Difference between revisions of "Talk:SubtiPathways"

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== 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/>
 
<br/>
 +
 
== Carbon metabolism ==
 
== Carbon metabolism ==
  
 
=== 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)
+
* 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
  
 +
<br/>
  
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<br/>
 
 
== Nitrogen and amino acid metabolism ==
 
== Nitrogen and amino acid metabolism ==
  
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* die Anordnung der einzelnen Teile in diesem Diagramm ist suboptimal, sie sollten noch mal verschoben werden (Jörg)
 
 
*write comments here
 
*write comments here
  
 
=== Alanine, glycine, serine ===
 
=== Alanine, glycine, serine ===
  
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* der Glycin-Abbau über gcvT, gcvPA, gcvPB und gcvH fehlt (Jörg)
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*write comments here
 
*write comments here
  
 
=== Aspartate, asparagine ===
 
=== Aspartate, asparagine ===
  
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* (warum ist YveA hier nicht drin?)
 
 
* write comments here
 
* write comments here
  
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* 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)
 
* 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)
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* Cystin-Aufnahme-Systeme mit aufnehmen: TcyP, TcyABC, TcyJKLMN (Jörg)
  
 
=== Histidine ===
 
=== Histidine ===
  
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*Repel: Description for HutU
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*write comments here
  
 
=== Isoleucine, valine, leucine ===
 
=== Isoleucine, valine, leucine ===
  
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*(beim Abbau Acyl-'''C'''oA nicht coA)
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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 ===
  
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* (SpoVF hieß das früher, jetzt sind es zwei Proteine (SpoVFA und SpoVFB), die kommen ja auch im Regulationsteil vor und sind richtig zu SubtiWiki verlinkt. Man sollte da also oben auch den Komplex aus beiden reinmachen und dann das Popup-Fenster entspechend verändern. Ich kopiere diese Message auhc mal auf die SubtiPathways-Wishlist, dann könnte  das in einer größeren Überarbeitungsaktion mal in Angriff genommen werden.)
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* write comments here
  
 
=== Phenylalanine, tyrosine, tryptophan ===
 
=== Phenylalanine, tyrosine, tryptophan ===
  
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* (pyr rot)
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* write comments here
−
* (Reaktionen Chorismat ---> Folat bzw. Menachinon stimmen nicht (sind viel komplizierter, dafür gibt es auch eigene Diagramme, am besten beide hier raus nehmen)) --> hab die Proteine an diesen Reaktionen herausgenommen und die Reaktionspfeile ersetzt, jetzt wird symbolisiert, dass bekannte Reaktionen zu Chorismat und Menachinon führen --> jetzt vielleicht Verlinkung zu den entsprechenden Diagrammen?
 
  
 
=== Proline ===
 
=== Proline ===
  
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*write comments here
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* 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 ===
  
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*(dut nicht in SubtiWiki --> ist vermutlich yncF (dUTP diphosphatase, Bezeichnung dut aus Paper Goelzer), im Diagramm ändern, Dut als Synonym übernehmen?)
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* write comments here
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*(RpsA nicht in SubtiWiki --> ist vermutlich ypfD (RpsA = Homolog aus E.coli, Bezeichnung aus Paper Goelzer), im Diagramm ändern!)
 
  
 
=== Nucleosides catabolism ===
 
=== Nucleosides catabolism ===
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=== Purine salvage pathways ===
 
=== Purine salvage pathways ===
  
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*(RelA muss groß geschrieben werden)
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* write comments here
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* (GucA nicht in SubtiWiki)
 
  
 
=== Pyrimidine metabolism ===
 
=== Pyrimidine metabolism ===
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<br/>
 
<br/>
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== Metabolism of cofactors ==
 
== Metabolism of cofactors ==
  
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*write comments here
 
*write comments here
 +
 +
=== Riboflavin and FAD synthesis ===
 +
 +
* write comments here
 +
 +
=== Thiamin synthesis ===
 +
 +
* write comments here
 +
 +
=== Biotin synthesis ===
 +
 +
* write comments here
  
 
<br/>
 
<br/>
 +
 
== Other pathways ==
 
== Other pathways ==
  
 
=== Cellwall ===
 
=== 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
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 +
=== Murein recycling ===
  
 
*write comments here
 
*write comments here
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=== Stress response ===
 
=== Stress response ===
  
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* (PurP muss PurS sein)
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* write comments here
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* (SpoVt muss SpoVT sein)
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* (sigB groß)
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=== Phosphorelay ===
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* (sigF groß)
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* 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.
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* (glutamate (bei Prolinsynthese) lila)
 
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* OpuAABCD muss OpuB(ABCD) sein
 
  
 
=== Sulfate assimilation ===
 
=== Sulfate assimilation ===
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=== tRNA charging ===
 
=== tRNA charging ===
  
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*Arne, wir hatten doch eine Extra-Diskussion über die Rolle von TilS. Das fehlt hier aber! Jörg
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* write comments here
 +
 
 +
=== Biofilm formation ===
 +
 
 +
* SlrR bind SinR, according to Losick {{PubMed|20351052}}
 +
 
 +
=== Protein secretion ===
 +
 
 +
* 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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