Difference between revisions of "Sandbox"

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−
* '''Description:''' competence transcription factor (CTF) <br/><br/>
+
* '''Description:''' D-alanyl-aminopeptidase <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'''
−
|''comK''
+
|''dppA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dciAA ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || competence transcription factor (CTF)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || D-alanyl-aminopeptidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of competence and DNA uptake
+
|style="background:#ABCDEF;" align="center"|'''Function''' || degradation of cell wall peptides
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 7.669  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 5.19  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 576 bp, 192 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 822 bp, 274 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhzC]]'', ''[[yhxD]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[proG]]'', ''[[dppB]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12882&#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:CAB13149&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:comK_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:dppA_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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__TOC__
 
__TOC__
  
−
<br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU10420
+
* '''Locus tag:''' BSU12920
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/comK.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dppABCDE.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11059]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10842]
  
 
=== Additional information===
 
=== Additional information===
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:'''
+
* '''Protein family:''' peptidase M55 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[MecA]]-[[ComK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/10447896 PubMed]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
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=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1HI9 1HI9]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P40396 P40396]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P26902 P26902]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10420]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU12920]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[dppA]]-[[dppB]]-[[dppC]]-[[dppD]]-[[dppE]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/1766371 PubMed]
 +
 +
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1766371 PubMed]
  
−
* '''[[Sigma factor]]:'''
+
* '''Regulation:''' repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1766371PubMed] repressed by glucose (2.9-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], expressed postexponentially ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1766371 PubMed], repressed by [[CodY]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
  
−
* '''Regulation:''' repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12586407PubMed] repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]   
+
* '''Regulatory mechanism:''' [[AbrB]]:  transcription repression [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1766371 PubMed], [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed1]  [http://www.ncbi.nlm.nih.gov/sites/entrez/18083814 PubMed2]
  
−
* '''Regulatory mechanism:''' [[AbrB]]:  transcription repression
+
* '''Additional information:'''
−
 
 
−
* '''Additional information:'''  
 
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Oscar Kuipers]], University of Groningen, The Netherlands
 
−
[http://molgen.biol.rug.nl/molgen/index.php Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed> 10447896, 12028382, 8016067, 10361283, 11703662, 12107147, 17581123, 17493123,16391071,16436435 </pubmed>
+
<pubmed>12850135 16493705, </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]
 +
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 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 19:28, 10 June 2009

  • Description: D-alanyl-aminopeptidase

Gene name dppA
Synonyms dciAA
Essential no
Product D-alanyl-aminopeptidase
Function degradation of cell wall peptides
MW, pI 30 kDa, 5.19
Gene length, protein length 822 bp, 274 aa
Immediate neighbours proG, dppB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
DppA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU12920

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: peptidase M55 family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylated on ser/ thr/ tyr PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: repressed during logrithmic growth (AbrB) [4] repressed by glucose (2.9-fold) PubMed, expressed postexponentially (AbrB) PubMed, repressed by CodY PubMed
  • 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

Alain Lévine, Françoise Vannier, Cédric Absalon, Lauriane Kuhn, Peter Jackson, Elaine Scrivener, Valérie Labas, Joëlle Vinh, Patrick Courtney, Jérôme Garin, Simone J Séror
Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes.
Proteomics: 2006, 6(7);2157-73
[PubMed:16493705] [WorldCat.org] [DOI] (P p)

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. Lévine et al. (2006) Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6: 2157-2173 PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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