Difference between revisions of "Sandbox"

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−
* '''Description:''' general stress protein, similar to isochorismatase <br/><br/>
+
* '''Description:''' tRNA specific adenosine deaminase<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'''
−
|''yaaI''
+
|''yaaJ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || tRNA specific adenosine deaminase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || survival of ethanol stress
+
|style="background:#ABCDEF;" align="center"|'''Function''' || tRNA modification
 
|-
 
|-
−
|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=BSU00170 yaaI]
+
|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=BSU00180 yaaJ]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 4.674  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 5.636  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 543 bp, 181 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 483 bp, 161 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaH]]'', ''[[yaaJ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaI]]'', ''[[scr]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00170 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00170 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00170 DNA_with_flanks]
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00180 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00180 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00180 DNA_with_flanks]
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yaaI_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yaaJ_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=yaaI_25221_25766_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yaaI_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00170]]
+
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tadA_25852_26337_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yaaJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00180]]
 
|-
 
|-
 
|}
 
|}
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= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}}
+
{{SubtiWiki category|[[translation]]}}
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
{{SubtiWiki regulon|[[SigB regulon]]}}
+
 
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00170
+
* '''Locus tag:''' BSU00180
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaJ-scr.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10081]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10082]
  
 
=== Additional information===
 
=== Additional information===
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:'''
+
* '''Protein family:''' cytidine and deoxycytidylate deaminase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
* '''The corresponding gene in ''E. coli'':''' [http://ecoliwiki.net/colipedia/index.php/tadA EcoliWiki]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2B3J 2B3J] (the protein of ''Staphylococcus aureus'', complex with RNA) {{PubMed|16415880}}
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37532 P37532]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P21335 P21335]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00170]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00180]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.chem.qmul.ac.uk/iubmb/enzyme/EC3/5/4/ 3.5.4.-]
  
 
=== Additional information===
 
=== Additional information===
−
 
−
important for survival of ethanol stress [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''''' [[yaaJ]]-[[scr]]''
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaI_25221_25766_-1 yaaI] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tadA_25852_26337_1 yaaJ] {{PubMed|22383849}}
  
−
* '''Sigma factor:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
+
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
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=References=
 
=References=
  
−
<pubmed>15805528 15805528, </pubmed>
+
<pubmed>19087206, 12110595, 16415880 </pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 14:54, 11 November 2013

  • Description: tRNA specific adenosine deaminase

Gene name yaaJ
Synonyms
Essential no
Product tRNA specific adenosine deaminase
Function tRNA modification
Gene expression levels in SubtiExpress: yaaJ
MW, pI 17 kDa, 5.636
Gene length, protein length 483 bp, 161 aa
Immediate neighbours yaaI, scr
Sequences Protein DNA DNA_with_flanks
Genetic context
YaaJ context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YaaJ expression.png
























Categories containing this gene/protein

translation

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU00180

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: cytidine and deoxycytidylate deaminase family (according to Swiss-Prot)
  • Paralogous protein(s):
  • The corresponding gene in E. coli: EcoliWiki

Extended information on the protein

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

Database entries

  • Structure: 2B3J (the protein of Staphylococcus aureus, complex with RNA) PubMed
  • KEGG entry: [3]

Additional information

Expression and regulation

  • 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

Takashi Inaoka, Takenori Satomura, Yasutaro Fujita, Kozo Ochi
Novel gene regulation mediated by overproduction of secondary metabolite neotrehalosadiamine in Bacillus subtilis.
FEMS Microbiol Lett: 2009, 291(2);151-6
[PubMed:19087206] [WorldCat.org] [DOI] (I p)

Heather C Losey, Alexander J Ruthenburg, Gregory L Verdine
Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA.
Nat Struct Mol Biol: 2006, 13(2);153-9
[PubMed:16415880] [WorldCat.org] [DOI] (P p)

Jeannette Wolf, André P Gerber, Walter Keller
tadA, an essential tRNA-specific adenosine deaminase from Escherichia coli.
EMBO J: 2002, 21(14);3841-51
[PubMed:12110595] [WorldCat.org] [DOI] (P p)

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