Difference between revisions of "Sandbox"

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−
* '''Description:''' tryptophan operon RNA-binding attenuation protein (TRAP) <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'''
−
|''mtrB''
+
|''serA''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || tryptophan operon RNA-binding attenuation protein (TRAP)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglycerate dehydrogenase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of tryptophan biosynthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of serine
−
(and translation) attenuation in the trp operon);
 
−
repression of the folate operon
 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 7.333  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.617  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 225 bp, 75 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1575 bp, 525 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[hepS]]'', ''[[mtrA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ypzE]]'', ''[[aroC]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/mtrB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/serA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/mtrB_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/serA_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:mtrB_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>
 
|-
 
|-
Line 44: Line 42:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mtrAB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/serA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10278]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10509]
  
 
=== Additional information===
 
=== Additional information===
Line 57: Line 55:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' mtrB family
+
* '''Protein family:''' ACT domain
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' membrane [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+BSU22770]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23070]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 121: Line 119:
 
=References=
 
=References=
  
−
# Antson AA, Otridge J, Brzozowski AM, Dodson EJ, Dodson GG, Wilson KS, Smith TM, Yang M, Kurecki T, Gollnick P (1995) The structure of ''trp'' RNA-binding protein. Nature 374:693-700. [http://www.ncbi.nlm.nih.gov/sites/entrez/7715723 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]
−
# Antson AA, Dodson EJ, Dodson G, Greaves RB, Chen XP, Gollnick P (1999) Structure of the ''trp'' RNA-binding attenuation protein, TRAP, bound to RNA. Nature 401:235-242. [http://www.ncbi.nlm.nih.gov/sites/entrez/10499579 PubMed]
 
−
# Babitzke P, Gollnick P (2001) Posttransription iniation control of tryptophan metabolism in ''Bacillus subtilis'' by the trp RNA-binding attenuation protein (TRAP), anti-TRAP, and RNA structure. J Bacteriol 183:5795-5802. [http://www.ncbi.nlm.nih.gov/sites/entrez/11566976 PubMed]
 
−
# Babitzke P, Stults JT, Shire SJ, Yanofsky C (1994) TRAP, the trp RNA-binding attenuation protein of ''Bacillus subtilis'', is a multisubunit complex that appears  to recognize G/UAG repeats in the ''trpEDCFBA'' and ''trpG'' transcripts. J Biol Chem 269:16597-16604. [http://www.ncbi.nlm.nih.gov/sites/entrez/7515880 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 05:21, 12 April 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
Gene sequence (+200bp) Protein sequence
Genetic context
SerA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: ACT domain
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: membrane 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. 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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