Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' dipeptide ABC transporter (ATP-binding protein) <br/><br/>
+
* '''Description:''' dipeptide ABC transporter (dipeptide-binding protein) <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'''
−
|''dppD''
+
|''dppE''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dciAD ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dciAE ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || dipeptide ABC transporter (ATP-binding protein)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || dipeptide ABC transporter (dipeptide-binding protein)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || uptake of dipeptides  
+
|style="background:#ABCDEF;" align="center"|'''Function''' || uptake of dipeptides
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 7.516  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 5.523  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1005 bp, 335 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1647 bp, 549 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dppC]]'', ''[[dppE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dppD]]'', ''[[ykfA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13152&#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:CAB13153&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:dppD_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:dppE_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>
 
|-
 
|-
Line 29: Line 31:
 
__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU12950
+
* '''Locus tag:''' BSU12960
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 45:
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dppABCDE.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dppABCDE.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10845]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10846]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 56:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' ABC transporter family (according to Swiss-Prot)
+
* '''Protein family:''' bacterial solute-binding protein 5 family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[OppA]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 62: Line 64:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:''' ABC transporter domain (according to Swiss-Prot)
+
* '''Domains:'''  
  
 
* '''Modification:'''
 
* '''Modification:'''
Line 72: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:''' membrane protein [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 78: Line 80:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P26905 P26905]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P26906 P26906]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU12950]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU12960]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 104: Line 106:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP1110 (spc), available in [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 122: Line 124:
 
=References=
 
=References=
  
−
<pubmed>1766371, </pubmed>
+
<pubmed>1766371,18763711, </pubmed>
 +
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 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 10:51, 12 June 2009

  • Description: dipeptide ABC transporter (dipeptide-binding protein)

Gene name dppE
Synonyms dciAE
Essential no
Product dipeptide ABC transporter (dipeptide-binding protein)
Function uptake of dipeptides
MW, pI 62 kDa, 5.523
Gene length, protein length 1647 bp, 549 aa
Immediate neighbours dppD, ykfA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
DppE context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Locus tag: BSU12960

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: bacterial solute-binding protein 5 family (according to Swiss-Prot)
  • Paralogous protein(s): OppA

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: membrane protein PubMed

Database entries

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

Additional information

Expression and regulation

  • Regulation: expressed postexponentially (AbrB) PubMed, repressed by CodY PubMed
    • repressed during growth in the presence of branched chain amino acids (CodY) PubMed
    • repressed during logrithmic growth (AbrB) PubMed
  • Additional information:

Biological materials

  • Mutant: GP1110 (spc), available in Stülke lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

F J Slack, J P Mueller, M A Strauch, C Mathiopoulos, A L Sonenshein
Transcriptional regulation of a Bacillus subtilis dipeptide transport operon.
Mol Microbiol: 1991, 5(8);1915-25
[PubMed:1766371] [WorldCat.org] [DOI] (P p)

  1. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://134.76.20.203/wiki//index.php?title=Sandbox&oldid=91654"