Difference between revisions of "Sandbox"

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* '''Description:''' spore killing factor <br/><br/>
+
* '''Description:''' synthesis of spore killing factor <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'''
|''skfA''
+
|''skfB''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybcO''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybcP, ybcQ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || spore killing factor
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || killing of sister cells
+
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of spore killing factor
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 10.648  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 4.934  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 165 bp, 55 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1230 bp, 410 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybcM]]'', ''[[skfB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[skfA]]'', ''[[skfC]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11984&#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:CAB11985&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:ybcO_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ybcP_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:''' BSU01910
+
* '''Locus tag:''' BSU01920
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/skf.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/skf.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12713]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12714]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
* '''Protein family:'''
+
* '''Protein family:''' moaA/nifB/pqqE family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
* '''Localization:''' secreted (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31422 O31422]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31423 O31423]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU01910]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU01920]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/16452424 PubMed]
 
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/16452424 PubMed]
  
* '''Regulation:''' repressed by glucose (33-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
+
* '''Regulation:'''  
 
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
 
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
  
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** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
 
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
  
* '''Additional information:'''
+
* '''Additional information:''' Northern blotting during during phosphate limitation showed an intense 0.25 kb ''skfA''-specific transcript, and a weaker 6.5 kb ''[[skfA]]-[[skfB]]-[[skfC]]-[[skfD]]-[[skfE]]-[[skfF]]-[[skfG]]-[[skfH]]'' transcript. The ''[[skfA]]'' transcript is stabilized by a stem-loop structure in the ''[[skfA]]-[[skfB]]'' intergenic region. [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
** Northern blotting during during phosphate limitation showed an intense 0.25 kb ''skfA''-specific transcript, and a weaker 6.5 kb ''[[skfA]]-[[skfB]]-[[skfC]]-[[skfD]]-[[skfE]]-[[skfF]]-[[skfG]]-[[skfH]]'' transcript.  
 
** The ''[[skfA]]'' transcript is stabilized by a stem-loop structure in the ''[[skfA]]-[[skfB]]'' intergenic region. [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
 
**  The mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
 
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
<pubmed>12850135, </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 13:47, 11 June 2009

  • Description: synthesis of spore killing factor

Gene name skfB
Synonyms ybcP, ybcQ
Essential no
Product unknown
Function synthesis of spore killing factor
MW, pI 45 kDa, 4.934
Gene length, protein length 1230 bp, 410 aa
Immediate neighbours skfA, skfC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YbcP context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU01920

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: moaA/nifB/pqqE 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

  • Regulation:
  • Regulatory mechanism:
  • Additional information: Northern blotting during during phosphate limitation showed an intense 0.25 kb skfA-specific transcript, and a weaker 6.5 kb skfA-skfB-skfC-skfD-skfE-skfF-skfG-skfH transcript. The skfA transcript is stabilized by a stem-loop structure in the skfA-skfB intergenic region. PubMed

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed