SEED Subsystems in Ralstonia solanacearum IBSBF1503

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 3
  Glycine and Serine Utilization 17
  Glycine cleavage system 5
  Serine Biosynthesis 8
Amino Acids and Derivatives : Arginine; urea cycle, polyamines Arginine Biosynthesis extended 14
  Arginine Deiminase Pathway 1
  Arginine and Ornithine Degradation 10
  Polyamine Metabolism 9
  Urea decomposition 14
Amino Acids and Derivatives : Aromatic amino acids and derivatives Aromatic amino acid degradation 9
  Aromatic amino acid interconversions with aryl acids 2
  Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. 3
  Chorismate Synthesis 13
  Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 10
  Phenylalanine and Tyrosine Branches from Chorismate 5
  Tryptophan synthesis 8
Amino Acids and Derivatives : Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis 24
  HMG CoA Synthesis 8
  Isoleucine degradation 19
  Ketoisovalerate oxidoreductase 5
  Leucine Biosynthesis 7
  Leucine Degradation and HMG-CoA Metabolism 14
  Valine degradation 22
Amino Acids and Derivatives : Glutamine, glutamate, aspartate, asparagine; ammonia assimilation Glutamate dehydrogenases 1
  Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 27
  Glutamine synthetases 2
Amino Acids and Derivatives : Histidine Metabolism Histidine Biosynthesis 12
  Histidine Degradation 7
Amino Acids and Derivatives : Lysine, threonine, methionine, and cysteine Cysteine Biosynthesis 19
  Lysine Biosynthesis DAP Pathway 10
  Lysine degradation 3
  Methionine Biosynthesis 26
  Methionine Degradation 9
  Threonine anaerobic catabolism gene cluster 3
  Threonine and Homoserine Biosynthesis 14
  Threonine degradation 8
Amino Acids and Derivatives : Proline and 4-hydroxyproline Proline, 4-hydroxyproline uptake and utilization 4
  Proline Synthesis 3
Carbohydrates Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway 4
Carbohydrates : Aminosugars Chitin and N-acetylglucosamine utilization 1
  N-Acetyl-Galactosamine and Galactosamine Utilization 1
Carbohydrates : CO2 fixation Calvin-Benson cycle 8
  Carboxysome 3
  Photorespiration (oxidative C2 cycle) 16
Carbohydrates : Central carbohydrate metabolism Entner-Doudoroff Pathway 22
  Glycolate, glyoxylate interconversions 7
  Glycolysis and Gluconeogenesis 12
  Glycolysis and Gluconeogenesis, including Archaeal enzymes 9
  Methylglyoxal Metabolism 12
  Pentose phosphate pathway 7
  Pyruvate Alanine Serine Interconversions 12
  Pyruvate metabolism I: anaplerotic reactions, PEP 10
  Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 19
  TCA Cycle 15
Carbohydrates : Di- and oligosaccharides Beta-Glucoside Metabolism 1
  Lactose and Galactose Uptake and Utilization 4
  Maltose and Maltodextrin Utilization 6
  Sucrose utilization 3
  Sucrose utilization Shewanella 1
  Trehalose Biosynthesis 10
  Trehalose Uptake and Utilization 1
Carbohydrates : Fermentation Acetoin, butanediol metabolism 3
  Acetyl-CoA fermentation to Butyrate 20
  Butanol Biosynthesis 12
  Fermentations: Lactate 3
  Fermentations: Mixed acid 11
Carbohydrates : Glycoside hydrolases Predicted carbohydrate hydrolases 2
Carbohydrates : Monosaccharides D-Galacturonate and D-Glucuronate Utilization 10
  D-Sorbitol(D-Glucitol) and L-Sorbose Utilization 1
  D-galactarate, D-glucarate and D-glycerate catabolism 11
  D-gluconate and ketogluconates metabolism 4
  D-ribose utilization 6
  Deoxyribose and Deoxynucleoside Catabolism 2
  Fructose utilization 8
  L-rhamnose utilization 3
  Mannose Metabolism 1
  Xylose utilization 3
Carbohydrates : One-carbon Metabolism One-carbon metabolism by tetrahydropterines 4
  Serine-glyoxylate cycle 24
Carbohydrates : Organic acids Isobutyryl-CoA to Propionyl-CoA Module 9
  Lactate utilization 5
  Methylcitrate cycle 8
  Propionate-CoA to Succinate Module 8
  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
  Inositol catabolism 12
  Mannitol Utilization 5
  Propanediol utilization 1
  Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 2
Cell Division and Cell Cycle Bacterial Cytoskeleton 24
  Control of cell elongation - division cycle in Bacilli 1
  Macromolecular synthesis operon 6
  Two cell division clusters relating to chromosome partitioning 11
Cell Wall and Capsule Peptidoglycan Biosynthesis 24
  UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis 6
  YjeE 1
Cell Wall and Capsule : Capsular and extracellular polysacchrides Alginate metabolism 5
  CMP-N-acetylneuraminate Biosynthesis 2
  Capsular heptose biosynthesis 1
  Colanic acid biosynthesis 3
  O-Methyl Phosphoramidate Capsule Modification in Campylobacter 2
  Polysaccharide deacetylases 1
  Rhamnose containing glycans 9
  Sialic Acid Metabolism 7
  dTDP-rhamnose synthesis 6
Cell Wall and Capsule : Cell wall of Mycobacteria linker unit-arabinogalactan synthesis 9
  mycolic acid synthesis 21
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 ) 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 2
  Teichuronic acid biosynthesis 2
Clustering-based subsystems Bacterial Cell Division 27
  Bacterial RNA-metabolizing Zn-dependent hydrolases 9
  CBSS-214092.1.peg.3450 2
  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 2
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 12
Clustering-based subsystems : proteosome related Cluster-based Subsystem Grouping Hypotheticals - perhaps Proteosome Related 2
Cofactors, Vitamins, Prosthetic Groups, Pigments Thiamin biosynthesis 9
Cofactors, Vitamins, Prosthetic Groups, Pigments : Biotin Biotin biosynthesis 12
Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme A Coenzyme A Biosynthesis 11
Cofactors, Vitamins, Prosthetic Groups, Pigments : Folate and pterines Folate Biosynthesis 18
  Molybdenum cofactor biosynthesis 18
  Pterin biosynthesis 2
  p-Aminobenzoyl-Glutamate Utilization 2
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 17
  NAD regulation 10
  PnuC-like transporters 1
Cofactors, Vitamins, Prosthetic Groups, Pigments : Pyridoxine Pyridoxin (Vitamin B6) Biosynthesis 14
Cofactors, Vitamins, Prosthetic Groups, Pigments : Quinone cofactors Plastoquinone Biosynthesis 3
  Tocopherol Biosynthesis 3
  Ubiquinone Biosynthesis 8
Cofactors, Vitamins, Prosthetic Groups, Pigments : Riboflavin, FMN, FAD Riboflavin, FMN and FAD metabolism 4
Cofactors, Vitamins, Prosthetic Groups, Pigments : Tetrapyrroles Cobalamin synthesis 12
  Coenzyme B12 biosynthesis 24
  Experimental tye 15
  Heme and Siroheme Biosynthesis 12
DNA Metabolism DNA structural proteins, bacterial 6
  Restriction-Modification System 2
  YcfH 2
DNA Metabolism : CRISPs CRISPRs 2
DNA Metabolism : DNA recombination RuvABC plus a hypothetical 3
DNA Metabolism : DNA repair 2-phosphoglycolate salvage 5
  DNA Repair Base Excision 11
  DNA repair, UvrABC system 4
  DNA repair, bacterial 22
  DNA repair, bacterial DinG and relatives 1
  DNA repair, bacterial MutL-MutS system 2
  DNA repair, bacterial RecFOR pathway 6
  DNA repair, bacterial UvrD and related helicases 5
DNA Metabolism : DNA replication DNA-replication 23
  DNA replication, archaeal 1
  DNA topoisomerases, Type II, ATP-dependent 4
  Plasmid replication 4
Fatty Acids, Lipids, and Isoprenoids Polyhydroxybutyrate metabolism 21
Fatty Acids, Lipids, and Isoprenoids : Fatty acids Fatty Acid Biosynthesis FASII 29
Fatty Acids, Lipids, and Isoprenoids : Isoprenoids Archaeal lipids 1
  Carotenoids 3
  Isoprenoid Biosynthesis 8
  Polyprenyl Diphosphate Biosynthesis 1
  polyprenyl synthesis 5
Fatty Acids, Lipids, and Isoprenoids : Phospholipids Glycerolipid and Glycerophospholipid Metabolism in Bacteria 33
Fatty Acids, Lipids, and Isoprenoids : Triacylglycerols Triacylglycerol metabolism 1
Iron acquisition and metabolism Campylobacter Iron Metabolism 8
  Heme, hemin uptake and utilization systems in GramPositives 1
  Hemin transport system 5
  Iron acquisition in Vibrio 16
  Transport of Iron 13
Iron acquisition and metabolism : Siderophores Siderophore Staphylobactin 2
Membrane Transport ECF class transporters 2
  Ton and Tol transport systems 19
  Transport of Manganese 2
  Transport of Molybdenum 5
  Transport of Nickel and Cobalt 2
  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) 29
  ABC transporter dipeptide (TC 3.A.1.5.2) 5
  ABC transporter oligopeptide (TC 3.A.1.5.1) 9
  ABC transporter tungstate (TC 3.A.1.6.2) 3
Membrane Transport : Protein and nucleoprotein secretion system, Type IV Type 4 conjugative transfer system, IncI1 type 1
  Type IV pilus 38
  pVir Plasmid of Campylobacter 1
Membrane Transport : Protein secretion system, Type II Widespread colonization island 16
Membrane Transport : Protein translocation across cytoplasmic membrane Twin-arginine translocation system 3
Membrane Transport : Sugar Phosphotransferase Systems, PTS Fructose and Mannose Inducible PTS 3
Metabolism of Aromatic Compounds Aromatic Amin Catabolism 2
  Benzoate transport and degradation cluster 3
  Gentisare degradation 3
Metabolism of Aromatic Compounds : Metabolism of central aromatic intermediates 4-Hydroxyphenylacetic acid catabolic pathway 2
  Catechol branch of beta-ketoadipate pathway 9
  Central meta-cleavage pathway of aromatic compound degradation 1
  Homogentisate pathway of aromatic compound degradation 14
  N-heterocyclic aromatic compound degradation 6
  Protocatechuate branch of beta-ketoadipate pathway 15
  Salicylate and gentisate catabolism 8
Metabolism of Aromatic Compounds : Peripheral pathways for catabolism of aromatic compounds Benzoate degradation 7
  Chloroaromatic degradation pathway 4
  Naphtalene and antracene degradation 3
  Phenylpropanoid compound degradation 9
  Quinate degradation 2
  Salicylate ester degradation 2
  Toluene degradation 1
  n-Phenylalkanoic acid degradation 12
  p-Hydroxybenzoate degradation 2
Miscellaneous Muconate lactonizing enzyme family 1
  YaaA 1
  YbbK 4
  ZZ gjo need homes 12
Miscellaneous : Plant-Prokaryote DOE project Conserved gene cluster possibly involved in RNA metabolism 3
Motility and Chemotaxis Bacterial Chemotaxis 35
Motility and Chemotaxis : Flagellar motility in Prokaryota Flagellar motility 23
  Flagellum 45
  Flagellum in Campylobacter 5
Motility and Chemotaxis : Social motility and nonflagellar swimming in bacteria Rhamnolipids in Pseudomonas 2
Nitrogen Metabolism Allantoin Utilization 5
  Ammonia assimilation 18
  Cyanate hydrolysis 3
  Denitrification 6
  Dissimilatory nitrite reductase 1
  Nitrate and nitrite ammonification 17
  Nitric oxide synthase 2
  Nitrosative stress 3
Nucleosides and Nucleotides Hydantoin metabolism 3
  Ribonucleotide reduction 5
Nucleosides and Nucleotides : Detoxification Nudix proteins (nucleoside triphosphate hydrolases) 7
Nucleosides and Nucleotides : Purines De Novo Purine Biosynthesis 11
  Purine Utilization 8
  Purine conversions 18
Nucleosides and Nucleotides : Pyrimidines De Novo Pyrimidine Synthesis 10
  Pyrimidine utilization 1
Phages, Prophages, Transposable elements, Plasmids : Pathogenicity islands Staphylococcal pathogenicity islands SaPI 5
Phages, Prophages, Transposable elements, Plasmids : Phages, Prophages IbrA and IbrB: co-activators of prophage gene expression 2
Phosphorus Metabolism Alkylphosphonate utilization 6
  High affinity phosphate transporter and control of PHO regulon 10
  Phosphate metabolism 29
  Phosphonate metabolism 1
Potassium metabolism Glutathione-regulated potassium-efflux system and associated functions 4
  Potassium homeostasis 13
Protein Metabolism : Protein biosynthesis Ribosome LSU bacterial 29
  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 11
  Putative TldE-TldD proteolytic complex 1
Protein Metabolism : Protein folding GroEL GroES 2
  Peptidyl-prolyl cis-trans isomerase 3
  Periplasmic disulfide interchange 5
  Protein chaperones 8
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 4
RNA Metabolism : RNA processing and modification ATP-dependent RNA helicases, bacterial 3
  Polyadenylation bacterial 4
  Queuosine-Archaeosine Biosynthesis 29
  RNA 3'-terminal phosphate cyclase 5
  RNA processing and degradation, bacterial 7
  Ribonuclease H 2
  Wyeosine-MimG Biosynthesis 4
  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 10
Regulation and Cell signaling DNA-binding regulatory proteins, strays 6
  Orphan regulatory proteins 10
  Sex pheromones in Enterococcus faecalis and other Firmicutes 6
  Stringent Response, (p)ppGpp metabolism 2
  Two-component regulatory systems in Campylobacter 7
  cAMP signaling in bacteria 11
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 6
  Biogenesis of cbb3-type cytochrome c oxidases 3
  Biogenesis of cytochrome c oxidases 9
  Carbon monoxide dehydrogenase maturation factors 4
  Formate hydrogenase 6
  Soluble cytochromes and functionally related electron carriers 9
Respiration : ATP synthases F0F1-type ATP synthase 7
Respiration : Electron accepting reactions Anaerobic respiratory reductases 12
  Terminal cytochrome C oxidases 15
  Terminal cytochrome O ubiquinol oxidase 4
  Terminal cytochrome d ubiquinol oxidases 4
  Terminal cytochrome oxidases 8
  Ubiquinone Menaquinone-cytochrome c reductase complexes 3
Respiration : Electron donating reactions CO Dehydrogenase 7
  Formate dehydrogenase 1
  Respiratory Complex I 14
  Respiratory dehydrogenases 1 7
  Succinate dehydrogenase 4
Secondary Metabolism : Aromatic amino acids and derivatives Cinnamic Acid Degradation 2
Secondary Metabolism : Bacterial cytostatics, differentiation factors and antibiotics Phenazine biosynthesis 1
Secondary Metabolism : Biosynthesis of phenylpropanoids Phenylpropionate Degradation 2
Secondary Metabolism : Plant Hormones Auxin biosynthesis 6
  Auxin degradation 1
Stress Response Bacterial hemoglobins 10
  Flavohaemoglobin 3
  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 4
Stress Response : Oxidative stress Glutaredoxins 4
  Glutathione: Biosynthesis and gamma-glutamyl cycle 5
  Glutathione: Non-redox reactions 11
  Glutathione: Redox cycle 2
  Oxidative stress 25
  Redox-dependent regulation of nucleus processes 4
  Rubrerythrin 2
Sulfur Metabolism Sulfur oxidation 12
  Thioredoxin-disulfide reductase 11
Sulfur Metabolism : Organic sulfur assimilation Alkanesulfonate assimilation 15
  Alkanesulfonates Utilization 7
  Taurine Utilization 3
  Utilization of glutathione as a sulphur source 3
Virulence, Disease and Defense : Detection MLST 4
Virulence, Disease and Defense : Invasion and intracellular resistance Listeria surface proteins: Internalin-like proteins 1
Virulence, Disease and Defense : Resistance to antibiotics and toxic compounds Arsenic resistance 2
  Beta-lactamase 2
  Cobalt-zinc-cadmium resistance 21
  Copper homeostasis 13
  Copper homeostasis: copper tolerance 5
  Mercuric reductase 1
  Methicillin resistance in Staphylococci 3
  Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 6
  Multidrug Resistance Efflux Pumps 21
  Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) 13
  Resistance to fluoroquinolones 4