Difference between revisions of "Sandbox"

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−
* '''Description:''' bacteriocin-like product <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'''
−
|''sboX''
+
|''comK''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || bacteriocin-like product
+
|style="background:#ABCDEF;" align="center"| '''Product''' || competence transcription factor (CTF)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of competence and DNA uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 9.857  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 7.669  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 150 bp, 50 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 576 bp, 192 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sboA]]'', ''[[albA]]''
+
|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:CAE01468&#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:sboX_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:comK_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:''' BSU37360
+
* '''Locus tag:''' BSU10420
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sboAX-albABCDEFG.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/comK.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14182]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11059]
  
 
=== Additional information===
 
=== Additional information===
Line 70: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[MecA]]-[[ComK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/10447896 PubMed]
  
 
* '''Localization:'''
 
* '''Localization:'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q7WY57 Q7WY57]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P40396 P40396]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37360]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10420]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[sboA]]-[[sboX]]-[[albA]]-[[albB]]-[[albC]]-[[albD]]-[[albE]]-[[albF]]-[[albG]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] 
−
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10572140,17720793 PubMed]
+
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12586407 PubMed]
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10572140,17720793 PubMed]
+
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12586407 PubMed]
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 113: Line 113:
  
 
=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=
  
 
=References=
 
=References=
 +
 +
<pubmed> 10447896, 12028382, 8016067, 10361283, 11703662, 12107147, 17581123, 17493123,16391071,16436435 </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 11:12, 11 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
  • Regulatory mechanism:
  • 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

Wiep Klaas Smits, Cristina Bongiorni, Jan-Willem Veening, Leendert W Hamoen, Oscar P Kuipers, Marta Perego
Temporal separation of distinct differentiation pathways by a dual specificity Rap-Phr system in Bacillus subtilis.
Mol Microbiol: 2007, 65(1);103-20
[PubMed:17581123] [WorldCat.org] [DOI] (P p)

Wiep Klaas Smits, Tran Thu Hoa, Leendert W Hamoen, Oscar P Kuipers, David Dubnau
Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein.
Mol Microbiol: 2007, 64(2);368-81
[PubMed:17493123] [WorldCat.org] [DOI] (P p)

Kim A Susanna, Fabrizia Fusetti, Andy-Mark W H Thunnissen, Leendert W Hamoen, Oscar P Kuipers
Functional analysis of the competence transcription factor ComK of Bacillus subtilis by characterization of truncation variants.
Microbiology (Reading): 2006, 152(Pt 2);473-483
[PubMed:16436435] [WorldCat.org] [DOI] (P p)

Kim A Susanna, Chris D den Hengst, Leendert W Hamoen, Oscar P Kuipers
Expression of transcription activator ComK of Bacillus subtilis in the heterologous host Lactococcus lactis leads to a genome-wide repression pattern: a case study of horizontal gene transfer.
Appl Environ Microbiol: 2006, 72(1);404-11
[PubMed:16391071] [WorldCat.org] [DOI] (P p)

Ulrike Mäder, Georg Homuth, Christian Scharf, Knut Büttner, Rüdiger Bode, Michael Hecker
Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability.
J Bacteriol: 2002, 184(15);4288-95
[PubMed:12107147] [WorldCat.org] [DOI] (P p)

Michiko M Nakano, Shunji Nakano, Peter Zuber
Spx (YjbD), a negative effector of competence in Bacillus subtilis, enhances ClpC-MecA-ComK interaction.
Mol Microbiol: 2002, 44(5);1341-9
[PubMed:12028382] [WorldCat.org] [DOI] (P p)

M M Nakano, F Hajarizadeh, Y Zhu, P Zuber
Loss-of-function mutations in yjbD result in ClpX- and ClpP-independent competence development of Bacillus subtilis.
Mol Microbiol: 2001, 42(2);383-94
[PubMed:11703662] [WorldCat.org] [DOI] (P p)

M Persuh, K Turgay, I Mandic-Mulec, D Dubnau
The N- and C-terminal domains of MecA recognize different partners in the competence molecular switch.
Mol Microbiol: 1999, 33(4);886-94
[PubMed:10447896] [WorldCat.org] [DOI] (P p)

M Ogura, L Liu, M Lacelle, M M Nakano, P Zuber
Mutational analysis of ComS: evidence for the interaction of ComS and MecA in the regulation of competence development in Bacillus subtilis.
Mol Microbiol: 1999, 32(4);799-812
[PubMed:10361283] [WorldCat.org] [DOI] (P p)

L Kong, D Dubnau
Regulation of competence-specific gene expression by Mec-mediated protein-protein interaction in Bacillus subtilis.
Proc Natl Acad Sci U S A: 1994, 91(13);5793-7
[PubMed:8016067] [WorldCat.org] [DOI] (P p)


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