Difference between revisions of "Sandbox"

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* '''Description:''' 4.5 S RNA<br/><br/>
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* '''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'''
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|''scr''
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|''dnaX''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dna-8132 ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
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|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || small cytoplasmic RNA (scRNA, 4.5S RNA),  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase III (gamma and tau subunits) (EC 2.7.7.7)
−
 
+
|-
−
signal recognition particle-like (SRP) component
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|style="background:#ABCDEF;" align="center"|'''Function''' || DNA replication
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 5.488 
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1689 bp, 563 aa
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || presecretory protein translocation
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[scr]]'', ''[[yaaK]]''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaJ]]'', ''[[dnaX]]''
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|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/dnaX_protein.txt Protein sequence]'''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/scr_nucleotide.txt    Gene sequence      (+200bp)  ]'''
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/scr_protein.txt Protein sequence]'''
 
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:scr_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dnaX_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 ===
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* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00095]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10083]
 +
 
 +
=== 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:''' [[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]
 +
 
 +
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:'''
 +
 
 +
* '''Swiss prot entry:'''
 +
 
 +
* '''KEGG entry:'''
 +
 
 +
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[yaaJ]]-[[scr]],  [[scr]]''
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]] (both promoters)
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' transcribed as 354 nt precursor, cleaved at the 5' end by [[rnc| RNase III]] and at the 3' site by [[rnjA| RNase J1]] to yield a 275 nt molecule, final trimming to 271 nt sc RNA by [[rph| RNase PH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17576666 PubMed]
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
 +
 +
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
 +
 +
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# Yao, S., Blaustein, J. B. & Bechhofer, D. H. (2007). Processing of ''Bacillus subtilis'' small cytoplasmic RNA: evidence for an additional endonuclease cleavage site. Nucleic Acids Res. 35:4464-4473. [http://www.ncbi.nlm.nih.gov/sites/entrez/17576666 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]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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 13:46, 10 March 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: The sequence for this gene in SubtiList contains errors
Genetic context
DnaX context.gif



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

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:
  • 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
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