Difference between revisions of "SkfD"

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m (YbcT moved to SkfD)
(→‎Extended information on the protein)
 
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* '''Description:''' write here <br/><br/>
+
* '''Description:''' This gene has been deleted due to its merger with ''[[skfC]]'' according to Barbe et al. (2009) <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'''
−
|''ybcT''
+
|''skfD''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''skfD''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybcT''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' ||  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' ||
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 7.198   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 7.198   
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 933 bp, 311 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' ||  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
−
|-
 
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ybcT_nucleotide.txt    Gene sequence      (+200bp)  ]'''
 
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ybcT_protein.txt Protein sequence]'''
 
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ybcT_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ybcT_context.gif]]
 +
<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 ===
  
−
* '''Coordinates:'''
+
* '''Locus tag:''' BSU01940
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ybcT.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/skf.html]
  
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12717]
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12717]
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''[[SubtInteract|Interactions]]:'''
  
−
* '''Localization:'''
+
* '''[[Localization]]:''' membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:'''
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/O31426 O31426]
  
−
* '''KEGG entry:'''
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01940]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[skfA]]-[[skfB]]-[[skfC]]-[[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:'''  
 +
** expressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647,15687200 PubMed]
 +
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[Spo0A]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647,15687200 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]]-[[skfE]]-[[skfF]]-[[skfG]]-[[skfH]]'' transcript. [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
 +
==Reviews==
 +
<pubmed>20955377 </pubmed>
 +
==Original Publications==
 +
<pubmed>12817086,15812018,,16816204,14651647,15687200,15687200,17720793,17449691,18840696  </pubmed>
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
[[Category:Protein-coding genes]]

Latest revision as of 20:48, 19 December 2011

  • Description: This gene has been deleted due to its merger with skfC according to Barbe et al. (2009)

Gene name skfD
Synonyms ybcT
Essential no
Product unknown
Function
MW, pI 34 kDa, 7.198
Gene length, protein length
Immediate neighbours
Genetic context
YbcT context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU01940

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:

Database entries

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

Additional information

Expression and regulation

  • Regulation:
    • expressed under conditions that trigger sporulation (Spo0A) PubMed
    • repressed during logrithmic growth (AbrB) 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-skfE-skfF-skfG-skfH transcript. PubMed

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

Reviews

José Eduardo González-Pastor
Cannibalism: a social behavior in sporulating Bacillus subtilis.
FEMS Microbiol Rev: 2011, 35(3);415-24
[PubMed:20955377] [WorldCat.org] [DOI] (I p)

Original Publications

Allison V Banse, Arnaud Chastanet, Lilah Rahn-Lee, Errett C Hobbs, Richard Losick
Parallel pathways of repression and antirepression governing the transition to stationary phase in Bacillus subtilis.
Proc Natl Acad Sci U S A: 2008, 105(40);15547-52
[PubMed:18840696] [WorldCat.org] [DOI] (I p)

Mark A Strauch, Benjamin G Bobay, John Cavanagh, Fude Yao, Angelo Wilson, Yoann Le Breton
Abh and AbrB control of Bacillus subtilis antimicrobial gene expression.
J Bacteriol: 2007, 189(21);7720-32
[PubMed:17720793] [WorldCat.org] [DOI] (P p)

Akihito Ochiai, Takafumi Itoh, Akiko Kawamata, Wataru Hashimoto, Kousaku Murata
Plant cell wall degradation by saprophytic Bacillus subtilis strains: gene clusters responsible for rhamnogalacturonan depolymerization.
Appl Environ Microbiol: 2007, 73(12);3803-13
[PubMed:17449691] [WorldCat.org] [DOI] (P p)

Nicholas E E Allenby, Carys A Watts, Georg Homuth, Zoltán Prágai, Anil Wipat, Alan C Ward, Colin R Harwood
Phosphate starvation induces the sporulation killing factor of Bacillus subtilis.
J Bacteriol: 2006, 188(14);5299-303
[PubMed:16816204] [WorldCat.org] [DOI] (P p)

Helga Westers, Peter G Braun, Lidia Westers, Haike Antelmann, Michael Hecker, Jan D H Jongbloed, Hirofumi Yoshikawa, Teruo Tanaka, Jan Maarten van Dijl, Wim J Quax
Genes involved in SkfA killing factor production protect a Bacillus subtilis lipase against proteolysis.
Appl Environ Microbiol: 2005, 71(4);1899-908
[PubMed:15812018] [WorldCat.org] [DOI] (P p)

Masaya Fujita, José Eduardo González-Pastor, Richard Losick
High- and low-threshold genes in the Spo0A regulon of Bacillus subtilis.
J Bacteriol: 2005, 187(4);1357-68
[PubMed:15687200] [WorldCat.org] [DOI] (P p)

Virginie Molle, Masaya Fujita, Shane T Jensen, Patrick Eichenberger, José E González-Pastor, Jun S Liu, Richard Losick
The Spo0A regulon of Bacillus subtilis.
Mol Microbiol: 2003, 50(5);1683-701
[PubMed:14651647] [WorldCat.org] [DOI] (P p)

José E González-Pastor, Errett C Hobbs, Richard Losick
Cannibalism by sporulating bacteria.
Science: 2003, 301(5632);510-3
[PubMed:12817086] [WorldCat.org] [DOI] (I p)

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