Difference between revisions of "Sandbox"

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−
* '''Description:''' involved in isopentenol (isoprenoid) biosynthesis <br/><br/>
+
* '''Description:''' similar to biotin biosynthesis <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'''
−
|''yhfR''
+
|''yhfU''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|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''' || unknown  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || isoprenoid biosynthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 5.164  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 10.681  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 579 bp, 193 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 558 bp, 186 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhfQ]]'', ''[[yhfS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhfT]]'', ''[[hemAT]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12874&#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:CAB12877&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yhfR_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yhfU_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:''' BSU10340
+
* '''Locus tag:''' BSU10370
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
no detectable phenotype  [http://www.ncbi.nlm.nih.gov/sites/entrez/10869096 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
Line 45: Line 43:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13062]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13065]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' unknown  [http://www.ncbi.nlm.nih.gov/sites/entrez/10869096 PubMed]
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' GpmB subfamily (according to Swiss-Prot) similar to 2,3-diphosphoglycerate-dependent phosphoglycerate mutases  [http://www.ncbi.nlm.nih.gov/sites/entrez/10869096 PubMed]
+
* '''Protein family:''' bioY family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cell membrane (according to Swiss-Prot),  membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O07617 O07617]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O07620 O07620]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10340]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10370]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 98: Line 96:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' weakly expressed  [http://www.ncbi.nlm.nih.gov/sites/entrez/10869096 PubMed]
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 118:
 
=References=
 
=References=
  
−
<pubmed>10869096, </pubmed>
+
<pubmed>18763711, </pubmed>
−
# Pearson CL, Loshon CA, Pedersen LB, Setlow B, Setlow P (2000) Analysis of the function of a putative 2,3-diphosphoglyceric acid-dependent phosphoglycerate mutase from ''Bacillus subtilis''. ''J. Bacteriol.'' '''182:''' 4121-4123. [http://www.ncbi.nlm.nih.gov/sites/entrez/10869096 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 13:45, 8 June 2009

  • Description: similar to biotin biosynthesis

Gene name yhfU
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 19 kDa, 10.681
Gene length, protein length 558 bp, 186 aa
Immediate neighbours yhfT, hemAT
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YhfU context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU10370

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: bioY 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 membrane (according to Swiss-Prot), membrane associated PubMed

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • 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

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)

  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
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