Difference between revisions of "Sandbox"

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* '''Description:''' write here <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"  
 +
|-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''yaaB''
+
|''dnaX''
 +
|-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dna-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-8132 ''
 +
|-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 +
|-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase III (gamma and tau subunits) (EC 2.7.7.7)
 +
|-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-
 +
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA replication
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 5.488 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' ||
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1689 bp, 563 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 8.796 
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 156 bp, 52 aa
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[scr]]'', ''[[yaaK]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[recF]]'', ''[[gyrB]]''
+
|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/yaaB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yaaB_protein.txt Protein sequence]'''
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-goettingen.de/dnaX_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 +
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-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: The sequence for this gene in SubtiList contains errors'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yaaB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dnaX_context.gif]]
 +
|-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 
|-
 
|-
 
|}
 
|}
Line 40: Line 66:
  
 
===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/yaaA-recF-yaaB-gyrB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaX.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10069]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10083]
  
 
=== Additional information===
 
=== Additional information===
Line 72: Line 100:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[DnaX]]-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-[[DnaB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14757052 PubMed]
  
−
* '''Localization:'''
+
* '''Localization:''' nucleoid region (mid-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-cell spot) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 90: Line 122:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[yaaA]]-[[recF]]-[[yaaB]]-[[gyrB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 98: Line 130:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 110: Line 142:
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:'''  
+
* '''two-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-hybrid system:'''  
  
 
* '''Antibody:'''
 
* '''Antibody:'''
Line 120: Line 154:
 
=References=
 
=References=
  
−
# 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:''' 2267-2279. [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
# Haroniti et al. (2004) The clamp-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-loader-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-helicase interaction in ''Bacillus''. Atomic force microscopy reveals the structural organisation of the DnaB-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-tau complex in ''Bacillus''.''J. Mol. Biol.'' '''336:''' 381-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-393. [http://www.ncbi.nlm.nih.gov/sites/entrez/14757052 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-
 +
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 +
|-2146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

Revision as of 12:14, 23 February 2009

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

Caution: The sequence for this gene in SubtiList contains errors
Gene name dnaX
Caution: The sequence for this gene in SubtiList contains errors
Synonyms dnaH, dna- Caution: The sequence for this gene in SubtiList contains errors
Caution: The sequence for this gene in SubtiList contains errors
Essential yes PubMed
Caution: The sequence for this gene in SubtiList contains errors
Product DNA polymerase III (gamma and tau subunits) (EC 2.7.7.7)
Caution: The sequence for this gene in SubtiList contains errors
Function DNA replication
Caution: The sequence for this gene in SubtiList contains errors
MW, pI 62 kDa, 5.488
Caution: The sequence for this gene in SubtiList contains errors
Gene length, protein length 1689 bp, 563 aa
Caution: The sequence for this gene in SubtiList contains errors
Immediate neighbours scr, yaaK
Caution: The sequence for this gene in SubtiList contains errors
[http://subtiwiki.uni- Caution: The sequence for this gene in SubtiList contains errors
[http://subtiwiki.uni- Caution: The sequence for this gene in SubtiList contains errors
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
DnaX context.gif
Caution: The sequence for this gene in SubtiList contains errors



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:
  • Interactions: DnaX-

|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | Caution: The sequence for this gene in SubtiList contains errors |-DnaB PubMed

  • Localization: nucleoid region (mid-

|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | Caution: The sequence for this gene in SubtiList contains errors |-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-

|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | Caution: The sequence for this gene in SubtiList contains errors |-hybrid system:

  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Haroniti et al. (2004) The clamp-

|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | Caution: The sequence for this gene in SubtiList contains errors |-loader- |colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | Caution: The sequence for this gene in SubtiList contains errors |-helicase interaction in Bacillus. Atomic force microscopy reveals the structural organisation of the DnaB- |colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | Caution: The sequence for this gene in SubtiList contains errors |-tau complex in Bacillus.J. Mol. Biol. 336: 381- |colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | Caution: The sequence for this gene in SubtiList contains errors |-393. 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: 2135-

|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | Caution: The sequence for this gene in SubtiList contains errors |-2146. PubMed

Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=23407"