Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' unknown <br/><br/>
+
* '''Description:''' replication initiation protein <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
Line 6: Line 6:
 
  |-
 
  |-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''yaaB''
+
|''dnaA''
 
|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''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dnaJ, dnaK ''
 
|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"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|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"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || replication initiation protein
 
|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"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA replication
 
|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"| '''MW, pI''' || 5 kDa, 8.796  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 6.035  
 
|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''' || 156 bp, 52 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1338 bp, 446 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''' || ''[[recF]]'', ''[[gyrB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpmH]]'', ''[[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>
Line 40: Line 40:
 
|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/yaaB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
  |-goettingen.de/dnaA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 
|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/yaaB_protein.txt Protein sequence]'''
+
  |-goettingen.de/dnaA_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:yaaB_context.gif]].*
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dnaA_context.gif]]
−
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
+
|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>
 
  |-
 
  |-
Line 65: Line 64:
  
 
===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/yaaAcontext.gif]].*
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html]
−
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
−
|-recFcontext.gif]].*
 
−
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
−
|-yaaBcontext.gif]].*
 
−
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
−
|-gyrB.html]
 
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10069]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10065]
  
 
=== Additional information===
 
=== Additional information===
Line 103: Line 98:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[DnaA]]context.gif]].*
 +
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 +
|-[[YabA]]context.gif]].*
 +
<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]].*
 +
<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]
  
−
* '''Localization:'''
+
* '''Localization:''' throughout the cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 115: Line 116:
 
* '''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+BSU00050]
+
  |-bin/www_bget?bsu+BSU00010]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 123: Line 124:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[yaaA]]context.gif]].*
+
* '''Operon:''' ''[[dnaA]]context.gif]].*
−
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
−
|-[[recF]]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>
−
  |-[[yaaB]]context.gif]].*
+
  |-[[dnaN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
−
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 
−
|-[[gyrB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
 
  
−
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' negatively controlled by [[DnaA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2168872 PubMed] and [[Spo0A]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
Line 156: Line 153:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
[[Philippe Noirot]], Jouycontext.gif]].*
 +
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 +
|-encontext.gif]].*
 +
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 +
|-Josas, France [http://locus.jouy.inra.fr/cms/index.php?id=18 homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 161: Line 163:
 
=References=
 
=References=
  
 +
# Imai et al. (2000) Subcellular localization of Dnacontext.gif]].*
 +
<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]].*
 +
<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]
 +
# Ishigocontext.gif]].*
 +
<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]].*
 +
<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]
 +
# Noirotcontext.gif]].*
 +
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 +
|-Gros et al. (2002) An expanded view of bacterial DNA replication. ''Proc. Natl. Acad. Sci. USA'' '''99:''' 8342context.gif]].*
 +
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 +
|-8347. [http://www.ncbi.nlm.nih.gov/sites/entrez/12060778 PubMed]
 +
# Noirotcontext.gif]].*
 +
<div align="right"> <small>this image is kindly was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>
 +
|-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]].*
 +
<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]
 
# 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]].*
 
# 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>
 
  |-2279. [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
 
  |-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]].*
 +
<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]

Revision as of 10:34, 23 March 2009

  • Description: replication initiation protein

context.gif]].*
this image is kindly was kindly provided by SubtiList
Gene name dnaA context.gif]].*
this image is kindly was kindly provided by SubtiList
Synonyms dnaH, dnaJ, 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 replication initiation protein 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 50 kDa, 6.035 context.gif]].*
this image is kindly was kindly provided by SubtiList
Gene length, protein length 1338 bp, 446 aa context.gif]].*
this image is kindly was kindly provided by SubtiList
Immediate neighbours rpmH, dnaN 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
DnaA context.gif 		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, DnaAcontext.gif]].*
this image is kindly was kindly provided by SubtiList 
|-DnaD PubMed
  • Localization: throughout the cytoplasm PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [5]].*
this image is kindly was kindly provided by SubtiList 
|-bin/www_bget?bsu+BSU00010]
  • E.C. number:

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. Imai et al. (2000) Subcellular localization of Dnacontext.gif]].*
this image is kindly was kindly provided by SubtiList 
|-initiation proteins of Bacillus subtilis: evidence that chromosome replication begins at either edge of the nucleoids. Mol. Microbiol. 36: 1037context.gif]].*
this image is kindly was kindly provided by SubtiList 
|-1048. PubMed
  1. Ishigocontext.gif]].*
this image is kindly was kindly provided by SubtiList 
|-Oka et al. (2001) DnaD protein of Bacillus subtilis interacts with DnaA, the initiator protein of replication. J. Bacteriol. 183: 2148context.gif]].*
this image is kindly was kindly provided by SubtiList 
|-2150. 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. 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. 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. Author1, Author2 & Author3 (year) Title Journal volume: pagecontext.gif]].*
this image is kindly was kindly provided by SubtiList 
|-page. PubMed