Difference between revisions of "Sandbox"

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* '''Description:''' small RNA <br/><br/>
+
* '''Description:''' cystine transporter, membrane 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'''
−
|''surC''
+
|''tcyP''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yhcL''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || small RNA
+
|style="background:#ABCDEF;" align="center"| '''Product''' || cystine transporter, membrane protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || cystine uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length''' ||  bp
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 9.471  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaJ]]'', ''[[dnaK]]''
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1389 bp, 463 aa
 
|-
 
|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt    Gene sequence      (+200bp)  ]'''  
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhcK]]'', ''[[yhcM]]''
 
|-
 
|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:SurC_context.jpeg]]
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12741&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:yhcL_context.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
 
|}
 
|}
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<br/><br/>
 
<br/><br/>
  
−
<br/><br/><br/><br/><br/>
 
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:'''
+
* '''Locus tag:''' BSU09130
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 43:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' no entry
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11590]
−
 
−
* '''Structure:'''
 
  
 
=== Additional information===
 
=== Additional information===
  
 +
 +
=The protein=
 +
 +
=== Basic information/ Evolution ===
 +
 +
* '''Catalyzed reaction/ biological activity:'''
 +
 +
* '''Protein family:'''
 +
 +
* '''Paralogous protein(s):'''
 +
 +
=== Extended information on the protein ===
 +
 +
* '''Kinetic information:'''
 +
 +
* '''Domains:'''
 +
 +
* '''Modification:'''
 +
 +
* '''Cofactor(s):'''
 +
 +
* '''Effectors of protein activity:'''
 +
 +
* '''Interactions:'''
 +
 +
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
 +
 +
=== Database entries ===
 +
 +
* '''Structure:'''
 +
 +
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54596 P54596]
 +
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU09130]
 +
 +
* '''E.C. number:'''
 +
 +
=== Additional information===
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''surC'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]
+
* '''Operon:''' ''tcyP''
  
−
* '''Sigma factor:''' [[SigK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' expressed during sporulation in the mother cell ([[SigK]], [[GerE]])[http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]
+
* '''Regulation:''' repressed in the presence of cysteine ([[CymR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16513748 PubMed]
  
−
* '''Regulatory mechanism:''' [[GerE]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]
+
* '''Regulatory mechanism:''' [[CymR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16513748 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 +
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
  
−
=Labs working on this gene/RNA=
+
* '''Antibody:'''
  
 +
=Labs working on this gene/protein=
  
 +
[[Isabelle Martin-Verstraete]], Institute Pasteur, Paris, France
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>16385044, </pubmed>
+
<pubmed>18763711, </pubmed>
−
# Silvaggi JM, Perkins JB, Losick R (2006) Genes for small, noncoding RNAs under sporulation control in ''Bacillus subtilis''. ''J. Bacteriol.'' '''188:''' 532-541. [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 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]

Revision as of 14:38, 8 June 2009

  • Description: cystine transporter, membrane protein

Gene name tcyP
Synonyms yhcL
Essential no
Product cystine transporter, membrane protein
Function cystine uptake
MW, pI 48 kDa, 9.471
Gene length, protein length 1389 bp, 463 aa
Immediate neighbours yhcK, yhcM
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YhcL context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU09130

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:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

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

Additional information

Expression and regulation

  • Operon: tcyP
  • Regulation: repressed in the presence of cysteine (CymR) PubMed
  • Regulatory mechanism: CymR: transcription repression PubMed
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Isabelle Martin-Verstraete, Institute Pasteur, Paris, France

Your additional remarks

References

  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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