SEED Subsystems in Sphingobium sp. HT1-2

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 : Alanine, serine, and glycine Alanine biosynthesis 9
  Glycine Biosynthesis 1
  Glycine and Serine Utilization 15
  Glycine cleavage system 5
  Serine Biosynthesis 8
Amino Acids and Derivatives : Arginine; urea cycle, polyamines Arginine Biosynthesis extended 9
  Arginine Deiminase Pathway 2
  Arginine and Ornithine Degradation 10
  Cyanophycin Metabolism 1
  Polyamine Metabolism 8
Amino Acids and Derivatives : Aromatic amino acids and derivatives Aromatic amino acid degradation 7
  Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. 5
  Chorismate Synthesis 16
  Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 10
  Phenylalanine and Tyrosine Branches from Chorismate 7
  Tryptophan synthesis 6
Amino Acids and Derivatives : Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis 16
  HMG CoA Synthesis 9
  Isoleucine degradation 33
  Ketoisovalerate oxidoreductase 4
  Leucine Biosynthesis 5
  Leucine Degradation and HMG-CoA Metabolism 15
  Valine degradation 37
Amino Acids and Derivatives : Glutamine, glutamate, aspartate, asparagine; ammonia assimilation Glutamate dehydrogenases 1
  Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 19
  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 12
  Lysine Biosynthesis DAP Pathway 8
  Methionine Biosynthesis 21
  Methionine Degradation 5
  Methionine Salvage 1
  Threonine anaerobic catabolism gene cluster 5
  Threonine and Homoserine Biosynthesis 14
  Threonine degradation 5
Amino Acids and Derivatives : Proline and 4-hydroxyproline Proline, 4-hydroxyproline uptake and utilization 15
  Proline Synthesis 3
Carbohydrates Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway 4
Carbohydrates : Aminosugars Chitin and N-acetylglucosamine utilization 17
  N-Acetyl-Galactosamine and Galactosamine Utilization 2
Carbohydrates : CO2 fixation Calvin-Benson cycle 9
  Carboxysome 4
  Photorespiration (oxidative C2 cycle) 19
Carbohydrates : Central carbohydrate metabolism Entner-Doudoroff Pathway 26
  Glycolate, glyoxylate interconversions 2
  Glycolysis and Gluconeogenesis 13
  Glycolysis and Gluconeogenesis, including Archaeal enzymes 10
  Methylglyoxal Metabolism 11
  Pentose phosphate pathway 10
  Pyruvate Alanine Serine Interconversions 7
  Pyruvate metabolism I: anaplerotic reactions, PEP 8
  Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 25
  TCA Cycle 17
Carbohydrates : Di- and oligosaccharides Beta-Glucoside Metabolism 4
  Fructooligosaccharides(FOS) and Raffinose Utilization 4
  Lactose and Galactose Uptake and Utilization 12
  Lactose utilization 7
  Maltose and Maltodextrin Utilization 12
  Sucrose utilization 3
  Sucrose utilization Shewanella 3
  Trehalose Biosynthesis 5
  Trehalose Uptake and Utilization 1
Carbohydrates : Fermentation Acetoin, butanediol metabolism 5
  Acetyl-CoA fermentation to Butyrate 38
  Butanol Biosynthesis 30
  Fermentations: Lactate 7
  Fermentations: Mixed acid 16
Carbohydrates : Glycoside hydrolases Predicted carbohydrate hydrolases 1
Carbohydrates : Monosaccharides D-Galacturonate and D-Glucuronate Utilization 21
  D-Sorbitol(D-Glucitol) and L-Sorbose Utilization 1
  D-galactarate, D-glucarate and D-glycerate catabolism 4
  D-galactonate catabolism 5
  D-gluconate and ketogluconates metabolism 4
  D-ribose utilization 1
  Deoxyribose and Deoxynucleoside Catabolism 2
  Fructose utilization 10
  L-Arabinose utilization 7
  L-fucose utilization 2
  L-fucose utilization temp 4
  L-rhamnose utilization 12
  Mannose Metabolism 11
  Xylose utilization 13
Carbohydrates : One-carbon Metabolism One-carbon metabolism by tetrahydropterines 4
  Serine-glyoxylate cycle 33
Carbohydrates : Organic acids Isobutyryl-CoA to Propionyl-CoA Module 19
  Lactate utilization 8
  Propionate-CoA to Succinate Module 2
  Propionyl-CoA to Succinyl-CoA Module 5
Carbohydrates : Polysaccharides Glycogen metabolism 5
Carbohydrates : Sugar alcohols Di-Inositol-Phosphate biosynthesis 3
  Ethanolamine utilization 4
  Glycerol and Glycerol-3-phosphate Uptake and Utilization 11
  Glycerol fermenation to 1,3-propanediol 1
  Inositol catabolism 1
  Mannitol Utilization 7
  Propanediol utilization 2
  Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 5
Cell Division and Cell Cycle Bacterial Cytoskeleton 24
  Control of cell elongation - division cycle in Bacilli 1
  Macromolecular synthesis operon 7
  Two cell division clusters relating to chromosome partitioning 16
Cell Wall and Capsule Peptidoglycan Biosynthesis 26
  UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis 9
  YjeE 1
Cell Wall and Capsule : Capsular and extracellular polysacchrides Alginate metabolism 13
  CMP-N-acetylneuraminate Biosynthesis 1
  Capsular Polysaccharide (CPS) of Campylobacter 3
  Capsular heptose biosynthesis 1
  Colanic acid biosynthesis 2
  O-Methyl Phosphoramidate Capsule Modification in Campylobacter 1
  Rhamnose containing glycans 15
  Sialic Acid Metabolism 7
  dTDP-rhamnose synthesis 7
Cell Wall and Capsule : Cell wall of Mycobacteria linker unit-arabinogalactan synthesis 11
  mycolic acid synthesis 29
Cell Wall and Capsule : Gram-Negative cell wall components KDO2-Lipid A biosynthesis 5
  Lipid A-Ara4N pathway ( Polymyxin resistance ) 3
Cell Wall and Capsule : Gram-Positive cell wall components Teichoic and lipoteichoic acids biosynthesis 2
  Teichuronic acid biosynthesis 3
Clustering-based subsystems Bacterial Cell Division 26
  Bacterial RNA-metabolizing Zn-dependent hydrolases 10
  Conserved gene cluster associated with Met-tRNA formyltransferase 13
  LMPTP YfkJ cluster 3
  LMPTP YwlE cluster 4
  NusA-TFII Cluster 4
  Putative hemin transporter 2
  Putative sulfate assimilation cluster 1
Clustering-based subsystems : Clustering-based subsystems CBSS-262719.3.peg.410 2
  Conenzyme B12 related Hypothetical: Clusters with cobST 3
Clustering-based subsystems : proteosome related Cluster-based Subsystem Grouping Hypotheticals - perhaps Proteosome Related 2
Cofactors, Vitamins, Prosthetic Groups, Pigments Thiamin biosynthesis 4
Cofactors, Vitamins, Prosthetic Groups, Pigments : Biotin Biotin biosynthesis 10
Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme A Coenzyme A Biosynthesis 7
Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme F420 Coenzyme F420 synthesis 2
Cofactors, Vitamins, Prosthetic Groups, Pigments : Folate and pterines Folate Biosynthesis 17
  Molybdenum cofactor biosynthesis 14
  Pterin biosynthesis 5
Cofactors, Vitamins, Prosthetic Groups, Pigments : Lipoic acid Lipoic acid metabolism 2
Cofactors, Vitamins, Prosthetic Groups, Pigments : NAD and NADP NAD and NADP cofactor biosynthesis global 12
  NAD regulation 9
  PnuC-like transporters 1
Cofactors, Vitamins, Prosthetic Groups, Pigments : Pyridoxine Pyridoxin (Vitamin B6) Biosynthesis 11
Cofactors, Vitamins, Prosthetic Groups, Pigments : Quinone cofactors Menaquinone Biosynthesis via Futalosine 1
  Menaquinone and Phylloquinone Biosynthesis 3
  Plastoquinone Biosynthesis 3
  Pyrroloquinoline Quinone biosynthesis 1
  Tocopherol Biosynthesis 3
  Ubiquinone Biosynthesis 6
Cofactors, Vitamins, Prosthetic Groups, Pigments : Riboflavin, FMN, FAD Riboflavin, FMN and FAD metabolism 3
Cofactors, Vitamins, Prosthetic Groups, Pigments : Tetrapyrroles Cobalamin synthesis 12
  Coenzyme B12 biosynthesis 30
  Experimental tye 13
  Heme and Siroheme Biosynthesis 14
DNA Metabolism DNA structural proteins, bacterial 4
  Restriction-Modification System 2
  YcfH 1
DNA Metabolism : DNA recombination RuvABC plus a hypothetical 3
DNA Metabolism : DNA repair 2-phosphoglycolate salvage 2
  DNA Repair Base Excision 13
  DNA repair, UvrABC system 4
  DNA repair, bacterial 21
  DNA repair, bacterial DinG and relatives 1
  DNA repair, bacterial MutL-MutS system 2
  DNA repair, bacterial RecFOR pathway 8
  DNA repair, bacterial UvrD and related helicases 1
DNA Metabolism : DNA replication DNA-replication 28
  DNA replication, archaeal 1
  DNA topoisomerases, Type I, ATP-independent 2
  DNA topoisomerases, Type II, ATP-dependent 5
  Plasmid replication 10
Fatty Acids, Lipids, and Isoprenoids Polyhydroxybutyrate metabolism 31
Fatty Acids, Lipids, and Isoprenoids : Fatty acids Fatty Acid Biosynthesis FASII 37
Fatty Acids, Lipids, and Isoprenoids : Isoprenoids Archaeal lipids 6
  Carotenoids 6
  Isoprenoid Biosynthesis 12
  Polyprenyl Diphosphate Biosynthesis 1
  polyprenyl synthesis 6
Fatty Acids, Lipids, and Isoprenoids : Phospholipids Glycerolipid and Glycerophospholipid Metabolism in Bacteria 32
Fatty Acids, Lipids, and Isoprenoids : Triacylglycerols Triacylglycerol metabolism 1
Iron acquisition and metabolism Campylobacter Iron Metabolism 4
  Heme, hemin uptake and utilization systems in GramPositives 1
  Hemin transport system 13
  Iron acquisition in Vibrio 8
  Transport of Iron 8
Iron acquisition and metabolism : Siderophores Siderophore Pyoverdine 1
Membrane Transport Choline Transport 1
  ECF class transporters 2
  Ton and Tol transport systems 33
  Transport of Molybdenum 4
  Transport of Nickel and Cobalt 1
  Transport of Zinc 3
Membrane Transport : ABC transporters ABC transporter dipeptide (TC 3.A.1.5.2) 2
  ABC transporter oligopeptide (TC 3.A.1.5.1) 1
  ABC transporter peptide (TC 3.A.1.5.5) 1
Membrane Transport : Protein and nucleoprotein secretion system, Type IV Type IV pilus 4
  pVir Plasmid of Campylobacter 4
Membrane Transport : Protein secretion system, Type II Widespread colonization island 12
Membrane Transport : Protein translocation across cytoplasmic membrane Twin-arginine translocation system 3
Membrane Transport : Sugar Phosphotransferase Systems, PTS Fructose and Mannose Inducible PTS 3
Membrane Transport : Uni- Sym- and Antiporters Na(+) H(+) antiporter 2
  Sodium Hydrogen Antiporter 1
Metabolism of Aromatic Compounds Aromatic Amin Catabolism 1
  Benzoate transport and degradation cluster 2
  Gentisare degradation 3
Metabolism of Aromatic Compounds : Metabolism of central aromatic intermediates Catechol branch of beta-ketoadipate pathway 10
  Central meta-cleavage pathway of aromatic compound degradation 4
  Homogentisate pathway of aromatic compound degradation 9
  N-heterocyclic aromatic compound degradation 4
  Protocatechuate branch of beta-ketoadipate pathway 8
  Salicylate and gentisate catabolism 6
Metabolism of Aromatic Compounds : Peripheral pathways for catabolism of aromatic compounds Benzoate degradation 5
  Biphenyl Degradation 1
  Chloroaromatic degradation pathway 3
  Naphtalene and antracene degradation 1
  Phenylpropanoid compound degradation 3
  Quinate degradation 4
  Salicylate ester degradation 2
  n-Phenylalkanoic acid degradation 18
  p-Hydroxybenzoate degradation 1
Miscellaneous Muconate lactonizing enzyme family 3
  YaaA 1
  YbbK 2
  ZZ gjo need homes 15
Miscellaneous : Plant-Prokaryote DOE project Conserved gene cluster possibly involved in RNA metabolism 3
  Synechocystis experimental 1
Motility and Chemotaxis Bacterial Chemotaxis 19
Motility and Chemotaxis : Flagellar motility in Prokaryota Flagellar motility 19
  Flagellum 34
  Flagellum in Campylobacter 6
Nitrogen Metabolism Allantoin Utilization 3
  Ammonia assimilation 9
  Cyanate hydrolysis 3
  Dissimilatory nitrite reductase 3
  Nitrate and nitrite ammonification 7
  Nitric oxide synthase 4
  Nitrosative stress 3
Nucleosides and Nucleotides Adenosyl nucleosidases 1
  Hydantoin metabolism 2
  Ribonucleotide reduction 3
Nucleosides and Nucleotides : Detoxification Nudix proteins (nucleoside triphosphate hydrolases) 8
Nucleosides and Nucleotides : Purines De Novo Purine Biosynthesis 16
  Purine Utilization 3
  Purine conversions 17
Nucleosides and Nucleotides : Pyrimidines De Novo Pyrimidine Synthesis 8
  Pyrimidine utilization 3
Phages, Prophages, Transposable elements : Bacteriophage structural proteins Phage capsid proteins 1
Phages, Prophages, Transposable elements, Plasmids : Pathogenicity islands Staphylococcal pathogenicity islands SaPI 4
Phages, Prophages, Transposable elements, Plasmids : Phages, Prophages Staphylococcal phi-Mu50B-like prophages 1
Phages, Prophages, Transposable elements, Plasmids : Transposable elements Tn552 5
Phosphorus Metabolism Alkylphosphonate utilization 3
  High affinity phosphate transporter and control of PHO regulon 9
  Phosphate metabolism 34
Potassium metabolism Glutathione-regulated potassium-efflux system and associated functions 1
  Potassium homeostasis 13
Protein Metabolism : Protein biosynthesis Programmed frameshift 1
  Ribosome LSU bacterial 32
  Ribosome SSU bacterial 19
  Ribosome activity modulation 1
  Ribosome biogenesis bacterial 9
  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 1
  Universal GTPases 14
  tRNA aminoacylation, Glu and Gln 2
Protein Metabolism : Protein degradation Proteasome bacterial 6
  Protein degradation 2
  Proteolysis in bacteria, ATP-dependent 10
  Putative TldE-TldD proteolytic complex 2
Protein Metabolism : Protein folding GroEL GroES 4
  Peptidyl-prolyl cis-trans isomerase 1
  Periplasmic disulfide interchange 6
  Protein chaperones 9
Protein Metabolism : Protein processing and modification N-linked Glycosylation in Bacteria 4
  Ribosomal protein S12p Asp methylthiotransferase 3
  Ribosomal protein S5p acylation 1
  Signal peptidase 4
Protein Metabolism : Selenoproteins Glycine reductase, sarcosine reductase and betaine reductase 4
RNA Metabolism : RNA processing and modification ATP-dependent RNA helicases, bacterial 2
  Polyadenylation bacterial 3
  Queuosine-Archaeosine Biosynthesis 19
  RNA processing and degradation, bacterial 4
  Ribonuclease H 2
  Wyeosine-MimG Biosynthesis 6
  tRNA nucleotidyltransferase 1
  tRNA processing 9
RNA Metabolism : Transcription RNA polymerase bacterial 4
  Rrf2 family transcriptional regulators 5
  Transcription factors bacterial 10
  Transcription factors cyanobacterial RpoD-like sigma factors 1
  Transcription initiation, bacterial sigma factors 6
Regulation and Cell signaling DNA-binding regulatory proteins, strays 7
  Orphan regulatory proteins 7
  Oxygen and light sensor PpaA-PpsR 2
  Sex pheromones in Enterococcus faecalis and other Firmicutes 4
  Stringent Response, (p)ppGpp metabolism 1
  Two-component regulatory systems in Campylobacter 3
  cAMP signaling in bacteria 8
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
Respiration Biogenesis of c-type cytochromes 13
  Biogenesis of cbb3-type cytochrome c oxidases 3
  Biogenesis of cytochrome c oxidases 6
  Carbon monoxide dehydrogenase maturation factors 2
  Formate hydrogenase 2
  Soluble cytochromes and functionally related electron carriers 14
Respiration : ATP synthases F0F1-type ATP synthase 12
Respiration : Electron accepting reactions Anaerobic respiratory reductases 23
  Terminal cytochrome C oxidases 11
  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 4
  Hydrogenases 1
  Membrane-bound Ni, Fe-hydrogenase 1
  Respiratory Complex I 16
  Respiratory dehydrogenases 1 14
  Succinate dehydrogenase 6
Secondary Metabolism : Bacterial cytostatics, differentiation factors and antibiotics Phenazine biosynthesis 1
Secondary Metabolism : Biosynthesis of phenylpropanoids Phenylpropionate Degradation 1
Secondary Metabolism : Plant Hormones Auxin biosynthesis 4
  Auxin degradation 1
Stress Response Bacterial hemoglobins 17
  Flavohaemoglobin 2
  Hfl operon 4
  Universal stress protein family 1
Stress Response : Acid stress Acid resistance mechanisms 1
Stress Response : Detoxification Glutathione-dependent pathway of formaldehyde detoxification 3
Stress Response : Heat shock Heat shock dnaK gene cluster extended 15
Stress Response : Osmotic stress Choline and Betaine Uptake and Betaine Biosynthesis 3
  Ectoine biosynthesis and regulation 6
Stress Response : Oxidative stress Glutaredoxins 4
  Glutathione: Biosynthesis and gamma-glutamyl cycle 7
  Glutathione: Non-redox reactions 13
  Glutathione: Redox cycle 2
  Glutathionylspermidine and Trypanothione 1
  Oxidative stress 26
  Redox-dependent regulation of nucleus processes 3
  Rubrerythrin 3
Sulfur Metabolism Galactosylceramide and Sulfatide metabolism 8
  Sulfur oxidation 1
  Thioredoxin-disulfide reductase 14
Sulfur Metabolism : Organic sulfur assimilation Alkanesulfonate assimilation 9
  Alkanesulfonates Utilization 4
  Taurine Utilization 4
  Utilization of glutathione as a sulphur source 4
Virulence : Type III, Type IV, Type VI, ESAT secretion systems Type 4 secretion and conjugative transfer 26
Virulence, Disease and Defense : Detection MLST 9
Virulence, Disease and Defense : Resistance to antibiotics and toxic compounds Arsenic resistance 4
  Beta-lactamase 8
  Cobalt-zinc-cadmium resistance 25
  Copper homeostasis 20
  Copper homeostasis: copper tolerance 3
  Mercuric reductase 1
  Mercury resistance operon 3
  Methicillin resistance in Staphylococci 2
  Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 4
  Multidrug Resistance Efflux Pumps 17
  Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) 10
  Resistance to fluoroquinolones 5
  Zinc resistance 1