Here is a list of subsystems that people are working on.
| 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) 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_nitrit |
