Difference between revisions of "Sandbox"

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Line 1: Line 1:
−
* '''Description:''' general stress protein, survival of ethanol  stress, spore coat protein <br/><br/>
+
* '''Description:''' similar to erythromycin esterase <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'''
−
|''yaaH''
+
|''ybfO''
 
|-
 
|-
 
|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''' || spore coat protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || survival of ethanol  stress
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.618  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 6.678  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1281 bp, 427 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1338 bp, 446 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dgk]]'', ''[[yaaI]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybfN]]'', ''[[ybfP]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11792&#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:CAB12025&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yaaH_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ybfO_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:''' BSU00160
+
* '''Locus tag:''' BSU02310
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaH.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ybfO.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10080]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12743]
  
 
=== Additional information===
 
=== Additional information===
Line 72: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' spore wall (according to Swiss-Prot),  spore coat [http://www.ncbi.nlm.nih.gov/sites/entrez/11964120 PubMed]
+
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 78: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37531 P37531]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00160]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02310]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
−
required for survival of ethanol stress [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''yaaH'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10419957 PubMed]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigE]] [http://www.ncbi.nlm.nih.gov/sites/entrez/10419957 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed], expressed during sporulation [http://www.ncbi.nlm.nih.gov/sites/entrez/10419957 PubMed]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 118:
 
=References=
 
=References=
  
−
<pubmed>15805528 10419957 15805528 11964120, </pubmed>
+
<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]
+
# 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]
−
# Kodama et al. (1999) The ''Bacillus subtilis yaaH'' gene is transcribed by SigE RNA polymerase during sporulation, and its product is involved in germination of spores.''J. Bacteriol.'' '''181:''' 4584-4591. [http://www.ncbi.nlm.nih.gov/sites/entrez/10419957 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Höper et al. (2005) Comprehensive characterization of the contribution of individual SigB-dependent general stress genes to stress resistance of ''Bacillus subtilis''.''J.Bacteriol.'' '''187:''' 2810-2826. [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
 
−
# Aronson (2002) Sporulation and delta-endotoxin synthesis by ''Bacillus thuringiensis''.''Cell. Mol. Life Sci.'' '''59:''' 417-425. [http://www.ncbi.nlm.nih.gov/sites/entrez/11964120 PubMed]
 

Revision as of 13:42, 8 June 2009

  • Description: similar to erythromycin esterase

Gene name ybfO
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 51 kDa, 6.678
Gene length, protein length 1338 bp, 446 aa
Immediate neighbours ybfN, ybfP
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YbfO context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU02310

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: extracellular (signal peptide) 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. Voigt et al. (2009) Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis. J Mol Microbiol Biotechnol. 16: 53-68 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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