The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining

Abstract

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolism and related biotransformations, primarily for environmental pollutants. Currently, it contains information on over 130 metabolic pathways, 800 reactions, 750 compounds and 500 enzymes. In the past two years, it has increased its breath to include more examples of microbial metabolism of metals and metalloids; and expanded the types of information it includes to contain microbial biotransformations of, and binding interactions with many chemical elements. It has also increased the ways in which this data can be accessed (mined). Structure-based searching was added, for exact matches, similarity, or substructures. Analysis of UM-BBD reactions has lead to a prototype, guided, pathway prediction system. Guided prediction means that the user is shown all possible biotransformations at each step and guides the process to its conclusion. Mining the UM-BBD's data provides a unique view into how the microbial world recycles organic functional groups. UM-BBD users are encouraged to comment on all aspects of the database, including the information it contains and the tools by which it can be mined. The database and prediction system develop under the direction of the scientific community.

Figure 1

Excerpt from the UM-BBD webpage for the element arsenic. If users selects the ‘chemical properties’ link, they are transferred to the Web Elements (http://www.webelements.com/) page for the element; if they select the ‘UM-BBD compounds’ link, they are transferred to a dynamically-generated list of all UM-BBD compound pages that contain that element. The complete page is found at: http://umbbd.ahc.umn.edu/periodic/elements/as.html.

Figure 2

Excerpts from the UM-BBD Guided Pathway Prediction starting from the compound benzyl alcohol, see text. (A) First step, showing six possible biotransformations. The user proceeds by selecting ‘next’ to indicate the next compound to be transformed, or ‘rule’ to see the biotransformation (bt) rule for that transformation, including, where possible, a link to a UM-BBD reaction with bibliographic reference. (B) Last step in one predicted pathway branch. The compounds in the pathway are numbered 1–6, in pathway order. Additional rules are needed to handle the degradation of the last compound.

Figure 2

Excerpts from the UM-BBD Guided Pathway Prediction starting from the compound benzyl alcohol, see text. (A) First step, showing six possible biotransformations. The user proceeds by selecting ‘next’ to indicate the next compound to be transformed, or ‘rule’ to see the biotransformation (bt) rule for that transformation, including, where possible, a link to a UM-BBD reaction with bibliographic reference. (B) Last step in one predicted pathway branch. The compounds in the pathway are numbered 1–6, in pathway order. Additional rules are needed to handle the degradation of the last compound.