Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' subtilosin A <br/><br/>
+
* '''Description:''' probable spore coat protein <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''
+
|''cotP''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sbo ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydfT ''
 
|-
 
|-
 
|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''' || probable spore coat protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || antimicrobial peptide
+
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance of the spore
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 4 kDa, 4.569  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 4.56  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 129 bp, 43 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 429 bp, 143 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywiB]]'', ''[[sboX]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydfS]]'', ''[[ydgA]]''
 
|-
 
|-
−
|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:CAB12362&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:sboA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:cotP_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:''' BSU37350
+
* '''Locus tag:''' BSU05550
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sboAX-albABCDEFG.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ydgBA-cotP.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12671]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12167]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' bacteriocin class V family (according to Swiss-Prot)
+
* '''Protein family:''' small heat shock protein (HSP20) family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 72: Line 72:
 
* '''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/P96698 P96698]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37350]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05550]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 88:
 
=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 124: Line 118:
 
=References=
 
=References=
  
−
<pubmed>15743949,10809710,10572140,17720793, </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 20:46, 12 June 2009

  • Description: probable spore coat protein

Gene name cotP
Synonyms ydfT
Essential no
Product probable spore coat protein
Function resistance of the spore
MW, pI 16 kDa, 4.56
Gene length, protein length 429 bp, 143 aa
Immediate neighbours ydfS, ydgA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CotP context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU05550

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: small heat shock protein (HSP20) 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: [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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=92537"