SEED Subsystems in Azospirillum brasilense Sp245

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 4
Amino Acids and Derivatives : Alanine, serine, and glycine Alanine biosynthesis 10
  Glycine Biosynthesis 1
  Glycine and Serine Utilization 13
  Glycine cleavage system 5
  Serine Biosynthesis 7
Amino Acids and Derivatives : Arginine; urea cycle, polyamines Arginine Biosynthesis extended 15
  Arginine Deiminase Pathway 6
  Arginine and Ornithine Degradation 22
  Cyanophycin Metabolism 2
  Polyamine Metabolism 35
  Urea decomposition 11
Amino Acids and Derivatives : Aromatic amino acids and derivatives Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. 8
  Chorismate Synthesis 9
  Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 6
  Phenylalanine and Tyrosine Branches from Chorismate 4
  Tryptophan synthesis 8
Amino Acids and Derivatives : Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis 22
  HMG CoA Synthesis 10
  Isoleucine degradation 26
  Ketoisovalerate oxidoreductase 4
  Leucine Biosynthesis 9
  Leucine Degradation and HMG-CoA Metabolism 11
  Valine degradation 29
Amino Acids and Derivatives : Glutamine, glutamate, aspartate, asparagine; ammonia assimilation Glutamate dehydrogenases 2
  Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 20
  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 18
  Lysine Biosynthesis DAP Pathway 10
  Lysine degradation 4
  Methionine Biosynthesis 30
  Methionine Degradation 10
  Methionine Salvage 3
  Threonine anaerobic catabolism gene cluster 7
  Threonine and Homoserine Biosynthesis 17
  Threonine degradation 6
Amino Acids and Derivatives : Proline and 4-hydroxyproline Proline, 4-hydroxyproline uptake and utilization 5
  Proline Synthesis 4
Carbohydrates Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway 11
Carbohydrates : Aminosugars Chitin and N-acetylglucosamine utilization 3
  N-Acetyl-Galactosamine and Galactosamine Utilization 1
Carbohydrates : CO2 fixation CO2 uptake, carboxysome 1
  Calvin-Benson cycle 10
  Carboxysome 6
  Photorespiration (oxidative C2 cycle) 19
Carbohydrates : Central carbohydrate metabolism Dihydroxyacetone kinases 1
  Entner-Doudoroff Pathway 21
  Glycolate, glyoxylate interconversions 9
  Glycolysis and Gluconeogenesis 16
  Glycolysis and Gluconeogenesis, including Archaeal enzymes 11
  Methylglyoxal Metabolism 16
  Pentose phosphate pathway 8
  Pyruvate Alanine Serine Interconversions 8
  Pyruvate metabolism I: anaplerotic reactions, PEP 7
  Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 24
  TCA Cycle 17
Carbohydrates : Di- and oligosaccharides Beta-Glucoside Metabolism 1
  Fructooligosaccharides(FOS) and Raffinose Utilization 3
  Lactose and Galactose Uptake and Utilization 15
  Lactose utilization 2
  Maltose and Maltodextrin Utilization 13
  Melibiose Utilization 1
  Sucrose utilization 2
  Sucrose utilization Shewanella 2
  Trehalose Biosynthesis 12
Carbohydrates : Fermentation Acetoin, butanediol metabolism 10
  Acetyl-CoA fermentation to Butyrate 38
  Butanol Biosynthesis 26
  Fermentations: Lactate 6
  Fermentations: Mixed acid 19
Carbohydrates : Monosaccharides D-Galacturonate and D-Glucuronate Utilization 14
  D-Tagatose and Galactitol Utilization 2
  D-galactarate, D-glucarate and D-glycerate catabolism 3
  D-galactonate catabolism 2
  D-gluconate and ketogluconates metabolism 6
  D-ribose utilization 8
  Deoxyribose and Deoxynucleoside Catabolism 7
  Fructose utilization 7
  L-Arabinose utilization 3
  L-rhamnose utilization 4
  Mannose Metabolism 2
  Xylose utilization 3
Carbohydrates : One-carbon Metabolism Formaldehyde assimilation: Ribulose monophosphate pathway 1
  Methanogenesis 4
  One-carbon metabolism by tetrahydropterines 7
  Serine-glyoxylate cycle 29
Carbohydrates : Organic acids Isobutyryl-CoA to Propionyl-CoA Module 11
  Lactate utilization 11
  Methylcitrate cycle 2
  Propionate-CoA to Succinate Module 3
  Propionyl-CoA to Succinyl-CoA Module 4
Carbohydrates : Polysaccharides Glycogen metabolism 10
Carbohydrates : Sugar alcohols Di-Inositol-Phosphate biosynthesis 2
  Ethanolamine utilization 7
  Glycerol and Glycerol-3-phosphate Uptake and Utilization 16
  Inositol catabolism 1
  Mannitol Utilization 3
  Propanediol utilization 3
  Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 6
Cell Division and Cell Cycle Bacterial Cytoskeleton 30
  Control of cell elongation - division cycle in Bacilli 3
  Cyanobacterial Circadian Clock 1
  Macromolecular synthesis operon 7
  Two cell division clusters relating to chromosome partitioning 18
Cell Wall and Capsule Peptidoglycan Biosynthesis 22
  UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis 7
  YjeE 1
Cell Wall and Capsule : Capsular and extracellular polysacchrides Alginate metabolism 5
  CMP-N-acetylneuraminate Biosynthesis 1
  Capsular heptose biosynthesis 6
  Colanic acid biosynthesis 3
  O-Methyl Phosphoramidate Capsule Modification in Campylobacter 2
  Rhamnose containing glycans 20
  Sialic Acid Metabolism 7
  dTDP-rhamnose synthesis 9
Cell Wall and Capsule : Cell wall of Mycobacteria linker unit-arabinogalactan synthesis 21
  mycolic acid synthesis 28
Cell Wall and Capsule : Gram-Negative cell wall components KDO2-Lipid A biosynthesis 10
  LOS core oligosaccharide biosynthesis 9
  Lipid A-Ara4N pathway ( Polymyxin resistance ) 6
  Lipid A modifications 2
  Lipopolysaccharide-related cluster in Alphaproteobacteria 2
Cell Wall and Capsule : Gram-Positive cell wall components Teichoic and lipoteichoic acids biosynthesis 3
  Teichuronic acid biosynthesis 4
Clustering-based subsystems Bacterial Cell Division 28
  Bacterial RNA-metabolizing Zn-dependent hydrolases 12
  CBSS-214092.1.peg.3450 1
  Conserved gene cluster associated with Met-tRNA formyltransferase 14
  LMPTP YfkJ cluster 3
  LMPTP YwlE cluster 5
  NusA-TFII Cluster 3
  Putative hemin transporter 2
  Putative sulfate assimilation cluster 2
Clustering-based subsystems : Clustering-based subsystems CBSS-262719.3.peg.410 3
  Conenzyme B12 related Hypothetical: Clusters with cobST 2
Clustering-based subsystems : Lysine, threonine, methionine, and cysteine YeiH 2
Clustering-based subsystems : Type III secretion system related CBSS-343509.6.peg.2644 1
Clustering-based subsystems : proteosome related Cluster-based Subsystem Grouping Hypotheticals - perhaps Proteosome Related 3
Cofactors, Vitamins, Prosthetic Groups, Pigments Thiamin biosynthesis 23
Cofactors, Vitamins, Prosthetic Groups, Pigments : Biotin Biotin biosynthesis 6
Cofactors, Vitamins, Prosthetic Groups, Pigments : Coenzyme A Coenzyme A Biosynthesis 10
Cofactors, Vitamins, Prosthetic Groups, Pigments : Folate and pterines Folate Biosynthesis 20
  Molybdenum cofactor biosynthesis 22
  Pterin biosynthesis 2
  p-Aminobenzoyl-Glutamate Utilization 1
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 14
  NAD regulation 7
Cofactors, Vitamins, Prosthetic Groups, Pigments : Pyridoxine Pyridoxin (Vitamin B6) Biosynthesis 15
Cofactors, Vitamins, Prosthetic Groups, Pigments : Quinone cofactors Coenzyme PQQ synthesis 2
  Menaquinone and Phylloquinone Biosynthesis 1
  Pyrroloquinoline Quinone biosynthesis 3
  Ubiquinone Biosynthesis 10
Cofactors, Vitamins, Prosthetic Groups, Pigments : Riboflavin, FMN, FAD Flavodoxin 1
  Riboflavin, FMN and FAD metabolism 4
Cofactors, Vitamins, Prosthetic Groups, Pigments : Tetrapyrroles Cobalamin synthesis 11
  Coenzyme B12 biosynthesis 24
  Experimental tye 13
  Heme and Siroheme Biosynthesis 12
DNA Metabolism DNA structural proteins, bacterial 5
  YcfH 1
DNA Metabolism : DNA recombination RuvABC plus a hypothetical 2
DNA Metabolism : DNA repair 2-phosphoglycolate salvage 4
  DNA Repair Base Excision 8
  DNA repair, UvrABC system 4
  DNA repair, bacterial 17
  DNA repair, bacterial MutL-MutS system 2
  DNA repair, bacterial RecFOR pathway 7
  DNA repair, bacterial UvrD and related helicases 1
DNA Metabolism : DNA replication DNA-replication 24
  DNA replication, archaeal 1
  DNA topoisomerases, Type I, ATP-independent 3
  DNA topoisomerases, Type II, ATP-dependent 3
  Plasmid replication 13
Fatty Acids, Lipids, and Isoprenoids Polyhydroxybutyrate metabolism 28
Fatty Acids, Lipids, and Isoprenoids : Fatty acids Fatty Acid Biosynthesis FASII 35
Fatty Acids, Lipids, and Isoprenoids : Isoprenoids Archaeal lipids 3
  Carotenoids 9
  Isoprenoid Biosynthesis 9
  Polyprenyl Diphosphate Biosynthesis 2
  polyprenyl synthesis 3
Fatty Acids, Lipids, and Isoprenoids : Phospholipids Glycerolipid and Glycerophospholipid Metabolism in Bacteria 29
Fatty Acids, Lipids, and Isoprenoids : Triacylglycerols Triacylglycerol metabolism 2
Iron acquisition and metabolism Campylobacter Iron Metabolism 10
  Heme, hemin uptake and utilization systems in GramPositives 3
  Hemin transport system 3
  Iron acquisition in Vibrio 25
  Transport of Iron 17
Iron acquisition and metabolism : Siderophores Siderophore Aerobactin 4
  Siderophore Enterobactin 1
  Siderophore Pyoverdine 5
Membrane Transport Choline Transport 2
  ECF class transporters 3
  Ton and Tol transport systems 21
  Transport of Manganese 3
  Transport of Molybdenum 8
  Transport of Nickel and Cobalt 3
  Transport of Zinc 4
Membrane Transport : ABC transporters ABC transporter alkylphosphonate (TC 3.A.1.9.1) 4
  ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 80
  ABC transporter dipeptide (TC 3.A.1.5.2) 25
  ABC transporter oligopeptide (TC 3.A.1.5.1) 22
  ABC transporter tungstate (TC 3.A.1.6.2) 2
Membrane Transport : Protein and nucleoprotein secretion system, Type IV Type IV pilus 3
  pVir Plasmid of Campylobacter 3
Membrane Transport : Protein secretion system, Type II Widespread colonization island 1
Membrane Transport : Protein translocation across cytoplasmic membrane Twin-arginine translocation system 4
Membrane Transport : Sugar Phosphotransferase Systems, PTS Fructose and Mannose Inducible PTS 2
Membrane Transport : Uni- Sym- and Antiporters Na(+) H(+) antiporter 1
  Sodium Hydrogen Antiporter 5
Metabolism of Aromatic Compounds Aromatic Amin Catabolism 2
  Benzoate transport and degradation cluster 1
  Gentisare degradation 3
Metabolism of Aromatic Compounds : Metabolism of central aromatic intermediates Catechol branch of beta-ketoadipate pathway 6
  Central meta-cleavage pathway of aromatic compound degradation 2
  Homogentisate pathway of aromatic compound degradation 10
  N-heterocyclic aromatic compound degradation 3
  Protocatechuate branch of beta-ketoadipate pathway 7
  Salicylate and gentisate catabolism 6
Metabolism of Aromatic Compounds : Peripheral pathways for catabolism of aromatic compounds Benzoate degradation 2
  Chloroaromatic degradation pathway 3
  Naphtalene and antracene degradation 1
  Phenylpropanoid compound degradation 1
  Quinate degradation 1
  Salicylate ester degradation 1
  n-Phenylalkanoic acid degradation 16
  p-Hydroxybenzoate degradation 1
Miscellaneous Muconate lactonizing enzyme family 1
  YbbK 1
  ZZ gjo need homes 18
Miscellaneous : Plant-Prokaryote DOE project Conserved gene cluster possibly involved in RNA metabolism 4
  Synechocystis experimental 1
Motility and Chemotaxis Bacterial Chemotaxis 55
Motility and Chemotaxis : Flagellar motility in Prokaryota Flagellar motility 45
  Flagellum 63
  Flagellum in Campylobacter 7
Nitrogen Metabolism Allantoin Utilization 4
  Ammonia assimilation 7
  Cyanate hydrolysis 2
  Denitrification 17
  Dissimilatory nitrite reductase 2
  Nitrate and nitrite ammonification 17
  Nitric oxide synthase 2
  Nitrogen fixation 27
  Nitrosative stress 3
Nucleosides and Nucleotides Adenosyl nucleosidases 1
  Hydantoin metabolism 7
  Ribonucleotide reduction 4
Nucleosides and Nucleotides : Detoxification Nudix proteins (nucleoside triphosphate hydrolases) 8
Nucleosides and Nucleotides : Purines De Novo Purine Biosynthesis 16
  Purine Utilization 6
  Purine conversions 22
Nucleosides and Nucleotides : Pyrimidines De Novo Pyrimidine Synthesis 11
  Pyrimidine utilization 4
Phages, Prophages, Transposable elements : Bacteriophage structural proteins Phage capsid proteins 1
Phages, Prophages, Transposable elements, Plasmids : Pathogenicity islands Staphylococcal pathogenicity islands SaPI 9
Phages, Prophages, Transposable elements, Plasmids : Phages, Prophages Staphylococcal phi-Mu50B-like prophages 1
Phages, Prophages, Transposable elements, Plasmids : Transposable elements Tn552 1
Phosphorus Metabolism Alkylphosphonate utilization 1
  High affinity phosphate transporter and control of PHO regulon 9
  Phosphate metabolism 43
Potassium metabolism Glutathione-regulated potassium-efflux system and associated functions 2
  Potassium homeostasis 13
Protein Metabolism : Protein biosynthesis Ribosome LSU bacterial 32
  Ribosome SSU bacterial 18
  Ribosome activity modulation 1
  Ribosome biogenesis bacterial 10
  Trans-translation by stalled ribosomes 1
  Translation elongation factor G family 3
  Translation elongation factors eukaryotic and archaeal 1
  Translation initiation factors eukaryotic and archaeal 1
  Universal GTPases 15
  tRNA aminoacylation, Glu and Gln 2
Protein Metabolism : Protein degradation Proteasome bacterial 8
  Protein degradation 3
  Proteolysis in bacteria, ATP-dependent 13
Protein Metabolism : Protein folding GroEL GroES 7
  Peptidyl-prolyl cis-trans isomerase 2
  Periplasmic disulfide interchange 5
  Protein chaperones 11
  Thermosome, archaeal 1
Protein Metabolism : Protein processing and modification N-linked Glycosylation in Bacteria 13
  Ribosomal protein S12p Asp methylthiotransferase 3
  Ribosomal protein S5p acylation 1
  Signal peptidase 3
Protein Metabolism : Selenoproteins Glycine reductase, sarcosine reductase and betaine reductase 6
RNA Metabolism : RNA processing and modification ATP-dependent RNA helicases, bacterial 1
  Polyadenylation bacterial 3
  Queuosine-Archaeosine Biosynthesis 23
  RNA processing and degradation, bacterial 5
  Ribonuclease H 2
  Wyeosine-MimG Biosynthesis 5
  tRNA nucleotidyltransferase 1
  tRNA processing 7
RNA Metabolism : Transcription RNA polymerase bacterial 3
  Rrf2 family transcriptional regulators 5
  Transcription factors bacterial 7
  Transcription factors cyanobacterial RpoD-like sigma factors 1
  Transcription initiation, bacterial sigma factors 13
Regulation and Cell signaling DNA-binding regulatory proteins, strays 6
  Orphan regulatory proteins 9
  Oxygen and light sensor PpaA-PpsR 2
  Sex pheromones in Enterococcus faecalis and other Firmicutes 9
  Stringent Response, (p)ppGpp metabolism 1
  Two-component regulatory systems in Campylobacter 15
  cAMP signaling in bacteria 25
Regulation and Cell signaling : Programmed Cell Death and Toxin-antitoxin Systems Murein hydrolase regulation and cell death 5
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 6
  Biogenesis of cytochrome c oxidases 7
  Carbon monoxide dehydrogenase maturation factors 4
  Formate hydrogenase 17
  Soluble cytochromes and functionally related electron carriers 13
Respiration : ATP synthases F0F1-type ATP synthase 7
Respiration : Electron accepting reactions Anaerobic respiratory reductases 18
  Terminal cytochrome C oxidases 18
  Terminal cytochrome O ubiquinol oxidase 4
  Terminal cytochrome d ubiquinol oxidases 3
  Terminal cytochrome oxidases 7
  Tetrathionate respiration 4
  Ubiquinone Menaquinone-cytochrome c reductase complexes 3
  trimethylamine N-oxide (TMAO) reductase 3
Respiration : Electron donating reactions CO Dehydrogenase 12
  Formate dehydrogenase 1
  Hydrogenases 6
  Membrane-bound Ni, Fe-hydrogenase 4
  NiFe hydrogenase maturation 6
  Respiratory Complex I 15
  Respiratory dehydrogenases 1 14
  Succinate dehydrogenase 4
Secondary Metabolism : Aromatic amino acids and derivatives Cinnamic Acid Degradation 1
Secondary Metabolism : Biosynthesis of phenylpropanoids Flavanone biosynthesis 1
Secondary Metabolism : Plant Hormones Auxin biosynthesis 5
Stress Response Bacterial hemoglobins 16
  Flavohaemoglobin 1
  Hfl operon 4
  SigmaB stress responce regulation 4
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 18
Stress Response : Osmotic stress Choline and Betaine Uptake and Betaine Biosynthesis 12
Stress Response : Oxidative stress Glutaredoxins 3
  Glutathione: Biosynthesis and gamma-glutamyl cycle 5
  Glutathione: Non-redox reactions 19
  Glutathione: Redox cycle 3
  Oxidative stress 32
  Redox-dependent regulation of nucleus processes 3
  Rubrerythrin 1
Sulfur Metabolism Galactosylceramide and Sulfatide metabolism 3
  Sulfur oxidation 3
  Thioredoxin-disulfide reductase 12
Sulfur Metabolism : Organic sulfur assimilation Alkanesulfonate assimilation 32
  Alkanesulfonates Utilization 18
  Taurine Utilization 10
  Utilization of glutathione as a sulphur source 2
Virulence, Disease and Defense : Detection MLST 8
Virulence, Disease and Defense : Resistance to antibiotics and toxic compounds Arsenic resistance 4
  Beta-lactamase 6
  Cobalt-zinc-cadmium resistance 17
  Copper homeostasis 8
  Copper homeostasis: copper tolerance 4
  Methicillin resistance in Staphylococci 2
  Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 1
  Multidrug Resistance Efflux Pumps 14
  Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) 7
  Resistance to fluoroquinolones 3
  Zinc resistance 1