Difference between revisions of "Sandbox"

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−
* '''Description:''' thymidylate kinase <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"  
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|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''tmk''
+
|''dnaX''
 
|-
 
|-
 
|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'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yaaP ''
+
|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'''
 
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
Line 18: Line 20:
 
|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'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || thymidylate kinase (EC 2.7.4.9)
+
|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'''
 
|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''' || nucleotide biosynthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA replication
 
|-
 
|-
 
|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'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 4.866  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 5.488  
 
|-
 
|-
 
|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'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1689 bp, 563 aa  
 
|-
 
|-
 
|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'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaO]]'', ''[[yaaQ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[scr]]'', ''[[yaaK]]''
 
|-
 
|-
 
|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'''
Line 40: Line 42:
 
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-
 
|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'''
 
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
−
|-goettingen.de/tmk_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|-goettingen.de/dnaX_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-
 
|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'''
 
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
−
|-goettingen.de/tmk_protein.txt Protein sequence]'''
+
|-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:tmk_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'''
 
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
Line 69: Line 71:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/tmk.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaX.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10092]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10083]
  
 
=== Additional information===
 
=== Additional information===
Line 98: 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 148: Line 154:
 
=References=
 
=References=
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-
+
# 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'''
 
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
−
|-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
|-2146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

Revision as of 12:18, 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

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