Difference between revisions of "Sandbox"

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−
* '''Description:''' extracellular alkaline serine protease (subtilisin E) <br/><br/>
+
* '''Description:''' competence transcription factor (CTF) <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'''
−
|''aprE''
+
|''comK''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sprE ''
+
|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''' || extracellular alkaline serine protease (subtilisin E))
+
|style="background:#ABCDEF;" align="center"| '''Product''' || competence transcription factor (CTF)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of competence and DNA uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 9.342  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 7.669  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1143 bp, 381 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 576 bp, 192 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhfN]]'', ''[[yhfO]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhzC]]'', ''[[yhxD]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12870&#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:CAB12882&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:comK_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:aprE_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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__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/>
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU10300
+
* '''Locus tag:''' BSU10420
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/aprE.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/comK.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10190]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11059]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1 (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' peptidase S8 family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[AprE]]-[[PaiA]]
+
* '''Interactions:''' [[MecA]]-[[ComK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/10447896 PubMed]
  
−
* '''Localization:''' secreted (according to Swiss-Prot),  extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1SBC 1SBC]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P04189 P04189]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P40396 P40396]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10300]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10420]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] 
−
** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1898931 PubMed]
+
** repressed by [[Rok]] [http://www.ncbi.nlm.nih.gov/sites/entrez/11849533 PubMed]
−
** repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467 PubMed]
+
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/8830686 PubMed]
−
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584 PubMed]
+
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12586407 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1898931 PubMed]
+
** [[Rok]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/11849533 PubMed]
−
** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467 PubMed]
+
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/8830686 PubMed]
−
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584 PubMed]
+
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12586407 PubMed]
  
−
* '''Additional information:''' the mRNA is extremely stable (more than 25 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/11101663 PubMed]
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Oscar Kuipers]], University of Groningen, The Netherlands
 +
[http://molgen.biol.rug.nl/molgen/index.php Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>2504584,18957862 11101663 12055299, </pubmed>
+
<pubmed>12586407, 10447896, 12028382, 8016067, 10361283, 11703662, 12107147, 17581123, 17493123,16391071,16436435 </pubmed>
−
# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
 
−
# Hambraeus, G., Persson, M. & Rutberg, B. (2000). The ''aprE'' leader is a determinant of extreme mRNA stability in ''Bacillus subtilis''. Microbiology 146, 3051-3059. [http://www.ncbi.nlm.nih.gov/sites/entrez/11101663 PubMed]
 
−
# Hambraeus, G., Karhumaa, K. & Rutberg, B. (2002). A 5' stem-loop and ribosome binding but not translation are important for the stability of ''Bacillus subtilis aprE'' leader mRNA. Microbiology 148, 1795-1803. [http://www.ncbi.nlm.nih.gov/sites/entrez/12055299 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 10:37, 12 June 2009

  • Description: competence transcription factor (CTF)

Gene name comK
Synonyms
Essential no
Product competence transcription factor (CTF)
Function regulation of competence and DNA uptake
MW, pI 22 kDa, 7.669
Gene length, protein length 576 bp, 192 aa
Immediate neighbours yhzC, yhxD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ComK context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Locus tag: BSU10420

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:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation: repressed by casamino acids PubMed
    • repressed by Rok PubMed
    • repressed during growth in the presence of branched chain amino acids (CodY) PubMed
    • repressed during logrithmic growth (AbrB) PubMed
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Oscar Kuipers, University of Groningen, The Netherlands Homepage

Your additional remarks

References


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