Protein Info for DDA3937_RS05535 in Dickeya dadantii 3937
Annotation: (2E,6E)-farnesyl 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: 72% identical to ISPA_ECOLI: Farnesyl diphosphate synthase (ispA) from Escherichia coli (strain K12)
KEGG orthology group: K00795, farnesyl diphosphate synthase [EC: 2.5.1.1 2.5.1.10] (inferred from 100% identity to ddd:Dda3937_01961)MetaCyc: 72% identical to geranyl diphosphate/farnesyl diphosphate synthase (Escherichia coli K-12 substr. MG1655)
Geranyltranstransferase. [EC: 2.5.1.10]; Dimethylallyltranstransferase. [EC: 2.5.1.10, 2.5.1.1]
Predicted SEED Role
"Octaprenyl diphosphate synthase (EC 2.5.1.90) / Dimethylallyltransferase (EC 2.5.1.1) / (2E,6E)-farnesyl diphosphate 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 2.5.1.1, EC 2.5.1.10, EC 2.5.1.29, EC 2.5.1.90)
MetaCyc Pathways
- superpathway of chorismate metabolism (54/59 steps found)
- superpathway of ubiquinol-8 biosynthesis (early decarboxylation) (12/12 steps found)
- superpathway of menaquinol-8 biosynthesis I (10/10 steps found)
- superpathway of demethylmenaquinol-8 biosynthesis I (9/9 steps found)
- superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) (11/12 steps found)
- taxadiene biosynthesis (engineered) (11/13 steps found)
- polyisoprenoid biosynthesis (E. coli) (5/5 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)
- 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 phylloquinol biosynthesis (8/15 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 menaquinol-8 biosynthesis III (2/9 steps found)
- fusicoccin A biosynthesis (1/8 steps found)
- superpathway of menaquinol-8 biosynthesis II (2/10 steps found)
- viridicatumtoxin biosynthesis (1/9 steps found)
- superpathway of ergosterol biosynthesis II (10/26 steps found)
- superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis (12/33 steps found)
- superpathway of ergosterol biosynthesis I (3/26 steps found)
- Methanobacterium thermoautotrophicum biosynthetic metabolism (22/56 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
- Terpenoid biosynthesis
Isozymes
Compare fitness of predicted isozymes for: 2.5.1.90
Use Curated BLAST to search for 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)
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 E0SD48 at UniProt or InterPro
Protein Sequence (303 amino acids)
>DDA3937_RS05535 (2E,6E)-farnesyl diphosphate synthase (Dickeya dadantii 3937) MTDFLKQLTAHHQRINATLNQFISTLPFQSSPLVEAMAHGALLGGKRLRPFLVYTTGQLF GISQNNLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGQPTCHVRFGEDKAILAGDALQT LAFSILADAPMPEVSDRDRLAMISELASASGVAGMCGGQALDLEAEGHQVDLLALERIHR HKTGALIRASVRLGALAAGERGRLALPCLDRYANAVGLAFQVQDDILDVIGDSATTGKRQ GADQQLGKSTYPALLGLEQAKIKARELCQESLSALNELEDTLDNPAAIAPLRSLANYVVE RDK