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. 2001 Jan 1;29(1):340-3.
doi: 10.1093/nar/29.1.340.

The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes

L B Ellis  1 , C D Hershberger, E M Bryan, L P Wackett
Affiliations

The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes

L B Ellis et al. Nucleic Acids Res. .

Abstract

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolic enzymes and their organization into metabolic pathways. Currently, it contains information on over 400 enzymes. In the last year the enzyme page was enhanced to contain more internal and external links; it also displays the different metabolic pathways in which each enzyme participates. In collaboration with the Nomenclature Commission of the International Union of Biochemistry and Molecular Biology, 35 UM-BBD enzymes were assigned complete EC codes during 2000. Bacterial oxygenases are heavily represented in the UM-BBD; they are known to have broad substrate specificity. A compilation of known reactions of naphthalene and toluene dioxygenases were recently added to the UM-BBD; 73 and 108 were listed respectively. In 2000 the UM-BBD is mirrored by two prestigious groups: the European Bioinformatics Institute and KEGG (the Kyoto Encyclopedia of Genes and Genomes). Collaborations with other groups are being developed. The increased emphasis on UM-BBD enzymes is important for predicting novel metabolic pathways that might exist in nature or could be engineered. It also is important for current efforts in microbial genome annotation.

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Figures

Figure 1
Figure 1
Excerpt from a UM-BBD enzyme page. This page for the enzyme haloalkane dehalogenase includes, among other information: (A) a link to the BRENDA database; (B) a dynamic search of the GenBank database; (C) a dynamic search of the GenPept database; and (D) a dynamic search of the PDB database. The complete enzyme page is available at http://umbbd.ahc.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=e0003.
Figure 2
Figure 2
Excerpt from a UM-BBD reaction page. This page for the reaction from 1,2-dichloroethane to 2-chloroethanol includes, among other information, (A) a link to a Medline abstract which contains information on the enzyme’s structure; (B) a link to the UM-BBD enzyme page for its enzyme, excerpt shown in Figure 1; and (C) a link to a generated pathway starting from this reaction. An example of the latter is shown in Figure 3. The complete reaction page is available at http://umbbd.ahc.umn.edu/servlets/pageservlet?ptype=r&reacID=r0001.
Figure 3
Figure 3
Excerpt from a UM-BBD generated metabolic pathway. This pathway was generated starting from the reaction from dimethyl sulfoxide to dimethyl sulfide. In the original all enzyme and compound names are hyperlinked to UM-BBD reaction and compound pages, respectively. The complete generated pathway page is available at http://umbbd.ahc.umn.edu/cgi-bin/page.cgi?ptype=p&reacID=r0207.
Figure 4
Figure 4
Prototype improved visualization of UM-BBD generated pathways. This is an excerpt that displays the same generated pathway shown in Figure 3. Compared to Figure 3, the prototype is more compact, more attractive and loops are displayed more intuitively.
See this image and copyright information in PMC

References

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