Difference between revisions of "Sandbox"

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−
* '''Description:''' acetate kinase <br/><br/>
+
* '''Description:''' alkyl hydroperoxide reductase (large subunit) / NADH dehydrogenase <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'''
−
|''ackA''
+
|''ahpF''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ndh ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || acetate kinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || alkyl hydroperoxide reductase (large subunit) / NADH dehydrogenase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || overflow metabolism
+
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance against peroxide stres
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 5.191  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54 kDa, 4.705  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1185 bp, 395 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1527 bp, 509 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[moaB]]'', ''[[ytxK]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ahpC]]'', ''[[bglA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14925&#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:CAB16047&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ackA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ahpF_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:''' BSU29470
+
* '''Locus tag:''' BSU40100
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ackA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ahpCF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10813]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11204]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATP + acetate = ADP + acetyl phosphate (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' NADH + acceptor = NAD<sup>+</sup> + reduced acceptor (according to Swiss-Prot)  
  
−
* '''Protein family:''' acetokinase family (according to Swiss-Prot)
+
* '''Protein family:''' class-II pyridine nucleotide-disulfide oxidoreductase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 64: Line 64:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on (Ser-48 OR Ser-49) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot)
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37877 P37877]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42974 P42974]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29470]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40100]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.2.1 2.7.2.1]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[ahpC]]-[[ahpF]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8932314 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8932314 PubMed]
  
−
* '''Regulation:''' expression activated by glucose (2.5 fold) (CcpA) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+
* '''Regulation:''' induced by H2O2 ([[PerR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11532148 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[PerR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/11532148 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 113: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>12850135 8226682 9811655, </pubmed>
+
<pubmed>17218307, </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]
+
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
−
# Grundy FJ, Waters DA, Allen SH, Henkin TM (1993) Regulation of the Bacillus subtilis acetate kinase gene by CcpA. J Bacteriol 175:7348-7355 [http://www.ncbi.nlm.nih.gov/sites/entrez/8226682 PubMed]
 
−
# Turinsky, A. J., Grundy, F. J., Kim, J. H., Chambliss, G. H., and Henkin, T. M. 1998. Transcriptional activation of the Bacillus subtilis ackA gene requires sequences upstream of the promoter. J. Bacteriol. 180: 5961-5967. [http://www.ncbi.nlm.nih.gov/sites/entrez/9811655 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 13:55, 8 June 2009

  • Description: alkyl hydroperoxide reductase (large subunit) / NADH dehydrogenase

Gene name ahpF
Synonyms ndh
Essential no
Product alkyl hydroperoxide reductase (large subunit) / NADH dehydrogenase
Function resistance against peroxide stres
MW, pI 54 kDa, 4.705
Gene length, protein length 1527 bp, 509 aa
Immediate neighbours ahpC, bglA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AhpF context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU40100

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: NADH + acceptor = NAD+ + reduced acceptor (according to Swiss-Prot)
  • Protein family: class-II pyridine nucleotide-disulfide oxidoreductase family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on (Ser-48 OR Ser-49) PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cell membrane (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulatory mechanism: PerR: transcription repression PubMed
  • 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

Boris Macek, Ivan Mijakovic, Jesper V Olsen, Florian Gnad, Chanchal Kumar, Peter R Jensen, Matthias Mann
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis.
Mol Cell Proteomics: 2007, 6(4);697-707
[PubMed:17218307] [WorldCat.org] [DOI] (P p)

  1. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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