Difference between revisions of "Sandbox"

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* '''Description:''' DNA polymerase III (gamma and tau subunits)DNA polymerase III (gamma and tau subunits)<br/><br/>
+
* '''Description:''' inhibitor of pro-[[SigK]] processing<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'''
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|''dnaX''
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|''bofA''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dna-8132 ''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase III (gamma and tau subunits) (EC 2.7.7.7)
+
|style="background:#ABCDEF;" align="center"| '''Product''' ||  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA replication
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|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of the pro-sigma-K processing machinery
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 5.488  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 9.32  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1689 bp, 563 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 261 bp, 87 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[scr]]'', ''[[yaaK]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaL]]'', ''[[rrnA-16S]]''
 
|-
 
|-
−
|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_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dnaX_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/bofA_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: The sequence for this gene in SubtiList contains errors
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:dnaX_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:bofA_context.gif]]
 
|-
 
|-
 
|}
 
|}
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===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/dnaX.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/bofA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10083]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10087]
  
 
=== Additional information===
 
=== Additional information===
Line 74: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[DnaX]]-[[DnaB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14757052 PubMed]
+
* '''Interactions:''' [[BofA]]-[[SpoIVB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15292188 PubMed]
−
 
 
−
* '''Localization:''' nucleoid region (mid-cell spot) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
 
  
 +
* '''Localization:'''
 +
 
=== Database entries ===
 
=== Database entries ===
  
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''bofA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
  
−
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigE]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' expressed during sporulation  [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' repressed by [[SpoIIID]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 117: Line 115:
  
 
=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 122: Line 122:
 
=References=
 
=References=
  
−
# 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]
+
# 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]
−
# 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]
+
# 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]

Revision as of 12:31, 23 February 2009

  • Description: inhibitor of pro-SigK processing

Gene name bofA
Synonyms
Essential no
Product
Function inhibition of the pro-sigma-K processing machinery
MW, pI 8 kDa, 9.32
Gene length, protein length 261 bp, 87 aa
Immediate neighbours yaaL, rrnA-16S
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
BofA context.gif



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

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:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: expressed during sporulation PubMed
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Simon Cutting, London, UK homepage

Your additional remarks

References

  1. 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. PubMed
  2. Ireton & Grossman (1992 ) Interactions among mutations that cause altered timing of gene expression during sporulation in Bacillus subtilis. J. Bacteriol. 174: 3185-3195. PubMed
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