Difference between revisions of "Sandbox"

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* '''Description:''' replication initiation protein <br/><br/>
+
* '''Description:''' DNA polymerase  III (gamma and tau subunits) <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
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  |-
 
  |-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''dnaA''
+
|''dnaN''
 
|context.gif]].*
 
|context.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  |-
 
  |-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dnaJ, dnaK ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaG, dnaK ''
 
|context.gif]].*
 
|context.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
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  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  |-
 
  |-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || replication initiation protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase  III (gamma and tau subunits)
 
|context.gif]].*
 
|context.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
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  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  |-
 
  |-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 6.035  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.718  
 
|context.gif]].*
 
|context.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  |-
 
  |-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1338 bp, 446 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1134 bp, 378 aa  
 
|context.gif]].*
 
|context.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  |-
 
  |-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpmH]]'', ''[[dnaN]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaA]]'', ''[[yaaA]]''
 
|context.gif]].*
 
|context.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.unicontext.gif]].*
 
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.unicontext.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
−
  |-goettingen.de/dnaA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
  |-goettingen.de/dnaN_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.unicontext.gif]].*
 
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.unicontext.gif]].*
 
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  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
−
  |-goettingen.de/dnaA_protein.txt Protein sequence]'''
+
  |-goettingen.de/dnaN_protein.txt Protein sequence]'''
 
|context.gif]].*
 
|context.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  |-
 
  |-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:dnaA_context.gif]].*
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dnaN_context.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  |-|context.gif]].*
 
  |-|context.gif]].*
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10065]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10066]
  
 
=== Additional information===
 
=== Additional information===
Line 103: Line 103:
 
  |-[[YabA]]context.gif]].*
 
  |-[[YabA]]context.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
−
  |-[[DnaN]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12060778 PubMed], [[DnaA]]context.gif]].*
+
  |-[[DnaN]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12060778 PubMed]
 +
 
 +
* '''Localization:''' nucleoid (midcontext.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
−
  |-[[DnaD]] [http://www.ncbi.nlm.nih.gov/sites/entrez/11222620 PubMed]
+
  |-cell spot) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
−
 
 
−
* '''Localization:''' throughout the cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
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* '''KEGG entry:''' [http://www.genome.jp/dbgetcontext.gif]].*
 
* '''KEGG entry:''' [http://www.genome.jp/dbgetcontext.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
−
  |-bin/www_bget?bsu+BSU00010]
+
  |-bin/www_bget?bsu+BSU00020]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' 2.7.7.7
  
 
=== Additional information===
 
=== Additional information===
Line 164: Line 164:
 
=References=
 
=References=
  
−
# Imai et al. (2000) Subcellular localization of Dnacontext.gif]].*
+
# Ogasawara et al. (1985) Structure and function of the region of the replication origin of the ''Bacillus subtilis'' chromosome. IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames.''Nucl. Acids Res.'' '''11:''' 2267context.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
−
  |-initiation proteins of ''Bacillus subtilis'': evidence that chromosome replication begins at either edge of the nucleoids. ''Mol. Microbiol.'' '''36:''' 1037context.gif]].*
+
  |-2279. [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
 +
# Fukuoka et al.  (1990) Purification and characterization of an initiation protein for chromosomal replication, DnaA, in ''Bacillus subtilis''. ''J. Biochem.'' '''107:''' 732context.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
−
  |-1048. [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed]
+
  |-739. [http://www.ncbi.nlm.nih.gov/sites/entrez/2168872 PubMed]
−
# Ishigocontext.gif]].*
+
# 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:''' 2135context.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
−
  |-Oka et al. (2001) DnaD protein of ''Bacillus subtilis'' interacts with DnaA, the initiator protein of replication. ''J. Bacteriol.'' '''183:''' 2148context.gif]].*
+
  |-2146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
 +
# Molle et al. (2003) The Spo0A regulon of ''Bacillus subtilis''.''Mol. Microbiol.'' '''50:''' 1683context.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
−
  |-2150. [http://www.ncbi.nlm.nih.gov/sites/entrez/11222620 PubMed]
+
  |-1701. [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
 
# Noirotcontext.gif]].*
 
# Noirotcontext.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
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  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  |-2373. [http://www.ncbi.nlm.nih.gov/sites/entrez/16461910 PubMed]
 
  |-2373. [http://www.ncbi.nlm.nih.gov/sites/entrez/16461910 PubMed]
−
# Ogasawara et al. (1985) Structure and function of the region of the replication origin of the ''Bacillus subtilis'' chromosome. IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames.''Nucl. Acids Res.'' '''11:''' 2267context.gif]].*
 
−
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
−
|-2279. [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
 
−
# Fukuoka et al.  (1990) Purification and characterization of an initiation protein for chromosomal replication, DnaA, in ''Bacillus subtilis''. ''J. Biochem.'' '''107:''' 732context.gif]].*
 
−
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
−
|-739. [http://www.ncbi.nlm.nih.gov/sites/entrez/2168872 PubMed]
 
−
# Molle et al. (2003) The Spo0A regulon of ''Bacillus subtilis''.''Mol. Microbiol.'' '''50:''' 1683context.gif]].*
 
−
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
−
|-1701. [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
 
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' pagecontext.gif]].*
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' pagecontext.gif]].*
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  <div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
  |-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
  |-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 10:32, 23 March 2009

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

this image is kindly was kindly provided by SubtiList
context.gif]].*
this image is kindly was kindly provided by SubtiList
Gene name dnaN context.gif]].*
this image is kindly was kindly provided by SubtiList
Synonyms dnaG, dnaK context.gif]].*
this image is kindly was kindly provided by SubtiList
Essential yes PubMed context.gif]].*
this image is kindly was kindly provided by SubtiList
Product DNA polymerase III (gamma and tau subunits) context.gif]].*
this image is kindly was kindly provided by SubtiList
Function DNA replication context.gif]].*
this image is kindly was kindly provided by SubtiList
MW, pI 41 kDa, 4.718 context.gif]].*
this image is kindly was kindly provided by SubtiList
Gene length, protein length 1134 bp, 378 aa context.gif]].*
this image is kindly was kindly provided by SubtiList
Immediate neighbours dnaA, yaaA context.gif]].*
this image is kindly was kindly provided by SubtiList
[1]].*
this image is kindly was kindly provided by SubtiList
[2]].*
this image is kindly was kindly provided by SubtiList
context.gif]].*
this image is kindly was kindly provided by SubtiList
Genetic context
DnaN context.gif.*
this image is kindly was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

Database entries

  • DBTBS entry: [3]
  • SubtiList entry: [4]

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:
this image is kindly was kindly provided by SubtiList 
|-YabAcontext.gif]].*
this image is kindly was kindly provided by SubtiList 
|-DnaN PubMed
  • Localization: nucleoid (midcontext.gif]].*
this image is kindly was kindly provided by SubtiList 
|-cell spot) PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [5]].*
this image is kindly was kindly provided by SubtiList 
|-bin/www_bget?bsu+BSU00020]
  • E.C. number: 2.7.7.7

Additional information

Expression and regulation

this image is kindly was kindly provided by SubtiList 
|-dnaN  PubMed
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • twocontext.gif]].*
this image is kindly was kindly provided by SubtiList 
|-hybrid system:
  • Antibody:

Labs working on this gene/protein

Philippe Noirot, Jouycontext.gif]].*

this image is kindly was kindly provided by SubtiList 
|-encontext.gif]].*
this image is kindly was kindly provided by SubtiList 
|-Josas, France homepage

Your additional remarks

References

  1. Ogasawara et al. (1985) Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames.Nucl. Acids Res. 11: 2267context.gif]].*
this image is kindly was kindly provided by SubtiList 
|-2279. PubMed
  1. Fukuoka et al. (1990) Purification and characterization of an initiation protein for chromosomal replication, DnaA, in Bacillus subtilis. J. Biochem. 107: 732context.gif]].*
this image is kindly was kindly provided by SubtiList 
|-739. PubMed
  1. 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: 2135context.gif]].*
this image is kindly was kindly provided by SubtiList 
|-2146. PubMed
  1. Molle et al. (2003) The Spo0A regulon of Bacillus subtilis.Mol. Microbiol. 50: 1683context.gif]].*
this image is kindly was kindly provided by SubtiList 
|-1701. PubMed
  1. Noirotcontext.gif]].*
this image is kindly was kindly provided by SubtiList 
|-Gros et al. (2002) An expanded view of bacterial DNA replication. Proc. Natl. Acad. Sci. USA 99: 8342context.gif]].*
this image is kindly was kindly provided by SubtiList 
|-8347. PubMed
  1. Noirotcontext.gif]].*
this image is kindly was kindly provided by SubtiList 
|-Gros et al. (2002) Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus Title Proc. Natl. Acad. Sci. USA 103: 2368context.gif]].*
this image is kindly was kindly provided by SubtiList 
|-2373. PubMed
  1. Author1, Author2 & Author3 (year) Title Journal volume: pagecontext.gif]].*
this image is kindly was kindly provided by SubtiList 
|-page. PubMed