Difference between revisions of "Sandbox"

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* '''Description:''' threonyl-tRNA synthetase (minor) <br/><br/>
+
* '''Description:''' penicillin-binding protein 2d <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'''
−
|''thrZ''
+
|''pbpG''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''thrS2 ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywhE ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || threonyl-tRNA synthetase (minor)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || penicillin-binding protein 2d
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || bifunctional glucosyltransferase/ transpeptidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 73 kDa, 5.753  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 71 kDa, 9.392  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1914 bp, 638 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1941 bp, 647 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywhA]]'', ''[[mmr]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[speE]]'', ''[[ywhD]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15778&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ywhE_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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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/thrZ-ywhA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywhE.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10421]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12459]
  
 
=== Additional information===
 
=== Additional information===
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* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''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]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 74: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' prespore [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37560]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37510]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 86:
 
=== Additional information===
 
=== Additional information===
  
−
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
 
=Expression and regulation=
 
=Expression and regulation=
  
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigF]],  [[SigG]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' expressed in prespore
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:'''  
+
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jeff Errington]] lab
  
 
* '''Antibody:'''
 
* '''Antibody:'''
Line 121: Line 118:
 
=References=
 
=References=
  
−
# 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]
 
 
# 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 23:54, 16 April 2009

  • Description: penicillin-binding protein 2d

Gene name pbpG
Synonyms ywhE
Essential no
Product penicillin-binding protein 2d
Function bifunctional glucosyltransferase/ transpeptidase
MW, pI 71 kDa, 9.392
Gene length, protein length 1941 bp, 647 aa
Immediate neighbours speE, ywhD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YwhE context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

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:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation: expressed in prespore
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jeff Errington lab
  • 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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