Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' ATP-dependent Clp protease ATP-binding subunit (class III heat-shock protein) <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'''
−
|''clpX''
+
|''yqeK''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
Line 10: Line 10:
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent Clp protease ATP-binding subunit
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 5.967 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.645 
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 558 bp, 186 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1260 bp, 420 aa
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqeL]]'', ''[[nadD]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lonB]]'', ''[[tig]]''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14505&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14782&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yqeK_context.gif]]
−
|-
 
−
|-
 
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:clpX_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>
 
|-
 
|-
Line 39: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU28220
+
* '''Locus tag:''' BSU25630
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 45: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/clpX.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11387]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11639]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATPase/chaperone
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' clpX chaperone family (according to Swiss-Prot) ClpX (IP004487) [http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004487 InterPro], AAA+ -type ATPase (IPR013093) [http://www.ebi.ac.uk/interpro/IEntry?ac=IPR013093 InterPro] (PF07724) [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM]
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[ClpC]], [[ClpE]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 66: Line 62:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:''' AAA-ATPase [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM], Zinc finger [http://pfam.sanger.ac.uk/family?acc=PF06689 PFAM]
+
* '''Domains:'''  
  
 
* '''Modification:'''
 
* '''Modification:'''
Line 74: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[ClpP]]-[[ClpX]]
+
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasmic polar clusters, excluded from the nucleoid, induced clustering upon heatshock, colocalization with [[ClpP]] [http://www.ncbi.nlm.nih.gov/pubmed/18786145 Pubmed]
+
* '''Localization:'''
−
[[File:ClpX.jpg‎ ]]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' homologue structure resolved [http://www.rcsb.org/pdb/explore/explore.do?structureId=1UM8 1UM8], structural model of ''B. subtilis'' ClpX available from [http://subtiwiki.uni-goettingen.de/wiki/index.php/User:Hstrahl hstrahl]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P50866 P50866]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54456 P54456]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28220]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25630]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 105: Line 100:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' ''clpX::kan'', ''clpX::spec'' and ''clpX::cat'' available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 111: Line 106:
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
−
* '''GFP fusion:''' C-terminal GFP fusions (both single copy and 2th copy in ''amyE'' locus, also as CFP and YFP variants) available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
+
* '''GFP fusion:'''
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
Line 118: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
[[Leendert Hamoen]], Newcastle University, UK [http://www.ncl.ac.uk/camb/staff/profile/l.hamoen homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
−
 
−
<pubmed> 19136590 , 9643546, 18786145 </pubmed>
 
  
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 20:55, 12 June 2009

  • Description: unknown

Gene name yqeK
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 21 kDa, 5.967
Gene length, protein length 558 bp, 186 aa
Immediate neighbours yqeL, nadD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YqeK context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU25630

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:
  • Interactions:
  • Localization:

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • 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

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=92555"