Difference between revisions of "Sandbox"

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−
* '''Description:''' late competence operon required for DNA binding and uptake <br/><br/>
+
* '''Description:''' DNA transport machinery <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'''
−
|''comEC''
+
|''comGB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''comD ''
+
|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''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA transport machinery
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || compentence
+
|style="background:#ABCDEF;" align="center"|'''Function''' || competence, DNA uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 86 kDa, 6.964  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 8.654  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2328 bp, 776 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 969 bp, 323 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[holA]]'', ''[[comEB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[comGC]]'', ''[[comGA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14499&#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:CAB14403&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:comEC_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:comGB_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:''' BSU25570
+
* '''Locus tag:''' BSU24720
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/comEABC.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/comGABCDEFG-yqzE.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10482]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10484]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:'''
+
* '''Protein family:''' GSP F family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cell surface (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39695 P39695]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P25954 P25954]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25570]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU24720]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[comEA]]-[[comEB]]-[[comEC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7968523 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/19028902 PubMed2]
+
* '''Operon:''' ''[[comGA]]-[[comGB]]-[[comGC]]-[[comGD]]-[[comGE]]-[[comGF]]-[[comGG]]'' [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] 
  
−
* '''Regulatory mechanism:''' post-translational control by [[ComN]], ''[[yutB]]'' is required for transcription [http://www.ncbi.nlm.nih.gov/sites/entrez/19028902 PubMed]
+
* '''Regulatory mechanism:'''  
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 118: Line 118:
 
=References=
 
=References=
  
−
<pubmed>19028902, </pubmed>
+
<pubmed>12107147, </pubmed>
−
# Ogura, M. and T. Tanaka (2009) The ''Bacillus subtilis'' Late Competence Operon ''comE'' Is Transcriptionally Regulated by ''yutB'' and under Post-Transcription Initiation Control by ''comN'' (''yrzD'') ''J. Bacteriol.'' '''191:''' 949-958. [http://www.ncbi.nlm.nih.gov/sites/entrez/19028902 PubMed]
+
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 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 13:59, 8 June 2009

  • Description: DNA transport machinery

Gene name comGB
Synonyms
Essential no
Product DNA transport machinery
Function competence, DNA uptake
MW, pI 36 kDa, 8.654
Gene length, protein length 969 bp, 323 aa
Immediate neighbours comGC, comGA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ComGB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU24720

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: GSP F family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cell surface (according to Swiss-Prot)

Database entries

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

Additional information

Expression and regulation

  • Regulation: repressed by casamino acids PubMed
  • Regulatory mechanism:
  • 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

Ulrike Mäder, Georg Homuth, Christian Scharf, Knut Büttner, Rüdiger Bode, Michael Hecker
Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability.
J Bacteriol: 2002, 184(15);4288-95
[PubMed:12107147] [WorldCat.org] [DOI] (P p)

  1. Mäder et al. (2002) Transcriptome and Proteome Analysis of Bacillus subtilis Gene Expression Modulated by Amino Acid Availability. J. Bacteriol 184: 1844288-4295 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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