Abstract:The nucleic acid sequences and amino acid sequences of farnesyl diphosphate synthase (FPPS) from Lycopersicon esculentum, Hevea brasiliensis, Musa acuminata, Malus x domestica, Helianthus annuus and Vitis vinifera, which were registered in GenBank, were analyzed and predicted by the tools of bioinformatics in the following aspects: the composition of nucleic acid sequences and amino acid sequences, transit peptides, transmembrane topological structures, hydrophobicity or hydrophilicity, secondary and tertiary structure of protein, molecular phylogenetic evolution. The full-length gene of FPPS contains an opening reading frame, a 5’-untranslated region, and a 3’-untranslated region. FPPS is a hydrophilic and non-transmembrane protein without transit peptides at its N-terminal end. The amino acid sequences of FPPS include 5 conserved structural regions, out of which two are Asp-rich motifs. α-helix and random coil are the major motifs of predicted secondary structure of FPPS. β-turn and extended strands spread in the secondary structure of the protein. A large central cavity formed from the α-helices is present within the predicted tertiary structure of functional regions of FPPS. Five conserved amino acid sequences are on the surface of this cavity, two of which are conserved Asp-rich motifs on the inner walls of the cavity.