Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' inhibitor of pro-[[SigK]] processing<br/><br/>
+
* '''Description:''' DNA polymerase III (gamma and tau subunits)DNA polymerase III (gamma and tau subunits)<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'''
−
|''bofA''
+
|''dnaX''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dna-8132 ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' ||  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase III (gamma and tau subunits) (EC 2.7.7.7)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of the pro-sigma-K processing machinery
+
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA replication
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 9.32  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 5.488  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 261 bp, 87 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1689 bp, 563 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaL]]'', ''[[rrnA-16S]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[scr]]'', ''[[yaaK]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/bofA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dnaX_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/bofA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dnaX_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: Arne has a very small and smelling pimple between his legs'''
 
|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:bofA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dnaX_context.gif]]
 
|-
 
|-
 
|}
 
|}
Line 41: Line 41:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/bofA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaX.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10087]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10083]
  
 
=== Additional information===
 
=== Additional information===
Line 73: Line 75:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[BofA]]-[[SpoIVB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15292188 PubMed]
+
* '''Interactions:''' [[DnaX]]-[[DnaB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14757052 PubMed]
 +
 
 +
* '''Localization:''' nucleoid region (mid-cell spot) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
−
* '''Localization:'''
 
−
 
 
=== Database entries ===
 
=== Database entries ===
  
Line 91: Line 93:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''bofA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigE]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' expressed during sporulation  [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' repressed by [[SpoIIID]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 116: Line 118:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
Simon Cutting, London, UK [http://personal.rhul.ac.uk/uhba/009/bacillus/simon_cutting.html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 123: Line 123:
 
=References=
 
=References=
  
−
# Dong & Cutting (2004) The PDZ domain of the SpoIVB transmembrane signaling protein enables cis-trans interactions involving multiple partners leading to the activation of the pro-sigmaK processing complex in ''Bacillus subtilis''.''J. Biol. Chem.'' '''279:''' 43468-43478. [http://www.ncbi.nlm.nih.gov/sites/entrez/15292188 PubMed]
+
# Haroniti et al. (2004) The clamp-loader-helicase interaction in ''Bacillus''. Atomic force microscopy reveals the structural organisation of the DnaB-tau complex in ''Bacillus''.''J. Mol. Biol.'' '''336:''' 381-393. [http://www.ncbi.nlm.nih.gov/sites/entrez/14757052 PubMed]
−
# Ireton & Grossman (1992 ) Interactions among mutations that cause altered timing of gene expression during sporulation in ''Bacillus subtilis''. ''J. Bacteriol.'' '''174:''' 3185-3195. [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
# Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory ''Proteomics'' '''6:''' 2135-2146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

Revision as of 12:23, 23 February 2009

  • Description: DNA polymerase III (gamma and tau subunits)DNA polymerase III (gamma and tau subunits)

Gene name dnaX
Synonyms dnaH, dna-8132
Essential yes PubMed
Product DNA polymerase III (gamma and tau subunits) (EC 2.7.7.7)
Function DNA replication
MW, pI 62 kDa, 5.488
Gene length, protein length 1689 bp, 563 aa
Immediate neighbours scr, yaaK
Gene sequence (+200bp) Protein sequence
Caution: Arne has a very small and smelling pimple between his legs
Genetic context
DnaX context.gif



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

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:
  • Localization: nucleoid region (mid-cell spot) PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • 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

  1. Haroniti et al. (2004) The clamp-loader-helicase interaction in Bacillus. Atomic force microscopy reveals the structural organisation of the DnaB-tau complex in Bacillus.J. Mol. Biol. 336: 381-393. PubMed
  2. Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory Proteomics 6: 2135-2146. PubMed
Retrieved from "http://134.76.20.203/wiki//index.php?title=Sandbox&oldid=23414"