Difference between revisions of "Sandbox"

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−
* '''Description:''' dipeptide ABC transporter (dipeptide-binding protein) <br/><br/>
+
* '''Description:''' GTP-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'''
−
|''dppE''
+
|''era''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dciAE ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''bex, yqfH ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || dipeptide ABC transporter (dipeptide-binding protein)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || GTP-binding protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || uptake of dipeptides
+
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 5.523  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 8.376  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1647 bp, 549 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 903 bp, 301 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dppD]]'', ''[[ykfA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[recO]]'', ''[[cdd]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14458&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:era_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>
 
|-
 
|-
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__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 37: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU12960
+
* '''Locus tag:''' BSU25290
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dppABCDE.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cdd-era.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10846]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11188]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Binds and hydrolyzes GTP and readily exchanges GDP for GTP
  
−
* '''Protein family:''' bacterial solute-binding protein 5 family (according to Swiss-Prot)
+
* '''Protein family:''' Era subfamily (according to Swiss-Prot) Era/Obg family
  
−
* '''Paralogous protein(s):''' [[OppA]]
+
* '''Paralogous protein(s):''' [[Era]], [[Obg]], [[YphC]], [[YsxC]], [[RbgA]], [[YqeH]], [[ThdF]], [[YyaF]], [[YnbA]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' membrane protein [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P26906 P26906]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42182 P42182]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU12960]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25290]
  
 
* '''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:'''  
−
 
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1766371 PubMed]
 
  
−
* '''Regulation:''' 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]
+
* '''Sigma factor:'''  
  
−
* '''Regulatory mechanism:''' [[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 PubMed] 
+
* '''Regulation:'''  
  
−
* '''Additional information:'''
+
* '''Regulatory mechanism:'''
 +
 
 +
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP1110 (spc), available in [[Stülke]] lab
+
* '''Mutant:'''
  
−
* '''Expression vector:'''
+
* '''Expression vector:''' pGP93 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
 
          
 
          
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Naotake Ogasawara]], Nara, Japan
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>18763711, </pubmed>
+
<pubmed>12427945, </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]
+
# Morimoto T, Loh PC, Hirai T, Asai K, Kobayashi K, Moriya S, Ogasawara N (2002) Six GTP-binding proteins of the Era/Obg family are essential for cell growth in ''Bacillus subtilis''. ''Microbiology'' '''148:''' 3539-3552. [http://www.ncbi.nlm.nih.gov/sites/entrez/12427945 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 14:02, 8 June 2009

  • Description: GTP-binding protein

Gene name era
Synonyms bex, yqfH
Essential yes PubMed
Product GTP-binding protein
Function
MW, pI 33 kDa, 8.376
Gene length, protein length 903 bp, 301 aa
Immediate neighbours recO, cdd
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
Era context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU25290

Phenotypes of a mutant

essential PubMed

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Binds and hydrolyzes GTP and readily exchanges GDP for GTP
  • Protein family: Era subfamily (according to Swiss-Prot) Era/Obg family

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

  • Operon:
  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector: pGP93 (N-terminal Strep-tag, purification from B. subtilis, for SPINE, in pGP380), available in Stülke lab
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Naotake Ogasawara, Nara, Japan

Your additional remarks

References

  1. Morimoto T, Loh PC, Hirai T, Asai K, Kobayashi K, Moriya S, Ogasawara N (2002) Six GTP-binding proteins of the Era/Obg family are essential for cell growth in Bacillus subtilis. Microbiology 148: 3539-3552. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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