Difference between revisions of "Sandbox"

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* '''Description:''' small acid-soluble spore protein (minor) <br/><br/>
+
* '''Description:''' required for activity of PurR <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'''
−
|''sspF''
+
|''yabJ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || small acid-soluble spore protein (minor)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || protection of spore DNA
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of purine biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 9.647  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 5.134  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 183 bp, 61 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[veg]]'', ''[[ispE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[purR]]'', ''[[spoVG]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11821&#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:CAB11824&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:sspF_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yabJ_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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=== Database entries ===
 
=== Database entries ===
  
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sspF.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/purR-yabJ.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10108]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10111]
  
 
=== Additional information===
 
=== Additional information===
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' alpha/beta-type SASP family
+
* '''Protein family:''' YjgF family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' forms a trimer [http://www.ncbi.nlm.nih.gov/sites/entrez/10557275 PubMed]
  
−
* '''Localization:'''
+
* '''Localization:''' Cytoplasm
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' 1QD9 [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=11484 NCBI] [http://www.ncbi.nlm.nih.gov/sites/entrez/10557275 PubMed]
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00450]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00480]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''sspF'' [http://www.ncbi.nlm.nih.gov/sites/entrez/6205155 PubMed]
+
* '''Operon:''' ''[[purR]]-[[yabJ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed]
  
−
* '''[[Sigma factor]]:''' [[SigG]] [http://www.ncbi.nlm.nih.gov/sites/entrez/6205155 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' switched on during stage  III of sporulation [http://www.ncbi.nlm.nih.gov/sites/entrez/6205155 PubMed]
+
* '''Regulation:''' negative autoregulation [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' repression by [[PurR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed]
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
# Stephens et al. (1984) A promoter whose utilization is temporally regulated during sporulation in ''Bacillus subtilis''. ''J. Mol. Biol.'' '''176:''' 333-348. [http://www.ncbi.nlm.nih.gov/sites/entrez/6205155 PubMed]
+
# Weng et al. (1995) Identification of the ''Bacillus subtilis pur'' operon repressor. ''Proc. Natl. Acad. Sci. USA'' '''92:''' 7455-7459. [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed]
 +
# Sinha et al. (1999) Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family.''Proc. Natl. Acad. Sci. USA'' '''96:''' 13074-13079. [http://www.ncbi.nlm.nih.gov/sites/entrez/10557275 PubMed]
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 17:26, 21 April 2009

  • Description: required for activity of PurR

Gene name yabJ
Synonyms
Essential no
Product unknown
Function regulation of purine biosynthesis
MW, pI 13 kDa, 5.134
Gene length, protein length 375 bp, 125 aa
Immediate neighbours purR, spoVG
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YabJ context.gif
This image was kindly provided by SubtiList



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: YjgF family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions: forms a trimer PubMed
  • Localization: Cytoplasm

Database entries

  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: negative autoregulation PubMed
  • 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. Weng et al. (1995) Identification of the Bacillus subtilis pur operon repressor. Proc. Natl. Acad. Sci. USA 92: 7455-7459. PubMed
  2. Sinha et al. (1999) Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family.Proc. Natl. Acad. Sci. USA 96: 13074-13079. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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