Genome Res., 8, 203-210 (1998)
Reconstruction of Amino Acid Biosynthesis Pathways from the Complete Genome
Sequence
Hidemasa Bono, Hiroyuki Ogata, Susumu Goto, Minoru Kanehisa*
Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
Abstract
The complete genome sequence of an organism contains information that has not been
fully utilized in the current prediction methods of gene functions, which are based on
piece-by-piece similarity searches of individual genes. We present here a method that
utilizes a higher level information of molecular pathways to reconstruct a complete
functional unit from a set of genes. Specifically, a genome-by-genome comparison is
first made for identifying enzyme genes and assigning EC numbers, which is followed
by the reconstruction of selected portions of the metabolic pathways using the reference
biochemical knowledge. The completeness of the reconstructed pathway is an indicator
of the correctness of the initial gene function assignment. This feature has become
possible because of our efforts to computerize the current knowledge of metabolic
pathways under the KEGG project. We found that the biosynthesis pathways of all 20
amino acids were completely reconstructed in E. coli, H. influenzae, and B. subtilis,
and probably in Synechocystis and S. cerevisiae as well, although it was necessary to
assume wider substrate specificity for aspartate aminotransferases.
*Corresponding author:
Minoru Kanehisa
Institute for Chemical Research, Kyoto University
Uji, Kyoto 611, Japan
Telephone: +81-774-38-3270
Fax: +81-774-38-3269
E-mail: kanehisa@kuicr.kyoto-u.ac.jp