Difference between revisions of "Sandbox"

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* '''Description:''' general stress protein, survival of salt and ethanol  stresses <br/><br/>
+
* '''Description:''' similar to transcriptional regulator (MarR family) <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'''
|''yfkM''
+
|''ydgG''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Product''' || unknown  
 
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || survival of salt and ethanol  stresses
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 18 kDa, 4.722  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 5.623  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 516 bp, 172 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 456 bp, 152 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yfkN]]'', ''[[yfkL]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dinB]]'', ''[[ydgH]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12614&#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:CAB12371&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:yfkM_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ydgG_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 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
* '''Locus tag:''' BSU07850
+
* '''Locus tag:''' BSU05640
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yfkM.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ydgGH.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12929]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12174]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
* '''Protein family:''' PfpI endopeptidase domain (according to Swiss-Prot)
+
* '''Protein family:'''
  
* '''Paralogous protein(s):''' [[YraA]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 78: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80876 P80876]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P96705 P96705]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU07850]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05640]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 90:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
+
* '''[[Sigma factor]]:'''  
  
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
Line 118: Line 118:
 
=References=
 
=References=
  
<pubmed>15805528, </pubmed>
 
# 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]
 
 
# 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 13:02, 11 June 2009

  • Description: similar to transcriptional regulator (MarR family)

Gene name ydgG
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 17 kDa, 5.623
Gene length, protein length 456 bp, 152 aa
Immediate neighbours dinB, ydgH
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YdgG context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU05640

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:
  • 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