Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' anti-[[SigW]] <br/><br/>
+
* '''Description:''' 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'''
−
|''rsiW''
+
|''skfA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbM''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybcO''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || anti-[[SigW]]
+
|style="background:#ABCDEF;" align="center"| '''Product''' || spore killing factor
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[SigW]] activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || killing of sister cells
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 6.646  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 10.648  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 624 bp, 208 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 165 bp, 55 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sigW]]'', ''[[ybbP]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybcM]]'', ''[[skfB]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11950&#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:CAB11984&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ybcO_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ybbM_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 37: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU01740
+
* '''Locus tag:''' BSU01910
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sigW-ybbM.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/skf.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11574]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12713]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' anti-sigma-W factor family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 72: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[PrsW]]-[[RsiW]],  [[RasP]]-[[RsiW]],  [[RsiW]]-[[SigW]]
+
* '''Interactions:'''
  
−
* '''Localization:''' membrane (according to Swiss-Prot)
+
* '''Localization:''' secreted (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
Line 80: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q45588 Q45588]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31422 O31422]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU01740]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU01910]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[skfA]]-[[skfB]]-[[skfC]]-[[skfD]]-[[skfE]]-[[skfF]]-[[skfG]]-[[skfH]]'' [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/16452424 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose (33-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
−
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12076816 PubMed]
+
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12076816 PubMed]
+
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
  
−
* '''Additional information:'''  the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
+
* '''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]
 +
** The mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
  
 
=Biological materials =
 
=Biological materials =
Line 117: Line 118:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Thomas Wiegert]], University of Bayreuth, Germany [http://www.genetik.uni-bayreuth.de/LSGenetik1/Thomas%20Wiegert-Dateien/Thomas%20Wiegert.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 124: Line 123:
 
=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 13:45, 11 June 2009

  • Description: spore killing factor

Gene name skfA
Synonyms ybcO
Essential no
Product spore killing factor
Function killing of sister cells
MW, pI 5 kDa, 10.648
Gene length, protein length 165 bp, 55 aa
Immediate neighbours ybcM, skfB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YbcO context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU01910

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: secreted (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: repressed by glucose (33-fold) PubMed
  • 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
    • The mRNA is very stable (half-life > 15 min) PubMed

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

Hans-Matti Blencke, Georg Homuth, Holger Ludwig, Ulrike Mäder, Michael Hecker, Jörg Stülke
Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways.
Metab Eng: 2003, 5(2);133-49
[PubMed:12850135] [WorldCat.org] [DOI] (P p)

  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
Retrieved from "http://subtiwiki-test.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=90942"