Difference between revisions of "Sandbox"
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− | * '''Description:''' | + | * '''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''' | ||
− | |'' | + | |''yabJ'' |
|- | |- | ||
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' '' | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' '' | ||
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''Essential''' || | + | |style="background:#ABCDEF;" align="center"| '''Essential''' || no |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''Product''' || | + | |style="background:#ABCDEF;" align="center"| '''Product''' || unknown |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"|'''Function''' || | + | |style="background:#ABCDEF;" align="center"|'''Function''' || regulation of purine biosynthesis |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || | + | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 5.134 |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || | + | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ | + | |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+[EMBLCDS: | + | |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11824]+-newId sequences] <br/> (Barbe ''et al.'', 2009)''' |
|- | |- | ||
− | |colspan="2" | '''Genetic context''' <br/> [[Image: | + | |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> | ||
|- | |- | ||
Line 38: | Line 38: | ||
===Phenotypes of a mutant === | ===Phenotypes of a mutant === | ||
− | |||
− | |||
=== Database entries === | === Database entries === | ||
− | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ | + | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/purR-yabJ.html] |
− | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+ | + | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10111] |
=== Additional information=== | === Additional information=== | ||
Line 56: | Line 54: | ||
* '''Catalyzed reaction/ biological activity:''' | * '''Catalyzed reaction/ biological activity:''' | ||
− | * '''Protein family:''' | + | * '''Protein family:''' YjgF family |
* '''Paralogous protein(s):''' | * '''Paralogous protein(s):''' | ||
Line 72: | Line 70: | ||
* '''Effectors of protein activity:''' | * '''Effectors of protein activity:''' | ||
− | * '''Interactions:''' | + | * '''Interactions:''' forms a trimer [http://www.ncbi.nlm.nih.gov/sites/entrez/10557275 PubMed] |
* '''Localization:''' Cytoplasm | * '''Localization:''' Cytoplasm | ||
Line 78: | Line 76: | ||
=== 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+ | + | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00480] |
* '''E.C. number:''' | * '''E.C. number:''' | ||
Line 90: | Line 88: | ||
=Expression and regulation= | =Expression and regulation= | ||
− | * '''Operon:''' '' | + | * '''Operon:''' ''[[purR]]-[[yabJ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed] |
* '''[[Sigma factor]]:''' | * '''[[Sigma factor]]:''' | ||
− | * '''Regulation:''' | + | * '''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 = | ||
Line 120: | Line 118: | ||
=References= | =References= | ||
+ | # 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] | # Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed] |
Revision as of 01:11, 30 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 ![]() This image was kindly provided by SubtiList
|
Contents
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
- Weng et al. (1995) Identification of the Bacillus subtilis pur operon repressor. Proc. Natl. Acad. Sci. USA 92: 7455-7459. 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. PubMed
- Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed