Difference between revisions of "Sandbox"

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* '''Description:''' bacteriocin producer immunity protein <br/><br/>
+
* '''Description:''' small RNA <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'''
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|''sunI''
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|''surC''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yolF ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || bacteriocin producer immunity protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || small RNA
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || immunity to sublancin
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 9.222  
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|style="background:#ABCDEF;" align="center"| '''Gene length''' ||  bp
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 315 bp, 105 aa
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaJ]]'', ''[[dnaK]]''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sunA]]'', ''[[uvrX]]''
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt    Gene sequence      (+200bp)  ]'''  
 
|-
 
|-
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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:CAB14067&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" | '''Genetic context''' <br/> [[Image:SurC_context.jpeg]]
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|-
 
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|colspan="2" | '''Genetic context''' <br/> [[Image:yolF_context.gif]]
 
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<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
 
|-
 
|-
 
|}
 
|}
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<br/><br/>
 
<br/><br/>
  
 +
<br/><br/><br/><br/><br/>
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU21490
+
* '''Locus tag:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 41:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13584]
+
* '''SubtiList entry:''' no entry
 +
 +
* '''Structure:'''
  
 
=== Additional information===
 
=== Additional information===
  
−
 
−
=The protein=
 
−
 
−
=== Basic information/ Evolution ===
 
−
 
−
* '''Catalyzed reaction/ biological activity:''' mediates immunity to sublancin [http://www.ncbi.nlm.nih.gov/sites/entrez/19047653 PubMed]
 
−
 
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* '''Protein family:''' ribosomal protein S1P family (according to Swiss-Prot)
 
−
 
−
* '''Paralogous protein(s):'''
 
−
 
−
=== Extended information on the protein ===
 
−
 
−
* '''Kinetic information:'''
 
−
 
−
* '''Domains:'''
 
−
 
−
* '''Modification:'''
 
−
 
−
* '''Cofactor(s):'''
 
−
 
−
* '''Effectors of protein activity:'''
 
−
 
−
* '''Interactions:'''
 
−
 
−
* '''Localization:''' membrane anchored protein [http://www.ncbi.nlm.nih.gov/sites/entrez/19047653 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
 
−
 
−
=== Database entries ===
 
−
 
−
* '''Structure:'''
 
−
 
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31989 O31989]
 
−
 
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU21490]
 
−
 
−
* '''E.C. number:'''
 
−
 
−
=== Additional information===
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''surC'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]
  
−
* '''[[[[Sigma factor]]]]:'''  
+
* '''Sigma factor:''' [[SigK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' expressed during sporulation in the mother cell ([[SigK]], [[GerE]])[http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[GerE]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]
  
 
* '''Additional information:'''  
 
* '''Additional information:'''  
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* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
−
* '''GFP fusion:'''
 
−
 
−
* '''two-hybrid system:'''
 
  
−
* '''Antibody:'''
+
=Labs working on this gene/RNA=
  
−
=Labs working on this gene/protein=
 
  
−
[[Jan Maarten van Dijl]], Groningen, Netherlands
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>18763711 19047653, </pubmed>
+
<pubmed>16385044, </pubmed>
−
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
# Silvaggi JM, Perkins JB, Losick R (2006) Genes for small, noncoding RNAs under sporulation control in ''Bacillus subtilis''. ''J. Bacteriol.'' '''188:''' 532-541. [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]
−
# Dubois et al. (2009) Immunity to the bacteriocin sublancin 168 Is determined by the SunI (YolF) protein of ''Bacillus subtilis''. ''Antimicrob. Agents Chemother.'' '''53:''' 651-661. [http://www.ncbi.nlm.nih.gov/sites/entrez/19047653 PubMed]
 
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 

Revision as of 13:38, 8 June 2009

  • Description: small RNA

Gene name surC
Synonyms
Essential no
Product small RNA
Function unknown
Gene length bp
Immediate neighbours dnaJ, dnaK
Gene sequence (+200bp)
Genetic context
SurC context.jpeg








The gene

Basic information

  • Locus tag:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: no entry
  • Structure:

Additional information

Expression and regulation

  • Regulation: expressed during sporulation in the mother cell (SigK, GerE)PubMed
  • Regulatory mechanism: GerE: transcription repression PubMed
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:


Labs working on this gene/RNA

Your additional remarks

References

Jessica M Silvaggi, John B Perkins, Richard Losick
Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis.
J Bacteriol: 2006, 188(2);532-41
[PubMed:16385044] [WorldCat.org] [DOI] (P p)

  1. Silvaggi JM, Perkins JB, Losick R (2006) Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis. J. Bacteriol. 188: 532-541. PubMed
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