M-path: a compass for navigating potential metabolic pathways.
BACKGROUND
Construction of synthetic metabolic pathways promises sustainable production of diverse chemicals and materials. To design synthetic metabolic pathways of high value, computational methods are needed to expand present knowledge by mining comprehensive chemical and enzymatic information databases. Several computational methods have been already reported for the metabolic pathway design, but until now computation complexity has limited the diversity of chemical and enzymatic data used.


RESULTS
We introduce a computational platform, M-path, to explore synthetic metabolic pathways including putative enzymatic reactions and compounds. M-path is an iterative random algorithm, which makes efficient use of chemical and enzymatic databases to find potential synthetic metabolic pathways. M-path can readily control the search space and perform well compared with exhaustively enumerating possible pathways. A web-based pathway viewer is also developed to check extensive metabolic pathways with evaluation scores on the basis of chemical similarities. We further produce extensive synthetic metabolic pathways for a comprehensive set of alpha amino acids. The scalable nature of M-path enables us to calculate potential metabolic pathways for any given chemicals.
Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.
Michihiro
M
Araki
Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.
Robert Sidney
RS
Cox
Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.
Hiroki
H
Makiguchi
Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.
Teppei
T
Ogawa
Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.
Takeshi
T
Taniguchi
Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.
Kohei
K
Miyaoku
Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.
Masahiko
M
Nakatsui
Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.
Kiyotaka Y
KY
Hara
Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Mitsui Knowledge Industry (MKI) Co., Osaka 530-0005, MCHC R&D Synergy Center, Inc., Yokohama 227-8502 and Mitsubishi Chemical Group Science and Technology Research Center (MCRC) Inc., Yokohama 227-8502, Japan.
Akihiko
A
Kondo
D000465:Algorithms; D000596:Amino Acids / Q000378:metabolism; D016208:Databases, Factual; D053858:Metabolic Networks and Pathways; D012984:Software
D000596:Amino Acids