Difference between revisions of "Sandbox"

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−
* '''Description:''' Fur-regulated basic protein, acts as RNA chaperone for fsrA <br/><br/>
+
* '''Description:''' valyl-tRNA synthetase <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'''
−
|''fbpA''
+
|''valS''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbN''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|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''' || Fur-regulated basic protein, <br/>acts as RNA chaperone for fsrA
+
|style="background:#ABCDEF;" align="center"| '''Product''' || valyl-tRNA synthetase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA chaperone
+
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || xx,x kDa, 9.50
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 101 kDa, 4.868 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 159 bp, 53 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2640 bp, 880 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fbpB]]'', ''[[ydbO]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[folC]]'', ''[[ysxE]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt    Gene sequence      (+200bp)  ]'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14769&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_protein.txt Protein sequence]'''
 
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:FbpA_fbpB_context.jpeg]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:valS_context.gif]]
 +
<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/>
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:'''
+
* '''Locus tag:''' BSU28090
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/valS-folC.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12081]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10321]
  
 
=== Additional information===
 
=== Additional information===
  
−
The sequence of the former ydbN gene was corrected, and does now contain two genes, [[fbpA]] and [[fbpB]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]
 
  
 
=The protein=
 
=The protein=
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val) (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' ValS type 1 subfamily (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q05873 Q05873]
  
−
* '''KEGG entry:''' no entry
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28090]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/6.1.1.9 6.1.1.9]
  
 
=== Additional information===
 
=== Additional information===
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* '''Expression vector:'''
 
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
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=References=
 
=References=
  
−
<pubmed>18697947, </pubmed>
 
−
# Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD. (2008) The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins.  ''Proc Natl Acad Sci U S A.'' '''Aug 19;105(33):''' 11927-32. [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 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 00:01, 13 June 2009

  • Description: valyl-tRNA synthetase

Gene name valS
Synonyms
Essential yes PubMed
Product valyl-tRNA synthetase
Function translation
MW, pI 101 kDa, 4.868
Gene length, protein length 2640 bp, 880 aa
Immediate neighbours folC, ysxE
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ValS context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU28090

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: ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val) (according to Swiss-Prot)
  • Protein family: ValS type 1 subfamily (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry: [3]

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

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