Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' alkyl hydroperoxide reductase (small subunit) <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'''
−
|''ahpC''
+
|''ahpF''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''perR ''
+
|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''' || alkyl hydroperoxide reductase (small subunit)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || alkyl hydroperoxide reductase (large subunit) / NADH dehydrogenase
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance against peroxide stres  
 
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance against peroxide stres  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 4.283  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54 kDa, 4.705  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 561 bp, 187 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1527 bp, 509 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gntZ]]'', ''[[ahpF]]''
+
|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:CAB16046&#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:ahpC_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>
 
|-
 
|-
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU40090
+
* '''Locus tag:''' BSU40100
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 43:
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ahpCF.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ahpCF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11385]
+
* '''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:''' 2 R'-SH + ROOH = R'-S-S-R' + H<sub>2</sub>O + ROH (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' NADH + acceptor = NAD<sup>+</sup> + reduced acceptor (according to Swiss-Prot)  
  
−
* '''Protein family:''' ahpC/TSA 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:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]  
+
* '''Modification:''' phosphorylation on (Ser-48 OR Ser-49) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 72: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
Line 78: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80239 P80239]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42974 P42974]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40090]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40100]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 118: Line 118:
 
=References=
 
=References=
  
−
<pubmed>16493705, </pubmed>
+
<pubmed>17218307, </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]
+
# 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]
 
# 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 10:13, 11 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
Retrieved from "http://subtiwiki-test.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=90340"