Protein Info for Atu0634 in Agrobacterium fabrum C58
Annotation: octaprenyl-diphosphate synthase
These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.
Protein Families and Features
Best Hits
Swiss-Prot: 46% identical to ISPB_ECOLI: Octaprenyl diphosphate synthase (ispB) from Escherichia coli (strain K12)
KEGG orthology group: K02523, octaprenyl-diphosphate synthase [EC: 2.5.1.90] (inferred from 100% identity to atu:Atu0634)MetaCyc: 46% identical to all-trans-octaprenyl-diphosphate synthase (Escherichia coli K-12 substr. MG1655)
RXN-8992 [EC: 2.5.1.90]
Predicted SEED Role
"Octaprenyl-diphosphate synthase (EC 2.5.1.-) / Dimethylallyltransferase (EC 2.5.1.1) / Geranyltranstransferase (farnesyldiphosphate synthase) (EC 2.5.1.10) / Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.29)" in subsystem Archaeal lipids or Isoprenoid Biosynthesis or Carotenoids or Polyprenyl Diphosphate Biosynthesis (EC 2.5.1.-, EC 2.5.1.1, EC 2.5.1.10, EC 2.5.1.29)
MetaCyc Pathways
- polyisoprenoid biosynthesis (E. coli) (5/5 steps found)
- superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) (10/12 steps found)
- taxadiene biosynthesis (engineered) (10/13 steps found)
- trans, trans-farnesyl diphosphate biosynthesis (2/2 steps found)
- geranyl diphosphate biosynthesis (1/1 steps found)
- geranylgeranyl diphosphate biosynthesis (1/1 steps found)
- octaprenyl diphosphate biosynthesis (1/1 steps found)
- (3R)-linalool biosynthesis (1/2 steps found)
- (3S)-linalool biosynthesis (1/2 steps found)
- linalool biosynthesis I (1/2 steps found)
- all-trans-farnesol biosynthesis (2/4 steps found)
- methyl phomopsenoate biosynthesis (2/4 steps found)
- ophiobolin F biosynthesis (1/3 steps found)
- plaunotol biosynthesis (1/3 steps found)
- superpathway of linalool biosynthesis (1/3 steps found)
- superpathway of ubiquinol-8 biosynthesis (early decarboxylation) (7/12 steps found)
- ipsdienol biosynthesis (1/4 steps found)
- bisabolene biosynthesis (engineered) (2/6 steps found)
- mono-trans, poly-cis decaprenyl phosphate biosynthesis (1/5 steps found)
- stellatic acid biosynthesis (3/8 steps found)
- superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) (4/10 steps found)
- paspaline biosynthesis (1/6 steps found)
- brassicicene C biosynthesis (1/7 steps found)
- superpathway of chorismate metabolism (38/59 steps found)
- superpathway of menaquinol-8 biosynthesis III (2/9 steps found)
- fusicoccin A biosynthesis (1/8 steps found)
- superpathway of menaquinol-8 biosynthesis I (2/10 steps found)
- superpathway of menaquinol-8 biosynthesis II (2/10 steps found)
- superpathway of demethylmenaquinol-8 biosynthesis I (1/9 steps found)
- viridicatumtoxin biosynthesis (1/9 steps found)
- superpathway of ergosterol biosynthesis II (9/26 steps found)
- superpathway of phylloquinol biosynthesis (1/15 steps found)
- superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis (13/33 steps found)
- superpathway of ergosterol biosynthesis I (3/26 steps found)
- Methanobacterium thermoautotrophicum biosynthetic metabolism (18/56 steps found)
- superpathway of cholesterol biosynthesis (3/38 steps found)
KEGG Metabolic Maps
- Biosynthesis of alkaloids derived from terpenoid and polyketide
- Biosynthesis of plant hormones
- Biosynthesis of terpenoids and steroids
- Carotenoid biosynthesis - General
- Methionine metabolism
- Porphyrin and chlorophyll metabolism
- Riboflavin metabolism
- Terpenoid biosynthesis
- Tryptophan metabolism
- Ubiquinone and menaquinone biosynthesis
Isozymes
Compare fitness of predicted isozymes for: 2.5.1.-, 2.5.1.1, 2.5.1.10, 2.5.1.29, 2.5.1.90
Use Curated BLAST to search for 2.5.1.- or 2.5.1.1 or 2.5.1.10 or 2.5.1.29 or 2.5.1.90
Sequence Analysis Tools
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
Compare to protein structures
Predict protein localization: PSORTb (Gram-negative bacteria)
Predict transmembrane helices and signal peptides: Phobius
Check the current SEED with FIGfam search
Find homologs in fast.genomics or the ENIGMA genome browser
See Q7D122 at UniProt or InterPro
Protein Sequence (338 amino acids)
>Atu0634 octaprenyl-diphosphate synthase (Agrobacterium fabrum C58) MGVVIPLEESKNKLASVKPLVDLTRPDMERVNQLILSRAGSDVQMIPEVANHLISSGGKR LRPMLTLASASMFGYEGDNHIKLATSVEFMHTATLLHDDVVDESDLRRGKSTARTIWGNQ ASVLVGDFLLGQAFRMMVDVGSLDALDVLSTAASVIAEGEVLQLSVAKNMETTEDDYLQV IRAKTAALFAAAAEVGPIVAKTDKASRSALKSYGMNLGLAFQLVDDVLDYGGKSADLGKN TGDDFREGKITLPVILSYRRGTQDERAFWRNAIEKGESSDENLEKALGLITKYNGLGDTI GRATHYGTIARDALAPLPQSPWKNALLEVIDFCIERLN