Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' acetolactate synthase <br/><br/>
+
* '''Description:''' aminopeptidase <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'''
−
|''alsS''
+
|''ampS''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
Line 10: Line 10:
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || acetolactate synthase)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || aminopeptidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || overflow metabolism
+
|style="background:#ABCDEF;" align="center"|'''Function''' || required for  biofilm formation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61 kDa, 5.164  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 4.954  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1713 bp, 571 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1230 bp, 410 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[alsD]]'', ''[[alsR]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykpB]]'', ''[[ykpC]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15618&#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:CAB13318&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:alsS_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ampS_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:''' BSU36010
+
* '''Locus tag:''' BSU14450
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/alsSD.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10471]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10986]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 2 pyruvate = 2-acetolactate + CO<sub>2</sub> (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' TPP enzyme family (according to Swiss-Prot)
+
* '''Protein family:''' peptidase M29 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 78: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q04789 Q04789]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39762 P39762]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36010]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14450]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.2.1.6 2.2.1.6]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
Line 88: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[alsS]]-[[alsD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' induction by acetate ([[AlsR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed], repressed as long as terminal electron acceptors are available for respiration ([[Rex]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16428414 PubMed]
+
* '''Regulation:'''  
−
Note: since acetate formation requires ''[[ackA]]'' activation by [[CcpA]] there is an indirect effect of [[CcpA]] on the ''alsSD'' operon: the operon is not expressed in ''[[ccpA]]'' mutants
 
  
−
* '''Regulatory mechanism:''' [[AlsR]]: transcription activation in the presence of acetate [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed], [[Rex]]: transcription repression if the ratio NADH2/NAD is high [http://www.ncbi.nlm.nih.gov/sites/entrez/16428414 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 118: Line 117:
  
 
=References=
 
=References=
−
 
−
<pubmed> 19383131, 7685336, 16428414  </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 08:53, 3 June 2009

  • Description: aminopeptidase

Gene name ampS
Synonyms
Essential no
Product aminopeptidase
Function required for biofilm formation
MW, pI 45 kDa, 4.954
Gene length, protein length 1230 bp, 410 aa
Immediate neighbours ykpB, ykpC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AmpS context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU14450

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: peptidase M29 family (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
Retrieved from "https://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=84100"