Difference between revisions of "Sandbox"

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* '''Description:''' preprotein translocase subunit <br/><br/>
+
* '''Description:''' phosphoglycerate dehydrogenase <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'''
−
|''secY''
+
|''serA''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || preprotein translocase subunit
+
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglycerate dehydrogenase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || protein secretion
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of serine
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 10.209  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.617  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1293 bp, 431 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1575 bp, 525 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rplO]]'', ''[[adk]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ypzE]]'', ''[[aroC]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11912&#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:CAB14239&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:secY_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:serA_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU01360
+
* '''Locus tag:''' BSU23070
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
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/serA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10445]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10509]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' 3-phospho-D-glycerate + NAD<sup>+</sup> = 3-phosphonooxypyruvate + NADH (according to Swiss-Prot)
  
−
* '''Protein family:''' secY/SEC61-alpha family (according to Swiss-Prot)
+
* '''Protein family:''' D-isomer specific 2-hydroxyacid dehydrogenase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 66: Line 64:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' S-cysteinylation after diamide stress (C410)[http://www.ncbi.nlm.nih.gov/sites/entrez/17611193 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[SecA]]-[[SecY]]
+
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot),  membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]  
+
* '''Localization:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P16336 P16336]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P35136 P35136]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU01360]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23070]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.95 1.1.1.95]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''serA''
  
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =

Revision as of 13:36, 8 June 2009

  • Description: phosphoglycerate dehydrogenase

Gene name serA
Synonyms
Essential no
Product phosphoglycerate dehydrogenase
Function biosynthesis of serine
MW, pI 56 kDa, 5.617
Gene length, protein length 1575 bp, 525 aa
Immediate neighbours ypzE, aroC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SerA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU23070

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: 3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH (according to Swiss-Prot)
  • Protein family: D-isomer specific 2-hydroxyacid dehydrogenase family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: S-cysteinylation after diamide stress (C410)PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: membrane PubMed

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Operon: serA
  • 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

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

  1. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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