Difference between revisions of "Sandbox"

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−
* '''Description:''' inhibitor of pro-[[SigK]] processing<br/><br/>
+
* '''Description:''' thymidylate kinase <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'''
−
|''bofA''
+
|''tmk''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yaaP ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' ||  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || thymidylate kinase (EC 2.7.4.9)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of the pro-sigma-K processing machinery
+
|style="background:#ABCDEF;" align="center"|'''Function''' || nucleotide biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 9.32  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 4.866  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 261 bp, 87 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaL]]'', ''[[rrnA-16S]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaO]]'', ''[[yaaQ]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/bofA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/tmk_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/bofA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/tmk_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:bofA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:tmk_context.gif]]
 
|-
 
|-
 
|}
 
|}
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===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/bofA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/tmk.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10087]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10092]
  
 
=== Additional information===
 
=== Additional information===
Line 73: Line 75:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[BofA]]-[[SpoIVB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15292188 PubMed]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
−
+
 
 
=== Database entries ===
 
=== Database entries ===
  
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''bofA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigE]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' expressed during sporulation  [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' repressed by [[SpoIIID]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 116: Line 118:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
Simon Cutting, London, UK [http://personal.rhul.ac.uk/uhba/009/bacillus/simon_cutting.html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 123: Line 123:
 
=References=
 
=References=
  
−
# Dong & Cutting (2004) The PDZ domain of the SpoIVB transmembrane signaling protein enables cis-trans interactions involving multiple partners leading to the activation of the pro-sigmaK processing complex in ''Bacillus subtilis''.''J. Biol. Chem.'' '''279:''' 43468-43478. [http://www.ncbi.nlm.nih.gov/sites/entrez/15292188 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Ireton & Grossman (1992 ) Interactions among mutations that cause altered timing of gene expression during sporulation in ''Bacillus subtilis''. ''J. Bacteriol.'' '''174:''' 3185-3195. [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
 

Revision as of 12:25, 23 February 2009

  • Description: thymidylate kinase

Gene name tmk
Synonyms yaaP
Essential yes PubMed
Product thymidylate kinase (EC 2.7.4.9)
Function nucleotide biosynthesis
MW, pI 23 kDa, 4.866
Gene length, protein length 636 bp, 212 aa
Immediate neighbours yaaO, yaaQ
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
Tmk context.gif



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:
  • Localization:

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-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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