Difference between revisions of "Sandbox"

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−
* '''Description:''' repair, recombination <br/><br/>
+
* '''Description:''' unknown <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'''
−
|''recR''
+
|''yaaL''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''recM ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|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''' || [[DNA repair/ recombination]]
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|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]
+
|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=BSU00220 yaaL]
 
|-
 
|-
−
|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"| '''MW, pI''' || 9 kDa, 10.329 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 5.301 
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 222 bp, 74 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 594 bp, 198 aa
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[recR]]'', ''[[bofA]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaK]]'', ''[[yaaL]]''
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00220 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00220 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00220 DNA_with_flanks]
 
|-
 
|-
−
|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:yaaL_context.gif]]
−
|-
 
−
|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=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]]
+
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaL_29481_29705_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yaaL_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00220]]
 
|-
 
|-
 
|}
 
|}
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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|[[DNA repair/ recombination]]}}
+
{{SubtiWiki category|[[proteins of unknown function]]}}
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
Line 49: Line 51:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00210
+
* '''Locus tag:''' BSU00220
  
 
===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+BG10085]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10086]
  
 
=== Additional information===
 
=== Additional information===
Line 70: Line 72:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' recR family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 87: Line 89:
  
 
* '''[[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/P24277 P24277]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37533 P37533]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00210]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00220]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=recR_28867_29463_1 recR] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaL_29481_29705_1 yaaL] {{PubMed|22383849}}
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''Regulatory mechanism:'''  
 
* '''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 =
Line 138: Line 137:
  
 
=References=
 
=References=
−
== Reviews ==
 
−
<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: unknown

Gene name yaaL
Synonyms
Essential no
Product unknown
Function unknown
Gene expression levels in SubtiExpress: yaaL
MW, pI 9 kDa, 10.329
Gene length, protein length 222 bp, 74 aa
Immediate neighbours recR, bofA
Sequences Protein DNA DNA_with_flanks
Genetic context
YaaL context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YaaL expression.png
























Categories containing this gene/protein

proteins of unknown function

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU00220

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:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • 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

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