Difference between revisions of "Sandbox"

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−
* '''Description:''' alkyl hydroperoxide reductase (large subunit) / NADH dehydrogenase <br/><br/>
+
* '''Description:''' regulation of anaerobic genes <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'''
−
|''ahpF''
+
|''arfM''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ndh ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywiD ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || alkyl hydroperoxide reductase (large subunit) / NADH dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance against peroxide stres
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of anaerobic genes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54 kDa, 4.705  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 5.842  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1527 bp, 509 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 474 bp, 158 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ahpC]]'', ''[[bglA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[narG]]'', ''[[ywiC]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15757&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ahpF_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:arfM_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:''' BSU40100
+
* '''Locus tag:''' BSU37290
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ahpCF.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/arfM.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11204]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11345]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' NADH + acceptor = NAD<sup>+</sup> + reduced acceptor (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' class-II pyridine nucleotide-disulfide oxidoreductase family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on (Ser-48 OR Ser-49) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42974 P42974]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P46910 P46910]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40100]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37290]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[ahpC]]-[[ahpF]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8932314 PubMed]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8932314 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' induced by H2O2 ([[PerR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11532148 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[PerR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/11532148 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 118: Line 118:
 
=References=
 
=References=
  
−
<pubmed>17218307, </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 10:10, 11 June 2009

  • Description: regulation of anaerobic genes

Gene name arfM
Synonyms ywiD
Essential no
Product unknown
Function regulation of anaerobic genes
MW, pI 17 kDa, 5.842
Gene length, protein length 474 bp, 158 aa
Immediate neighbours narG, ywiC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ArfM context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU37290

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

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

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

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

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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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