Application

ApplicationReconstruction of amino acid

biosynthesis pathways from the complete

genome sequence

Bono H, Ogata H, Goto S, Kanehisa M

Genome Res. 1998 Mar;8(3):203-10

MotivationThe complete genome sequence of an organism contains information that has not been fully utilized in the current prediction methods of gene function, which are based on piece by piece similarity searches of individual genes.

MethodA genome by genome comparison id first made for identifying enzyme gene and assigning EC number, which is followed by the reconstruction of selected proteins of the metabolic pathways by use of the reference biochemical knowledge.

Use Gene Function Identification Tool (GEIT) and orthologous gene table.

The completeness of the reconstructed pathway is a indicator of the correctness of the initial gene function assignment.

Reference pathway (pathway database)

+EC number assignment(ligand database)

+gene sequence(genes database)