Difference between revisions of "Sandbox"

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* '''Description:''' L-aspartase <br/><br/>
+
* '''Description:''' oligopeptide ABC transporter (permease) <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'''
−
|''ansB''
+
|''appC''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || L-aspartase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || oligopeptide ABC transporter (permease))
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || aspartate degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || uptake of oligopeptides
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 5.69  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 9.777  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1425 bp, 475 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 909 bp, 303 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mleN]]'', ''[[ansA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[appB]]'', ''[[yjbA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14289&#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:CAB12997&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:appC_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ansB_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:''' BSU23570
+
* '''Locus tag:''' BSU11400
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ansAB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/appDFABC.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10301]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11089]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' L-aspartate = fumarate + NH<sub>3</sub> (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' Aspartase subfamily (according to Swiss-Prot)
+
* '''Protein family:''' ABC transmembrane type-1 domain (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[CitG]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:''' cell membrane (according to Swiss-Prot),  membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P26899 P26899]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42063 P42063]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23570]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU11400]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.3.1.1 4.3.1.1]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[ansA]]-[[ansB]]''
+
* '''Operon:''' ''[[appD]]-[[appF]]-[[appA]]-[[appB]]-[[appC]]''
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by [[CodY]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed] 
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=References=
 
=References=
  
−
<pubmed>1711029, </pubmed>
+
<pubmed>18763711, </pubmed>
−
 
+
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
# Sun DX, Setlow P. (1991) Cloning, nucleotide sequence, and expression of the Bacillus subtilis ans operon, which codes for L-asparaginase and L-aspartase. ''J Bacteriol. '' '''Jun;173(12):''' 3831-45. [http://www.ncbi.nlm.nih.gov/sites/entrez/1711029 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 13:07, 8 June 2009

  • Description: oligopeptide ABC transporter (permease)

Gene name appC
Synonyms
Essential no
Product oligopeptide ABC transporter (permease))
Function uptake of oligopeptides
MW, pI 33 kDa, 9.777
Gene length, protein length 909 bp, 303 aa
Immediate neighbours appB, yjbA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AppC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU11400

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: ABC transmembrane type-1 domain (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cell membrane (according to Swiss-Prot), membrane associated PubMed

Database entries

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

Additional information

Expression and regulation

  • Regulatory mechanism: CodY: 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

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

  1. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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