Difference between revisions of "Sandbox"

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* '''Description:''' 2-oxoglutarate dehydrogenase (E1 subunit) <br/><br/>
+
* '''Description:''' 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 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'''
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|''odhA''
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|''odhB''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citK ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citM ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || 2-oxoglutarate dehydrogenase (E1 subunit)  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 2-oxoglutarate dehydrogenase complex
 +
(dihydrolipoamide transsuccinylase, E2 subunit)  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle  
 
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 105 kDa, 5.871  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 4.859  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2823 bp, 941 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1251 bp, 417 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yojO]], [[odhB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[odhA]], [[yocS]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
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|-
 
|-
 
|-
 
|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:odhA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:odhB_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/><br/><br/>
  
 
=The gene=
 
=The gene=
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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/odhAB.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/odhAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10272]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10273]
  
 
=== Additional information===
 
=== Additional information===
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19370]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19360]
  
−
* '''E.C. number:''' 1.2.4.2
+
* '''E.C. number:''' 2.3.1.61
  
 
=== Additional information===
 
=== Additional information===
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* '''Sigma factor:''' [[SigA]]
 
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:''' constitutive
+
* '''Regulation:''' repressed by glucose (2.4-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  constitutive
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP671 (spc), GP665 (aphA3), GP684 (cat), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
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=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]
 +
# 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]
 +
# Kobayashi et al. (2003) Essential ''Bacillus subtilis'' genes. Proc. Natl. Acad. Sci. USA 100: 4678-4683. [http://www.ncbi.nlm.nih.gov/pubmed/12682299 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 14:18, 15 April 2009

  • Description: 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit)

Gene name odhB
Synonyms citM
Essential yes PubMed
Product 2-oxoglutarate dehydrogenase complex

(dihydrolipoamide transsuccinylase, E2 subunit)

Function TCA cycle
MW, pI 45 kDa, 4.859
Gene length, protein length 1251 bp, 417 aa
Immediate neighbours odhA, yocS
Hier soll was neues rein
Genetic context
OdhB 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: membrane associated PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number: 2.3.1.61

Additional information

Expression and regulation

  • Regulation: repressed by glucose (2.4-fold) (CcpA) PubMed, constitutive
  • Regulatory mechanism: CcpA: transcription repression
  • 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. 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 PubMed
  2. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  3. Kobayashi et al. (2003) Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. USA 100: 4678-4683. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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