Difference between revisions of "Sandbox"

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Line 4: Line 4:
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''rbsD''
+
|''oppA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0KA ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || ribose ABC transporter (membrane protein)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || oligopeptide ABC transporter (binding protein)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || ribose transport
+
|style="background:#ABCDEF;" align="center"|'''Function''' || required for initiation of sporulation, competence development, and oligopeptide transport
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 4.987  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61 kDa, 5.722  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 393 bp, 131 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1635 bp, 545 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rbsK]]'', ''[[rbsA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trpS]]'', ''[[oppB]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rbsD_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/oppA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rbsD_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/oppA_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rbsD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:oppA_context.gif]]
 
|-
 
|-
 
|}
 
|}
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rbsRKDACB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/oppABCDF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10878]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10771]
  
 
=== Additional information===
 
=== Additional information===
Line 88: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[rbsR]]-[[rbsK]]-[[rbsD]]-[[rbsA]]-[[rbsC]]-[[rbsB]]''
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 96: Line 96:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 118: Line 118:
 
=References=
 
=References=
  
−
# Kim MS, Shin J, Lee W, Lee HS, Oh BH. (2003) Crystal structures of RbsD leading to the identification of cytoplasmic sugar-binding proteins with a novel folding architecture. ''J Biol Chem. '' '''Jul 25;278(30):''' 28173-80. [http://www.ncbi.nlm.nih.gov/sites/entrez/12738765 PubMed]
 
−
# Woodson K, Devine KM. (1994) Analysis of a ribose transport operon from Bacillus subtilis. ''Microbiology. '' '''Aug;140 ( Pt 8):''' 1829-38. [http://www.ncbi.nlm.nih.gov/sites/entrez/7921236 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 16:52, 9 March 2009

  • Description: write here

Gene name oppA
Synonyms spo0KA
Essential no
Product oligopeptide ABC transporter (binding protein)
Function required for initiation of sporulation, competence development, and oligopeptide transport
MW, pI 61 kDa, 5.722
Gene length, protein length 1635 bp, 545 aa
Immediate neighbours trpS, oppB
Gene sequence (+200bp) Protein sequence
Genetic context
OppA context.gif



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:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • 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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