Difference between revisions of "Sandbox"

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* '''Description:''' similar to to ribosomal-protein-alanine N-acetyltransferase <br/><br/>
+
* '''Description:''' transcriptional repressor of anaerobically expressed genes involved in anaerobic respiration and fermentation <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'''
|''ydiD''
+
|''rex''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydiH''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of fermentation and anaerobic respiration
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 5.673  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 6.772  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 453 bp, 151 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 645 bp, 215 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydiC]]'', ''[[gcp]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydiG]]'', ''[[tatAY]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12412&#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:CAB13085&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:ydiD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ydiH_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 43: Line 43:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12201]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12205]
  
 
=== Additional information===
 
=== Additional information===
Line 57: Line 57:
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
=== Genes/ operons controlled by Rex ===
 +
 +
''[[alsS]]-[[alsD]]'', ''[[cydA]]-[[cydB]]-[[cydC]]-[[cydD]]'', ''[[ldh]]-[[lctP]]'', ''[[ywcJ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16207915 PubMed]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 68: Line 72:
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' NADH (indication of low oxygen concentration) releases Rex from DNA [http://www.ncbi.nlm.nih.gov/sites/entrez/18485070 PubMed]
  
 
* '''Interactions:'''
 
* '''Interactions:'''
Line 80: Line 84:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05930]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05970]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 113: Line 117:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Claes von Wachenfeldt]], Lund University, Sweden [http://aron.ldc.lu.se/kundwebb/cellorg/mibiol/research/wachen/index.htm Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=

Revision as of 01:35, 30 April 2009

  • Description: transcriptional repressor of anaerobically expressed genes involved in anaerobic respiration and fermentation

Gene name rex
Synonyms ydiH
Essential no
Product transcriptional repressor
Function regulation of fermentation and anaerobic respiration
MW, pI 23 kDa, 6.772
Gene length, protein length 645 bp, 215 aa
Immediate neighbours ydiG, tatAY
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YdiH context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

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):

Genes/ operons controlled by Rex

alsS-alsD, cydA-cydB-cydC-cydD, ldh-lctP, ywcJ PubMed

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity: NADH (indication of low oxygen concentration) releases Rex from DNA PubMed
  • Interactions:
  • Localization: Cytoplasm

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

Claes von Wachenfeldt, Lund University, Sweden Homepage

Your additional remarks

References

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