Difference between revisions of "Sandbox"

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−
* '''Description:''' similar to iron-sulphur-binding reductase <br/><br/>
+
* '''Description:''' fatty acid degradation, similar to proline 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'''
−
|''fadF''
+
|''fadM''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywjF ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yusM''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || fatty acid degradation
 
|style="background:#ABCDEF;" align="center"|'''Function''' || fatty acid degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 79 kDa, 6.526  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 9.377  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2115 bp, 705 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 906 bp, 302 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[acdA]]'', ''[[ywjE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fadN]]'', ''[[yusN]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15746&#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:CAB15274&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ywjF_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yusM_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:''' BSU37180
+
* '''Locus tag:''' BSU32850
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywjF-acdA-rpoE.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yusMLKJ.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11311]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14025]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' proline dehydrogenase family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[YcgM]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 72: Line 72:
 
* '''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/P45866 P45866]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32179 O32179]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37180]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU32850]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 92: Line 92:
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by glucose (5-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
Line 118: Line 118:
 
=References=
 
=References=
  
−
<pubmed>12850135 17189250, </pubmed>
+
<pubmed>17189250, </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]
 
 
# Matsuoka H, Hirooka K, Fujita Y. (2007) Organization and function of the YsiA regulon of Bacillus subtilis involved in fatty acid degradation. ''J Biol Chem. '' '''Feb 23;282(8):''' 5180-94. [http://www.ncbi.nlm.nih.gov/sites/entrez/17189250 PubMed]
 
# Matsuoka H, Hirooka K, Fujita Y. (2007) Organization and function of the YsiA regulon of Bacillus subtilis involved in fatty acid degradation. ''J Biol Chem. '' '''Feb 23;282(8):''' 5180-94. [http://www.ncbi.nlm.nih.gov/sites/entrez/17189250 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: fatty acid degradation, similar to proline dehydrogenase

Gene name fadM
Synonyms yusM
Essential no
Product unknown
Function fatty acid degradation
MW, pI 34 kDa, 9.377
Gene length, protein length 906 bp, 302 aa
Immediate neighbours fadN, yusN
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YusM context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU32850

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor (according to Swiss-Prot)
  • Protein family: proline dehydrogenase family (according to Swiss-Prot)
  • Paralogous protein(s): YcgM

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. Matsuoka H, Hirooka K, Fujita Y. (2007) Organization and function of the YsiA regulon of Bacillus subtilis involved in fatty acid degradation. J Biol Chem. Feb 23;282(8): 5180-94. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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