Difference between revisions of "Sandbox"

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#REDIRECT [[PdxT]]
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* '''Description:''' seryl-tRNA-synthetase <br/><br/>
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{| align="right" border="1" cellpadding="2"
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|-
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|style="background:#ABCDEF;" align="center"|'''Gene name'''
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|''serS''
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|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
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|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || seryl-tRNA-synthetase
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|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || translation
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|-
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|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]
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|-
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|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]'''
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|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.193 
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|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1275 bp, 425 aa
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|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdxT]]'', ''[[trnSL-Ser1]]''
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|-
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|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]
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|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:serS_context.gif]]
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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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|-
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|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]]
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|-
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|}
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__TOC__
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<br/><br/><br/><br/>
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<br/><br/><br/><br/>
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<br/><br/><br/><br/>
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<br/><br/><br/><br/>
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<br/><br/><br/><br/>
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<br/><br/><br/><br/><br/><br/>
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= [[Categories]] containing this gene/protein =
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{{SubtiWiki category|[[translation]]}},
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{{SubtiWiki category|[[essential genes]]}}
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= This gene is a member of the following [[regulons]] =
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{{SubtiWiki regulon|[[T-box]]}}
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=The gene=
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 +
=== Basic information ===
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* '''Locus tag:''' BSU00130
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 +
===Phenotypes of a mutant ===
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 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
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 +
=== Database entries ===
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/serS.html]
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* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10077]
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=== Additional information===
 +
 
 +
 
 +
 
 +
 
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=The protein=
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 +
=== Basic information/ Evolution ===
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 +
* '''Catalyzed reaction/ biological activity:''' ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser) (according to Swiss-Prot)
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 +
* '''Protein family:''' Type-1 seryl-tRNA synthetase subfamily (according to Swiss-Prot)
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* '''Paralogous protein(s):'''
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 +
=== Extended information on the protein ===
 +
 
 +
* '''Kinetic information:'''
 +
 
 +
* '''Domains:'''
 +
 
 +
* '''Modification:'''
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* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
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* '''[[SubtInteract|Interactions]]:'''
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* '''[[Localization]]:'''
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** cytoplasm (according to Swiss-Prot)
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=== Database entries ===
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* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1SES 1SES] (from ''Thermus thermophilus'', 36% identity, 56% similarity) {{PubMed|8128224}}
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* '''UniProt:''' [http://www.uniprot.org/uniprot/P37464 P37464]
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00130]
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* '''E.C. number:''' [http://www.expasy.org/enzyme/6.1.1.11 6.1.1.11]
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=== Additional information===
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=Expression and regulation=
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* '''Operon:''' ''serS'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
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* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=serS_20880_22157_1 serS] {{PubMed|22383849}}
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* '''Sigma factor:'''
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* '''Regulation:'''
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** induced by serine limitation ([[T-box]]) {{PubMed|19258532}}
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* '''Regulatory mechanism:'''
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** [[T-box]]: [[RNA switch]], transcriptional antitermination {{PubMed|19258532}}
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* '''Additional information:'''
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=Biological materials =
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* '''Mutant:'''
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* '''Expression vector:'''
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* '''lacZ fusion:'''
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* '''GFP fusion:'''
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* '''two-hybrid system:'''
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* '''Antibody:'''
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=Labs working on this gene/protein=
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=Your additional remarks=
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=References=
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<pubmed>19258532,,8915527, </pubmed>
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''Biochimie'' '''78:''' 381-389. [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
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[[Category:Protein-coding genes]]

Revision as of 14:54, 11 November 2013

  • Description: seryl-tRNA-synthetase

Gene name serS
Synonyms
Essential yes PubMed
Product seryl-tRNA-synthetase
Function translation
Gene expression levels in SubtiExpress: serS
Metabolic function and regulation of this protein in SubtiPathways:
tRNA charging
MW, pI 48 kDa, 5.193
Gene length, protein length 1275 bp, 425 aa
Immediate neighbours pdxT, trnSL-Ser1
Sequences Protein DNA DNA_with_flanks
Genetic context
SerS context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
SerS expression.png




























Categories containing this gene/protein

translation, essential genes

This gene is a member of the following regulons

T-box

The gene

Basic information

  • Locus tag: BSU00130

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-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser) (according to Swiss-Prot)
  • Protein family: Type-1 seryl-tRNA synthetase subfamily (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure: 1SES (from Thermus thermophilus, 36% identity, 56% similarity) PubMed
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation:
  • 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

Ana Gutiérrez-Preciado, Tina M Henkin, Frank J Grundy, Charles Yanofsky, Enrique Merino
Biochemical features and functional implications of the RNA-based T-box regulatory mechanism.
Microbiol Mol Biol Rev: 2009, 73(1);36-61
[PubMed:19258532] [WorldCat.org] [DOI] (I p)

C Condon, M Grunberg-Manago, H Putzer
Aminoacyl-tRNA synthetase gene regulation in Bacillus subtilis.
Biochimie: 1996, 78(6);381-9
[PubMed:8915527] [WorldCat.org] [DOI] (P p)


Biochimie 78: 381-389. PubMed

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