"Need to know how microbes break down chemical
compounds not commonly found in nature? This award-winning
site provides a wealth of information on microbial
biocatalytic reactions and biodegradation pathways
for primarily xenobiotic organic compounds. The
database recently added its 100th pathway, after starting
with just four in 1995.
The database currently covers approximately 650
reactions, 600 compounds, 50 organic functional
groups, 400 enzymes, and 250 microorganisms. Most
known microbial catabolic reaction types are included.
You can search the database in a variety of ways
(including by name, formula, CAS registry number, and
EC number), and links are provided to other chemical
and biological databases. The site also contains an
extensive list of almost 100 Internet resources.
At the site, you can learn to use the database by
taking the "guided tour",
join the e-mail user list, or
even enroll in a graduate-level Internet course titled
"Biocatalysis and Biodegradation".
The co-directors of the site (Lynda Ellis (ACS '85)
and Larry Wackett (ACS '99)) and their Scientific
Advisory Board pay special attention to documenting
the credibility of the database information. Future
additions to the database will include additional mirror
sites, fold prediction for its sequenced enzymes, closer
ties to genome and microbial strain databases, and
the prediction of biodegradation pathways for
compounds not contained in the database."
Wedin, R. (2000) "Review: The University of Minnesota Biocatalysis/Biodegradation Database" Chemistry, Fall 2000, American Chemical Society, p. 6.
"Microbes that devour or otherwise help break down exotic chemicals are cleaning up the environment,
spawning new technologies, and deepening our understanding of microbial life. While biodegradation and
biocatalysis are young fields, much of what is known can be found in the University of Minnesota Biocatalysis/Biodegradation Database.
The site provides detailed explanations of 99 "pathways"--chains of reactions that break down various
chemicals --as well as data on hundreds of individual reactions, compounds, enzymes, and microorganisms.
The site focuses on the reactions that begin to break down compounds not commonly found in nature, for
example, those involving naphthalene, the stuff of mothballs. For information on the more common metabolic
pathways that complete the breakdown, the site links to databases such as the
Kyoto Encyclopedia of Genes and Genomes.
All data display their pedigrees, and a guided tour helps first-time visitors find their way around.
The site lacks only for style. Hyperlinked graphics accompany most pages of data; however, by default,
reactions and pathways are rendered in old-fashioned diagrams made with text and keyboard symbols. "We
made a conscious design decision to use text as much as possible," says computational biologist and site
co-director Lynda Ellis, "and to have the graphics a click away for those whose computers are fast enough to
use them."
Cho, A. (2000) "Munching on Strange Chemicals" Netwatch, Science, 288(5471): 1543.
