Difference between revisions of "Sandbox"

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* '''Description:''' tRNA:m1A22 methyl transferase <br/><br/>
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* '''Description:''' tRNA-Ile <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'''
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|''trmK''
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|''trnA-Ile''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqfN''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || tRNA:m1A22 methyl transferase
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|style="background:#ABCDEF;" align="center"| '''Product''' || transfer RNA-Ile
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || tRNA modification
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|style="background:#ABCDEF;" align="center"|'''Function''' || translation
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 5.272 
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|style="background:#ABCDEF;" align="center"| '''Gene length''' || 77 bp
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 648 bp, 216 aa
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rrnA-16S]]'', ''[[trnA-Ala]]''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfO]]'', ''[[cccA]]''
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/trnA-Ile_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 
|-
 
|-
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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:CAB14448&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
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|colspan="2" | '''Genetic context''' <br/> [[Image:trnA-Ile_context.gif]]
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|-
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<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
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|colspan="2" | '''Genetic context''' <br/> [[Image:yqfN_context.gif]]
 
 
|-
 
|-
 
|}
 
|}
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__TOC__
 
__TOC__
  
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<br/><br/>
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<br/><br/><br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
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* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
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* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11660]
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* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00012]
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=== Additional information===
 
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−
 
 
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=The protein=
 
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=== Basic information/ Evolution ===
 
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* '''Catalyzed reaction/ biological activity:'''
 
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* '''Protein family:'''
 
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* '''Paralogous protein(s):'''
 
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=== Extended information on the protein ===
 
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* '''Kinetic information:'''
 
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* '''Domains:'''
 
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* '''Modification:''' phosphorylation on Ser-48 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
 
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* '''Cofactor(s):'''
 
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* '''Effectors of protein activity:'''
 
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* '''Interactions:'''
 
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* '''Localization:'''
 
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=== Database entries ===
 
  
 
* '''Structure:'''
 
* '''Structure:'''
  
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* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54471 P54471]
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=== Additional information===
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* '''KEGG entry:'''
 
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* '''E.C. number:'''
 
  
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=== Additional information===
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:'''  
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* '''Operon:''' ''[[rrnA-16S]]-[[trnA-Ile]]-[[trnA-Ala]]-[[rrnA-23S]]-[[rrnA-5S]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
  
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* '''[[Sigma factor]]:'''  
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* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
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* '''Additional information:'''  
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* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
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* '''GFP fusion:'''
 
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
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* '''Antibody:'''
 
* '''Antibody:'''
  
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=Labs working on this gene/protein=
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=Labs working on this gene/RNA=
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
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<pubmed>17218307, </pubmed>
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<pubmed>6312418, </pubmed>
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# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
+
# Ogasawara et al. (1983) Structure and organization of rRNA operons in the region of the replication origin of the ''Bacillus subtilis'' chromosome.''Nucl. Acids Res.'' '''11:''' 6301-6318. [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 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 14:39, 8 June 2009

  • Description: tRNA-Ile

Gene name trnA-Ile
Synonyms
Essential no
Product transfer RNA-Ile
Function translation
Gene length 77 bp
Immediate neighbours rrnA-16S, trnA-Ala
Gene sequence (+200bp)
Genetic context
TrnA-Ile context.gif
This image was kindly provided by SubtiList







The gene

Basic information

  • Locus tag:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]
  • Structure:

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/RNA

Your additional remarks

References

  1. Ogasawara et al. (1983) Structure and organization of rRNA operons in the region of the replication origin of the Bacillus subtilis chromosome.Nucl. Acids Res. 11: 6301-6318. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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