University of Minnesota Biocatalysis/Biodegradation Database
Progress Report 161 - April 18, 2008
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- A pathway for the aerobic Phenol Family has been added. This includes
metabolism for phenol, phenylboronic acid, and diphenyl ether.
http://umbbd.msi.umn.edu/pba/pba_map.html
http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[upathway-id:'pba_map']
- 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). The first one is for angular
dioxygenation of polynuclear aromatic compounds bridged by an ether,
amine, or carbonyl. Test this with benzofuran, c1ccc2c(c1)oc3ccccc23,
which goes to 2,2',3-trihydroxybiphenyl in one step using the super
rule bt0374. The second one is for degradation of 2,4,6-trinitrophenol
(picric acid) and 2,4-dinitrophenol. Try this out by pasting
Picric acid, [O-]c1c(cc(cc1[N+]([O-])=O)[N+]([O-])=O)[N+]([O-])=O
into the PPS SMILE string box. It is transformed to
2,4-dinitrocyclohexanone in one step using the super rule bt0378.
Predictions for these classes of compounds are better and faster.
http://umbbd.msi.umn.edu/predict/
http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=bt0374
http://umbbd.msi.umn.edu/servlets/predict.jsp?bt=aerobic&query=c1ccc2c(c1)oc3ccccc23
http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=bt0378
- Relative reasoning, giving one btrule priority over another, was
announced last June. Now a list of all btrules using it, and which
rules each has priority over, is available. It is linked to on the
list of all rules and the main search and browse page.
http://umbbd.msi.umn.edu/cgi-bin/relative_reasoning.cgi
http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=allrules
http://umbbd.msi.umn.edu/search/
- Due to changes in the ATCC website, links to ATCC no longer
work. We will be moving UM-BBD microorganism links to the
WFCC-MIRCEN World Data Centre for Microorganisms. This change
has been made on the list of microorganisms, and will be made
on pathway map pages as time permits.
http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=allmicros
- On the Links page, a link was added for IPCS INCHEM: Chemical
Safety Information from Intergovernmental Organizations, and a
link was updated for the WFCC-MIRCEN World Data Centre for
Microorganisms.
http://umbbd.msi.umn.edu/resources.html
If you have comments on any aspect of the UM-BBD, please let us know.
Lynda Ellis <[log in to unmask]>
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