University of Minnesota Biocatalysis/Biodegradation Database
                   Progress Report 158 - January 23, 2008

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- The pathway for nicotine has been updated.
   http://umbbd.msi.umn.edu/nic/nic_map.html
   http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[upathway-id:'nic_map']

- The scrollable list of pathways on the UM-BBD home page is now so large
   that it has been reformatted for better user access.
   http://umbbd.msi.umn.edu/

- Two additional super rules, rules that include two or more contiguous
   btrules that form a small pathway of their own, have been added to the
   Pathway Prediction System (PPS). These are for the first and second
   steps in cleavage of pyridines and nicotines and their derivatives.
   Predictions for this class of compounds are better and faster.
   Try out these super rules using pyridine-2-carboxamide (picolinamide),
   a photolytic product of the herbicide Diquat, C1=CC=NC(=C1)C(=O)N.
   The amide is first removed to form 2-carboxypyridine, which is cleaved
   to 2,5-dihydroxypyridine using the first super rule (bt0362).  The
   latter is cleaved to fumarate and acetoacetate using the second
   (bt0363).  Prediction of decarboxylation (bt0051 and bt0082) has also
   been improved.
   http://umbbd.msi.umn.edu/predict/
   http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=bt0362
   http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=bt0363
   http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=bt0051
   http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=bt0082
http://umbbd.msi.umn.edu/servlets/predict.jsp?bt=aerobic&query=C1=CC=NC(=C1)C(=O)N

- In the PPS, when the Next button will take you to a readily degraded
   compound that will end a prediction, that button is now shaded green.
   You can chose it to end the prediction, or continue the prediction by
   choosing a non-green Next button.  This is described in more detail
   in the About the PPS tutorial.
   http://umbbd.msi.umn.edu/predict/aboutPPS.html

- On the Links page, links were added for BDPServer: prediction of
   environmental fate for chemical compounds, National Center for
   Biotechnology, Spain, and BiocatCollecction: International
   Collection of Biocatalysts.  The link for MetaRouter was removed.
   http://umbbd.msi.umn.edu/resources.html

- The What's New page restarts; 2007 activities have been archived.
   http://umbbd.msi.umn.edu/whatsnew.html

If you have comments on any aspect of the UM-BBD, please let us know.

Lynda Ellis <[log in to unmask]>