Difference between revisions of "Sandbox"

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* '''Description:''' malate dehydrogenase <br/><br/>
+
* '''Description:''' acetyl-CoA carboxylase (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'''
|''mdh''
+
|''accA''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || acetyl-CoA carboxylase (alpha subunit))
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || production of malonyl-CoA, the substrate for fatty acid biosynthesis
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 6.087  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 975 bp, 325 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[icd]], [[phoP]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pfkA]]'', ''[[accD]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14872&#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:CAB14880&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:mdh_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:accA_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 29: Line 29:
 
__TOC__
 
__TOC__
  
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 38: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/accDA.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12557]
  
 
=== Additional information===
 
=== Additional information===
Line 72: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
* '''Localization:''' Cytoplasm membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]  
+
* '''Localization:''' Cytoplasm Membrane-proximal (Spotty) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')
+
* '''Structure:'''
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29120]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29200]
  
* '''E.C. number:''' 1.1.1.37
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
 +
 +
=Expression and regulation=
  
 
* '''Operon:'''  
 
* '''Operon:'''  
**''[[citZ]]-[[icd]]-[[mdh]]''
 
**''[[icd]]-[[mdh]]''
 
 
* '''Sigma factor:''' [[SigA]]
 
  
* '''Regulation:''' ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
+
* '''[[Sigma factor]]:'''  
''[[mdh]]'': constitutive
 
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpC]]: transcription repression
 
  
 +
* '''Regulation:'''
  
 +
* '''Regulatory mechanism:'''
  
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
* '''Mutant:''' GP719 (spc), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 120: Line 120:
 
=References=
 
=References=
  
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
# Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in ''Bacillus subtilis'': identification of new proteins at the DNA replication factory ''Proteomics'' '''6:''' 2135-2146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 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 03:14, 30 April 2009

  • Description: acetyl-CoA carboxylase (alpha subunit)

Gene name accA
Synonyms
Essential yes PubMed
Product acetyl-CoA carboxylase (alpha subunit))
Function production of malonyl-CoA, the substrate for fatty acid biosynthesis
MW, pI 36 kDa, 6.087
Gene length, protein length 975 bp, 325 aa
Immediate neighbours pfkA, accD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AccA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

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:
  • Interactions:
  • Localization: Cytoplasm Membrane-proximal (Spotty) PubMed

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. Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory Proteomics 6: 2135-2146. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed