Difference between revisions of "Sandbox"

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−
* '''Description:''' flagellar hook-associated protein 3 (HAP3) <br/><br/>
+
* '''Description:''' two-component sensor kinase for exoenzyme and competence regulation <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'''
−
|''flgL''
+
|''degS''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yviD ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sacU ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || flagellar hook-associated protein 3 (HAP3)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component sensor kinase (NarL family)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || movement and chemotaxis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of degradative enzyme and genetic competence
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 4.42  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 44 kDa, 5.988  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 894 bp, 298 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yviE]]'', ''[[flgK]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[degU]]'', ''[[yvyE]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15557&#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:CAB15567&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:flgL_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:degS_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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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/comFABC-yvyF-flgM-yvyG-flgKL.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/degSU.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11936]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10392]
  
 
=== Additional information===
 
=== Additional information===
Line 64: Line 64:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Ser-76 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[DegS]]-[[DegU]]
  
−
* '''Localization:''' Cytoplasm
+
* '''Localization:''' Cytoplasm Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35400]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35500]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''''' [[degS]]-[[degU]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced in the presence of ammonium ([[TnrA]])
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[TnrA]]: repression, [[DegU]]: positive autoregulation
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 113: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Tarek Msadek]], Institut Pasteur, Paris, France
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 120:
 
=References=
 
=References=
  
 +
# Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in ''Bacillus subtilis'': identification of new proteins at the DNA replication factory ''Proteomics'' '''6:''' 2135-2146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
 +
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 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 03:38, 30 April 2009

  • Description: two-component sensor kinase for exoenzyme and competence regulation

Gene name degS
Synonyms sacU
Essential no
Product two-component sensor kinase (NarL family)
Function regulation of degradative enzyme and genetic competence
MW, pI 44 kDa, 5.988
Gene length, protein length 1155 bp, 385 aa
Immediate neighbours degU, yvyE
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
DegS context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

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: phosphorylation on Ser-76 PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: Cytoplasm Cytoplasm (Homogeneous) PubMed

Database entries

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

Additional information

Expression and regulation

  • Regulation: induced in the presence of ammonium (TnrA)
  • Regulatory mechanism: TnrA: repression, DegU: positive autoregulation
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Tarek Msadek, Institut Pasteur, Paris, France

Your additional remarks

References

  1. Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory Proteomics 6: 2135-2146. PubMed
  2. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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