Difference between revisions of "Sandbox"

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* '''Description:''' two-component sensor kinase, response to bacitracin <br/><br/>
+
* '''Description:''' general stress protein, similar to senescence marker protein-30 <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'''
−
|''liaS''
+
|''yvrE''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvqE''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component sensor kinase (NarL family)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of LiaR activity in response to bacitracin
+
|style="background:#ABCDEF;" align="center"|'''Function''' || survival of salt stress
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 7.333  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.617  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1080 bp, 360 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 876 bp, 292 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[liaR]]'', ''[[liaF]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvrD]]'', ''[[yvrG]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15299&#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:CAB15310&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yvqE_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yvrE_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/yvqIHGFEC.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yvrE.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14134]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14145]
  
 
=== Additional information===
 
=== Additional information===
Line 62: Line 62:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:''' two transmembrane segments, C-terminal histidine phosphotransferase domain
+
* '''Domains:'''  
  
 
* '''Modification:'''
 
* '''Modification:'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33090]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33200]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[liaI]]-[[liaH]]-[[liaG]]-[[liaF]]-[[liaS]]-[[liaR]]''
+
* '''Operon:'''  
−
''[[liaS]]-[[liaR]]''
 
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]  
  
−
* '''Regulation:''' ''[[liaI]]'': induced by bacitracin ([[LiaR]])
+
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
−
''[[liaS]]'': constitutive
 
  
−
* '''Regulatory mechanism:''' [[LiaR]]: transcription activation
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 115: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]
 
−
 
−
[[Thorsten Mascher]], Karlsruhe Institute of Technology, Germany [http://microbial-stress.iab.kit.edu/ link]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# Jordan, S., A. Junker, J. D. Helmann, and T. Mascher. 2006. Regulation of LiaRS-dependent gene expression in Bacillus subtilis: identification of inhibitor proteins, regulator binding sites, and target genes of a conserved cell envelope stress-sensing two-component system. J. Bacteriol. 188: 5153-5166. [http://www.ncbi.nlm.nih.gov/sites/entrez/16816187 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 03:28, 30 April 2009

  • Description: general stress protein, similar to senescence marker protein-30

Gene name yvrE
Synonyms
Essential no
Product unknown
Function survival of salt stress
MW, pI 33 kDa, 4.617
Gene length, protein length 876 bp, 292 aa
Immediate neighbours yvrD, yvrG
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YvrE 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: Cytoplasm

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • 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. 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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