Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' extracellular non-specific endonuclease, Rnase <br/><br/>
+
* '''Description:''' involved in isopentenol (isoprenoid) biosynthesis <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'''
−
|''yhcR''
+
|''yhfR''
 
|-
 
|-
 
|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''' || extracellular non-specific endonuclease, Rnase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of nucleic acids
+
|style="background:#ABCDEF;" align="center"|'''Function''' || isoprenoid biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 132 kDa, 4.693  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 5.164  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 3651 bp, 1217 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 579 bp, 193 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhcQ]]'', ''[[yhcS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhfQ]]'', ''[[yhfS]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12747&#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:CAB12874&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yhcR_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yhfR_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 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU09190
+
* '''Locus tag:''' BSU10340
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
no detectable phenotype  [http://www.ncbi.nlm.nih.gov/sites/entrez/10869096 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 43: Line 45:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11596]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13062]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' unknown  [http://www.ncbi.nlm.nih.gov/sites/entrez/10869096 PubMed]
  
−
* '''Protein family:'''
+
* '''Protein family:''' GpmB subfamily (according to Swiss-Prot) similar to 2,3-diphosphoglycerate-dependent phosphoglycerate mutases  [http://www.ncbi.nlm.nih.gov/sites/entrez/10869096 PubMed]
  
−
* '''Paralogous protein(s):''' [[YfkN]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 72: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
Line 78: Line 80:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54602 P54602]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O07617 O07617]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU09190]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10340]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 96: Line 98:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:''' weakly expressed  [http://www.ncbi.nlm.nih.gov/sites/entrez/10869096 PubMed]
  
 
=Biological materials =
 
=Biological materials =
Line 113: Line 115:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 120:
 
=References=
 
=References=
  
−
<pubmed>18957862, </pubmed>
+
<pubmed>10869096, </pubmed>
−
# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
# Pearson CL, Loshon CA, Pedersen LB, Setlow B, Setlow P (2000) Analysis of the function of a putative 2,3-diphosphoglyceric acid-dependent phosphoglycerate mutase from ''Bacillus subtilis''. ''J. Bacteriol.'' '''182:''' 4121-4123. [http://www.ncbi.nlm.nih.gov/sites/entrez/10869096 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 13:45, 8 June 2009

  • Description: involved in isopentenol (isoprenoid) biosynthesis

Gene name yhfR
Synonyms
Essential no
Product unknown
Function isoprenoid biosynthesis
MW, pI 21 kDa, 5.164
Gene length, protein length 579 bp, 193 aa
Immediate neighbours yhfQ, yhfS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YhfR context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU10340

Phenotypes of a mutant

no detectable phenotype PubMed

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: unknown PubMed
  • Protein family: GpmB subfamily (according to Swiss-Prot) similar to 2,3-diphosphoglycerate-dependent phosphoglycerate mutases PubMed
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information: weakly expressed PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

C L Pearson, C A Loshon, L B Pedersen, B Setlow, P Setlow
Analysis of the function of a putative 2,3-diphosphoglyceric acid-dependent phosphoglycerate mutase from Bacillus subtilis.
J Bacteriol: 2000, 182(14);4121-3
[PubMed:10869096] [WorldCat.org] [DOI] (P p)

  1. Pearson CL, Loshon CA, Pedersen LB, Setlow B, Setlow P (2000) Analysis of the function of a putative 2,3-diphosphoglyceric acid-dependent phosphoglycerate mutase from Bacillus subtilis. J. Bacteriol. 182: 4121-4123. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "https://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=89002"