Difference between revisions of "Sandbox"

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* '''Description:''' aspartate carbamoyltransferase <br/><br/>
+
* '''Description:''' dihydroorotase <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'''
−
|''pyrB''
+
|''pyrC''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || aspartate carbamoyltransferase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || dihydroorotase
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || pyrimidine biosynthesis
 
|style="background:#ABCDEF;" align="center"|'''Function''' || pyrimidine biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 5.341  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 5.427  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 912 bp, 304 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1284 bp, 428 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pyrP]]'', ''[[pyrC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pyrB]]'', ''[[pyrAA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13423&#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:CAB13424&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pyrC_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:pyrB_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:''' [http://dbtbs.hgc.jp/COG/prom/pyrRPBCAAABKDFE.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pyrRPBCAAABKDFE.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10713]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10714]
  
 
=== Additional information===
 
=== Additional information===
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' ATCase/OTCase family (according to Swiss-Prot)
+
* '''Protein family:''' Type 2 subfamily (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[PucH]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on Ser-303 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2AT2 2AT2]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P05654 P05654]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P25995 P25995]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15490]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15500]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.1.3.2 2.1.3.2]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.5.2.3 3.5.2.3]
  
 
=== 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=
  
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* '''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 =
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]
 
−
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 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 21:59, 11 May 2009

  • Description: dihydroorotase

Gene name pyrC
Synonyms
Essential no
Product dihydroorotase
Function pyrimidine biosynthesis
MW, pI 46 kDa, 5.427
Gene length, protein length 1284 bp, 428 aa
Immediate neighbours pyrB, pyrAA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PyrC 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: Type 2 subfamily (according to Swiss-Prot)
  • Paralogous protein(s): PucH

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • KEGG entry: [3]

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