Difference between revisions of "Sandbox"

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* '''Description:''' secreted peptide, controls LiaRS activity <br/><br/>
+
* '''Description:''' ABC transporter (resistance), permease <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'''
−
|''yydF''
+
|''yydI''
 
|-
 
|-
 
|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''' || secreted peptide
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ABC transporter (resistance), permease
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || control of LiaRS activity
 
|style="background:#ABCDEF;" align="center"|'''Function''' || control of LiaRS activity
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 9.567  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 8.387  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 147 bp, 49 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 627 bp, 209 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yydG]]'', ''[[fbp]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yydJ]]'', ''[[yydH]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16055&#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:CAB16052&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:yydF_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yydI_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU40180
+
* '''Locus tag:''' BSU40150
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yydFGHIJ.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11479]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11482]
  
 
=== Additional information===
 
=== Additional information===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40180]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40150]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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* '''Additional information:'''  
 
* '''Additional information:'''  
−
**  the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
 
−
** the ''yydF'' portion of the mRNA belongs to the most stable mRNAs in ''B. subtilis'' [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 PubMed]
 
  
 
=Biological materials =
 
=Biological materials =

Revision as of 13:54, 8 June 2009

  • Description: ABC transporter (resistance), permease

Gene name yydI
Synonyms
Essential no
Product ABC transporter (resistance), permease
Function control of LiaRS activity
MW, pI 23 kDa, 8.387
Gene length, protein length 627 bp, 209 aa
Immediate neighbours yydJ, yydH
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YydI context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU40150

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

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:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: activated after transition to stationary phase(AbrB) PubMed
  • Regulatory mechanism: AbrB: transcription repression 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

Bronwyn G Butcher, Yi-Pin Lin, John D Helmann
The yydFGHIJ operon of Bacillus subtilis encodes a peptide that induces the LiaRS two-component system.
J Bacteriol: 2007, 189(23);8616-25
[PubMed:17921301] [WorldCat.org] [DOI] (I p)

  1. Butcher BG, Lin YP, Helmann JD (2007) The yydFGHIJ operon of Bacillus subtilis encodes a peptide that induces the LiaRS two-component systemJ. Bacteriol 189: 8616-8625. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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