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New page: * '''Description:''' write here <br/><br/> {| align="right" border="1" cellpadding="2" |- |style="background:#ABCDEF;" align="center"|'''Gene name''' |''yqfR'' |- |style="background:#ABC...
 
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* '''Description:''' write here <br/><br/>
{{#bank: cshB}}
* '''Description:''' [[DEAD-box RNA helicases|DEAD-box RNA helicase]], important for adaptation to low temperatures<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'''
|''yqfR''
|''cshB ''
|-
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqfR''
|-
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|-
|style="background:#ABCDEF;" align="center"| '''Product''' ||  
|style="background:#ABCDEF;" align="center"| '''Product''' || [[DEAD-box RNA helicases|DEAD-box RNA helicase]]
|-
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
|-
|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=BSU25140 cshB]
|-
|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=CshB CshB]
|-
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 9.89   
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 9.89   
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1314 bp, 438 aa  
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1314 bp, 438 aa  
|-
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nfo]]'', ''[[yqfQ]]''
|-
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yqfR_nucleotide.txt    Gene sequence     (+200bp)  ]'''
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU25140 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU25140 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU25140 DNA_with_flanks]
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yqfR_protein.txt Protein sequence]'''
|-
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:yqfR_context.gif]]
|colspan="2" | '''Genetic context''' <br/> [[Image:yqfR_context.gif]]
<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=cshB_2594184_2595500_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:cshB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU25140]]
|-
|-
|}
|}


__TOC__
__TOC__
<br/><br/><br/><br/>
<br/><br/><br/><br/>
<br/><br/><br/><br/>
<br/><br/>
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[DEAD-box RNA helicases]]}},
{{SubtiWiki category|[[translation]]}}
= This gene is a member of the following [[regulons]] =


<br/><br/>


=The gene=
=The gene=
Line 35: Line 51:
=== Basic information ===
=== Basic information ===


* '''Coordinates:'''
* '''Locus tag:''' BSU25140


===Phenotypes of a mutant ===
===Phenotypes of a mutant ===
* poor growth at low temperatures (16 to 20°C) {{PubMed|23175651}}


=== Database entries ===
=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU25140&redirect=T BSU25140]


* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqfR.html]
* '''DBTBS entry:''' no entry


* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11664]
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11664]
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* '''Catalyzed reaction/ biological activity:'''  
* '''Catalyzed reaction/ biological activity:'''  
** RNA helicase
** required for [[ribosome]] assembly {{PubMed|23175651}}


* '''Protein family:'''
* '''Protein family:''' [[DEAD-box RNA helicases|DEAD-box RNA helicase]]


* '''Paralogous protein(s):'''
* '''Paralogous protein(s):''' [[CshA]], [[DeaD]], [[YfmL]]


=== Extended information on the protein ===
=== Extended information on the protein ===
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* '''Effectors of protein activity:'''
* '''Effectors of protein activity:'''


* '''Interactions:'''
* '''[[SubtInteract|Interactions]]:'''
** [[CshB]]-[[CspB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]
** [[CshB]]-[[DeaD]] {{PubMed|20572937}}


* '''Localization:'''
* '''[[Localization]]:''' cytoplasma, colocalizes with the ribosomes [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]


=== Database entries ===
=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU25140&redirect=T BSU25140]


* '''Structure:'''
* '''Structure:'''


* '''Swiss prot entry:'''
* '''UniProt:''' [http://www.uniprot.org/uniprot/P54475 P54475]


* '''KEGG entry:'''
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25140]


* '''E.C. number:'''
* '''E.C. number:'''
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* '''Operon:'''  
* '''Operon:'''  


* '''Sigma factor:'''  
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cshB_2594184_2595500_-1 cshB] {{PubMed|22383849}}
 
* '''[[Sigma factor]]:'''  


* '''Regulation:'''  
* '''Regulation:'''  
** well expressed in complex medium, poorly expressed in minimal medium {{PubMed|20572937}}
** expression declines in stationary phase {{PubMed|23175651,20572937}}


* '''Regulatory mechanism:'''  
* '''Regulatory mechanism:'''  


* '''Additional information:'''  
* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium): 141 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 526 {{PubMed|24696501}}


=Biological materials =
=Biological materials =


* '''Mutant:'''
* '''Mutant:'''  
** GP1051 (cat), available in [[Jörg Stülke]]'s lab


* '''Expression vector:'''
* '''Expression vector:'''
       
** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], expression from the native chromomsomal site: GP1064 (spc), available in [[Jörg Stülke]]'s lab
 
* '''lacZ fusion:'''
* '''lacZ fusion:'''


* '''GFP fusion:'''
* '''GFP fusion:'''


* '''two-hybrid system:'''  
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
 
* '''FLAG-tag construct:'''
** GP1011 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab


* '''Antibody:'''
* '''Antibody:'''


=Labs working on this gene/protein=
=Labs working on this gene/protein=
[[Mohamed Marahiel]], Marburg University, Germany [http://www.uni-marburg.de/fb15/fachgebiete/bio/marahiel?language_sync=1 homepage]


=Your additional remarks=
=Your additional remarks=


=References=
=References=
 
'''Additional publications:''' {{PubMed|20709848}}
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
<pubmed>16352840,, 12399512, 20572937 23175651</pubmed>
[[Category:Protein-coding genes]]

Latest revision as of 11:50, 10 November 2015

cshB

Gene name cshB
Synonyms yqfR
Essential no
Product DEAD-box RNA helicase
Function RNA helicase
Gene expression levels in SubtiExpress: cshB
Interactions involving this protein in SubtInteract: CshB
MW, pI 49 kDa, 9.89
Gene length, protein length 1314 bp, 438 aa
Immediate neighbours nfo, yqfQ
Sequences Protein DNA DNA_with_flanks
Genetic context
This image was kindly provided by SubtiList
Expression at a glance   PubMed















Categories containing this gene/protein

DEAD-box RNA helicases, translation

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU25140

Phenotypes of a mutant

  • poor growth at low temperatures (16 to 20°C) PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:

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:
  • Regulation:
    • well expressed in complex medium, poorly expressed in minimal medium PubMed
    • expression declines in stationary phase PubMed
  • Regulatory mechanism:
  • Additional information:
    • number of protein molecules per cell (minimal medium with glucose and ammonium): 141 PubMed
    • number of protein molecules per cell (complex medium with amino acids, without glucose): 526 PubMed

Biological materials

  • Expression vector:
    • for expression/ purification from B. subtilis with C-terminal Strep-tag, for SPINE, expression from the native chromomsomal site: GP1064 (spc), available in Jörg Stülke's lab
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jörg Stülke's lab
  • Antibody:

Labs working on this gene/protein

Mohamed Marahiel, Marburg University, Germany homepage

Your additional remarks

References

Additional publications: PubMed <pubmed>16352840,, 12399512, 20572937 23175651</pubmed>

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