Difference between revisions of "Sandbox"

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* '''Description:''' DNA-Gyrase (subunit A) <br/><br/>
+
* '''Description:''' 16S rRNA<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'''
−
|''gyrA''
+
|''rrnO-16S''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''nalA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || DNA-Gyrase (subunit A)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ribosomal RNA-16S
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA supercoiling, <br/>initation of replication cycle and DNA elongation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 91 kDa, 5.215 
+
|style="background:#ABCDEF;" align="center"| '''Gene length''' || 1553 bp
 +
|-|-
 +
 
 +
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gyrA]]'', ''[[trnO-Ile]]''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2463 bp, 821 aa
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rrnO-16S_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 +
|style="background:#FAF8CC;" align="center"|'''  '''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gyrB]]'', ''[[rrnO-16S]]''
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rrnO-16S_context.gif]]
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|-
 
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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:CAB11783&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:GyrA_context.png]]
 
 
  <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>
 
|-
 
|-
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__TOC__
 
__TOC__
  
−
<br/><br/><br/>
+
<br/><br/><br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00070
+
* '''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/gyrA.html]
+
* '''DBTBS entry:''' no entry
−
 
 
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10071]
 
−
 
 
−
=== Additional information===
 
−
 
 
−
 
 
−
=The protein=
 
−
 
 
−
=== Basic information/ Evolution ===
 
−
 
 
−
* '''Catalyzed reaction/ biological activity:''' ATP-dependent breakage, passage and rejoining of double-stranded DNA (according to Swiss-Prot)
 
  
−
* '''Protein family:''' topoisomerase gyrA/parC subunit family (according to Swiss-Prot)
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00005]
  
−
* '''Paralogous protein(s):''' [[ParC]]
+
* '''Structure:'''
−
 
 
−
=== Extended information on the protein ===
 
−
 
 
−
* '''Kinetic information:'''
 
−
 
 
−
* '''Domains:'''
 
−
 
 
−
* '''Modification:'''
 
−
 
 
−
* '''Cofactor(s):'''
 
−
 
 
−
* '''Effectors of protein activity:'''
 
−
 
 
−
* '''Interactions:''' [[GyrA]]-[[GyrB]]
 
−
 
 
−
* '''Localization:''' Nucleoid (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] nucleoid-associated in actively growing cells [http://www.ncbi.nlm.nih.gov/sites/entrez/9539793 PubMed]
 
−
 
 
−
=== Database entries ===
 
−
 
 
−
* '''Structure:'''
 
−
 
 
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P05653 P05653]
 
−
 
 
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00070]
 
−
 
 
−
* '''E.C. number:'''
 
  
 
=== Additional information===
 
=== Additional information===
−
 
−
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''gyrA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Operon:''' ''rrnO'' operon (''[[rrnO-16S]] - [[trnO-Ile]] - [[trnO-Ala]] -[[rrnO-23S]] - [[rrnO-5S]]'') [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed],  GyrA is subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Dagmar Klostermeier]], Biozentrum Basel, Switzerland [http://www.biozentrum.unibas.ch/klostermeier/index.html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>16479537,17981983 ,9539793 , 2987848  </pubmed>
+
 
 +
<pubmed> 6312418, 19447912 </pubmed>

Revision as of 12:48, 14 June 2009

  • Description: 16S rRNA

Gene name rrnO-16S
Synonyms
Essential no
Product ribosomal RNA-16S
Function translation
Gene length 1553 bp
Immediate neighbours gyrA, trnO-Ile
Gene sequence (+200bp)
Genetic context
RrnO-16S 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:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Yousuke Natori, Kazumi Tagami, Kana Murakami, Sawako Yoshida, Osamu Tanigawa, Yoonsuh Moh, Kenta Masuda, Tetsuya Wada, Shota Suzuki, Hideaki Nanamiya, Yuzuru Tozawa, Fujio Kawamura
Transcription activity of individual rrn operons in Bacillus subtilis mutants deficient in (p)ppGpp synthetase genes, relA, yjbM, and ywaC.
J Bacteriol: 2009, 191(14);4555-61
[PubMed:19447912] [WorldCat.org] [DOI] (I p)

N Ogasawara, S Moriya, H Yoshikawa
Structure and organization of rRNA operons in the region of the replication origin of the Bacillus subtilis chromosome.
Nucleic Acids Res: 1983, 11(18);6301-18
[PubMed:6312418] [WorldCat.org] [DOI] (P p)

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