Difference between revisions of "YbdK"

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* '''Description:''' [[two-component systems|two-component]] sensor kinase<br/><br/>
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{| align="right" border="1" cellpadding="2"  
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|-
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|style="background:#ABCDEF;" align="center"|'''Gene name'''
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|''ybdK''
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|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
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|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || [[two-component systems|two-component]] sensor kinase
 +
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
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|-
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU02010 ybdK]
 +
|-
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/YbdK YbdK]
 +
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 5.212 
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|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 960 bp, 320 aa
 +
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybdJ]]'', ''[[ybdL]]''
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|-
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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:CAB11995&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
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|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:ybdK_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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|-
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|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybdK_221950_222912_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ybdK_expression.png|500px]]
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|-
 +
|}
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__TOC__
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<br/><br/><br/><br/>
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<br/><br/><br/><br/>
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<br/><br/><br/><br/>
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<br/><br/><br/><br/>
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<br/><br/><br/><br/>
 +
 
 +
 
 +
<br/><br/>
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= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[protein modification]]}},
 +
{{SubtiWiki category|[[transcription factors and their control]]}},
 +
{{SubtiWiki category|[[membrane proteins]]}},
 +
{{SubtiWiki category|[[phosphoproteins]]}}
 +
 
 +
= This gene is a member of the following [[regulons]] =
 +
{{SubtiWiki regulon|[[ComK regulon]]}}
 +
 
 +
=The gene=
 +
 
 +
=== Basic information ===
 +
 
 +
* '''Locus tag:''' BSU02010
 +
 
 +
===Phenotypes of a mutant ===
 +
 
 +
=== Database entries ===
 +
 
 +
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ybdK.html]
 +
 
 +
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12724]
 +
 
 +
=== Additional information===
 +
 
 +
 
 +
 
 +
 
 +
=The protein=
 +
 
 +
=== Basic information/ Evolution ===
 +
 
 +
* '''Catalyzed reaction/ biological activity:''' autophosphorylation, phosphorylation of [[YbdJ]]
 +
 
 +
* '''Protein family:'''
 +
 
 +
* '''Paralogous protein(s):'''
 +
 
 +
=== Extended information on the protein ===
 +
 
 +
* '''Kinetic information:'''
 +
 
 +
* '''Domains:''' two transmembrane segments, C-terminal histidine phosphotransferase domain
 +
 
 +
* '''Modification:''' autophosphorylation on a His residue
 +
 
 +
* '''Cofactor(s):'''
 +
 
 +
* '''Effectors of protein activity:'''
 +
 
 +
* '''[[SubtInteract|Interactions]]:'''
 +
** [[YbdK]]-[[YbdJ]]
 +
 
 +
* '''[[Localization]]:''' cell membrane (according to Swiss-Prot)
 +
 
 +
=== Database entries ===
 +
 
 +
* '''Structure:'''
 +
 
 +
* '''UniProt:''' [http://www.uniprot.org/uniprot/O31433 O31433]
 +
 
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU02010]
 +
 
 +
* '''E.C. number:'''
 +
 
 +
=== Additional information===
 +
 
 +
=Expression and regulation=
 +
 
 +
* '''Operon:''' ''ybdK'' [http://dbtbs.hgc.jp/COG/prom/ybdK.html DBTBS]
 +
 
 +
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybdK_221950_222912_1 ybdK] {{PubMed|22383849}}
 +
 
 +
* '''Sigma factor:'''
 +
 
 +
* '''Regulation:'''
 +
 
 +
* '''Regulatory mechanism:''' [[ComK]]: positive regulation {{PubMed|11948146}}
 +
 
 +
* '''Additional information:'''
 +
 
 +
=Biological materials =
 +
 
 +
* '''Mutant:'''
 +
 
 +
* '''Expression vector:'''
 +
       
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* '''lacZ fusion:'''
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* '''GFP fusion:'''
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* '''two-hybrid system:'''
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* '''Antibody:'''
 +
 
 +
=Labs working on this gene/protein=
 +
 
 +
=Your additional remarks=
 +
 
 +
=References=
 +
 
 +
<pubmed>10094672,11948146 ,20035725  </pubmed>
 +
 
 +
[[Category:Protein-coding genes]]

Revision as of 20:12, 8 August 2012

Gene name ybdK
Synonyms
Essential no
Product two-component sensor kinase
Function unknown
Gene expression levels in SubtiExpress: ybdK
Interactions involving this protein in SubtInteract: YbdK
MW, pI 37 kDa, 5.212
Gene length, protein length 960 bp, 320 aa
Immediate neighbours ybdJ, ybdL
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YbdK context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YbdK expression.png
























Categories containing this gene/protein

protein modification, transcription factors and their control, membrane proteins, phosphoproteins

This gene is a member of the following regulons

ComK regulon

The gene

Basic information

  • Locus tag: BSU02010

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: autophosphorylation, phosphorylation of YbdJ
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains: two transmembrane segments, C-terminal histidine phosphotransferase domain
  • Modification: autophosphorylation on a His residue
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

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

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation:
  • Regulatory mechanism: ComK: positive regulation PubMed
  • 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

Young Pil Kim, Kwon Joo Yeo, Myung Hee Kim, Young-Chang Kim, Young Ho Jeon
Structural characterization of the intra-membrane histidine kinase YbdK from Bacillus subtilis in DPC micelles.
Biochem Biophys Res Commun: 2010, 391(3);1506-11
[PubMed:20035725] [WorldCat.org] [DOI] (I p)

Mitsuo Ogura, Hirotake Yamaguchi, Kazuo Kobayashi, Naotake Ogasawara, Yasutaro Fujita, Teruo Tanaka
Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK.
J Bacteriol: 2002, 184(9);2344-51
[PubMed:11948146] [WorldCat.org] [DOI] (P p)

C Fabret, V A Feher, J A Hoch
Two-component signal transduction in Bacillus subtilis: how one organism sees its world.
J Bacteriol: 1999, 181(7);1975-83
[PubMed:10094672] [WorldCat.org] [DOI] (P p)

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