Difference between revisions of "Sandbox"

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* '''Description:''' molecular chaperone involved in protein secretion <br/><br/>
+
* '''Description:''' pyruvate dehydrogenase (E1 alpha subunit)<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'''
−
|''csaA''
+
|''pdhA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''aceA ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || molecular chaperone
+
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate dehydrogenase (E1 alpha subunit)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || protein secretion
+
|style="background:#ABCDEF;" align="center"|'''Function''' || links glycolysis and TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 8.691  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.837  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 330 bp, 110 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1113 bp, 371 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bsrF]]'', ''[[yobQ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykyA]]'', ''[[pdhB]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13796&#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:CAB13331&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:csaA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pdhA_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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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 +
 +
''pdhA'' is essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10809]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10207]
  
 
=== Additional information===
 
=== Additional information===
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[CsaA]]-[[SdpC]],  
+
* '''Interactions:''' [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]], [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 76: Line 80:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1W88 1W88] (E1 in complex with subunit binding domain of E2, ''Geobacillus stearothermophilus'')
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19040]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14580]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' 1.2.4.1
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' expression activated by glucose (3.4) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 113: Line 117:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Arthur Aronson]], Purdue University, West Lafayette, USA [http://wwwdev.gradschool.purdue.edu/PULSe/faculty.cfm?fid=5&range=0 homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 124:
 
=References=
 
=References=
  
 +
# Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. Metab. Engn. '''5:''' 133-149. [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 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 00:06, 28 April 2009

  • Description: pyruvate dehydrogenase (E1 alpha subunit)

Gene name pdhA
Synonyms aceA
Essential yes
Product pyruvate dehydrogenase (E1 alpha subunit)
Function links glycolysis and TCA cycle
MW, pI 41 kDa, 5.837
Gene length, protein length 1113 bp, 371 aa
Immediate neighbours ykyA, pdhB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PdhA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

pdhA is essential PubMed

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:
  • Localization:

Database entries

  • Structure: 1W88 (E1 in complex with subunit binding domain of E2, Geobacillus stearothermophilus)
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number: 1.2.4.1

Additional information

Expression and regulation

  • Regulation: expression activated by glucose (3.4) PubMed
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Arthur Aronson, Purdue University, West Lafayette, USA homepage

Your additional remarks

References

  1. Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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