Difference between revisions of "Talk:SubtiPathways"
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<big>'''Discovered something unusual in the diagrams? Please leave a comment in the corresponding section!'''</big> | <big>'''Discovered something unusual in the diagrams? Please leave a comment in the corresponding section!'''</big> | ||
| − | + | __TOC__ | |
| + | |||
| + | == 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. | ||
| + | * write comments here | ||
| + | |||
| + | <br/> | ||
== Carbon metabolism == | == Carbon metabolism == | ||
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=== Central carbon metabolism === | === Central carbon metabolism === | ||
| − | write comments here | + | * write comments here |
=== Utilization of different carbon sources === | === Utilization of different carbon sources === | ||
| − | write comments here | + | * write comments here |
<br/> | <br/> | ||
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== Nitrogen and amino acid metabolism == | == Nitrogen and amino acid metabolism == | ||
=== Ammonium assimilation and glutamate metabolism (incl. glutamine and arginine) === | === Ammonium assimilation and glutamate metabolism (incl. glutamine and arginine) === | ||
| − | write comments here | + | |
| + | *write comments here | ||
=== Alanine, glycine, serine === | === Alanine, glycine, serine === | ||
| − | write comments here | + | |
| + | *write comments here | ||
=== Aspartate, asparagine === | === Aspartate, asparagine === | ||
| − | write comments here | + | * write comments here |
=== Cysteine, methionine === | === 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 === | === Histidine === | ||
| − | write comments here | + | *write comments here |
=== Isoleucine, valine, leucine === | === Isoleucine, valine, leucine === | ||
| − | + | * Isoleucin-Abbau: Bcd und YwaA sind zwei unterschiedliche Reaktionen, Bcd geht mit NAD, nicht mit 2-KG (Jörg) | |
=== Lysine, threonine === | === Lysine, threonine === | ||
| − | write comments here | + | * write comments here |
=== Phenylalanine, tyrosine, tryptophan === | === Phenylalanine, tyrosine, tryptophan === | ||
| − | write comments here | + | * write comments here |
=== Proline === | === Proline === | ||
| − | write comments here | + | * write comments here |
| + | |||
| + | === Utilization of other nitrogen sources === | ||
| + | |||
| + | * write comments here | ||
<br/> | <br/> | ||
| + | |||
| + | == 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 === | ||
| + | |||
| + | * write comments here | ||
| + | |||
== Nucleotides == | == Nucleotides == | ||
=== Gene regulation of nucleotides === | === Gene regulation of nucleotides === | ||
| − | write comments here | + | * write comments here |
=== Nucleosides catabolism === | === Nucleosides catabolism === | ||
| − | write comments here | + | *write comments here |
=== Purine metabolism === | === Purine metabolism === | ||
| − | write comments here | + | *write comments here |
| + | |||
| + | === Purine catabolism === | ||
| − | + | *write comments here | |
| − | + | === Purine salvage pathways === | |
| − | + | * write comments here | |
| − | + | === Pyrimidine metabolism === | |
| − | + | *write comments here | |
| − | |||
<br/> | <br/> | ||
| − | |||
| − | write comments here | + | == Metabolism of cofactors == |
| + | |||
| + | === CoA synthesis === | ||
| + | |||
| + | *write comments here | ||
| + | |||
| + | === Folate biosynthesis === | ||
| + | |||
| + | *write comments here | ||
| + | |||
| + | === Menaquinone === | ||
| + | |||
| + | *write comments here | ||
| + | |||
| + | === Riboflavin and FAD synthesis === | ||
| + | |||
| + | * write comments here | ||
| + | |||
| + | === Thiamin synthesis === | ||
| + | |||
| + | * write comments here | ||
| + | |||
| + | === Biotin synthesis === | ||
| + | |||
| + | * write comments here | ||
<br/> | <br/> | ||
| − | |||
| − | + | == Other pathways == | |
| − | + | === Cellwall === | |
| − | == tRNA charging == | + | 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). |
| + | *write comments here | ||
| + | |||
| + | === Murein recycling === | ||
| + | |||
| + | *write comments here | ||
| + | |||
| + | === Stress response === | ||
| + | |||
| + | * write comments here | ||
| + | |||
| + | === 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 === | ||
| + | |||
| + | *write comments here | ||
| + | |||
| + | === tRNA charging === | ||
| + | |||
| + | * write comments here | ||
| + | |||
| + | === Biofilm formation === | ||
| + | |||
| + | * SlrR bind SinR, according to Losick {{PubMed|20351052}} | ||
| + | |||
| + | === Protein secretion === | ||
| − | write comments here | + | * write comments here |
Latest revision as of 12:07, 13 December 2010
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.
- write comments here
Carbon metabolism
Central carbon metabolism
- write comments here
Utilization of different carbon sources
- write comments here
Nitrogen and amino acid metabolism
Ammonium assimilation and glutamate metabolism (incl. glutamine and arginine)
- write comments here
Alanine, glycine, serine
- write comments here
Aspartate, asparagine
- write comments here
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
- write comments here
Isoleucine, valine, leucine
- Isoleucin-Abbau: Bcd und YwaA sind zwei unterschiedliche Reaktionen, Bcd geht mit NAD, nicht mit 2-KG (Jörg)
Lysine, threonine
- write comments here
Phenylalanine, tyrosine, tryptophan
- write comments here
Proline
- write comments here
Utilization of other nitrogen sources
- write comments here
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
- write comments here
Nucleotides
Gene regulation of nucleotides
- write comments here
Nucleosides catabolism
- write comments here
Purine metabolism
- write comments here
Purine catabolism
- write comments here
Purine salvage pathways
- write comments here
Pyrimidine metabolism
- write comments here
Metabolism of cofactors
CoA synthesis
- write comments here
Folate biosynthesis
- write comments here
Menaquinone
- write comments here
Riboflavin and FAD synthesis
- write comments here
Thiamin synthesis
- write comments here
Biotin synthesis
- write comments here
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).
- write comments here
Murein recycling
- write comments here
Stress response
- write comments here
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
- write comments here
tRNA charging
- write comments here
Biofilm formation
- SlrR bind SinR, according to Losick PubMed
Protein secretion
- write comments here
