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Here is a list of subsystems that people are working on.
If you take one (or some other one), please edit this page.
| Level 1 | Level 2 | Level 3 | Subsystems | Author | Status* | Expertise level** | Forum Postings | ||
| Experimental Subsystems | |||||||||
| Essential gene lists | |||||||||
| Amino Acids and Derivatives - MikeK | |||||||||
| Glutamine, glutamate, aspartate, asparagine; ammonia assimilation | |||||||||
| Ammonia assimilation | |||||||||
![[WWW]](/SEEDWiki/img/moin-www.gif){kind=small} Ammonia assimilation | master:Ed | 2 | B | ||||||
| Glutamate | |||||||||
| Glutamate_biosynthesis | master:MattC | 4 | A | Forum posting | |||||
| Aspartate and asparagine | |||||||||
| Glutamate, aspartate and asparagine biosynthisis | master:MattC | 4 | A | ||||||
| Arginine; urea cycle, polyamines | |||||||||
| Arginine | |||||||||
| Arginine Biosynthesis | master:RickS | 2 | B | ||||||
| Arginine Putrescine and 4-aminobutyrate degradation | master:MattC | 2 | B | ||||||
| Polyamines | |||||||||
| Polyamine Metabolism | master:InesT_UCSD | 2 | B | ||||||
| Cyanophycin metabolism | master:MikeR | ||||||||
| Putrescine and 4-aminobutyrate degradation | master:MikeK | 2 | B | ||||||
| Proline and 4-hydroxyproline | |||||||||
| Proline Synthesis | master:RickS | 2 | B | ||||||
| Proline_degradation | |||||||||
| 4-hydroxyproline_degradation | |||||||||
| Alanine, serine, and glycine | |||||||||
| Alanine | |||||||||
| Pyruvate Alanine Serine Interconversions | master:JasonS_UCSD | 2 | B | ||||||
| Thermotoga Alanine Biosynthesis | master:rodionov | ||||||||
| Alanine Biosynthesis | master:Straw | ||||||||
| Serine | |||||||||
| Serine Biosynthesis | master:MikeK | 2 | B | ||||||
| Glycine_and_serine_utilisation | |||||||||
| Glycine | |||||||||
| Glycine_synthesis | master:MikeK | 2 | B | ||||||
| Glycine_and_serine_utilisation | |||||||||
| Lysine, threonine, methionine, and cysteine | |||||||||
| Lysine | |||||||||
| Lysine_Biosynthesis_DAP_Pathway | master:AndreiO | 3 | P | Subsystem diagram | |||||
| Aminoadipate_branch_of_lysine_degradation | |||||||||
| Threonine | |||||||||
| Threonine_synthesis | master:MikeK | 2 | B | ||||||
| Threonine_to_Isoleucine | master:RossO | 3 | B | ||||||
| Threonine_degradation | |||||||||
| Methionine, formylmethionine and SAM | |||||||||
| Methionine Metabolism | master:MonicaM_UCSD | 2 | B | ||||||
| Methionine Biosynthesis | master:rodionov | 3 | E | ||||||
| Cystein | |||||||||
| cysteine biosynthesis | master:RobE | 2 | B | ||||||
| Methionine_and_Cysteine_degradation | |||||||||
| Branhed-chain amino acids | |||||||||
| Leucine | |||||||||
| Leucine_synthesis | master:MikeK | 2 | B | ||||||
| Leucine_Degradation_and_HMG-CoA_Metabolism | master:VeronikaV | Subsystem diagram | |||||||
| HMG CoA Synthesis | master:VeronikaV | ||||||||
| Isoleucine | |||||||||
| Isoleucine Synthesis | master:BobO | 2 | B | ||||||
| Isoleucine_degradation | master:OlgaZ | 2 | B | ||||||
| Valine | |||||||||
| Valine_Synthesis | master:TerryD | 2 | B | ||||||
| Valine_degradation | master:OlgaZ | 2 | B | ||||||
| Aromatic amino acids and derivatives | |||||||||
| Shikimate, chorismate | |||||||||
| Chorismate Synthesis | master:VeronikaV | ||||||||
| Phenylalanine | |||||||||
| Phenylalanine synthesis | master:MikeK | 2 | B | ||||||
| Tyrosine | |||||||||
| Tyrosine_synthesis | master:MikeK | 2 | B | ||||||
| Tryptophane | |||||||||
| Tryptophan synthesis | master:VeronikaV | 4 | A | ||||||
| Aromatic amino acid degradation | |||||||||
| Aromatic_amino_acid_degradation | |||||||||
| Histidine | |||||||||
| Histidine Biosynthesis | master:RossO | 3 | A | ||||||
| Histidine Degradation | master:RossO | 3 | A | ||||||
| Nitrogen Metabolism - Ed Frank | |||||||||
| Ammonia assimilation | master:EdF | 2 | A | ||||||
| Ammonia oxidation | 1 | ||||||||
| Denitrification | master:rodionov | ||||||||
| Urea decomposition | master:rodionov | 2 | B | ||||||
| Allantoin degradation | master:MattC | 4 | A | forum posting | |||||
| Nitrate and Nitrite Reduction | master:rodionov | 2 | B | ||||||
| Nitrosative stress | master:rodionov | 2 | B | ||||||
| nitrogen fixation | master:FonsteinM | 1 | A | ||||||
| Sulfur Metabolism - Rob Edwards | |||||||||
| Sulfur Metabolism | master:RobE | ||||||||
| Inorganic sulfur assimilation | |||||||||
| Sulfate assimilation | master:MattC | ||||||||
| Inorganic Sulfur Assimilation | master:ChristianR | ||||||||
| Organic sulfur assimilation | |||||||||
| Utilization_of_taurine_as_a_sulphur_source | |||||||||
| Alkanesulfonate_assimilation | |||||||||
| Methanesulfonate_assimilation | |||||||||
| L-cysteate_assimilation | |||||||||
| Utilization_of_glutathione_as_a_sulphur_source | |||||||||
| Phosphorus Metabolism - RobE | |||||||||
| Metabolism of polyphosphates | |||||||||
| Phosphonate metabolism | |||||||||
| Uptake of inorganic phosphate | |||||||||
| P uptake (cyanobacteria) | master:acm@mit | ||||||||
| Uptake of organic phosphate | |||||||||
| Carbohydrates - SvetaG | |||||||||
| Central carbohydrate metabolism | |||||||||
| Glycolysis and gluconeogenesis | |||||||||
| Embden-Meyerhof and Gluconeogenesis | master:SvetaG | 3 | A | ||||||
| Archaeal Entner-Doudoroff Pathway | master:RossO | ||||||||
| Pentose Phosphate Pathway | |||||||||
| Pentose phosphate pathway (SG) | master:SvetaG | 3 | A | ||||||
| Tricarboxylic acid cycle (TCA) | |||||||||
| TCA Cycle | master:RickS | 1 | B | ||||||
| Glyoxylate Synthesis | master:RickS | 2 | B | ||||||
| glyoxylate degradation | master:MattC | 2 | B | ||||||
| Pyruvate metabolism | |||||||||
| Pyruvate, PEP and Acetyl-CoA (anaplerotic reactions) | master:GaryH_UCSD | 2 | A | ||||||
| Pyruvate Alanine Serine Interconversions | master:JasonS_UCSD | 2 | A | ||||||
| Acetoin metabolism | master:MikeD_UCSD | 2 | A | ||||||
| Fermentation | |||||||||
| Heterofermentative lactate fermentation | master:MaryP_UCSD | 2 | A | ||||||
| Homofermentative lactate fermentation | master:NeilJ_UCSD | 2 | A | ||||||
| Acetogenesis from Pyruvate | master:LienC_UCSD | 2 | A | ||||||
| Butyrate and Butanol Acetone fermentation | master:SouravB_UCSD | 2 | A | ||||||
| CO2 fixation | |||||||||
| CO2 transport and concentration mechanisms | |||||||||
| Calvin-Benson cycle | |||||||||
| Calvin-Benson cycle | master:SvetaG | 3 | A | Subsystem diagram | |||||
| Reductive TCA cycle | |||||||||
| Acetyl-CoA (Wood-Ljungdahl) pathway | |||||||||
| Hydroxypropionate pathway | |||||||||
| Merthanogenesis | |||||||||
| Methanogenesis | master:gjo | 3 | A | ||||||
| Polysaccharide Metabolism | |||||||||
| Glycogen metabolism | |||||||||
| Starch metabolism | |||||||||
| Cellulose metabolism | |||||||||
| Chitin metabolism | |||||||||
| Di- and oligosaccharides | |||||||||
| Lactose degradation | master:MattC | 3 | B | ||||||
| Sucrose Metabolism | master:NitinG_UCSD | ||||||||
| Trehalose biosynthesis | master:MattC | 4 | A | ||||||
| Monosaccharides | |||||||||
| D-arabinose degradation | master:MattC | ||||||||
| D-galactarate degradation | master:MattC | 2 | B | ||||||
| D-glucarate degradation | master:MattC | 2 | B | ||||||
| D-galacturonate degradation | master:MattC | 3 | B | ||||||
| Galactose degradation | master:MattC | 3 | A | ||||||
| Ketogluconate metabolism | master:MattC | 3 | B | ||||||
| L-ascorbate degradation | master:MattC | 3 | A | ||||||
| Fructose and Mannose metabolism | master:vasiliyP | 2 | A | ||||||
| Mannose and fructose metabolism | master:HanYuC_UCSD | 2 | A | ||||||
| mannose and GDP-mannose metabolism | master:MattC | 3 | A | ||||||
| superpathway of fucose and rhamnose degradation | master:MattC | 3 | A | ||||||
| Aminosugars | |||||||||
| Biosynthesis of aminosugars | |||||||||
| Nucleotide_Sugar__Biosynthesis_from_Glucose | |||||||||
| Nucleotide_sugar_biosynthesis_from_fructose | |||||||||
| UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis | master:vasiliyP | 4 | A | ||||||
| Nucleotide_sugar_biosynthesis_from_pentoses | |||||||||
| Nucleotide_sugar_biosynthesis_from_mannose,_galactose_and_fucose | |||||||||
| Nucleotide_sugar_biosynthesis_from_sucrose | |||||||||
| CMP-N-acetylneuraminate Biosynthesis | master:OlgaZ | 2 | A | ||||||
| Utilization of aminosugars | |||||||||
| N-Acetyl-D-Glucosamine Utilization | master:OlgaZ | 4 | P | Subsystem diagram | |||||
| Sugar alcohols | |||||||||
| Galactitol degradation | master:MattC | 4 | A | ||||||
| Inositol catabolism by VV | master:VeronikaV | ||||||||
| superpathway of hexitol degradation | master:MattC | 3 | A | ||||||
| Organic acids (Fermentation products/TCA cycle metabolites) | |||||||||
| Methylcitrate cycle | master:MattC | 2 | A | Subsystem diagram | |||||
| Tricarballylate Utilization | master:RossO | 2 | B | ||||||
| Alkanes | |||||||||
| Fatty Acids and Lipids - AndreiO | |||||||||
| Triacylglycerols | |||||||||
| Biosynthesis of Triacylglycerols | |||||||||
| Degradation of Triacylglycerols | |||||||||
| Glycerol Metabolism | master:MattC | 4 | A | ||||||
| Fatty acids | |||||||||
| Fatty Acid Biosynthesis FASII | master:AndreiO | 2 | P | Subsystem diagram | |||||
| Biosynthesis_of_branch_chain_fatty_acids | |||||||||
| Odd_carbon_number_fatty_acid_biosynthesis | |||||||||
| carnitine metabolism | master:MattC | 4 | A | ||||||
| fatty acid oxidation pathway | master:MattC | 2 | B | ||||||
| Alpha-oxidation_of_branch-chain_fatty_acid | master:MattC | 2 | B | ||||||
| Omega-oxidation_of_fatty_acid | master:MattC | 2 | B | ||||||
| fatty acid metabolism | master:MattC | 2 | B | ||||||
| Phospholipids | |||||||||
| Phospholipases | |||||||||
| Glycerophospholipids | |||||||||
| Glycerolipid metabolism | master:VasiliyP_UCSD | ||||||||
| Ether lipids | |||||||||
| Sphingophospholipids | |||||||||
| Sphingolipid biosynthesis | master:JorgeF | ||||||||
| Choline, betaine,sarcosine | |||||||||
| Betaine biosynthesis | master:MattC | 3 | A | ||||||
| Nucleosides and Nucleotides - RossO | |||||||||
| Ribonucleotide reduction | mater:rodionov | 3 | E | ||||||
| superpathway of ribose and deoxyribose phosphate metabolism | mater:MattC | 3 | A | ||||||
| Purines | |||||||||
| De Novo Purine Biosynthesis | master:RossO | 3 | A | ||||||
| purine conversions | master:RossO | ||||||||
| purine conversions 2 | master:RossO | ||||||||
| Pyrimidines | |||||||||
| De Novo Pyrimidine Synthesis | master:RossO | 3 | A | ||||||
| pyrimidine conversions | master:RossO | ||||||||
| Utilization of nucleotides as carbon and energy source | |||||||||
| Purine_utilization | master:RossO | ||||||||
| Pyrimidine_utilization | master:RossO | ||||||||
| Cofactors, Vitamins, Prosthetic Groups, Pigments - AndreiO | |||||||||
| NAD and NADP | |||||||||
| NAD and NADP cofactor biosynthesis global | master:AndreiO | 4 | E | Subsystem diagram | |||||
| Coenzyme A | |||||||||
| Coenzyme A Biosynthesis | master:AndreiA | 4 | E | Subsystem diagram | |||||
| Coenzyme M | |||||||||
| coenzyme M biosynthesis | master:AdamF | ||||||||
| Folate and pterines | |||||||||
| Folate biosynthesis | master:vcrecy | ||||||||
| Pterin biosynthesis | master:vcrecy | ||||||||
| methanopterin biosynthesis | master:AdamF | ||||||||
| Iron-sulfur clusters | |||||||||
| Fe-S cluster assembly | mater:rodionov | 3 | B | ||||||
| Biotin | |||||||||
| Biotin biosynthesis | mater:rodionov | Subsystem diagram | |||||||
| Biotin-Dependent Transcarboxylation | master:AndreiO | ||||||||
| Riboflavin, FMN, FAD | |||||||||
| Riboflavin metabolism | master:rodionov | 4 | E | ||||||
| FMN and FAD biosynthesis | master:AndreiO | 4 | E | Subsystem diagram | |||||
| Thiamin and thiamin pyrophosphate | |||||||||
| Thiamin biosynthesis | master:rodionov | 3 | E | ||||||
| Pyridoxine | master:rodionov | 1 | B | ||||||
| Cobalamin (vitamin B12) | master:rodionov | 1 | B | ||||||
| Lipoate and Lipoamide | |||||||||
| Tocopherol | |||||||||
| Tocopherol Biosynthesis | master:OlgaZ | 3 | A | Subsystem diagram | |||||
| Quinone cofactors | |||||||||
| Ubiquinone Biosynthesis | master:OlgaZ | 3 | A | Subsystem diagram | |||||
| Plastoquinone Biosynthesis | master:OlgaZ | 3 | A | Subsystem diagram | |||||
| Menaquinone and Phylloquinone Biosynthesis | master:OlgaZ | 3 | A | Subsystem diagram | |||||
| Pyrroloquinoline Quinone biosynthesis | master:OlgaZ | 3 | A | ||||||
| Isoprenoids | |||||||||
| Isoprenoid Biosynthesis | master:OlgaZ | 3 | P | Subsystem diagram | |||||
| polyisoprenoid biosynthesis | master:MattC | 2 | B | ||||||
| Carotenoids | master:OlgaV | 4 | A | Subsystem diagram | |||||
| polyprenyl synthesis | master:NJ | ||||||||
| Tetrapyrroles | Overview diagram | ||||||||
| Porphyrin, Heme, and Siroheme Biosynthesis | master:SvetaG | 3 | A | ||||||
| Chlorophyll Biosynthesis | master:VeronikaV | 2 | A | Subsystem diargam | |||||
| Bilin Biosynthesis | master:OlgaZ | 3 | A | ||||||
| Siderophores | |||||||||
| Enterobactin biosynthesis | master:MattC | 4 | A | ||||||
| Siderophore Yersiniabactin Biosynthesis | master:MikeK | 2 | B | ||||||
| Siderophore Aerobactin and Ferrichrome Biosynthesis | master:MikeK | 1 | B | ||||||
| Vibriobactin Biosynthesis | |||||||||
| Pseudobactin and Pyvoredines Biosynthesis | |||||||||
| Chysobactin Biosynthesis | |||||||||
| One-carbon metabolism -OlgaV | |||||||||
| Metabolism of Tetrahydrofolates | |||||||||
| One-carbon metabolism in methylotrophs | |||||||||
| Methane metabolism | master:MikeR | ||||||||
| Serine-isocytrate pathway | |||||||||
| Serine-glyoxylate_cycle | master:OlgaV | 3 | A | ||||||
| Glyoxylate-Hydroxypyruvate_Conversion | master:AndreiO | ||||||||
| Ribulose-monophosphate pathway | |||||||||
| Xylulose-monophosphate pathway | |||||||||
| Cell Wall and Capsule - OlgaZ | |||||||||
| Peptidoglycan biosynthesis | |||||||||
| Peptidoglycan Biosynthesis | master:RickS | 3 | A | Subsystem diagram | |||||
| Glycosylation | |||||||||
| N-linked Glycosylation in Bacteria | master:OlgaZ | 3 | A | ||||||
| O-linked flagella Glycosylation | master:OlgaZ | 3 | A | ||||||
| Gram-Positive cell wall components | |||||||||
| Teichoic and teichuronic acids | |||||||||
| Teichoic acid Biosynthesis | master:OlgaZ | 3 | A | ||||||
| D-alanyl lipoteichoic acid Biosynthesis | master:OlgaZ | 3 | A | ||||||
| S-layer | |||||||||
| Neutral polysaccharides | |||||||||
| Surface glycolipids | |||||||||
| Surface lipoproteins | |||||||||
| Surface proteins | |||||||||
| Gram-Negative cell wall components | General diagram | ||||||||
| Lipid A | |||||||||
| Lipid A biosynthesis | master:OlgaZ | 3 | A | ||||||
| Lipid A modifications | master:OlgaZ | 1 | A | ||||||
| Core polysaccharide | |||||||||
| LOS core oligosaccharide biosynthesis | master:OlgaZ | 3 | A | ||||||
| O-specific polysaccharide | |||||||||
| dTDP-rhamnose synthesis | master:MikeK | 2 | B | ||||||
| Surface lipoproteins | |||||||||
| Cell wall of Mycobacteria | |||||||||
| mycolic acid synthesis | master:NJ | 2 | E | ||||||
| linker unit-arabinogalactan synthesis | master:NJ | 2 | E | ||||||
| Archaeal cell wall | |||||||||
| Capsular and extracellular polysacchrides | |||||||||
| Capsular heptose biosynthesis | master:OlgaZ | 3 | A | ||||||
| Capsular polysaccharide biosynthesis | master:OlgaZ | 3 | A | ||||||
| Oxidative Phosphorylation - OlgaV | |||||||||
| Respiration | |||||||||
| Electron donating reactions | |||||||||
| Respiratory Complex I | master:OlgaV | 4 | A | ||||||
| Coenzyme_F420-H2_dehydrogenase_(methanophenazine) | master:gjo | 2 | |||||||
| Succinate dehydrogenase | master:OlgaV | 4 | A | ||||||
| Na(+)-translocating_NADH-quinone_oxidoreductase_and_rnf-like_group_of_electron_transport_complexes | master:OlgaV | 3 | A | ||||||
| Hydrogenases | master:OlgaV | 2 | A | ||||||
| NiFe_hydrogenase_maturation | master:gio | 2 | A | ||||||
| Membrane-bound_Ni,_Fe-hydrogenase | master:rodionov | 4 | |||||||
| Carbon monoxide dehydrohgenases | master:rodionov | ||||||||
| Formate hydrogenase | master:OlgaV | 3 | A | ||||||
| Respiratory_dehydrogenases | master:OlgaV | 3 | A | ||||||
| Quinone pool reductase | |||||||||
| Cytochrome B6-F complex | master:Sveta | 2 | A | ||||||
| Ubiquinone Menaquinone-cytochrome c reductase complexes | master:OlgaV | 4 | A | ||||||
| Soluble electron carries | |||||||||
| Soluble_cytochromes and functionally related electron carriers | master:OlgaV | 4 | A | ||||||
| Electron accepting reactions | |||||||||
| Terminal cytochrome C oxidases | master:OlgaV | |4|A | |||||||
| Terminal cytochrome oxidases | master:OlgaV | 4 | A | ||||||
| Anaerobic respiratory reductases | master:OlgaV | 3 | A | ||||||
| Nitrate_and_nitrite_ammonification | master:rodionov | 4 | |||||||
| Denitrification | master:rodionov | 4 | |||||||
| Fumarate reductase | master:OlgaV | 4 | A | ||||||
| ATP synthases | |||||||||
| F0F1-type ATP synthase | master:RickS | 4 | A | ||||||
| V-Type ATP synthaase | master:RickS | 4 | A | ||||||
| Transhydrogenation | |||||||||
| Photosynthesis - SvetaG | |||||||||
| Oxygenic photosynthesis | |||||||||
| Cytochrome B6-F complex | master:Sveta | 2 | A | ||||||
| Photosystem I | master:Sveta | 2 | P | ||||||
| Photosystem II | master:Sveta | 2 | P | ||||||
| Light harversting | |||||||||
| Phycobilisome | master:OlgaZ | 2 | A | ||||||
| Anoxygenic photosynthesis | |||||||||
| Purple sulfur phototrophs | |||||||||
| Purple nonsulfur phototrophs | |||||||||
| Green nonsulfur phototrophs | |||||||||
| Green sulfur phototrophs | |||||||||
| Heliobacteria | |||||||||
| Secondary metabolism/active compounds - OlgaV | |||||||||
| Bacterial cytostatics,differentiation factors and antibiotics | OlgaV | ||||||||
| 2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone and other bacterial morphogens | master:OlgaV | 2 | A | ||||||
| Clavulanic_acid biosynthesis | master:OlgaV | 1 | A | ||||||
| Anthracycline_biosynthesis | master:OlgaV | 1 | A | ||||||
| Streptomycin biosynthesis | master:OlgaV | 1 | A | ||||||
| Biologically active compounds in fungal cell defence and differentiation | OlgaV | ||||||||
| Fungal cytostatics | master:OlgaV | 1 | A | ||||||
| Fungal differentiation factors | master:OlgaV | 0 | A | ||||||
| Biologically active compounds in metazoan cell defence and differentiation | OlgaV | ||||||||
| Quinolinic_acid and its derivatives | master:OlgaV | 1 | A | ||||||
| Cytotoxic_Polyacetylenes | master:OlgaV | 0 | A | ||||||
| Steroid_sulfates | master:OlgaV | 2 | A | ||||||
| Bis-_and_Tris-Indole_alkaloids | master:OlgaV | 0 | A | ||||||
| Plant Octadecanoids | OlgaV | ||||||||
| Biosynthesis of Octadecanoids (Jasmonic acid and related compounds) | master:OlgaV | 2 | A | ||||||
| Plant Alkaloids | OlgaV | ||||||||
| Alkaloid biosynthesis from tyrosine | master:OlgaV | 1 | A | ||||||
| Alkaloid biosynthesis from L-lysine | master:OlgaV | 1 | A | ||||||
| Alkaloid biosynthesis from putrescine | master:OlgaV | 1 | A | ||||||
| Biosynthesis of phenylpropanoids | OlgaV | ||||||||
| Flavanol biosynthesis | master:OlgaV | 2 | A | ||||||
| Phytoalexin biosynthesis | master:OlgaV | 2 | A | ||||||
| Tannin biosynthesis | master:OlgaV | 2 | A | ||||||
| Antocyanin biosynthesis | master:OlgaV | 2 | A | ||||||
| Apigenin derivatives | master:OlgaV | 2 | A | ||||||
| Biflavanoid biosynthesis | master:OlgaV | 2 | A | ||||||
| Salicylic_acid biosynthesis | master:OlgaV | 1 | A | ||||||
| Suberin biosynthesis | master:OlgaV | 2 | A | ||||||
| Lignin biosynthesis | master:OlgaV | 2 | A | ||||||
| Coumarin biosynthesis | master:OlgaV | 2 | A | ||||||
| Caffeic acid derivatives | master:OlgaV | 1 | A | ||||||
| Plant hormons | OlgaV | ||||||||
| Auxin biosynthesis and transport | master:OlgaV | 2 | A | ||||||
| Auxin degradation | master:OlgaV | 1 | A | ||||||
| Cell signalling intermediates | OlgaV | ||||||||
| Tyrosine-derived mediators | OlgaV | ||||||||
| Tryptophan-derived mediators | OlgaV | ||||||||
| Lipid-derived mediators | OlgaV | ||||||||
| Cannabinoid biosynthesis | master:OlgaV | 1 | A | ||||||
| Metabolism of aromatic compounds - OlgaV | |||||||||
| Metabolism of central aromatic intermediates | OlgaV | ||||||||
| Protocatechuate_branch_of_beta-ketoadipate_pathway | master:OlgaV | 3 | A | ||||||
| Catechol_branch_of_beta-ketoadipate_pathway | master:OlgaV | 3 | A | ||||||
| Homogentisate_pathway_of_aromatic_compound_degradation | master:OlgaV | 3 | A | ||||||
| Phenylacetate_pathway_of_aromatic_compound_degradation | master:OlgaV | 3 | A | ||||||
| N-heterocyclic_aromatic_compaund_degradation | master:OlgaV | 2 | A | ||||||
| Central_meta-cleavage_pathway_of_aromatic_compound_degradation | master:OlgaV | 2 | A | ||||||
| Peripheral pathways for catabolism of aromatic compounds | OlgaV | ||||||||
| Benzoate_degradation | master:OlgaV | 2 | A | ||||||
| Anaerobic_benzoate_metabolism | master:OlgaV | 2 | A | ||||||
| Aromatic_Amin_Catabolism | master:OlgaV | 2 | A | ||||||
| Aromatic_amino_acid_degradation | master:OlgaV | 2 | A | ||||||
| p-Hydroxybenzoate_degradation | |||||||||
| Quinate_degradation | |||||||||
| Biphenyl_Degradation | master:OlgaV | 2 | A | ||||||
| Phenylpropanoid_compound_degradation | master:OlgaV | 1 | A | ||||||
| Phenylpropionate_Degradation | master:OlgaV | 2 | A | ||||||
| n-Phenylalkanoic_acid_degradation | OlgaV | 2 | A | ||||||
| hpa catabolic pathway | master:YakovK | 1 | B | ||||||
| Phenylacetate_pathway_of_aromatic_compound_degradation | master:OlgaV | 2 | A | ||||||
| Salicylate ester degradation | master:OlgaV | 1 | A | ||||||
| Degradation of Xenobiotics - OlgaV | |||||||||
| Glutathione transferases | |||||||||
| UDP-Glucuronosyltransferases | |||||||||
| Cytochromes p450 | |||||||||
| Toluene_degradation | master:OlgaV | 2 | A | ||||||
| Naphtalene_and_antracene_degradation | master:OlgaV | 1 | A | ||||||
| Biodegradation of phosphonates | |||||||||
| Biodegradation of aromatic hydrocarbons | |||||||||
| Biodegradation of 2,4,6-trinitrotoluene | |||||||||
| Bacterial degradation of chlorophenols/polychlorobiphenils | |||||||||
| Biodegradation of C2 sulfonates | |||||||||
| Mobile genetic elements involved in the distribution of xenobiotic-catabolic capacity | |||||||||
| Xenobiotic efflux systems | |||||||||
| DNA metabolism - RobE | |||||||||
| DNA Replication | |||||||||
| DNA-replication | master:RickS | 3 | A | ||||||
| DNA Modification | |||||||||
| DNA Repair | |||||||||
| DNA Repair Base Excision | master:MikeK | 2 | A | ||||||
| DNA uptake, competence | |||||||||
| gram plus late competence | master:alexS | ||||||||
| RNA metabolism - RossO | |||||||||
| RNA polymerase I | master:gjo | 4 | E | ||||||
| RNA polymerase II | master:gjo | 4 | E | ||||||
| RNA polymerase III | master:gjo | 4 | E | ||||||
| RNA polymerase II initiation factors | master:gjo | 4 | E | ||||||
| RNA polymerase archaeal initiation factors | master:gjo | 4 | E | ||||||
| RNA polymerase archaeal | master:gjo | 4 | E | ||||||
| RNA polymerase bacterial | master:gjo | 4 | E | ||||||
| archaeal general transcription factors | master:gjo | 4 | E | ||||||
| Transcription factors bacterial | master:gjo | 4 | E | ||||||
| Transcription factors cyanobacterial RpoD-like sigma factors | master:gjo | 4 | E | ||||||
| tRNA aminoacylation | master:gjo | 4 | E | ||||||
| tRNA processing | master:gjo | 4 | E | ||||||
| tRNA splicing | master:gjo | 4 | E | ||||||
| RNA processing and modification | |||||||||
| Queuosine | master:vcrecy | 3 | A | ||||||
| RNA degradation | |||||||||
| Protein Metabolism - RossO | |||||||||
| Protein Biosynthesis | |||||||||
| Ribosome LSU bacterial | master:gjo | 4 | E | ||||||
| Ribosome SSU bacterial | master:gjo | 4 | E | ||||||
| Ribosome LSU eukaryotic and archaeal | master:gjo | 4 | E | ||||||
| Ribosome SSU eukaryotic and archaeal | master:gjo | 4 | E | ||||||
| Ribosome SSU chloroplast | master:gjo | 4 | E | ||||||
| tRNA aminoacylation | master:gjo | 4 | E | ||||||
| Translation factors bacterial | master:gjo | 4 | E | ||||||
| Protein Degradation | |||||||||
| Proteasome archaeal | master:gjo | 4 | E | ||||||
| Proteasome eukaryotic | master:gjo | 4 | E | ||||||
| Protein Folding | |||||||||
| Chaperones | master:MikeK | 2 | A | ||||||
| GroEL GroES | master:MikeK | 2 | A | ||||||
| Protein Processing and Modification | |||||||||
| Protein Processing | |||||||||
| Protein metylation | |||||||||
| Protein acetylation/deacetylation | |||||||||
| Protein prenylation | |||||||||
| Protein glycosylation | |||||||||
| Modification of sulfhydryl groups | |||||||||
| Selenoproteins | |||||||||
| Protein Export and Secretion | |||||||||
| General secretory pathway (Sec-SRP) complex (TC 3.A.5.1.1) | master:MattC | ||||||||
| Type II secretion system | master:MikeK | 2 | A | ||||||
| Type III secretion system | master:MikeK | 2 | B | ||||||
| Type IV secretion system | master:MikeK | 1 | A | ||||||
| Membrane Transport - MattC | |||||||||
| Channel/pore type transporters | |||||||||
| Uni-, Sym- and Antiporters | |||||||||
| Phosphotransferase Systems (PTS) | |||||||||
| Transport ATPases | |||||||||
| ABC transporters | |||||||||
| ABC transporter alkylphosphonate (TC 3.A.1.9.1) | master:MattC | ||||||||
| ABC transporter arabinose (TC 3.A.1.2.2) | master:MattC | ||||||||
| ABC transporter branched-chain amino acid (TC 3.A.1.4.1) | master:MattC | ||||||||
| ABC transporter dipeptide (TC 3.A.1.5.2) | master:MattC | ||||||||
| ABC transporter ferric enterobactin (TC 3.A.1.14.2) | master:MattC | ||||||||
| ABC transporter ferrichrome (TC 3.A.1.14.3) | master:MattC | ||||||||
| ABC transporter galactose | master:MattC | ||||||||
| ABC transporter glutamate | master:MattC | ||||||||
| ABC transporter glutamine | master:MattC | ||||||||
| ABC transporter glycerol | master:MattC | ||||||||
| ABC transporter heme | master:MattC | ||||||||
| ABC transporter histidine | master:MattC | ||||||||
| ABC transporter iron(III) dicitrate | master:MattC | ||||||||
| ABC transporter leucine | master:MattC | ||||||||
| ABC transporter lysine arginine ornithine | master:MattC | ||||||||
| ABC transporter macrolide | master:MattC | ||||||||
| ABC transporter maltose | master:MattC | ||||||||
| ABC transporter molybdenum | master:MattC | ||||||||
| ABC transporter nickel | master:MattC | ||||||||
| ABC transporter oligopeptide | master:MattC | ||||||||
| Oligopeptide ABC transporters | master:SvetaG | ||||||||
| ABC transporter peptide | master:MattC | ||||||||
| ABC transporter phosphate | master:MattC | ||||||||
| ABC transporter polyamine putrescine spermidine (TC 3.A.1.11.1) | master:MattC | ||||||||
| ABC transporter potassium 3.A.3.7.1 | master:MattC | ||||||||
| Transport_of_Nickel_and_Cobalt | master:MattC | ||||||||
| Cell Division and Cell Cycle - OlgaV | |||||||||
| Cell cycle in Eukaryota | |||||||||
| Cell cycle in Prokaryota | |||||||||
| Bacterial Cell Division | master:RickS | ||||||||
| Cyanobacterial Circadian Clock | master:OlgaZ | 3 | A | Subsystem diagram | |||||
| Phytochromes | master:OlgaZ | 2 | A | ||||||
| Motility and Chemotaxis - OlgaV | |||||||||
| Cell motility in Eukaryota | |||||||||
| Chemotaxis in Eukaryota | |||||||||
| Flagellar motility in bacteria | |||||||||
| Flagellum | master:RickS | ||||||||
| Social motility and nonflagellar swimming in bacteria | |||||||||
| Bacterial_motility:Gliding | master:OlgaV | ||||||||
| Listeria factors of actine assembly | |||||||||
| Multiple stress signal integration - OlgaV | |||||||||
| Oxidative stres | |||||||||
| Protection_from_Reactive_Oxygen_Species | master:MikeK | ||||||||
| Regulation_of_Oxidative_Stress_Response | master:MikeK | ||||||||
| Oxidative_stress | master:OlgaV | ||||||||
| Redox-dependent regulation of nucleus processes | master:OlgaV | ||||||||
| Glutathione Redox Metabolism | master:Neema_UCSD | ||||||||
| Redox-dependent regulation of cellular functions | |||||||||
| Iron stress response | |||||||||
| Osmotic stress | |||||||||
| Heat shock | |||||||||
| Alkali stress | |||||||||
| Starvation response | |||||||||
| ppGpp biosynthesis | master:MikeK | ||||||||
| Phosphate starvation response | |||||||||
| Carbon starvation response | |||||||||
| Nitrogen starvation response | |||||||||
| Stationary phase | |||||||||
| Biofilm formation | |||||||||
| Competence development | |||||||||
| Bacterial differentiation/sporulation | |||||||||
| Phytochromes | master:OlgaZ | 2 | A | ||||||
| Detoxification | |||||||||
| Cell signaling - OlgaV | |||||||||
| Signal transduction in eukaryota | OlgaV | 1 | P| | ||||||
| Signal transduction in prokaryota | | | ||||||||
| KdpFABC potassium regulation | master:JustinG | ||||||||
| Phytochromes | master:OlgaZ | 2 | A | ||||||
| Quorum sensing, biofilm formation | | | ||||||||
| Quorum Sensing: Autoinducer-2 Synthesis | master:AndrewJ | ||||||||
| VIRULENCE - Core annotators | |||||||||
| Adhesion | |||||||||
| Fimbriae (Pili) | |||||||||
| Mannose-sensitive hemagglutinin type 4 pilus | RobE | 3 | A | ||||||
| Afimbrial adhesins | |||||||||
| Invasion | |||||||||
| Listeria surface proteins: Internalin-like proteins | SvetaG | 2 | A | ||||||
| Listeria surface proteins: LPXTG motif | SvetaG | 2 | A | ||||||
| Invasins | |||||||||
| Growth in Macrophages | |||||||||
| superoxide dismutases | |||||||||
| Macrophage induced proteins | |||||||||
| Toxins | |||||||||
| Cytolethal distending toxin of Campylobacter jejuni | OlgaZ | 4 | A | ||||||
| Superantigens | |||||||||
| Specific Enzymes | |||||||||
| Staphylococcal enterotoxin (e.g PMID:12704169) | |||||||||
| Matrix binding proteins | |||||||||
| Resistance to Antibiotics | |||||||||
| Beta-lactam | MikeK | 1 | B | ||||||
| Glycopeptides | |||||||||
| Aminoglycosides | |||||||||
| Tetracyclines | |||||||||
| Macrolides | |||||||||
| Lincosamides | |||||||||
| Oxazolidinones | |||||||||
| Fluoroquinolones | MattC | 1 | B | fourum posting | |||||
| Rifampin | |||||||||
| Trimethoprim | |||||||||
| Mupirocin | |||||||||
| Nutrient Acquisition in Host | |||||||||
| Iron Acquisition Mechanisms | MikeK | 1 | B | ||||||
| Virulence Islands, Prophages | |||||||||
| Listeria Pathogenicity Island LIPI-1 | SvetaG | 2 | A | ||||||
| Listeria Pathogenicity Island LIPI-1 extended | SvetaG | 2 | A | ||||||
| Plasmids, Transposable Elements, Viruses, and Phages - RobE | |||||||||
| Replication | |||||||||
| Packaging | |||||||||
| Cell lysis | |||||||||
| Lysogeny | |||||||||
| Morons | |||||||||
| Transposition | |||||||||
*There are 5 options for the status field:
0 = you have claimed this subsystem but have done no work on it
1 = you have defined the roles for this susbystem
2 = there are a handful of organisms in your subsystem representing some phylogenetic divergence
3 = you have extended the subsystem and marked the variants
4 = you have taken it as far as you can go and posted open questions to the forum at http://subsys.info\\
**Use the following guidelines while self-evaluating your expertise level with respect to a subsystem. This self-assessment is provided for usersightforward projection from basic resources such as KEGG, Michael book etc. Analysis may (or may not) include 1-2 basic reviews around 1-2 model organisms.
A = "Advanced": addition of components and variants beyond basic: alternative grouping of elements, functional variants, naming conventions. Some additional reading is implied.
Encoding at levels "B" and "A" make a tremendous contribution to annotation clean-up and set the stage for the next level of analysis (g is based on a more serious analysis and substantial critical reading of research articles on the subject. Some expertise in the field is implied.
E = "Expert": the most detailed knowledge and understanding of a subsystem is implied. We hope that some experts will be researchers actively working on aspects of a subsystem.
