Difference between revisions of "Sandbox"

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* '''Description:''' alpha-L-arabinofuranosidase <br/><br/>
+
* '''Description:''' oligopeptide ABC transporter (permease) <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'''
−
|''abfA''
+
|''oppC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0KC ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || alpha-L-arabinofuranosidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || oligopeptide ABC transporter (permease)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of sporulation, competence development
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 10.107 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.344 
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 915 bp, 305 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1500 bp, 500 aa
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[oppB]]'', ''[[oppD]]''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cstA]]'', ''[[araQ]]''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13002&#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:CAB14832&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" | '''Genetic context''' <br/> [[Image:oppC_context.gif]]
−
|-
 
−
|-
 
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:abfA_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/><br/>
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU28720
+
* '''Locus tag:''' BSU11450
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 45: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/araABDLMNPQ-abfA.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11900]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10773]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' glycosyl hydrolase 51 family (according to Swiss-Prot)
+
* '''Protein family:''' ABC transmembrane type-1 domain (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1QW8 1QW8] (complex with Ara-alpha-Xyl, Geobacillus stearothermophilus),  [http://www.rcsb.org/pdb/explore.do?structureId=1PZ3 1PZ3] (Geobacillus stearothermophilus)
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94531 P94531]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P24139 P24139]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28720]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU11450]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.2.1.55 3.2.1.55]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[araA]]-[[araB]]-[[araD]]-[[araL]]-[[araM]]-[[araN]]-[[araP]]-[[araQ]]-[[abfA]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by glucose ([[CcpA]])
+
* '''Regulation:'''  
−
** repressed in the absence of arabinose ([[AraR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10417639 PubMed]
+
** expressed in the absence of good nitrogen sources (glutamine or ammonium) ([[TnrA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12823818 PubMed]
 +
** repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10383984 PubMed]
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
+
* '''Regulatory mechanism:'''  
−
** [[AraR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10417639 PubMed]
+
** [[TnrA]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12823818 PubMed]
 +
** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10383984 PubMed]
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>12949161 9084180, </pubmed>
+
<pubmed>12823818,10383984, </pubmed>
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 15:24, 12 June 2009

  • Description: oligopeptide ABC transporter (permease)

Gene name oppC
Synonyms spo0KC
Essential no
Product oligopeptide ABC transporter (permease)
Function initiation of sporulation, competence development
MW, pI 33 kDa, 10.107
Gene length, protein length 915 bp, 305 aa
Immediate neighbours oppB, oppD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
OppC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU11450

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: ABC transmembrane type-1 domain (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 membrane (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation:
    • expressed in the absence of good nitrogen sources (glutamine or ammonium) (TnrA) PubMed
    • repressed during exponential growth (ScoC) 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

Ken-ichi Yoshida, Hirotake Yamaguchi, Masaki Kinehara, Yo-hei Ohki, Yoshiko Nakaura, Yasutaro Fujita
Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box.
Mol Microbiol: 2003, 49(1);157-65
[PubMed:12823818] [WorldCat.org] [DOI] (P p)

A Koide, M Perego, J A Hoch
ScoC regulates peptide transport and sporulation initiation in Bacillus subtilis.
J Bacteriol: 1999, 181(13);4114-7
[PubMed:10383984] [WorldCat.org] [DOI] (P p)

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