Protein Info for GFF2365 in Xanthobacter sp. DMC5

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: 42% identical to ISPB_HAEIN: Octaprenyl diphosphate synthase (ispB) from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

KEGG orthology group: K02523, octaprenyl-diphosphate synthase [EC: 2.5.1.90] (inferred from 94% identity to xau:Xaut_1373)

MetaCyc: 38% identical to solanesyl diphosphate synthase (Rhodobacter capsulatus)
TRANS-OCTAPRENYLTRANSTRANSFERASE-RXN [EC: 2.5.1.84]

Predicted SEED Role

"Decaprenyl diphosphate synthase (EC 2.5.1.91)" (EC 2.5.1.91)

MetaCyc Pathways

polyisoprenoid biosynthesis (E. coli) (5/5 steps found)
all-trans-decaprenyl diphosphate biosynthesis (1/1 steps found)
nonaprenyl diphosphate biosynthesis I (1/1 steps found)
octaprenyl diphosphate biosynthesis (1/1 steps found)
superpathway of chorismate metabolism (41/59 steps found)
superpathway of plastoquinol biosynthesis (2/5 steps found)
superpathway of ubiquinol-8 biosynthesis (early decarboxylation) (7/12 steps found)
superpathway of menaquinol-10 biosynthesis (5/10 steps found)
superpathway of menaquinol-8 biosynthesis I (5/10 steps found)
superpathway of menaquinol-9 biosynthesis (5/10 steps found)
superpathway of demethylmenaquinol-8 biosynthesis I (4/9 steps found)
superpathway of demethylmenaquinol-9 biosynthesis (4/9 steps found)
ubiquinol-10 biosynthesis (late decarboxylation) (4/9 steps found)
superpathway of menaquinol-8 biosynthesis III (2/9 steps found)
superpathway of menaquinol-8 biosynthesis II (2/10 steps found)

Isozymes

Compare fitness of predicted isozymes for: 2.5.1.90

Use Curated BLAST to search for 2.5.1.84 or 2.5.1.90 or 2.5.1.91

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

Find the best match in UniProt

Protein Sequence (335 amino acids)

>GFF2365 Octaprenyl diphosphate synthase (Xanthobacter sp. DMC5)
LAVVLPFEPNEPSLEALVALVKADMERVNTVILARTGSDVAMIPEVANHLISSGGKRLRP
MLTLACAALAGYRGEGHVKLAASVEFMHTATLLHDDVVDESDMRRGKLAARKLWGNEASV
LVGDFLLGQAFKMMVEVGSMTCLDILSTAACVIAEGEVMQLAAAKNTATSEDDYLAVIRG
KTAELFAAACEVGAVLAQRPKAEQAACRSYGMNLGIAFQLVDDALDYGGSQAKLGKNVGD
DFREGKITLPVLLAFRRGDEKERAFWQRCLENSEASDADLDQAIGLMTKHRAIADTVERA
RHYGAIAKDALALFPAGPAKAALMEAVDFCLSRAH