Difference between revisions of "Sandbox"

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* '''Description:''' ribosomal protein  <br/><br/>
+
* '''Description:''' transcriptional repressor of the ribose operon <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'''
−
|''rpmH''
+
|''rbsR''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || ribosomal protein L34
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor (LacI family)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of ribose utilization
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 13  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 5.577  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 132 bp, 44 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 978 bp, 326 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rnpA]]'', ''[[dnaA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[capB]]'', ''[[rbsK]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16143&#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:CAB15608&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ThdF_jag_spoIIIJ_rnpA_rpmH_context.png]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rbsR_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/rpmH.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rbsRKDACB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10064]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10876]
  
 
=== Additional information===
 
=== Additional information===
Line 72: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[RnpA]]-[[RpmH]],  
+
* '''Interactions:''' [[PtsH]]-[[RbsR]],  
  
 
* '''Localization:'''
 
* '''Localization:'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU41060]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35910]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[rbsR]]-[[rbsK]]-[[rbsD]]-[[rbsA]]-[[rbsC]]-[[rbsB]]''
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose (10-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 118:
 
=References=
 
=References=
  
 +
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
 +
# Woodson K, Devine KM. (1994) Analysis of a ribose transport operon from Bacillus subtilis. ''Microbiology. '' '''Aug;140 ( Pt 8):''' 1829-38. [http://www.ncbi.nlm.nih.gov/sites/entrez/7921236 PubMed]
 +
# Müller W, Horstmann N, Hillen W, Sticht H. (2006) The transcription regulator RbsR represents a novel interaction partner of the phosphoprotein HPr-Ser46-P in Bacillus subtilis. '' FEBS J.'' '''Mar;273(6):''' 1251-61. [http://www.ncbi.nlm.nih.gov/sites/entrez/16519689 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 00:27, 28 April 2009

  • Description: transcriptional repressor of the ribose operon

Gene name rbsR
Synonyms
Essential no
Product transcriptional repressor (LacI family)
Function regulation of ribose utilization
MW, pI 35 kDa, 5.577
Gene length, protein length 978 bp, 326 aa
Immediate neighbours capB, rbsK
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
RbsR 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:
  • Localization:

Database entries

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

Additional information

Expression and regulation

  • Regulation: repressed by glucose (10-fold) (CcpA) PubMed
  • Regulatory mechanism: CcpA: transcription repression
  • 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. Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 5: 133-149 PubMed
  2. Woodson K, Devine KM. (1994) Analysis of a ribose transport operon from Bacillus subtilis. Microbiology. Aug;140 ( Pt 8): 1829-38. PubMed
  3. Müller W, Horstmann N, Hillen W, Sticht H. (2006) The transcription regulator RbsR represents a novel interaction partner of the phosphoprotein HPr-Ser46-P in Bacillus subtilis. FEBS J. Mar;273(6): 1251-61. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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