Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' phosphofructokinase, glycolytic enzyme <br/><br/>
+
* '''Description:''' acetyl-CoA carboxylase (alpha subunit) <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'''
−
|''pfkA''
+
|''accA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pfk''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || 6-phosphofructokinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || acetyl-CoA carboxylase (alpha subunit))
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || production of malonyl-CoA, the substrate for fatty acid biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34,1 kDa, 6.14
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 6.087 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 957 bp, 319 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 975 bp, 325 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[accA]]'', ''[[pyk]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pfkA]]'', ''[[accD]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14879&#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:CAB14880&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:pfkA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:accA_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 ===
  
−
* '''Coordinates:''' 2985630 - 2986586
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pfkA-pyk-ytzA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/accDA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12644]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12557]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 53: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' phosphofructokinase family
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 64: Line 65:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
−
** 3 x nucleotide binding domain (ATP) (21–25), (154–158), (171–187)
 
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):''' ATP
+
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' inhibited by citrate, ATP, PEP, Ca2+, and others (in ''B. licheniformes'') [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed]
+
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[PfkA]]-[[Pgm]], [[PfkA]]-[[Eno]], [[PfkA]]-[[Rny]], [[PfkA]]-[[PnpA]], [[PfkA]]-[[RnjA]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
+
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot),  Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+
* '''Localization:''' cytoplasm (according to Swiss-Prot),  Membrane-proximal (Spotty) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=58449 NCBI], Mutant form, complex with fructose-6-phosphate ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=21480 NCBI]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34529 O34529] [http://www.uniprot.org/uniprot/O34529]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34847 O34847]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29190]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29200]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.11 2.7.1.11]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''pfkA [[pyk]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
+
* '''Operon:'''  
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' twofold induced by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 105: Line 104:
 
* '''Mutant:'''
 
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP393 (N-terminal His-tag, in [[pWH844]]), pGP87 (N-terminal Strep-tag, for SPINE, expression in ''B. subtilis'', in [[pGP380]]), available in [[Stülke]] lab
+
* '''Expression vector:'''
−
+
       
−
* '''lacZ fusion:''' pGP511 (in [[pAC6]]), available in [[Stülke]] lab
+
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''two-hybrid system:'''  
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 124: Line 121:
  
 
# Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in ''Bacillus subtilis'': identification of new proteins at the DNA replication factory ''Proteomics'' '''6:''' 2135-2146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
 
# Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in ''Bacillus subtilis'': identification of new proteins at the DNA replication factory ''Proteomics'' '''6:''' 2135-2146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
−
# Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. (2009) Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. Mol. Cell. Proteomics in press [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M., and Stülke, J. (2001) Transcription of glycolytic genes and operons in ''Bacillus subtilis'': evidence for the presence of multiple levels of control of the ''gapA'' operon. Mol Microbiol 41, 409-422. [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
 

Revision as of 23:14, 1 May 2009

  • Description: acetyl-CoA carboxylase (alpha subunit)

Gene name accA
Synonyms
Essential yes PubMed
Product acetyl-CoA carboxylase (alpha subunit))
Function production of malonyl-CoA, the substrate for fatty acid biosynthesis
MW, pI 36 kDa, 6.087
Gene length, protein length 975 bp, 325 aa
Immediate neighbours pfkA, accD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AccA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

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:
  • Localization: cytoplasm (according to Swiss-Prot), Membrane-proximal (Spotty) PubMed

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. Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory Proteomics 6: 2135-2146. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=65870"