Difference between revisions of "Sandbox"

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−
* '''Description:''' phytase <br/><br/>
+
* '''Description:''' involved in polyketide synthesis <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'''
−
|''phy''
+
|''pksE''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yodV, yzxA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || 3-phytase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || untilization of inositol hexakisphosphate (phytate)
+
|style="background:#ABCDEF;" align="center"|'''Function''' || polyketide synthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.936  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 85 kDa, 7.376  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1146 bp, 382 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2301 bp, 767 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cgeB]]'', ''[[yodU]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pksD]]'', ''[[acpK]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13871&#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:CAB13584&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:phy_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pksE_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:''' BSU19800
+
* '''Locus tag:''' BSU17120
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/phy.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11198]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12651]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Myo-inositol hexakisphosphate + H<sub>2</sub>O = 1D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' msrA Met sulfoxide reductase family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1QLG 1QLG] (enzyme from B. amyloliquefaciens, 72% identity)
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42094 P42094]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19800]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17120]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.3.8 3.1.3.8]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose (6-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
Line 118: Line 118:
 
=References=
 
=References=
  
−
<pubmed>18957862, </pubmed>
+
<pubmed>12850135, </pubmed>
−
# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
# 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]
 
# 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 13:29, 8 June 2009

  • Description: involved in polyketide synthesis

Gene name pksE
Synonyms
Essential no
Product unknown
Function polyketide synthesis
MW, pI 85 kDa, 7.376
Gene length, protein length 2301 bp, 767 aa
Immediate neighbours pksD, acpK
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PksE context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU17120

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

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:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation: repressed by glucose (6-fold) PubMed
  • 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. 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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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