Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' similar to Mn catalase <br/><br/>
+
* '''Description:''' P-loop ATPase <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'''
−
|''ydhU''
+
|''ydiB''
 
|-
 
|-
 
|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''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || P-loop ATPase
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 5.165  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 4.597  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 453 bp, 151 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 474 bp, 158 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gmuG]]'', ''[[trnE-Arg]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[thiL]]'', ''[[ydiC]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ydhU_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|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/ydhU_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ydiB_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ydhU_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ydiB_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 39:
  
 
===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 ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ydhU.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12198]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12199]
  
 
=== Additional information===
 
=== Additional information===
Line 55: Line 57:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' manganese catalase family
+
* '''Protein family:''' UPF0079 family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 61: Line 63:
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
  
−
* '''Kinetic information:'''
+
* '''Kinetic information:''' K(M) for ATP: 60 myM, V(max) 10 nmol/min  [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
  
 
* '''Domains:'''  
 
* '''Domains:'''  
Line 71: Line 73:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' dimerizes and oligomerizes  [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
  
−
* '''Localization:'''
+
* '''Localization:''' cytoplasm with the excepton of the nucleoid region  [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 81: Line 83:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05890]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05910]
  
 
* '''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 91: Line 95:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 119: Line 123:
 
=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 03:32, 12 April 2009

  • Description: P-loop ATPase

Gene name ydiB
Synonyms
Essential no
Product P-loop ATPase
Function unknown
MW, pI 17 kDa, 4.597
Gene length, protein length 474 bp, 158 aa
Immediate neighbours thiL, ydiC
Gene sequence (+200bp) Protein sequence
Genetic context
YdiB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

reduced growth rate PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: UPF0079 family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information: K(M) for ATP: 60 myM, V(max) 10 nmol/min PubMed
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions: dimerizes and oligomerizes PubMed
  • Localization: cytoplasm with the excepton of the nucleoid region PubMed

Database entries

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

Additional information

ATPase activity is required for in vivo function of the protein PubMed

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. 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. PubMed
  2. 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. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=52632"