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>
  
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__NOTOC__
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__TOC__
  
 
== General comments about all diagrams ==
 
== 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.
 
* There seem to be some compatibility problems using Google Chrome. Nonetheless, Mozilla Firefox, Netscape, Microsoft Explorer, Safari, and Opera are working properly.
−
* Comments in brackets have been changed in the original files, but have not been uploaded yet.
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* write comments here
 +
 
 +
<br/>
  
 
== Carbon metabolism ==
 
== Carbon metabolism ==
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=== Central carbon metabolism ===
 
=== Central carbon metabolism ===
  
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Please check whether the "y" genes in the diagrams have already new names. For example, yqjH is polY1. If you are on the PolY1 page in subtiwiki and you get the link to the pathway it is not obvious whtat to look for (PolY1) is not in the list. Jörg
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* write comments here
  
 
=== Utilization of different carbon sources ===  
 
=== Utilization of different carbon sources ===  
  
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*(sugar between gluconate and xylose = '''beta'''-xylosides)
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* write comments here  
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<br/>
 
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== Cellwall ==
 
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write comments here
 
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<br/>
 
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== CoA synthesis ==
 
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−
write comments here
 
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<br/>
 
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== Folate biosynthesis ==
 
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−
write comments here
 
  
 
<br/>
 
<br/>
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== Menaquinone ==
 
−
 
−
write comments here
 
  
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<br/>
 
 
== 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
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 +
*write comments here
  
 
=== Aspartate, asparagine ===
 
=== Aspartate, asparagine ===
  
−
write comments here
+
* write comments here
  
 
=== Cysteine, methionine ===
 
=== Cysteine, methionine ===
  
−
write comments here
+
* 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
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*write comments here
  
 
=== Isoleucine, valine, leucine ===
 
=== Isoleucine, valine, leucine ===
  
−
write comments here
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* 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
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* 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
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*write comments here
  
 
=== Purine metabolism ===
 
=== Purine metabolism ===
  
−
write comments here
+
*write comments here
 +
 
 +
=== Purine catabolism ===
  
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=== Purines catabolism ===
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*write comments here
  
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write comments here
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=== Purine salvage pathways ===
  
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=== Purines salvage pathways ===
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* write comments here
  
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(RelA muss groß geschrieben werden)
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=== Pyrimidine metabolism ===
  
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=== Pyrimidines metabolism ===
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*write comments here
  
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write comments here
 
  
 
<br/>
 
<br/>
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== Stress response ==
 
  
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*PurP muss PurS sein
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== Metabolism of cofactors ==
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*SpoVt muss SpoVT sein
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=== 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/>
  
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== Sulfate assimilation ==
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== Other pathways ==
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=== 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
  
−
write comments here
+
=== Biofilm formation ===
  
−
<br/>
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* SlrR bind SinR, according to Losick {{PubMed|20351052}}
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== tRNA charging ==
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 +
=== Protein secretion ===
  
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Arne, wir hatten doch eine Extra-Diskussion über die Rolle von TilS. Das fehlt hier aber! Jörg
+
* 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!

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
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