Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' P-loop ATPase <br/><br/>
+
* '''Description:''' similar to ABC transporter (ATP-binding protein) <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'''
−
|''ydiB''
+
|''ydiF''
 
|-
 
|-
 
|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''' || P-loop ATPase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 4.597  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 73 kDa, 4.868  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 474 bp, 158 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1926 bp, 642 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[thiL]]'', ''[[ydiC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gcp]]'', ''[[ydiG]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ydiB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ydiF_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ydiB_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ydiF_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ydiB_context.gif]]
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:ydiF_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 39: Line 41:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
reduced growth rate  [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
Line 46: Line 46:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12199]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12203]
  
 
=== Additional information===
 
=== Additional information===
Line 57: Line 57:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' UPF0079 family
+
* '''Protein family:''' EF3 subfamily
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 63: Line 63:
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
  
−
* '''Kinetic information:''' K(M) for ATP: 60 myM, V(max) 10 nmol/min  [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
+
* '''Kinetic information:'''
  
 
* '''Domains:'''  
 
* '''Domains:'''  
Line 73: Line 73:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' dimerizes and oligomerizes  [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
+
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm with the excepton of the nucleoid region  [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
Line 83: Line 83:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05910]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05950]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
−
ATPase activity is required for ''in vivo'' function of the protein  [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
 
  
 
=Expression and regulation=
 
=Expression and regulation=
Line 95: Line 93:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 123: Line 121:
 
=References=
 
=References=
  
−
# Hunt, A., Rawlins, J. P., Thomaides, H. B., and Errington, J. (2006) Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152, 2895-2907. [http://www.ncbi.nlm.nih.gov/sites/entrez/17005971 PubMed]
 
−
# Karst JC, Foucher AE, Campbell TL, Di Guilmi AM, Stroebel D, Mangat CS, Brown ED, Jault JM (2009) The ATPase activity of an 'essential' ''Bacillus subtilis'' enzyme, YdiB, is required for its cellular function and is modulated by oligomerization. ''Microbiology'' '''155:''' 944-965. [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 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 03:33, 12 April 2009

  • Description: similar to ABC transporter (ATP-binding protein)

Gene name ydiF
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 73 kDa, 4.868
Gene length, protein length 1926 bp, 642 aa
Immediate neighbours gcp, ydiG
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
YdiF context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: EF3 subfamily
  • 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: [2]
  • 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=52633"