EcoCyc is an electronic reference source for E. coli biologists, and for biologists who work with related microorganisms. Scientists can use the Pathway/Genome Navigator user interface within EcoCyc to visualize the layout of genes within the E. coli chromosome, or of an individual biochemical reaction, or of a complete biochemical pathway (with compound structures displayed). The navigation capabilities of the software allow a user to move from a display of an enzyme to a display of a reaction that the enzyme catalyzes, or to the gene that encodes the enzyme. The interface also supports a variety of queries, such as generating a display of the map positions of all genes that code for enzymes within a given biochemical pathway. As well as being used as a reference source to look up individual facts, EcoCyc supports computational studies of the metabolism, such as design of novel biochemical pathways for biotechnology, studies of the evolution of metabolic pathways, and simulation of metabolic pathways. EcoCyc is also used for computer-based education in biochemistry.
EcoCyc describes all known metabolic pathways and signal-transduction pathways of E. coli. It describes each metabolic enzyme of E. coli, including its cofactors, activators, inhibitors, and subunit structure. When known, the genes encoding the subunits of an enzyme are listed, as well as the map position of a gene on the E. coli chromosome. The project is also annotating E. coli transport proteins, as well as all tRNAs. The database tracks the ongoing functional identifications of E. coli genes that are reported in the literature.
EcoCyc is linked to other biological databases containing protein and nucleic-acid sequence data, bibliographic data, protein structures, and descriptions of different E. coli strains. In addition, the Pathway Tools software that underlies EcoCyc is not specific to E. coli, but has been applied to manage genomic and biochemical data for a variety of organisms.
"EcoCyc" is pronounced "eeko-sike". It sounds like "eclipse" and like "encyclopedia".
DoubleTwist, Inc. is the exclusive world-wide distributor of EcoCyc, MetaCyc, and Pathway tools.
Karp, P., Riley, M., Paley, S., Pellegrini-Toole, A., Krummenacker, M.
EcoCyc: Electronic Encyclopedia of E. coli Genes and Metabolism,
Nucleic Acids Research, 27(1):55 1999.
Additional EcoCyc publications:
Karp, P.D., Krummenacker, M., Paley, S., and Wagg, J. (1999, in press)
Integrated pathway/genome databases and their role in drug discovery,
Trends in Biotechnology.
Karp, P.D., (1999, in press)
EcoCyc: The Resource and the Lessons Learned,
Kluwer Academic Publishers.
P. Karp and S. Paley
Integrated
access to metabolic and genomic data,
Journal of Computational Biology, 3(1):191-212 1996.
P. Karp and M. Riley
"Representations
of metabolic knowledge,"
in Proceedings of the First International
Conference on Intelligent Systems for Molecular Biology (L. Hunter,
D. Searls, and J. Shavlik, eds.), (Menlo Park, CA), pp. 207-215, AAAI Press,
1993.
P. Karp and S. Paley
"Representations
of metabolic knowledge: Pathways,"
in Proceedings of the Second
International Conference on Intelligent Systems for Molecular Biology
(Altman, R. and Brutlag, D. and Karp, P. and Lathrop, R. and Searls, D.
eds.), (Menlo Park, CA), AAAI Press, 1994.