Difference between revisions of "Sandbox"

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* '''Description:''' dihydrolipoamide dehydrogenase E3 subunit of both pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes  <br/><br/>
+
* '''Description:''' arginine decarboxylase <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'''
|''pdhD''
+
|''speA''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citL ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cad ''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || dihydrolipoamide dehydrogenase E3 subunit<br/> of both pyruvate dehydrogenase and 2-oxoglutarate<br/> dehydrogenase complexes
+
|style="background:#ABCDEF;" align="center"| '''Product''' || arginine decarboxylase
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || links glycolysis and TCA cycle, enzyme in TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || spermidine, polyamine biosynthesis
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 4.76  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 53 kDa, 5.081  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1410 bp, 470 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1470 bp, 490 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdhC]]'', ''[[slp]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sr1]]'', ''[[yktA]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13334&#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:CAB13336&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:pdhD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:speA_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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__TOC__
 
__TOC__
  
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 38: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 
defects in sporulation and unable to grow on glucose as single carbon source [http://www.ncbi.nlm.nih.gov/pubmed/11976308 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]
+
* '''DBTBS entry:''' no entry
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10210]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10212]
  
 
=== Additional information===
 
=== Additional information===
Line 58: Line 56:
 
* '''Protein family:'''
 
* '''Protein family:'''
  
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[YaaO]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 72: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
* '''Interactions:''' [[OdhA]]-[[OdhB]]-[[PdhD]],  [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]
+
* '''Interactions:'''
  
 
* '''Localization:''' Cytoplasm
 
* '''Localization:''' Cytoplasm
Line 78: Line 76:
 
=== Database entries ===
 
=== Database entries ===
  
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EBD 1EBD] (complex with binding domain of dihydrolipoamide acetylase, ''Geobacillus stearothermophilus'')
+
* '''Structure:'''
  
* '''Swiss prot entry:'''  
+
* '''Swiss prot entry:'''
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14610]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14630]
  
* '''E.C. number:''' 1.8.1.4
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
Line 90: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:''' ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]''
+
* '''Operon:'''  
  
* '''Sigma factor:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
* '''Regulation:''' expression activated by glucose (2.0 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 118:
 
=References=
 
=References=
  
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
 
# Gao et al. (2002) The E1beta and E2 subunits of the ''Bacillus subtilis'' pyruvate dehydrogenase complex are involved in regulation of sporulation.''J. Bacteriol.'' '''184:''' 2780-2788. [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]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 02:09, 30 April 2009

  • Description: arginine decarboxylase

Gene name speA
Synonyms cad
Essential no
Product arginine decarboxylase
Function spermidine, polyamine biosynthesis
MW, pI 53 kDa, 5.081
Gene length, protein length 1470 bp, 490 aa
Immediate neighbours sr1, yktA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SpeA 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): YaaO

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