Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' GTP-binding protein<br/><br/>
+
* '''Description:''' beta-ketoacyl-acyl carrier protein synthase III <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'''
−
|''era''
+
|''fabHB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''bex, yqfH ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yhfB ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || GTP-binding protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || beta-ketoacyl-acyl carrier protein synthase III
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
+
|style="background:#ABCDEF;" align="center"|'''Function''' || fatty acid biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 8.376  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 5.684  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 903 bp, 301 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 975 bp, 325 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[recO]]'', ''[[cdd]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhgE]]'', ''[[yhfC]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14458&#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:CAB12857&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:era_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:fabHB_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:''' BSU25290
+
* '''Locus tag:''' BSU10170
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cdd-era.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fabHB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11188]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13048]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Binds and hydrolyzes GTP and readily exchanges GDP for GTP
+
* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + malonyl-[acyl-carrier-protein] = acetoacyl-[acyl-carrier-protein] + CoA + CO<sub>2</sub> (according to Swiss-Prot)
  
−
* '''Protein family:''' Era subfamily (according to Swiss-Prot) Era/Obg family
+
* '''Protein family:''' fabH family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[Era]], [[Obg]], [[YphC]], [[YsxC]], [[RbgA]], [[YqeH]], [[ThdF]], [[YyaF]], [[YnbA]]
+
* '''Paralogous protein(s):''' [[FabHA]], one of the two proteins has to be present for viability [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 74: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
Line 80: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42182 P42182]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O07600 O07600]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25290]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10170]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.1.180 2.3.1.180]
  
 
=== Additional information===
 
=== Additional information===
Line 92: Line 90:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 104: Line 102:
 
* '''Mutant:'''
 
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP93 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
+
* '''Expression vector:'''
 
          
 
          
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
Line 115: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Naotake Ogasawara]], Nara, Japan
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 118:
 
=References=
 
=References=
  
−
<pubmed>12427945, </pubmed>
+
<pubmed>17114254, </pubmed>
−
# Morimoto T, Loh PC, Hirai T, Asai K, Kobayashi K, Moriya S, Ogasawara N (2002) Six GTP-binding proteins of the Era/Obg family are essential for cell growth in ''Bacillus subtilis''. ''Microbiology'' '''148:''' 3539-3552. [http://www.ncbi.nlm.nih.gov/sites/entrez/12427945 PubMed]
+
# Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 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 14:02, 8 June 2009

  • Description: beta-ketoacyl-acyl carrier protein synthase III

Gene name fabHB
Synonyms yhfB
Essential no
Product beta-ketoacyl-acyl carrier protein synthase III
Function fatty acid biosynthesis
MW, pI 35 kDa, 5.684
Gene length, protein length 975 bp, 325 aa
Immediate neighbours yhgE, yhfC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
FabHB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU10170

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Acetyl-CoA + malonyl-[acyl-carrier-protein] = acetoacyl-[acyl-carrier-protein] + CoA + CO2 (according to Swiss-Prot)
  • Protein family: fabH family (according to Swiss-Prot)
  • Paralogous protein(s): FabHA, one of the two proteins has to be present for viability PubMed

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [3]

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

Helena B Thomaides, Ella J Davison, Lisa Burston, Hazel Johnson, David R Brown, Alison C Hunt, Jeffery Errington, Lloyd Czaplewski
Essential bacterial functions encoded by gene pairs.
J Bacteriol: 2007, 189(2);591-602
[PubMed:17114254] [WorldCat.org] [DOI] (P p)

  1. Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. 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=89102"