Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' penicillin-binding protein 5, D-alanyl-D-alanine carboxypeptidase <br/><br/>
+
* '''Description:''' riboflavin synthase (beta subunit) <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'''
−
|''dacB''
+
|''ribH''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
Line 10: Line 10:
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || penicillin-binding protein 5*, D-alanyl-D-alanine carboxypeptidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || riboflavin synthase (beta subunit)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || carboxypeptidase
+
|style="background:#ABCDEF;" align="center"|'''Function''' || riboflavin biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 9.725  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 5.196  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1146 bp, 382 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 462 bp, 154 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spmA]]'', ''[[ypuI]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ribT]]'', ''[[ribA]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dacB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ribH_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dacB_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ribH_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:dacB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ribH_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 42: Line 42:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dacB-spmAB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ypuE-ribDEAHT.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10527]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10521]
  
 
=== Additional information===
 
=== Additional information===
Line 55: Line 55:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' peptidase S11 family
+
* '''Protein family:''' DMRL synthase family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 81: Line 81:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23190]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23250]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 89: Line 89:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[dacB]]-[[spmA]]-[[spmB]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigE]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' expressed during sporulation in the mother cell [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =

Revision as of 05:22, 12 April 2009

  • Description: riboflavin synthase (beta subunit)

Gene name ribH
Synonyms
Essential no
Product riboflavin synthase (beta subunit)
Function riboflavin biosynthesis
MW, pI 16 kDa, 5.196
Gene length, protein length 462 bp, 154 aa
Immediate neighbours ribT, ribA
Gene sequence (+200bp) Protein sequence
Genetic context
RibH 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: DMRL synthase 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: [3]
  • E.C. number:

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
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=53072"