Protein Info for Psest_0401 in Pseudomonas stutzeri RCH2
Annotation: isopentenyl-diphosphate delta-isomerase, type 2
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: 92% identical to IDI2_PSEU5: Isopentenyl-diphosphate delta-isomerase (fni) from Pseudomonas stutzeri (strain A1501)
KEGG orthology group: K01823, isopentenyl-diphosphate delta-isomerase [EC: 5.3.3.2] (inferred from 92% identity to psa:PST_3876)Predicted SEED Role
"Isopentenyl-diphosphate delta-isomerase, FMN-dependent (EC 5.3.3.2)" in subsystem Archaeal lipids or Isoprenoid Biosynthesis (EC 5.3.3.2)
MetaCyc Pathways
- superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) (12/12 steps found)
- taxadiene biosynthesis (engineered) (12/13 steps found)
- methylerythritol phosphate pathway I (9/9 steps found)
- methylerythritol phosphate pathway II (9/9 steps found)
- isoprene biosynthesis I (9/10 steps found)
- all-trans-farnesol biosynthesis (3/4 steps found)
- bisabolene biosynthesis (engineered) (3/6 steps found)
- mono-trans, poly-cis decaprenyl phosphate biosynthesis (2/5 steps found)
- superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) (5/10 steps found)
- mevalonate pathway I (eukaryotes and bacteria) (2/7 steps found)
- mevalonate pathway II (haloarchaea) (2/7 steps found)
- isoprene biosynthesis II (engineered) (2/8 steps found)
- mevalonate pathway III (Thermoplasma) (2/8 steps found)
- mevalonate pathway IV (archaea) (2/8 steps found)
- superpathway of ergosterol biosynthesis II (11/26 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
No predicted isozymesUse Curated BLAST to search for 5.3.3.2
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 L0GGY3 at UniProt or InterPro
Protein Sequence (346 amino acids)
>Psest_0401 isopentenyl-diphosphate delta-isomerase, type 2 (Pseudomonas stutzeri RCH2) MSKQSLVSRKNDHLDIVLDPARAAGATGTGFGAFRFEHCALPELHLDQIDLKGALFGRSL RAPLLISSMTGGAARSAAINAHLAEAAQHLGIAMAVGSQRVALETAGDQGLTGQLRQLAP DILLLANFGAAQLVRGYGVDEARRAVEMIDGDALIVHLNPLQEAVQPGGDRDWRGVLQAI EALARRLAVPVVIKEVGAGISATVARQLVDAGVAAIDVAGSGGTSWAAVEAERATDVSQR AIAQAFADWGIPTAQALQAVREACPGTPLIASGGIRDGVEAAKAICLGADLVGQAAGVLQ AAMLSSDAVVQHFEVLIEQLRIACFCTGSASLAELRQARLLQVSGY