Difference between revisions of "Sandbox"

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−
* '''Description:''' UDP glucose 6-dehydrogenase <br/><br/>
+
* '''Description:''' toxic peptide <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'''
−
|''tuaD''
+
|''txpA ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvhD ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqcR, yqdB''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || UDP glucose 6-dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || toxic peptide
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of teichuronic acid
+
|style="background:#ABCDEF;" align="center"|'''Function''' || toxin
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 6.107  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 8.139  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1383 bp, 461 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 177 bp, 59 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tuaE]]'', ''[[tuaC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqbN]]'', ''[[ratA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15575&#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:CAB14546&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:tuaD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yqdB_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 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU35580
+
* '''Locus tag:''' BSU26050
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/tuaABCDEFGH.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/txpA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12691]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11512]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' UDP-glucose + 2 NAD<sup>+</sup> + H<sub>2</sub>O = UDP-glucuronate + 2 NADH (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' UDP-glucose/GDP-mannose dehydrogenase family (according to Swiss-Prot)
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[YtcA]], [[YwqF]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on a Tyr residue by [[PtkA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' [[PtkA]]-dependent phosphorylation stimulates TuaD activity [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
+
* '''Effectors of protein activity:'''
  
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32271 O32271]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54373 P54373]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35580]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU26050]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.22 1.1.1.22]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''txpA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16166525 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16166525 PubMed]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' expression is prevented by the ''[[ratA]]'' antisense RNA [http://www.ncbi.nlm.nih.gov/sites/entrez/16166525 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 113: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Richard Losick]], Harvard University, Cambridge, USA [http://www.mcb.harvard.edu/Losick/ Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>12970183, </pubmed>
+
<pubmed>16166525, </pubmed>
−
# Mijakovic I, Poncet S, Boël G, Mazé A, Gillet S, Decottignies P, Grangeasse C, Jamet E, Doublet P, Le Maréchal P, Deutscher J (2003) Transmembrane modulator-dependent bacterial tyrosine kinase activates UDP-glucose dehydrogenases. EMBO J 22:4709-4718. [http://www.ncbi.nlm.nih.gov/sites/entrez/12970183 PubMed]
+
# Silvaggi JM, Perkins JB, Losick R (2005) Small untranslated RNA antitoxin in ''Bacillus subtilis''.''J. Bacteriol.'' '''187:''' 6641-6650. [http://www.ncbi.nlm.nih.gov/sites/entrez/16166525 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 13:41, 8 June 2009

  • Description: toxic peptide

Gene name txpA
Synonyms yqcR, yqdB
Essential no
Product toxic peptide
Function toxin
MW, pI 6 kDa, 8.139
Gene length, protein length 177 bp, 59 aa
Immediate neighbours yqbN, ratA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YqdB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU26050

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:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

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

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism: expression is prevented by the ratA antisense RNA PubMed
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Richard Losick, Harvard University, Cambridge, USA Homepage

Your additional remarks

References

Jessica M Silvaggi, John B Perkins, Richard Losick
Small untranslated RNA antitoxin in Bacillus subtilis.
J Bacteriol: 2005, 187(19);6641-50
[PubMed:16166525] [WorldCat.org] [DOI] (P p)

  1. Silvaggi JM, Perkins JB, Losick R (2005) Small untranslated RNA antitoxin in Bacillus subtilis.J. Bacteriol. 187: 6641-6650. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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