Difference between revisions of "Sandbox"

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* '''Description:''' threonyl-tRNA synthetase (major) <br/><br/>
+
* '''Description:''' threonyl-tRNA synthetase (minor) <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'''
|''thrS''
+
|''thrZ''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''thrS2 ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || threonyl-tRNA synthetase (major)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || threonyl-tRNA synthetase (minor)
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || translation  
 
|style="background:#ABCDEF;" align="center"|'''Function''' || translation  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 73 kDa, 5.214  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 73 kDa, 5.753  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1929 bp, 643 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1914 bp, 638 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ysaA]]'', ''[[ytxC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywhA]]'', ''[[mmr]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14855&#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:CAB15783&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
 
|-
 
|-
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:thrS_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:thrZ_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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__TOC__
 
__TOC__
  
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 37: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
* '''Locus tag:''' BSU28950
+
* '''Locus tag:''' BSU37560
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/thrS.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/thrZ-ywhA.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10362]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10421]
  
 
=== Additional information===
 
=== Additional information===
Line 58: Line 58:
 
* '''Protein family:''' class-II aminoacyl-tRNA synthetase family (according to Swiss-Prot)
 
* '''Protein family:''' class-II aminoacyl-tRNA synthetase family (according to Swiss-Prot)
  
* '''Paralogous protein(s):''' [[ThrZ]], one of the two proteins has to be present for viability [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
+
* '''Paralogous protein(s):''' [[ThrS]], one of the two proteins has to be present for viability [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 74: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
* '''Localization:'''
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
Line 80: Line 80:
 
* '''Structure:'''
 
* '''Structure:'''
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P18255 P18255]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P18256 P18256]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28950]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37560]
  
 
* '''E.C. number:''' [http://www.expasy.org/enzyme/6.1.1.3 6.1.1.3]
 
* '''E.C. number:''' [http://www.expasy.org/enzyme/6.1.1.3 6.1.1.3]
Line 121: Line 121:
 
=References=
 
=References=
  
<pubmed>8288542,1379177,19258532,7476165,12136084,,17114254, </pubmed>
+
<pubmed>19258532,8288542,,1379177,17114254, </pubmed>
 
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
# Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
 
# Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 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 08:58, 13 June 2009

  • Description: threonyl-tRNA synthetase (minor)

Gene name thrZ
Synonyms thrS2
Essential no
Product threonyl-tRNA synthetase (minor)
Function translation
MW, pI 73 kDa, 5.753
Gene length, protein length 1914 bp, 638 aa
Immediate neighbours ywhA, mmr
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ThrZ context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU37560

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr) (according to Swiss-Prot)
  • Protein family: class-II aminoacyl-tRNA synthetase family (according to Swiss-Prot)
  • Paralogous protein(s): ThrS, one of the two proteins has to be present for viability PubMed

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information: subject to Clp-dependent proteolysis upon glucose starvation PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 PubMed
  2. Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed