Difference between revisions of "Sandbox"

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−
* '''Description:''' inhibitor of pro-
+
* '''Description:''' thymidylate kinase <br/><br/>
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 
−
|-[[SigK]] processing<br/><br/>
 
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
Line 8: Line 6:
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''bofA''
+
|''tmk''
 
|-
 
|-
 
|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''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yaaP ''
 
|-
 
|-
 
|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"| '''Essential''' || no
+
|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'''
 
|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''' ||  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || thymidylate kinase (EC 2.7.4.9)
 
|-
 
|-
 
|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''' || inhibition of the pro-
+
|style="background:#ABCDEF;" align="center"|'''Function''' || nucleotide biosynthesis
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 
−
|-sigma-
 
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 
−
|-K processing machinery
 
 
|-
 
|-
 
|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''' || 8 kDa, 9.32  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 4.866  
 
|-
 
|-
 
|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''' || 261 bp, 87 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 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''' || ''[[yaaL]]'', ''[[rrnA-
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaO]]'', ''[[yaaQ]]''
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 
−
|-16S]]''
 
 
|-
 
|-
 
|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 48: Line 40:
 
|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/bofA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|-goettingen.de/tmk_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/bofA_protein.txt Protein sequence]'''
+
|-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]]
 
|-
 
|-
 
|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 72: 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/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 104: Line 98:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[BofA]]-
+
* '''Interactions:'''
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 
−
|-[[SpoIVB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15292188 PubMed]
 
  
 
* '''Localization:'''
 
* '''Localization:'''
−
+
 
 
=== Database entries ===
 
=== Database entries ===
  
Line 124: Line 116:
 
=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 151: Line 143:
  
 
=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 158: Line 148:
 
=References=
 
=References=
  
−
# Dong & Cutting (2004) The PDZ domain of the SpoIVB transmembrane signaling protein enables cis-
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 
−
|-trans interactions involving multiple partners leading to the activation of the pro-
 
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 
−
|-sigmaK processing complex in ''Bacillus subtilis''.''J. Biol. Chem.'' '''279:''' 43468-
 
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors'''
 
−
|-43478. [http://www.ncbi.nlm.nih.gov/sites/entrez/15292188 PubMed]
 
−
# Ireton & Grossman (1992 ) Interactions among mutations that cause altered timing of gene expression during sporulation in ''Bacillus subtilis''. ''J. Bacteriol.'' '''174:''' 3185-
 
 
|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'''
−
|-3195. [http://www.ncbi.nlm.nih.gov/sites/entrez/1315731 PubMed]
+
|-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 12:14, 23 February 2009

  • Description: thymidylate kinase

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

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

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

Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=23409"