Difference between revisions of "Sandbox"

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−
* '''Description:''' unknown <br/><br/>
+
* '''Description:''' repair, recombination <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'''
−
|''yaaA''
+
|''recF''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || repair, recombination
 
|-
 
|-
−
|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=BSU00030 YaaA]
+
|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=BSU00040 RecF]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 7 kDa, 4.332  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 7.015  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 213 bp, 71 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1110 bp, 370 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaN]]'', ''[[recF]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaA]]'', ''[[yaaB]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00030 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00030 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00030 DNA_with_flanks]
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00040 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00040 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00040 DNA_with_flanks]
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_context.png]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_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>
 
|-
 
|-
−
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaA_3206_3421_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:YaaA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00030]]
+
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=recF_3437_4549_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:recF_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00040]]
 
|-
 
|-
 
|}
 
|}
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<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|[[proteins of unknown function]]}}
+
{{SubtiWiki category|[[DNA repair/ recombination]]}}
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00030
+
* '''Locus tag:''' BSU00040
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaA-recF-yaaB-gyrB.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaA-recF-yaaB-gyrB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10067]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10068]
  
 
=== Additional information===
 
=== Additional information===
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:'''
+
* '''Protein family:''' recF family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''[[SubtInteract|Interactions]]:'''
 
* '''[[SubtInteract|Interactions]]:'''
  
−
* '''[[Localization]]:'''
+
* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P05650 P05650]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P05651 P05651]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00030]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00040]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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* '''Operon:''' ''[[yaaA]]-[[recF]]-[[yaaB]]-[[gyrB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
 
* '''Operon:''' ''[[yaaA]]-[[recF]]-[[yaaB]]-[[gyrB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaA_3206_3421_1 yaaA] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=recF_3437_4549_1 recF] {{PubMed|22383849}}
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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=References=
 
=References=
−
 
+
== Reviews ==
−
<pubmed>2987848, </pubmed>
+
<pubmed> 22933559 </pubmed>
 +
== Original publications ==
 +
<pubmed>2987848, 15186413 9207023 </pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 14:40, 11 November 2013

  • Description: repair, recombination

Gene name recF
Synonyms
Essential
Product unknown
Function repair, recombination
Gene expression levels in SubtiExpress: RecF
MW, pI 42 kDa, 7.015
Gene length, protein length 1110 bp, 370 aa
Immediate neighbours yaaA, yaaB
Sequences Protein DNA DNA_with_flanks
Genetic context
DnaA dnaN yaaA recF yaaB gyrB context.png
This image was kindly provided by SubtiList
Expression at a glance   PubMed
RecF expression.png
























Categories containing this gene/protein

DNA repair/ recombination

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU00040

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: recF family (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:
  • KEGG entry: [3]
  • E.C. number:

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

Reviews

Justin S Lenhart, Jeremy W Schroeder, Brian W Walsh, Lyle A Simmons
DNA repair and genome maintenance in Bacillus subtilis.
Microbiol Mol Biol Rev: 2012, 76(3);530-64
[PubMed:22933559] [WorldCat.org] [DOI] (I p)

Original publications

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