Difference between revisions of "Sandbox"

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* '''Description:''' thymidylate kinase <br/><br/>
+
* '''Description:''' DNA polymerase III (delta subunit) <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'''
|''tmk''
+
|''holB''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yaaP ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yaaS ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || thymidylate kinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase III (delta subunit)
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TTP biosynthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || replication
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 4.866  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 6.334  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 987 bp, 329 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaO]]'', ''[[yaaQ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaR]]'', ''[[yaaT]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11804&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11807&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:holB_context.gif]]
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:tmk_context.gif]]
 
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
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* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10092]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10095]
  
 
=== Additional information===
 
=== Additional information===
Line 58: Line 56:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
* '''Protein family:''' thymidylate kinase family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 76: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
* '''Localization:'''
+
* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] cytoplasm (homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 82: Line 80:
 
* '''Structure:'''
 
* '''Structure:'''
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37537 P37537]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37540 P37540]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00280]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00310]
  
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.4.9 2.7.4.9]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.7.7 2.7.7.7]
  
 
=== Additional information===
 
=== Additional information===
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=References=
 
=References=
  
 +
# 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]
 +
# 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(7):''' 2135-46. [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 15:08, 12 May 2009

  • Description: DNA polymerase III (delta subunit)

Gene name holB
Synonyms yaaS
Essential yes PubMed
Product DNA polymerase III (delta subunit)
Function replication
MW, pI 37 kDa, 6.334
Gene length, protein length 987 bp, 329 aa
Immediate neighbours yaaR, yaaT
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
HolB context.gif
This image was kindly provided by SubtiList



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:
  • Interactions:
  • Localization: Cytoplasm (Homogeneous) PubMed cytoplasm (homogeneous) PubMed

Database entries

  • Structure:
  • KEGG entry: [2]

Additional information

Expression and regulation

  • Operon:
  • 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. 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
  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(7): 2135-46. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed