptophan synthesis 7
Amino Acids and Derivatives : Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis 31
  HMG CoA Synthesis 13
  Isoleucine degradation 30
  Ketoisovalerate oxidoreductase 4
  Leucine Biosynthesis 9
  Leucine Degradation and HMG-CoA Metabolism 16
  Valine degradation 35
Amino Acids and Derivatives : Glutamine, glutamate, aspartate, asparagine; ammonia assimilation Glutamate dehydrogenases 2
  Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 34
  Glutamine synthetases 1
Amino Acids and Derivatives : Histidine Metabolism Histidine Biosynthesis 11
  Histidine Degradation 12
Amino Acids and Derivatives : Lysine, threonine, methionine, and cysteine Cysteine Biosynthesis 22
  Lysine Biosynthesis DAP Pathway 7
  Lysine degradation 6
  Methionine Biosynthesis 30
  Methionine Degradation 19
  Methionine Salvage 2
  Threonine anaerobic catabolism gene cluster 5
  Threonine and Homoserine Biosynthesis 19
  Threonine degradation 10
Amino Acids and Derivatives : Proline and 4-hydroxyproline Proline, 4-hydroxyproline uptake and utilization 23
  Proline Synthesis 4
Carbohydrates Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway 9
Carbohydrates : Aminosugars Chitin and N-acetylglucosamine utilization 9
Carbohydrates : CO2 fixation CO2 uptake, carboxysome 3
  Calvin-Benson cycle 21
  Carboxysome 7
  Photorespiration (oxidative C2 cycle) 26
Carbohydrates : Central carbohydrate metabolism Dihydroxyacetone kinases 4
  Entner-Doudoroff Pathway 40
  Glycolate, glyoxylate interconversions 10
  Glycolysis and Gluconeogenesis 17
  Glycolysis and Gluconeogenesis, including Archaeal enzymes 11
  Methylglyoxal Metabolism 26
  Pentose phosphate pathway 21
  Pyruvate Alanine Serine Interconversions 14
  Pyruvate metabolism I: anaplerotic reactions, PEP 12
  Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 36
  TCA Cycle 19
Carbohydrates : Di- and oligosaccharides Fructooligosaccharides(FOS) and Raffinose Utilization 3
  Lactose and Galactose Uptake and Utilization 15
  Lactose utilization 3
  Maltose and Maltodextrin Utilization 13
  Sucrose utilization 1
  Sucrose utilization Shewanella 1
  Trehalose Biosynthesis 14
  Trehalose Uptake and Utilization 4
Carbohydrates : Fermentation Acetoin, butanediol metabolism 12
  Acetyl-CoA fermentation to Butyrate 41
  Butanol Biosynthesis 25
  Fermentations: Lactate 5
  Fermentations: Mixed acid 14
Carbohydrates : Glycoside hydrolases Predicted carbohydrate hydrolases 2
Carbohydrates : Monosaccharides 2-Ketogluconate Utilization 6
  D-Galacturonate and D-Glucuronate Utilization 22
  D-Sorbitol(D-Glucitol) and L-Sorbose Utilization 1
  D-galactarate, D-glucarate and D-glycerate catabolism 15
  D-galactonate catabolism 6
  D-gluconate and ketogluconates metabolism 9
  D-ribose utilization 39
  Deoxyribose and Deoxynucleoside Catabolism 7
  Fructose utilization 13
  L-Arabinose utilization 13
  L-fucose utilization 2
  L-fucose utilization temp 6
  L-rhamnose utilization 17
  Mannose Metabolism 8
  Xylose utilization 16
Carbohydrates : One-carbon Metabolism Formaldehyde assimilation: Ribulose monophosphate pathway 1
  Methanogenesis 5
  One-carbon metabolism by tetrahydropterines 7
  Serine-glyoxylate cycle 35
Carbohydrates : Organic acids Isobutyryl-CoA to Propionyl-CoA Module 12
  Lactate utilization 12
  Malonate decarboxylase 10
  Methylcitrate cycle 10
  Propionate-CoA to Succinate Module 8
  Propionyl-CoA to Succinyl-CoA Module 4
Carbohydrates : Polysaccharides Glycogen metabolism 10
Carbohydrates : Sugar alcohols Di-Inositol-Phosphate biosynthesis 1
  Erythritol utilization 1
  Ethanolamine utilization 7
  Glycerol and Glycerol-3-phosphate Uptake and Utilization 22
  Glycerol fermenation to 1,3-propanediol 1
  Inositol catabolism 16
  Mannitol Utilization 8
  Propanediol utilization 1
  Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 25
Cell Division and Cell Cycle Bacterial Cytoskeleton 26
  Control of cell elongation - division cycle in Bacilli 1
  Cyanobacterial Circadian Clock 2
  Macromolecular synthesis operon 8
  Two cell division clusters relating to chromosome partitioning 11
Cell Wall and Capsule Peptidoglycan Biosynthesis 27
  UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis 10
  YjeE 1
Cell Wall and Capsule : Capsular and extracellular polysacchrides Alginate metabolism 11
  CMP-N-acetylneuraminate Biosynthesis 1
  Capsular heptose biosynthesis 6
  Colanic acid biosynthesis 14
  O-Methyl Phosphoramidate Capsule Modification in Campylobacter 2
  Phosphorylcholine incorporation in LPS 1
  Polysaccharide deacetylases 2
  Rhamnose containing glycans 18
  Sialic Acid Metabolism 15
  dTDP-rhamnose synthesis 8
Cell Wall and Capsule : Cell wall of Mycobacteria linker unit-arabinogalactan synthesis 15
  mycolic acid synthesis 36
Cell Wall and Capsule : Gram-Negative cell wall components KDO2-Lipid A biosynthesis 13
  LOS core oligosaccharide biosynthesis 11
  Lipid A-Ara4N pathway ( Polymyxin resistance ) 7
  Lipid A modifications 2
  Lipopolysaccharide-related cluster in Alphaproteobacteria 1
Cell Wall and Capsule : Gram-Positive cell wall components Teichoic and lipoteichoic acids biosynthesis 6
  Teichuronic acid biosynthesis 4
Clustering-based subsystems Bacterial Cell Division 31
  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 5
  LMPTP YwlE cluster 6
  NusA-TFII Cluster 3
  PA0057 cluster 1
  Putative hemin transporter 2
  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 3
Clustering-based subsystems : Type III secretion system, extended Type III secretion systems, extended 10
Clustering-based subsystems : proteosome related Cluster-based Subsystem Grouping Hypotheticals - perhaps Proteosome Related 2
Cofactors, Vitamins, Prosthetic Groups, Pigments Thiamin biosynthesis 17
Cofactors, Vitamins, Prosthetic Groups, Pigments : Biotin Biotin biosynthesis 16
Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme A Coenzyme A Biosynthesis 12
Cofactors, Vitamins, Prosthetic Groups, Pigments : Folate and pterines Folate Biosynthesis 25
  Molybdenum cofactor biosynthesis 18
  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 20
  NAD regulation 11
  PnuC-like transporters 1
Cofactors, Vitamins, Prosthetic Groups, Pigments : Pyridoxine Pyridoxin (Vitamin B6) Biosynthesis 15
Cofactors, Vitamins, Prosthetic Groups, Pigments : Quinone cofactors Coenzyme PQQ synthesis 4
  Menaquinone and Phylloquinone Biosynthesis 2
  Plastoquinone Biosynthesis 4
  Pyrroloquinoline Quinone biosynthesis 5
  Tocopherol Biosynthesis 4
  Ubiquinone Biosynthesis 17
Cofactors, Vitamins, Prosthetic Groups, Pigments : Riboflavin, FMN, FAD Riboflavin, FMN and FAD metabolism 4
Cofactors, Vitamins, Prosthetic Groups, Pigments : Tetrapyrroles Cobalamin synthesis 14
  Coenzyme B12 biosynthesis 27
  Experimental tye 15
  Heme and Siroheme Biosynthesis 15
DNA Metabolism DNA structural proteins, bacterial 6
  Restriction-Modification System 11
  YcfH 2
DNA Metabolism : DNA recombination RuvABC plus a hypothetical 3
DNA Metabolism : DNA repair 2-phosphoglycolate salvage 5
  DNA Repair Base Excision 17
  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 38
  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 38
Fatty Acids, Lipids, and Isoprenoids : Fatty acids Fatty Acid Biosynthesis FASII 46
Fatty Acids, Lipids, and Isoprenoids : Isoprenoids Archaeal lipids 1
  Carotenoids 6
  Isoprenoid Biosynthesis 9
  Polyprenyl Diphosphate Biosynthesis 1
  polyprenyl synthesis 6
Fatty Acids, Lipids, and Isoprenoids : Phospholipids Glycerolipid and Glycerophospholipid Metabolism in Bacteria 53
Fatty Acids, Lipids, and Isoprenoids : Triacylglycerols Triacylglycerol metabolism 1
Iron acquisition and metabolism Campylobacter Iron Metabolism 5
  Hemin transport system 8
  Iron acquisition in Vibrio 12
  Transport of Iron 8
Iron acquisition and metabolism : Siderophores Siderophore Aerobactin 2
  Siderophore Pyoverdine 1
Membrane Transport Choline Transport 2
  ECF class transporters 1
  Ton and Tol transport systems 24
  Transport of Manganese 3
  Transport of Molybdenum 6
  Transport of Nickel and Cobalt 2
  Transport of Zinc 5
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) 25
  ABC transporter dipeptide (TC 3.A.1.5.2) 16
  ABC transporter oligopeptide (TC 3.A.1.5.1) 18
Membrane Transport : Protein and nucleoprotein secretion system, Type IV Type IV pilus 15
  pVir Plasmid of Campylobacter 1
Membrane Transport : Protein secretion system, Type II Widespread colonization island 19
Membrane Transport : Protein translocation across cytoplasmic membrane Twin-arginine translocation system 3
Membrane Transport : Sugar Phosphotransferase Systems, PTS Fructose and Mannose Inducible PTS 4
Metabolism of Aromatic Compounds Aromatic Amin Catabolism 5
  Benzoate transport and degradation cluster 14
  Cresol degradation 1
  Gentisare degradation 11
  carbazol degradation cluster 1
Metabolism of Aromatic Compounds : Metabolism of central aromatic intermediates 4-Hydroxyphenylacetic acid catabolic pathway 10
  Catechol branch of beta-ketoadipate pathway 15
  Central meta-cleavage pathway of aromatic compound degradation 9
  Homogentisate pathway of aromatic compound degradation 32
  N-heterocyclic aromatic compound degradation 10
  Protocatechuate branch of beta-ketoadipate pathway 20
  Salicylate and gentisate catabolism 18
Metabolism of Aromatic Compounds : Peripheral pathways for catabolism of aromatic compounds Benzoate degradation 8
  Biphenyl Degradation 1
  Chloroaromatic degradation pathway 7
  Naphtalene and antracene degradation 2
  Phenylpropanoid compound degradation 16
  Quinate degradation 3
  Salicylate ester degradation 3
  n-Phenylalkanoic acid degradation 26
  p-Hydroxybenzoate degradation 8
Miscellaneous Luciferases 2
  Muconate lactonizing enzyme family 1
  YaaA 1
  YbbK 4
  ZZ gjo need homes 15
Miscellaneous : Plant-Prokaryote DOE project Conserved gene cluster possibly involved in RNA metabolism 3
Motility and Chemotaxis Bacterial Chemotaxis 56
Motility and Chemotaxis : Flagellar motility in Prokaryota Flagellar motility 38
  Flagellum 63
  Flagellum in Campylobacter 5
Nitrogen Metabolism Allantoin Utilization 10
  Ammonia assimilation 23
  Cyanate hydrolysis 3
  Dissimilatory nitrite reductase 3
  Nitrate and nitrite ammonification 31
  Nitric oxide synthase 1
  Nitrosative stress 1
Nucleosides and Nucleotides Hydantoin metabolism 11
  Ribonucleotide reduction 5
Nucleosides and Nucleotides : Detoxification Nudix proteins (nucleoside triphosphate hydrolases) 7
Nucleosides and Nucleotides : Purines De Novo Purine Biosynthesis 13
  Purine Utilization 20
  Purine conversions 26
Nucleosides and Nucleotides : Pyrimidines De Novo Pyrimidine Synthesis 11
  Pyrimidine utilization 8
Phages, Prophages, Transposable elements, Plasmids : Pathogenicity islands Staphylococcal pathogenicity islands SaPI 11
Phages, Prophages, Transposable elements, Plasmids : Transposable elements Tn552 2
Phosphorus Metabolism Alkylphosphonate utilization 6
  High affinity phosphate transporter and control of PHO regulon 9
  Phosphate metabolism 34
  Phosphonate metabolism 8
Potassium metabolism Glutathione-regulated potassium-efflux system and associated functions 2
  Potassium homeostasis 10
Protein Metabolism : Protein biosynthesis Ribosome LSU bacterial 32
  Ribosome SSU bacterial 20
  Ribosome activity modulation 1
  Ribosome biogenesis bacterial 11
  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 17
  tRNA aminoacylation, Glu and Gln 2
Protein Metabolism : Protein degradation Proteasome bacterial 8
  Protein degradation 4
  Proteolysis in bacteria, ATP-dependent 15
  Putative TldE-TldD proteolytic complex 3
Protein Metabolism : Protein folding GroEL GroES 7
  Peptidyl-prolyl cis-trans isomerase 2
  Periplasmic disulfide interchange 5
  Protein chaperones 9
Protein Metabolism : Protein processing and modification N-linked Glycosylation in Bacteria 10
  Ribosomal protein S12p Asp methylthiotransferase 4
  Ribosomal protein S5p acylation 1
  Signal peptidase 2
Protein Metabolism : Selenoproteins Glycine reductase, sarcosine reductase and betaine reductase 9
  Selenocysteine metabolism 2
RNA Metabolism : RNA processing and modification ATP-dependent RNA helicases, bacterial 4
  Polyadenylation bacterial 5
  Queuosine-Archaeosine Biosynthesis 25
  RNA processing and degradation, bacterial 8
  Ribonuclease H 2
  Wyeosine-MimG Biosynthesis 10
  tRNA nucleotidyltransferase 1
  tRNA processing 12
RNA Metabolism : Transcription RNA polymerase bacterial 4
  Rrf2 family transcriptional regulators 3
  Transcription factors bacterial 8
  Transcription factors cyanobacterial RpoD-like sigma factors 2
  Transcription initiation, bacterial sigma factors 16
Regulation and Cell signaling DNA-binding regulatory proteins, strays 13
  Orphan regulatory proteins 13
  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 21
Regulation and Cell signaling : Programmed Cell Death and Toxin-antitoxin Systems Murein hydrolase regulation and cell death 6
Regulation and Cell signaling : Quorum sensing and biofilm formation Quorum Sensing: Autoinducer-2 Synthesis 1
Respiration Biogenesis of c-type cytochromes 7
  Biogenesis of cytochrome c oxidases 9
  Carbon monoxide dehydrogenase maturation factors 7
  Formate hydrogenase 8
  Soluble cytochromes and functionally related electron carriers 21
Respiration : ATP synthases F0F1-type ATP synthase 7
Respiration : Electron accepting reactions Anaerobic respiratory reductases 22
  Terminal cytochrome C oxidases 17
  Terminal cytochrome O ubiquinol oxidase 4
  Terminal cytochrome d ubiquinol oxidases 7
  Terminal cytochrome oxidases 11
  Ubiquinone Menaquinone-cytochrome c reductase complexes 3
Respiration : Electron donating reactions CO Dehydrogenase 15
  Respiratory Complex I 15
  Respiratory dehydrogenases 1 18
  Succinate dehydrogenase 8
Secondary Metabolism : Aromatic amino acids and derivatives Cinnamic Acid Degradation 7
Secondary Metabolism : Plant Hormones Auxin biosynthesis 4
Stress Response Bacterial hemoglobins 16
  Flavohaemoglobin 3
  Hfl operon 6
  Universal stress protein family 3
Stress Response : Acid stress Acid resistance mechanisms 1
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 30
Stress Response : Oxidative stress Glutaredoxins 5
  Glutathione: Biosynthesis and gamma-glutamyl cycle 8
  Glutathione: Non-redox reactions 17
  Glutathione: Redox cycle 1
  Glutathionylspermidine and Trypanothione 1
  Oxidative stress 27
  Redox-dependent regulation of nucleus processes 5
  Rubrerythrin 6
Sulfur Metabolism Galactosylceramide and Sulfatide metabolism 3
  Sulfur oxidation 6
  Thioredoxin-disulfide reductase 18
Sulfur Metabolism : Organic sulfur assimilation Alkanesulfonate assimilation 33
  Alkanesulfonates Utilization 14
  Taurine Utilization 8
  Utilization of glutathione as a sulphur source 8
Virulence, Disease and Defense : Detection MLST 5
Virulence, Disease and Defense : Resistance to antibiotics and toxic compounds Arsenic resistance 7
  Beta-lactamase 6
  Cobalt-zinc-cadmium resistance 19
  Copper homeostasis 6
  Copper homeostasis: copper tolerance 6
  Mercuric reductase 2
  Methicillin resistance in Staphylococci 4
  Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 20
  Multidrug Resistance Efflux Pumps 21
  Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) 8
  Resistance to fluoroquinolones 4