Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' acetolactate decarboxylase <br/><br/>
+
* '''Description:''' similar to NAD(P)H oxidoreductase <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''alsD''
+
|''ywrO''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
Line 10: Line 10:
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || acetolactate decarboxylase)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || overflow metabolism
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 4.603  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 5.2  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 765 bp, 255 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 525 bp, 175 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywrO]]'', ''[[alsS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywsA]]'', ''[[alsD]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:alsD_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:ywrO_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/alsSD.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywrO.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10472]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12528]
  
 
=== Additional information===
 
=== Additional information===
Line 64: Line 66:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 80: Line 82:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36000]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35990]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[alsS]]-[[alsD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' induction by acetate ([[AlsR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed], repressed as long as terminal electron acceptors are available for respiration ([[Rex]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16428414 PubMed]
+
* '''Regulation:'''  
−
Note: since acetate formation requires ''[[ackA]]'' activation by [[CcpA]] there is an indirect effect of [[CcpA]] on the ''alsSD'' operon: the operon is not expressed in ''[[ccpA]]'' mutants
 
  
−
* '''Regulatory mechanism:''' [[AlsR]]: transcription activation in the presence of acetate [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed], [[Rex]]: transcription repression if the ratio NADH2/NAD is high [http://www.ncbi.nlm.nih.gov/sites/entrez/16428414 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 119: Line 120:
 
=References=
 
=References=
  
−
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
 
−
# Renna, M. C., Najimudin, N., Winik, L. R., and Zahler, S. A. (1993). Regulation of the ''Bacillus subtilis alsS'', ''alsD'', and ''alsR'' genes involved in post-exponential-phase production of acetoin. J. Bacteriol. 175, 3863-3875. [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed]
 
−
# Reents, H., R. Münch, T. Dammeyer, D. Jahn, and E. Härtig. 2006. The Fnr regulon of ''Bacillus subtilis''. J. Bacteriol. 188: 1103-1112. [http://www.ncbi.nlm.nih.gov/sites/entrez/16428414 PubMed]
 
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 17:28, 15 April 2009

  • Description: similar to NAD(P)H oxidoreductase

Gene name ywrO
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 19 kDa, 5.2
Gene length, protein length 525 bp, 175 aa
Immediate neighbours ywsA, alsD
Hier soll was neues rein
Genetic context
YwrO context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=54513"