Difference between revisions of "Sandbox"

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−
* '''Description:''' D-alanyl-aminopeptidase <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'''
−
|''dppA''
+
|''fabHA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dciAA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yjaX ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || D-alanyl-aminopeptidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || beta-ketoacyl-acyl carrier protein synthase III
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || degradation of cell wall peptides
+
|style="background:#ABCDEF;" align="center"|'''Function''' || fatty acid biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 5.19  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 5.045  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 822 bp, 274 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[proG]]'', ''[[dppB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yjzB]]'', ''[[fabF]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13149&#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:CAB12974&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
 
|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:dppA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:fabHA_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>
 
|-
 
|-
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU12920
+
* '''Locus tag:''' BSU11330
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dppABCDE.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fabHAF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10842]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13127]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''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:''' peptidase M55 family (according to Swiss-Prot)
+
* '''Protein family:''' fabH family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[FabHB]], 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 ===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1HI9 1HI9]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P26902 P26902]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34746 O34746]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU12920]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU11330]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.1.180 2.3.1.180]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[dppA]]-[[dppB]]-[[dppC]]-[[dppD]]-[[dppE]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/1766371 PubMed]
+
* '''Operon:'''  
−
 
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1766371 PubMed]
 
  
−
* '''Regulation:''' repressed by glucose (2.9-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], expressed postexponentially ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1766371 PubMed], repressed by [[CodY]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
+
* '''[[Sigma factor]]:'''
  
−
* '''Regulatory mechanism:''' [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1766371 PubMed], [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed1]  [http://www.ncbi.nlm.nih.gov/sites/entrez/18083814 PubMed2]
+
* '''Regulation:'''  
  
−
* '''Additional information:'''
+
* '''Regulatory mechanism:'''
 +
 
 +
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>12850135 16493705, </pubmed>
+
<pubmed>17114254, </pubmed>
−
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 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]
−
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 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 14:15, 8 June 2009

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

Gene name fabHA
Synonyms yjaX
Essential no
Product beta-ketoacyl-acyl carrier protein synthase III
Function fatty acid biosynthesis
MW, pI 33 kDa, 5.045
Gene length, protein length 936 bp, 312 aa
Immediate neighbours yjzB, fabF
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
FabHA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU11330

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): FabHB, 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

  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
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