Difference between revisions of "Sandbox"

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* '''Description:''' write here <br/><br/>
+
* '''Description:''' penicillin-binding protein 2C <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'''
|''wprA''
+
|''pbpF''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yisM ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ponA ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || cell wall-associated protein precursor (CWBP23, CWBP52) (EC 3.4.21.-)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || penicillin-binding protein 2C
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
+
|style="background:#ABCDEF;" align="center"|'''Function''' || involved in spore peptidoglycan synthesis
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 96 kDa, 9.58  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 79 kDa, 7.078  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2682 bp, 894 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2142 bp, 714 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yisL]]'', ''[[yisN]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhgC]]'', ''[[hemE]]''
 
|-
 
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/wprA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pbpF_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/wprA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pbpF_protein.txt Protein sequence]'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:wprA_context.gif]]
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:pbpF_context.gif]]
 
|-
 
|-
 
|}
 
|}
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/wprA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pbpF.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11846]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10428]
  
 
=== Additional information===
 
=== Additional information===
Line 72: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
* '''Localization:'''
+
* '''Localization:''' prespore [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
  
 
=== Database entries ===
 
=== Database entries ===
Line 88: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:''' ''[[wprA]]''  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
+
* '''Operon:'''  
  
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]], [[SigG]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
  
* '''Regulation:'''  
+
* '''Regulation:''' expressed in mother cell and prespore [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
  
* '''Regulatory mechanism:''' activated by [[YvrHb]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
+
* '''Regulatory mechanism:'''  
  
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 108: Line 110:
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
* '''two-hybrid system:'''  
+
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jeff Errington]] lab
  
 
* '''Antibody:'''
 
* '''Antibody:'''
Line 118: Line 120:
 
=References=
 
=References=
  
# Serizawa M, Kodama K, Yamamoto H, Kobayashi K, Ogasawara N, Sekiguchi J. (2005) Functional analysis of the YvrGHb two-component system of ''Bacillus subtilis'': identification of the regulated genes by DNA microarray and northern blot analyses. ''Biosci. Biotechnol. Biochem.'' '''69:''' 2155-2169. [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 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 15:48, 9 March 2009

  • Description: penicillin-binding protein 2C

Gene name pbpF
Synonyms ponA
Essential no
Product penicillin-binding protein 2C
Function involved in spore peptidoglycan synthesis
MW, pI 79 kDa, 7.078
Gene length, protein length 2142 bp, 714 aa
Immediate neighbours yhgC, hemE
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
PbpF context.gif



The gene

Basic information

  • Coordinates:

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:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jeff Errington lab
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed