Difference between revisions of "Sandbox"

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* '''Description:''' serine protease Do (heat-shock protein) <br/><br/>
+
* '''Description:''' glyoxal reductase, general stress protein <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'''
−
|''htrA''
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|''yvgN''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykdA ''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvsB ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || serine protease Do (heat-shock protein)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glyoxal reductase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || probably involved in processing, maturation, or secretion of extracellular enzymes
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.699  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.066  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1347 bp, 449 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 828 bp, 276 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykcC]]'', ''[[proG]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvgM]]'', ''[[yvgO]]''
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13147&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15345&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yvgN_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:htrA_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>
 
|-
 
|-
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/htrA.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12608]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14096]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Lactaldehyde + NADP<sup>+</sup> = methylglyoxal + NADPH
  
−
* '''Protein family:''' PDZ (DHR) domain (according to Swiss-Prot)
+
* '''Protein family:''' aldo/keto reductase family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[YyxA]]
+
* '''Paralogous protein(s):''' [[YtbE]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot),  extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=3B3E 3B3E]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34358 O34358]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32210 O32210]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU12900 BSU12900]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33400 BSU33400]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.283 1.1.1.283]
  
 
=== Additional information===
 
=== Additional information===
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* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed], repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 118:
 
=References=
 
=References=
  
−
Test.
+
# H&ouml;per et al. (2005) Comprehensive Characterization of the Contribution of Individual [[SigB]]-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
−
<pubmed> 12850135</pubmed>
 
−
 
 
−
 
 
−
# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 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 02:45, 23 May 2009

  • Description: glyoxal reductase, general stress protein

Gene name yvgN
Synonyms yvsB
Essential no
Product glyoxal reductase
Function unknown
MW, pI 31 kDa, 5.066
Gene length, protein length 828 bp, 276 aa
Immediate neighbours yvgM, yvgO
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YvgN context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Lactaldehyde + NADP+ = methylglyoxal + NADPH
  • Protein family: aldo/keto reductase family (according to Swiss-Prot)
  • Paralogous protein(s): YtbE

Extended information on the protein

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

Database entries

Additional information

Expression and regulation

  • Operon:
  • Regulatory mechanism: SinR: transcription repression PubMed
  • 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. Höper et al. (2005) Comprehensive Characterization of the Contribution of Individual SigB-Dependent General Stress Genes to Stress Resistance of Bacillus subtilis. J. Bact. 187: 2810-2826 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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