Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2006 Jan 1;34(Database issue):D517-21.
doi: 10.1093/nar/gkj076.

The University of Minnesota Biocatalysis/Biodegradation Database: the first decade

Lynda B M Ellis  1 , Dave Roe, Lawrence P Wackett
Affiliations

The University of Minnesota Biocatalysis/Biodegradation Database: the first decade

Lynda B M Ellis et al. Nucleic Acids Res. .

Abstract

As the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) starts its second decade, it includes information on over 900 compounds, over 600 enzymes, nearly 1000 reactions and about 350 microorganism entries. Its Biochemical Periodic Tables have grown to include biological information for almost all stable, non-noble-gas elements (http://umbbd.ahc.umn.edu/periodic/). Its Pathway Prediction System (PPS) (http://umbbd.ahc.umn.edu/predict/) is now an internationally recognized, open system for predicting microbial catabolism of organic compounds. Graphical display of PPS rules, a stand-alone version of the PPS and guidance for PPS users are being developed. The next decade should see the PPS, and the UM-BBD on which it is based, find increasing use by national and international government agencies, commercial organizations and educational institutions.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Excerpt from a PPS pathway prediction web page. The complete page appears if ‘Demo’ is chosen from the initial PPS page (). Predicted compounds 1 and 4 are in the UM-BBD; these are the only displays that include a Cpd button. That button links to their UM-BBD compound pages, and, from there, to reaction and pathway pages.
Figure 2
Figure 2
Excerpt from the web page for bt0005, a rule that has been moved to Reactor. One rule pattern graphic is displayed. Since more than one pattern is used for this rule, a link to a graphic showing all of them is to its right. Benzyl alcohol triggers both patterns for this rule at two different locations, producing predicted compounds 5 through 8 in Figure 1. A list of all rules is available at .
Figure 3
Figure 3
Excerpt from a prototype MEPPS page. The grayed out ‘Examples’ button at the bottom will link to the appropriate static UM-BBD rule web page (and from that to static reaction, enzyme, compound and pathway pages) once the prototype is complete.
See this image and copyright information in PMC

References

    1. Ellis L.B., Hershberger C.D., Wackett L.P. The University of Minnesota Biocatalysis/Biodegradation database: specialized metabolism for functional genomics. Nucleic Acids Res. 1999;27:373–376. - PMC - PubMed
    1. Ellis L.B., Hershberger C.D., Wackett L.P. The University of Minnesota Biocatalysis/Biodegradation database: microorganisms, genomics and prediction. Nucleic Acids Res. 2000;28:377–379. - PMC - PubMed
    1. Ellis L.B., Hershberger C.D., Bryan E.M., Wackett L.P. The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes. Nucleic Acids Res. 2001;29:340–343. - PMC - PubMed
    1. Ellis L.B., Hou B.K., Kang W., Wackett L.P. The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining. Nucleic Acids Res. 2003;31:262–265. - PMC - PubMed
    1. Hou B.K., Wackett L.P., Ellis L.B. Microbial pathway predicting: a functional group approach. J. Chem. Inf. Comput. Sci. 2003;43:1051–1057. - PubMed

Publication types