Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
* '''Description:''' acetoin dehydrogenase E3 component (dihydrolipoamide dehydrogenase) <br/><br/>
+
* '''Description:''' two-component response regulator <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'''
|''acoL''
+
|''yfiK''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yfjH ''
+
|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''' || acetoin dehydrogenase E3 component (dihydrolipoamide dehydrogenase)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component response regulator
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || acetoin utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.273  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 4.671  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1374 bp, 458 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 660 bp, 220 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[acoC]]'', ''[[acoR]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yfiJ]]'', ''[[yfiL]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12638&#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:CAB12659&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:acoL_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yfiK_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 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/acoABCL.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yfiJK.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12561]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12216]
  
 
=== Additional information===
 
=== Additional information===
Line 80: Line 80:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08090]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08300]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:''' ''[[acoA]]-[[acoB]]-[[acoC]]-[[acoL]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11274109  PubMed]
+
* '''Operon:'''  
  
* '''[[Sigma factor]]:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/sites/entrez/11274109  PubMed]
+
* '''[[Sigma factor]]:'''  
  
* '''Regulation:''' repressed by glucose ([[CcpA]]) ,  induced by acetoin ([[AcoR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11274109  PubMed]
+
* '''Regulation:'''  
  
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[AcoR]]: transcription activation (interaction with [[SigL]]-containing RNA polymerase) [http://www.ncbi.nlm.nih.gov/sites/entrez/11274109  PubMed]
+
* '''Regulatory mechanism:'''  
  
 
* '''Additional information:'''  
 
* '''Additional information:'''  
Line 113: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 
[[Michel Debarbouille]], Pasteur Institute, Paris, France [http://www.pasteur.fr/ip/easysite/go/03b-00000m-0ob/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-des-bacteries-pathogenes-a-gram-positif/les-membres-de-l-equipe Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 118:
 
=References=
 
=References=
  
 
# Ali, N. O., Bignon, J., Rapoport, G., and Débarbouillé, M. (2001) Regulation of the acetoin catabolic pathway is controlled by sigma L in Bacillus subtilis. J. Bacteriol. 183, 2497-2504. [http://www.ncbi.nlm.nih.gov/sites/entrez/11274109  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 01:44, 30 April 2009

  • Description: two-component response regulator

Gene name yfiK
Synonyms
Essential no
Product two-component response regulator
Function unknown
MW, pI 24 kDa, 4.671
Gene length, protein length 660 bp, 220 aa
Immediate neighbours yfiJ, yfiL
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YfiK context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

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:
  • Interactions:
  • Localization: Cytoplasm

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • 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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed