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'''
−
|''yaaK''
+
|''recR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''recM ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
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|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''' || [[DNA 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=BSU00200 yaaK]
+
|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=BSU00210 recR]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 4.536 
+
|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=RecR RecR]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 321 bp, 107 aa
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 5.301 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaX]]'', ''[[recR]]''
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 594 bp, 198 aa
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00200 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00200 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00200 DNA_with_flanks]
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaK]]'', ''[[yaaL]]''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yaaK_context.gif]]
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00210 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00210 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00210 DNA_with_flanks]
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:recR_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=yaaK_28529_28852_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yaaK_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00200]]
+
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=recR_28867_29463_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:recR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00210]]
 
|-
 
|-
 
|}
 
|}
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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]] =
Line 51: Line 49:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00200
+
* '''Locus tag:''' BSU00210
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10084]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10085]
  
 
=== Additional information===
 
=== Additional information===
−
* The ''E.coli'' homolog: [http://ecoliwiki.net/colipedia/index.php/ybaB ''ybaB'']
+
 
 +
 
 +
 
  
 
=The protein=
 
=The protein=
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' UPF0133 family (according to Swiss-Prot)
+
* '''Protein family:''' recR family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
−
 
−
* '''The corresponding gene in ''E. coli'':''' [http://ecoliwiki.net/colipedia/index.php/ybaB EcoliWiki] {{PubMed|19594923}}
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''[[SubtInteract|Interactions]]:'''
 
* '''[[SubtInteract|Interactions]]:'''
 +
** [[RecR]]-[[RecO]],  [[RecR]]:[[RecO]] molecular ratio of 2:1 (as judged from other bacteria  such as ''E. coli'' and ''Deinococcus radiodurans'') {{PubMed|17581636}}
  
−
* '''[[Localization]]:'''
+
* '''[[Localization]]:'''  
 +
** cytoplasm (homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
 
* '''Structure:'''
 
* '''Structure:'''
 +
** [http://www.rcsb.org/pdb/explore/explore.do?structureId=2V1C 2V1C] (the [[RecR]]-[[RecO]] complex from ''Deinococcus radiodurans'', [[RecR]]: 52% identity, 78% similarity, [[RecO]]: 30%/ 58%)  {{PubMed|17581636}}
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P24281 P24281]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P24277 P24277]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00200]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00210]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 108: Line 109:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaK_28529_28852_1 yaaK] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=recR_28867_29463_1 recR] {{PubMed|22383849}}
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 137: Line 138:
  
 
=References=
 
=References=
−
 
+
== Reviews ==
−
<pubmed>12884008,19594923, </pubmed>
+
<pubmed> 22933559 </pubmed>
 +
== Original publications ==
 +
<pubmed>12884008,17581636, 16479537 </pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 14:54, 11 November 2013

  • Description: repair, recombination

Gene name recR
Synonyms recM
Essential no
Product unknown
Function DNA repair/ recombination
Gene expression levels in SubtiExpress: recR
Interactions involving this protein in SubtInteract: RecR
MW, pI 21 kDa, 5.301
Gene length, protein length 594 bp, 198 aa
Immediate neighbours yaaK, yaaL
Sequences Protein DNA DNA_with_flanks
Genetic context
RecR context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
RecR 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: BSU00210

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: recR 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

  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information: the mRNA is very stable (half-life > 15 min) PubMed

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

Joanna Timmins, Ingar Leiros, Sean McSweeney
Crystal structure and mutational study of RecOR provide insight into its mode of DNA binding.
EMBO J: 2007, 26(13);3260-71
[PubMed:17581636] [WorldCat.org] [DOI] (P p)

Jean-Christophe Meile, Ling Juan Wu, S Dusko Ehrlich, Jeff Errington, Philippe Noirot
Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory.
Proteomics: 2006, 6(7);2135-46
[PubMed:16479537] [WorldCat.org] [DOI] (P p)

G Hambraeus, C von Wachenfeldt, L Hederstedt
Genome-wide survey of mRNA half-lives in Bacillus subtilis identifies extremely stable mRNAs.
Mol Genet Genomics: 2003, 269(5);706-14
[PubMed:12884008] [WorldCat.org] [DOI] (P p)

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