Difference between revisions of "Sandbox"

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* '''Description:''' 2-oxoglutarate dehydrogenase (E1 subunit) <br/><br/>
+
* '''Description:''' transcriptional activator (for SigL-dependent promoter) <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'''
|''odhA''
+
|''yplP''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citK ''
+
|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''' || 2-oxoglutarate dehydrogenase (E1 subunit)  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional activator (for SigL-dependent promoter)  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || required for survival at low temperatures
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 105 kDa, 5.871  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 9.295  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2823 bp, 941 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 993 bp, 331 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yojO]], [[odhB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ilvA]]'', ''[[yplQ]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13829&#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:CAB14096&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yplP_context.gif]]
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:odhA_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>
 
|-
 
|-
Line 40: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
The mutant is cold-sensitive [http://www.ncbi.nlm.nih.gov/sites/entrez/16585774  PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/odhAB.html]
+
* '''DBTBS entry:''' no entry
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10272]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11619]
  
 
=== Additional information===
 
=== Additional information===
Line 72: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
* '''Interactions:''' [[OdhA]]-[[OdhB]]-[[PdhD]],  
+
* '''Interactions:''' [[YplP]]-[[SigL]],  
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 82: Line 82:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19370]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU21780]
  
* '''E.C. number:''' 1.2.4.2
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
Line 90: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:''' ''[[odhA]]''-''[[odhB]]''
+
* '''Operon:'''  
  
* '''Sigma factor:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
* '''Regulation:''' constitutive
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
* '''Mutant:''' GP671 (spc), GP665 (aphA3), GP684 (cat), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 120: Line 120:
 
=References=
 
=References=
  
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Wiegeshoff et al.  (2006) Sigma L is important for cold shock adaptation of ''Bacillus subtilis''. J Bacteriol , 188: 3130-3133. [http://www.ncbi.nlm.nih.gov/sites/entrez/16585774  PubMed]

Revision as of 00:07, 28 April 2009

  • Description: transcriptional activator (for SigL-dependent promoter)

Gene name yplP
Synonyms
Essential no
Product transcriptional activator (for SigL-dependent promoter)
Function required for survival at low temperatures
MW, pI 37 kDa, 9.295
Gene length, protein length 993 bp, 331 aa
Immediate neighbours ilvA, yplQ
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YplP context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

The mutant is cold-sensitive PubMed

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:
  • Localization:

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • 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

  1. Wiegeshoff et al. (2006) Sigma L is important for cold shock adaptation of Bacillus subtilis. J Bacteriol , 188: 3130-3133. PubMed