Talk:SubtiPathways
Discovered something unusual in the diagrams? Please leave a comment in the corresponding section!
Contents
- 1 General comments about all diagrams
- 2 Carbon metabolism
- 3 Nitrogen and amino acid metabolism
- 3.1 Ammonium assimilation and glutamate metabolism (incl. glutamine and arginine)
- 3.2 Alanine, glycine, serine
- 3.3 Aspartate, asparagine
- 3.4 Cysteine, methionine
- 3.5 Histidine
- 3.6 Isoleucine, valine, leucine
- 3.7 Lysine, threonine
- 3.8 Phenylalanine, tyrosine, tryptophan
- 3.9 Proline
- 3.10 Utilization of other nitrogen sources
- 4 Lipid metabolism
- 5 Nucleotides
- 6 Metabolism of cofactors
- 7 Other pathways
General comments about all diagrams
- There seem to be some compatibility problems using Google Chrome. Nonetheless, Mozilla Firefox, Netscape, Microsoft Explorer, Safari, and Opera are working properly.
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Carbon metabolism
Central carbon metabolism
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Utilization of different carbon sources
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Nitrogen and amino acid metabolism
Ammonium assimilation and glutamate metabolism (incl. glutamine and arginine)
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Alanine, glycine, serine
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Aspartate, asparagine
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Cysteine, methionine
- Repel: Eventuell Einbindung von Extramarkern für die S-Box (bzw. alle riboswitches)???? Es gibt ja dafür extra Seiten im Subtiwiki. Sollte man aber erst mal mit Lope und Arne diskutieren (Jörg)
- Cystin-Aufnahme-Systeme mit aufnehmen: TcyP, TcyABC, TcyJKLMN (Jörg)
Histidine
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Isoleucine, valine, leucine
- Isoleucin-Abbau: Bcd und YwaA sind zwei unterschiedliche Reaktionen, Bcd geht mit NAD, nicht mit 2-KG (Jörg)
Lysine, threonine
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Phenylalanine, tyrosine, tryptophan
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Proline
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Utilization of other nitrogen sources
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Lipid metabolism
Fatty acid and phospholipid biosynthesis
- The structure of PDGP is wrong (although the name, CDP-diacylglycerol, seems right). Wrong PubChem ID?
- The same applies for phosphatidylglycerol, L-serine, and others.
Fatty acid degradation
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Nucleotides
Gene regulation of nucleotides
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Nucleosides catabolism
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Purine metabolism
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Purine catabolism
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Purine salvage pathways
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Pyrimidine metabolism
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Metabolism of cofactors
CoA synthesis
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Folate biosynthesis
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Menaquinone
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Riboflavin and FAD synthesis
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Thiamin synthesis
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Biotin synthesis
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Other pathways
Cellwall
In the reaction catalysed by MurE, Lysine is added as the third residue of the stempeptide. This is incorrect - In Bacillus subtilis this is meso-diaminopimelic acid (as in E. coli). For refs see eg Scheffers and Pinho, MMBR 2005, 585; or Foster and Popham, Chapter 4 p 21, in Bacillus subtilis and its closest relatives, 2002 ASM Press (ed Sonenshein).
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Murein recycling
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Stress response
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Phosphorelay
- In the interaction between KipI and KipA, that prevents the complex between KinA and KipI, KinA should be released from the complex. This has to be added to the diagram.
Sulfate assimilation
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tRNA charging
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Biofilm formation
- SlrR bind SinR, according to Losick PubMed
Protein secretion
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