Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' subtilosin A <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'''
−
|''sboA''
+
|''aapA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sbo ''
+
|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''' || subtilosin A
+
|style="background:#ABCDEF;" align="center"| '''Product''' || amino acid permease
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || antimicrobial peptide
+
|style="background:#ABCDEF;" align="center"|'''Function''' || amino acid uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 4 kDa, 4.569  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 9.675  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 129 bp, 43 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1377 bp, 459 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywiB]]'', ''[[sboX]]''
+
|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:CAB15763&#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:sboA_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>
 
|-
 
|-
Line 29: Line 31:
 
__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU37350
+
* '''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/sboAX-albABCDEFG.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12671]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12556]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 56:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' bacteriocin class V family (according to Swiss-Prot)
+
* '''Protein family:''' amino acid-polyamine-organocation (APC) superfamily (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 72: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' secreted (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1PXQ 1PXQ]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O07623 O07623]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O06005 O06005]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37350]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU27090]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[sboA]]-[[sboX]]-[[albA]]-[[albB]]-[[albC]]-[[albD]]-[[albE]]-[[albF]]-[[albG]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
−
** repressed by [[Rok]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15743949 PubMed]
 
−
** expressed under anaerobic conditions ([[ResD]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10809710 PubMed]
 
−
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10572140,17720793 PubMed]
 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[Rok]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15743949 PubMed]
 
−
** [[ResD]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/10809710 PubMed]
 
−
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10572140,17720793 PubMed]
 
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 123: Line 119:
  
 
=References=
 
=References=
−
 
−
<pubmed>10572140,17720793, </pubmed>
 
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 

Revision as of 11:11, 12 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

Retrieved from "http://subtiwiki-test.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=91662"