Difference between revisions of "Sandbox"

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* '''Description:''' RNA polymerase [[sigma factor]] SigB <br/><br/>
+
* '''Description:''' chaperonin <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'''
−
|''sigB''
+
|''groES''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rpoF ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase [[sigma factor]] SigB
+
|style="background:#ABCDEF;" align="center"| '''Product''' || chaperonin
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || general stress response
+
|style="background:#ABCDEF;" align="center"|'''Function''' || protein folding and re-folding
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.418  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 4.595  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 282 bp, 94 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbW]]'', ''[[rsbX]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydiL]]'', ''[[groEL]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12280&#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:CAB12421&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:sigB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:groES_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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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rsbRSTUVW-sigB-rsbX.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/groESL.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10735]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10422]
  
 
=== Additional information===
 
=== Additional information===
Line 57: Line 59:
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
−
 
−
=== Genes/ operons controlled by SigB ===
 
−
 
−
''[[csbB]]'', ''[[ctc]]'', ''[[gsiB]]'', ''[[katE]], [[lexA]],[[licR]], [[sfA]], [[xpf]], [[yaaH]], [[ydeC]], [[ytzE]], [[yvaN]], [[ywhH]]'',
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 74: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[SigB]]-[[RsbW]],  
+
* '''Interactions:''' [[GroEL]]-[[GroES]],  
  
 
* '''Localization:'''
 
* '''Localization:'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU04730]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU06020]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 94: Line 92:
 
* '''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:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 117: Line 115:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Wolfgang Schumann]], Bayreuth University, Germany [http://www.genetik.uni-bayreuth.de/LSGenetik1/schumann_research.htm Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 122:
 
=References=
 
=References=
  
−
# 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]
 
−
# Petersohn, A., Bernhardt, J., Gerth, U., Höper, D., Koburger, T., Völker, U. and Hecker, M. 1999. Identification of sigma(B)-dependent genes in Bacillus subtilis using a promoter consensus-directed search and oligonucleotide hybridization. J. Bacteriol. 181: 5718-5724. [http://www.ncbi.nlm.nih.gov/sites/entrez/10482513 PubMed]
 
−
# Petersohn, A., Brigulla, M., Haas, S., Hoheisel, J. D., Völker, U. and Hecker, M. 2001. Global analysis of the general stress reponse of Bacillus subtilis. J. Bacteriol. 183: 5617-5631. [http://www.ncbi.nlm.nih.gov/sites/entrez/11544224 PubMed]
 
−
# Price, C. W., Fawcett, P., Cérémonie, H., Su, N., Murphy, C. K. and Youngman, P. 2001. Genome-wide analysis of the general stress response in Bacillus subtilis. Mol. Microbiol. 41: 757-774. [http://www.ncbi.nlm.nih.gov/sites/entrez/11532142 PubMed]
 
−
# Ollington, J. F., Haldenwang, W. G., Huynh, T. V. and Losick, R. 1981. Developmentally regulated transcription in a cloned segment of the Bacillus subtilis chromosome. J. Bacteriol. 147: 432-442. [http://www.ncbi.nlm.nih.gov/sites/entrez/6790515 PubMed]
 
−
# Haldenwang, W. G. & Losick, R. (1979). A modified RNA polymerase transcribes a cloned gene under sporulation control in Bacillus subtilis. Nature 282, 256-260 [http://www.ncbi.nlm.nih.gov/pubmed/116131 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 23:51, 27 April 2009

  • Description: chaperonin

Gene name groES
Synonyms
Essential yes PubMed
Product chaperonin
Function protein folding and re-folding
MW, pI 10 kDa, 4.595
Gene length, protein length 282 bp, 94 aa
Immediate neighbours ydiL, groEL
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GroES context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

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:
  • 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

Wolfgang Schumann, Bayreuth University, Germany Homepage

Your additional remarks

References

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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