Difference between revisions of "Sandbox"

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−
* '''Description:''' transcriptional antiterminator for ''[[sacB]]'' and ''[[sacX]]-[[sacY]]'' (acts at high sucrose concentrations) <br/><br/>
+
* '''Description:''' amino acid 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'''
−
|''sacY''
+
|''aapA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-13r, sacS ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional antiterminator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || amino acid permease
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of sucrose utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || amino acid uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 5.883  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 9.675  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 840 bp, 280 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1377 bp, 459 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sacX]]'', ''[[gspA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[levR]]'', ''[[yrhP]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15868&#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:CAB14651&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:sacY_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:aapA_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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__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:'''
+
* '''Locus tag:''' BSU27090
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sacXY.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10559]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12556]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' binding to the mRNA of'' [[sacB]]'' and the ''[[sacX]]-[[sacY]]'' operon, causes transcription antitermination (in presence of sucrose)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' transcriptional antiterminator bglG family (according to Swiss-Prot) BglG family of antiterminators
+
* '''Protein family:''' amino acid-polyamine-organocation (APC) superfamily (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[LicT]], [[GlcT]], [[SacT]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[PtsH]]-[[SacY]]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 76: Line 78:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1AUU 1AUU] (RNA-binding domain)
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P15401 P15401]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O06005 O06005]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU38420 BSU38420]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU27090]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[sacX]]-[[sacY]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' induction by sucrose (at high concentration)
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' induction by [[SacY]]-dependent RNA switch (transcriptional antitermination)
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 113: Line 115:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# Crutz AM, Steinmetz M, Aymerich S, Richter R, Le Coq D (1990) Induction of levansucrase in Bacillus subtilis: an antitermination mechanism negatively controlled by the phosphotransferase system. J Bacteriol 172:1043-1050. [http://www.ncbi.nlm.nih.gov/sites/entrez/2105292 PubMed]
 
−
# Arnaud, M., Débarbouillé, M., Rapoport, G., Saier, M. H., and Reizer, J. (1996) In vitro reconstitution of transcriptional antitermination by the SacT and SacY proteins of ''Bacillus subtilis''. J Biol Chem 271: 18966-18972. [http://www.ncbi.nlm.nih.gov/sites/entrez/8702561 PubMed]
 
−
# Tortosa, P., Aymerich, S., Lindner, C., Saier, M.H., Jr., Reizer, J. and Le Coq, D. (1997) Multiple phosphorylation of SacY, a Bacillus subtilis antiterminator negatively controlled by the phosphotransferase system. J. Biol. Chem. 272, 17230-17237. [http://www.ncbi.nlm.nih.gov/sites/entrez/9202047  PubMed]
 
−
# Tortosa, P., Declerck, N., Dutartre, H., Lindner, C., Deutscher, J., and Le Coq, D. (2001) Sites of positive and negative regulation in the Bacillus subtilis antiterminators LicT and SacY. Mol Microbiol 41: 1381-1393. [http://www.ncbi.nlm.nih.gov/sites/entrez/11580842 PubMed]
 
−
# Aymerich, S. and Steinmetz, M. (1992) Specificity determinants and structural features in the RNA target of the bacterial antiterminator proteins of the BglG/SacY family. Proc. Natl. Acad. Sci. USA 89, 10410-10414. [http://www.ncbi.nlm.nih.gov/sites/entrez/1279678 PubMed]
 
−
# Manival, X., Yang, Y., Strub, M. P., Kochoyan, M., Steinmetz, M. and Aymerich, S. (1997) From genetic to structural characterization of a new class of RNA-binding domain within the SacY/BglG family of antiterminator proteins. EMBO J. 16, 5019-5029. [http://www.ncbi.nlm.nih.gov/sites/entrez/9305643 PubMed]
 
−
# van Tilbeurgh, H., Manival, X., Aymerich, S., Lhoste, J. M., Dumas, C. and Kochoyan, M. (1997) Crystal structure of a new RNA-binding domain from the antiterminator protein SacY of ''Bacillus subtilis''. EMBO J. 16, 5030-5036. [http://www.ncbi.nlm.nih.gov/sites/entrez/9305644 PubMed]
 
−
# Declerck, N., Vincent, F., Hoh, F., Aymerich, S. and van Tilbeurgh, H. (1999) RNA recognition by transcriptional antiterminators of the BglG/SacY family: functional and structural comparison of the CAT domains from SacY and LicT. J. Mol. Biol. 294, 389-402. [http://www.ncbi.nlm.nih.gov/sites/entrez/10610766 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 09:49, 3 June 2009

  • Description: amino acid permease

Gene name aapA
Synonyms
Essential no
Product amino acid permease
Function amino acid uptake
MW, pI 50 kDa, 9.675
Gene length, protein length 1377 bp, 459 aa
Immediate neighbours levR, yrhP
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AapA context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Locus tag: BSU27090

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: amino acid-polyamine-organocation (APC) superfamily (according to Swiss-Prot)
  • 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: [2]
  • 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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