Difference between revisions of "Sandbox"

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−
* '''Description:''' zinc transport in via ABC system <br/><br/>
+
* '''Description:''' general stress protein, similar to tellurium resistance protein <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'''
−
|''ycdH''
+
|''yceE''
 
|-
 
|-
 
|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''' || zinc transport in via ABC system (binding protein)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || zinc uptake
+
|style="background:#ABCDEF;" align="center"|'''Function''' || required for survival of ethanol stress and <br/>at low temperatures
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 5.146  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 4.391  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 957 bp, 319 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 576 bp, 192 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ycdG]]'', ''[[ycdI]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yceD]]'', ''[[yceF]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12079&#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:CAB12085&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ycdH_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yceE_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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__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/>
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU02850
+
* '''Locus tag:''' BSU02910
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ycdHI-yceA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yceCDEFGH.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12763]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12769]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' bacterial solute-binding protein 9 family (according to Swiss-Prot)
+
* '''Protein family:''' CAPAB/terDEXZ family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[MntA]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot),  extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed],  membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2O1E 2O1E]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34966 O34966]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34384 O34384]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02850]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02910]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[yceC]]-[[yceD]]-[[yceE]]-[[yceF]]-[[yceG]]-[[yceH]]'' [http://www.ncbi.nlm.nih.gov/pubmed/11866510 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>18957862 18763711, </pubmed>
+
<pubmed>15805528, </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]
+
# H&ouml;per et al. (2005) Comprehensive Characterization of the Contribution of Individual [[SigB]]-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 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]
 
 
# 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 13:42, 8 June 2009

  • Description: general stress protein, similar to tellurium resistance protein

Gene name yceE
Synonyms
Essential no
Product unknown
Function required for survival of ethanol stress and
at low temperatures
MW, pI 20 kDa, 4.391
Gene length, protein length 576 bp, 192 aa
Immediate neighbours yceD, yceF
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YceE context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Locus tag: BSU02910

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: CAPAB/terDEXZ family (according to Swiss-Prot)
  • 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

  • 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. Höper et al. (2005) Comprehensive Characterization of the Contribution of Individual SigB-Dependent General Stress Genes to Stress Resistance of Bacillus subtilis. J. Bact. 187: 2810-2826 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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