Difference between revisions of "Sandbox"

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* '''Description:''' inhibition of the pro-sigma-K processing machinery <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'''
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|''bofA''
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|''rrnA-16S''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
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|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || inhibitor of pro-[[SigK]] processing
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|style="background:#ABCDEF;" align="center"| '''Product''' || ribosomal RNA-16S
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[SigK]] activation
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|style="background:#ABCDEF;" align="center"|'''Function''' || translation
 
|-
 
|-
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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=BSU00230 bofA]
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|style="background:#ABCDEF;" align="center"| '''Gene length''' || 1553 bp
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=BofA BofA]
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bofA]]'', ''[[trnA-Ile]]''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 9.32 
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rrnA-16S_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 261 bp, 87 aa
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rrnA-16S_context.gif]]
−
|-
 
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaL]]'', ''[[rrnA-16S]]''
 
−
|-
 
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00230 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00230 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00230 DNA_with_flanks]
 
−
|-
 
−
|-
 
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:bofA_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=bofA_29772_30035_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:bofA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00230]]
 
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
 
<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|[[sigma factors and their control]]}},
+
{{SubtiWiki category|[[translation]]}}
−
{{SubtiWiki category|[[sporulation proteins]]}},
 
−
{{SubtiWiki category|[[membrane proteins]]}}
 
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
{{SubtiWiki regulon|[[SigE regulon]]}},
+
 
−
{{SubtiWiki regulon|[[SpoIIID regulon]]}}
 
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00230
+
* '''Locus tag:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/bofA.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10087]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00011]
−
 
 
−
=== 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:'''
 
−
 
 
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* '''Cofactor(s):'''
 
−
 
 
−
* '''Effectors of protein activity:'''
 
−
 
 
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* '''[[SubtInteract|Interactions]]:'''
 
−
** [[BofA]]-[[SpoIVB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15292188 PubMed]
 
−
** [[SpoIVFB]]-[[BofA]], to inhibit proteolytic activity of [[SpoIVFB]] {{PubMed|15087499}}
 
−
** [[SpoIVFA]]-[[BofA]], recruitment of [[BofA]] to [[SpoIVFB]] {{PubMed|11959848}}
 
−
 
 
−
* '''[[Localization]]:'''
 
−
** forespore outer membrane (according to Swiss-Prot)
 
−
** integral membrane protein {{PubMed|11959848}}
 
−
 
 
−
=== Database entries ===
 
  
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P24282 P24282]
+
=== Additional information===
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00230]
 
  
−
* '''E.C. number:'''
 
  
−
=== Additional information===
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''bofA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Operon:''' ''[[rrnA-16S]]-[[trnA-Ile]]-[[trnA-Ala]]-[[rrnA-23S]]-[[rrnA-5S]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
−
 
 
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=bofA_29772_30035_1 bofA] {{PubMed|22383849}}
 
  
−
* '''Sigma factor:''' [[SigE]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
  
−
* '''Regulation:''' expressed during sporulation  [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' repressed by [[SpoIIID]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
 
* '''Mutant:'''
 
* '''Mutant:'''
−
** 1S100 ( ''bofA''::''cat''), {{PubMed|1577688}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S100&Search=1S100 BGSC]
 
−
** 1S96 ( ''bofA''::''erm''), {{PubMed|1315731}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S96&Search=1S96 BGSC]
 
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
 
          
 
          
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
−
 
−
* '''GFP fusion:'''
 
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
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* '''Antibody:'''
 
* '''Antibody:'''
  
−
=Labs working on this gene/protein=
+
=Labs working on this gene/RNA=
−
 
 
−
Simon Cutting, London, UK [http://personal.rhul.ac.uk/uhba/009/bacillus/simon_cutting.html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
 +
'''Additional publications:''' {{PubMed|21303765}}
 +
<pubmed> 6312418, 19447912 20634236 </pubmed>
  
−
<pubmed>11959848, 9501233, 1577688, 15292188, 2115401, 12940997, 12884008,, 15292188 1315731, 15752199 16818230 15087499</pubmed>
+
[[Category:Ribosomal RNA]]
−
 
 
−
[[Category:Protein-coding genes]]
 

Revision as of 14:54, 11 November 2013

Gene name rrnA-16S
Synonyms
Essential
Product ribosomal RNA-16S
Function translation
Gene length 1553 bp
Immediate neighbours bofA, trnA-Ile
Gene sequence (+200bp)
Genetic context
RrnA-16S 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]
  • 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

Additional publications: PubMed

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