Difference between revisions of "Sandbox"

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−
* '''Description:''' excinuclease ABC (subunit A) <br/><br/>
+
* '''Description:''' phosphodiesterase/alkaline phosphatase <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'''
−
|''uvrA''
+
|''phoD''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ycbS ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || excinuclease ABC (subunit A)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphodiesterase/alkaline phosphatase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA repair after UV damage
+
|style="background:#ABCDEF;" align="center"|'''Function''' || aquisition of phosphate upon phosphoate starvation 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 105 kDa, 5.843  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 8.394  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2871 bp, 957 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1668 bp, 556 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvzB]]'', ''[[uvrB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ycbR]]'', ''[[tatAD]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15533&#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:CAB12056&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:uvrA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:phoD_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:''' BSU35160
+
* '''Locus tag:''' BSU02620
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/uvrBA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/phoD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12697]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11174]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' A phosphate monoester + H<sub>2</sub>O = an alcohol + phosphate (according to Swiss-Prot)
  
−
* '''Protein family:''' UvrA subfamily (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[TatAD]]-[[PhoD]]
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot)
+
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], secreted by the [[TatAD]]-[[TatCD]] complex  [http://www.ncbi.nlm.nih.gov/sites/entrez/19395490 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2R6F 2R6F] (Geobacillus stearothermophilus)
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34863 O34863]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42251 P42251]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35160]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02620]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.3.1 3.1.3.1]
  
 
=== Additional information===
 
=== Additional information===
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Oscar Kuipers]], University of Groningen, The Netherlands
 +
[http://molgen.biol.rug.nl/molgen/index.php Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
 
 +
<pubmed> 18957862, 19383693, 19395490 </pubmed>

Revision as of 13:06, 11 June 2009

  • Description: phosphodiesterase/alkaline phosphatase

Gene name phoD
Synonyms ycbS
Essential no
Product phosphodiesterase/alkaline phosphatase
Function aquisition of phosphate upon phosphoate starvation
MW, pI 62 kDa, 8.394
Gene length, protein length 1668 bp, 556 aa
Immediate neighbours ycbR, tatAD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PhoD context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU02620

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: A phosphate monoester + H2O = an alcohol + phosphate (according to Swiss-Prot)
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry: [3]

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

Oscar Kuipers, University of Groningen, The Netherlands Homepage

Your additional remarks

References

Anja N J A Ridder, Esther J de Jong, Jan D H Jongbloed, Oscar P Kuipers
Subcellular localization of TatAd of Bacillus subtilis depends on the presence of TatCd or TatCy.
J Bacteriol: 2009, 191(13);4410-8
[PubMed:19395490] [WorldCat.org] [DOI] (I p)

Robyn T Eijlander, Magdalena A Kolbusz, Erwin M Berendsen, Oscar P Kuipers
Effects of altered TatC proteins on protein secretion efficiency via the twin-arginine translocation pathway of Bacillus subtilis.
Microbiology (Reading): 2009, 155(Pt 6);1776-1785
[PubMed:19383693] [WorldCat.org] [DOI] (P p)

Birgit Voigt, Haike Antelmann, Dirk Albrecht, Armin Ehrenreich, Karl-Heinz Maurer, Stefan Evers, Gerhard Gottschalk, Jan Maarten van Dijl, Thomas Schweder, Michael Hecker
Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis.
J Mol Microbiol Biotechnol: 2009, 16(1-2);53-68
[PubMed:18957862] [WorldCat.org] [DOI] (I p)

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