Protein Info for Psest_3388 in Pseudomonas stutzeri RCH2
Annotation: Geranylgeranyl pyrophosphate 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: 52% 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 98% identity to psa:PST_0955)MetaCyc: 52% 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 2.5.1.90) / 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 geranylgeranyl diphosphate biosynthesis II (via MEP) (12/12 steps found)
- taxadiene biosynthesis (engineered) (12/13 steps found)
- superpathway of chorismate metabolism (44/59 steps found)
- polyisoprenoid biosynthesis (E. coli) (5/5 steps found)
- superpathway of ubiquinol-8 biosynthesis (early decarboxylation) (10/12 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)
- all-trans-farnesol biosynthesis (3/4 steps found)
- (3R)-linalool biosynthesis (1/2 steps found)
- (3S)-linalool biosynthesis (1/2 steps found)
- linalool biosynthesis I (1/2 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)
- bisabolene biosynthesis (engineered) (3/6 steps found)
- mono-trans, poly-cis decaprenyl phosphate biosynthesis (2/5 steps found)
- ipsdienol biosynthesis (1/4 steps found)
- superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) (5/10 steps found)
- superpathway of menaquinol-8 biosynthesis I (5/10 steps found)
- superpathway of demethylmenaquinol-8 biosynthesis I (4/9 steps found)
- stellatic acid biosynthesis (3/8 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 (11/26 steps found)
- superpathway of phylloquinol biosynthesis (3/15 steps found)
- superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis (14/33 steps found)
- superpathway of ergosterol biosynthesis I (4/26 steps found)
- Methanobacterium thermoautotrophicum biosynthetic metabolism (21/56 steps found)
- superpathway of cholesterol biosynthesis (4/38 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: 2.5.1.1, 2.5.1.10, 2.5.1.29, 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)
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 L0GM93 at UniProt or InterPro
Protein Sequence (322 amino acids)
>Psest_3388 Geranylgeranyl pyrophosphate synthase (Pseudomonas stutzeri RCH2) MQPQPFYQVVADDFAAVDGIIRKQLTSRVPLVEKIGDYITSAGGKRLRPLLVLLSGSALG HQGDQLRLLAAIIEFLHTSTLLHDDVVDMSGMRRGRSTANALWGNAPSVLVGDFLYARSF EMMVELDSMPVMRIISQATRVIAEGEVLQLSKVRDASTTEEIYMEVIRGKTAMLFEASTH SAATLAGASEEQREALRTFGDHLGIAFQLVDDLLDYQGDAETLGKNVGDDLAEGKPTLPL IYTMREGTTEQAALVRKAIQKGGLEDLESIRTAVEAAGALDYTAKLARDYAERAIACLEV IPANQYRDALVELCRFAVARTH