Difference between revisions of "Sandbox"

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* '''Description:''' seryl-tRNA-synthetase <br/><br/>
+
* '''Description:''' tRNA-Ser<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'''
−
|''serS''
+
|''trnSL-Ser1''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || seryl-tRNA-synthetase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transfer RNA-Ser
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || translation  
 
|style="background:#ABCDEF;" align="center"|'''Function''' || translation  
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00130 serS]
+
|style="background:#ABCDEF;" align="center"| '''Gene length''' || 93 bp
 +
|-|-
 +
 
 +
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[serS]]'', ''[[dck]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/tRNA_charging.html tRNA charging]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/trnSL-Ser1_nucleotide.txt    Gene sequence      (+200bp)  ]'''
 +
|style="background:#FAF8CC;" align="center"|'''  '''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.193 
+
|colspan="2" | '''Genetic context''' <br/> [[Image:trnSL-Ser1_context.gif]]
−
|-
 
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1275 bp, 425 aa
 
−
|-
 
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdxT]]'', ''[[trnSL-Ser1]]''
 
−
|-
 
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00130 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00130 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00130 DNA_with_flanks]
 
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:serS_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>
−
|-
 
−
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=serS_20880_22157_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:serS_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00130]]
 
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
−
<br/><br/><br/><br/>
 
−
<br/><br/><br/><br/>
 
−
<br/><br/><br/><br/>
 
−
<br/><br/><br/><br/>
 
−
<br/><br/><br/><br/>
 
−
 
  
−
<br/><br/><br/><br/><br/><br/>
+
<br/><br/>
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[translation]]}},
+
{{SubtiWiki category|[[translation]]}}
−
{{SubtiWiki category|[[essential genes]]}}
 
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
{{SubtiWiki regulon|[[T-box]]}}
+
 
  
 
=The gene=
 
=The gene=
Line 54: Line 41:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00130
+
* '''Locus tag:'''
  
 
===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/serS.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10077]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00010]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser) (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' Type-1 seryl-tRNA synthetase subfamily (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''[[SubtInteract|Interactions]]:'''
+
* '''Interactions:'''
  
−
* '''[[Localization]]:'''
+
* '''Localization:'''
−
** cytoplasm (according to Swiss-Prot)
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1SES 1SES] (from ''Thermus thermophilus'', 36% identity, 56% similarity) {{PubMed|8128224}}
+
* '''Structure:'''
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37464 P37464]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00130]
+
* '''KEGG entry:'''
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/6.1.1.11 6.1.1.11]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''serS'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
+
* '''Operon:'''  
−
 
 
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=serS_20880_22157_1 serS] {{PubMed|22383849}}
 
  
 
* '''Sigma factor:'''  
 
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
−
** induced by serine limitation ([[T-box]]) {{PubMed|19258532}}
 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[T-box]]: [[RNA switch]], transcriptional antitermination {{PubMed|19258532}}
 
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>19258532,,8915527, </pubmed>
+
[[Category:Transfer RNA]]
−
 
−
''Biochimie'' '''78:''' 381-389. [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
 
−
 
 
−
[[Category:Protein-coding genes]]
 

Revision as of 14:54, 11 November 2013

  • Description: tRNA-Ser

Gene name trnSL-Ser1
Synonyms
Essential no
Product transfer RNA-Ser
Function translation
Gene length 93 bp
Immediate neighbours serS, dck
Gene sequence (+200bp)
Genetic context
TrnSL-Ser1 context.gif
This image was kindly provided by SubtiList



Categories containing this gene/protein

translation

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag:

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:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • 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

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