Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
* '''Description:''' dihydoorotic acid dehydrogenase (catalytic subunit) <br/><br/>
+
* '''Description:''' orotidine 5'-phosphate decarboxylase <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'''
|''pyrD''
+
|''pyrF''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pyrDI ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || dihydoorotic acid dehydrogenase (catalytic subunit)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || orotidine-5'-phosphate decarboxylase
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || pyrimidine biosynthesis
 
|style="background:#ABCDEF;" align="center"|'''Function''' || pyrimidine biosynthesis
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 4.942  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 5.835  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 933 bp, 311 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 717 bp, 239 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pyrK]]'', ''[[pyrF]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pyrD]]'', ''[[pyrE]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13428&#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:CAB13429&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:pyrD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pyrF_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>
 
|-
 
|-
Line 43: Line 43:
 
* '''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+BG10718]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10719]
  
 
=== Additional information===
 
=== Additional information===
Line 72: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
* '''Localization:''' cytoplasm (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1DBT 1DBT]
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P25996 P25996]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P25971 P25971]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15540]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15550]
  
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.3.3.1 1.3.3.1]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.1.23 4.1.1.23]
  
 
=== Additional information===
 
=== Additional information===

Revision as of 22:00, 11 May 2009

  • Description: orotidine 5'-phosphate decarboxylase

Gene name pyrF
Synonyms
Essential no
Product orotidine-5'-phosphate decarboxylase
Function pyrimidine biosynthesis
MW, pI 25 kDa, 5.835
Gene length, protein length 717 bp, 239 aa
Immediate neighbours pyrD, pyrE
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PyrF 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 1 subfamily (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • 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