Difference between revisions of "Sandbox"

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−
* '''Description:''' D-alanyl-aminopeptidase <br/><br/>
+
* '''Description:''' bacteriocin-like product <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'''
−
|''dppA''
+
|''sboX''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dciAA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || D-alanyl-aminopeptidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || bacteriocin-like product
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || degradation of cell wall peptides
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 5.19  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 9.857  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 822 bp, 274 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 150 bp, 50 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[proG]]'', ''[[dppB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sboA]]'', ''[[albA]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAE01468&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sboX_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU12920
+
* '''Locus tag:''' BSU37360
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dppABCDE.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sboAX-albABCDEFG.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10842]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14182]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' peptidase M55 family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1HI9 1HI9]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P26902 P26902]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q7WY57 Q7WY57]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU12920]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37360]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[dppA]]-[[dppB]]-[[dppC]]-[[dppD]]-[[dppE]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/1766371 PubMed]
+
* '''Operon:''' ''[[sboA]]-[[sboX]]-[[albA]]-[[albB]]-[[albC]]-[[albD]]-[[albE]]-[[albF]]-[[albG]]''
−
+
 
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1766371 PubMed]
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:''' repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1766371,  PubMed] 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/10572140 PubMed]  
  
−
* '''Regulatory mechanism:''' [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1766371,  PubMed] [[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 [http://www.ncbi.nlm.nih.gov/sites/entrez/10572140 PubMed]  
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=References=
 
=References=
  
−
<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 21:11, 10 June 2009

  • Description: bacteriocin-like product

Gene name sboX
Synonyms
Essential no
Product bacteriocin-like product
Function unknown
MW, pI 5 kDa, 9.857
Gene length, protein length 150 bp, 50 aa
Immediate neighbours sboA, albA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SboX context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU37360

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:

Database entries

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

Additional information

Expression and regulation

  • Regulation: repressed during logrithmic growth (AbrB) PubMed
  • Regulatory mechanism: AbrB: transcription repression 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

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