What's New in the UM-BBD?

December 4, 2008
A pathway was added for quinaldine, (US) or (UK), and the pathway for vanillin, (US) or (UK), was updated. The quinaldine pathway was started by a student in the 2008 Biocatalysis and Biodegradation class. Thanks to programming changes to make full use of recent server upgrades, predictions using the Pathway Prediction System (PPS) are now twice as fast. Test this with the PPS Demo. On the Links page, a link was updated for the Agency for Toxic Substances and Disease Registry's ToxFAQs.

November 13, 2008
A pathway was added for 2,4-dinitrotoluene, (US) or (UK). This pathway was started by a student in the 2008 Biocatalysis and Biodegradation class. In the Pathway Prediction System (PPS), all rules that handle CoA thioesters have been simplified to instead use carboxylates. Users now enter carboxylates rather than CoA thioesters; for example, 4-hydroxybenzoate instead of 4-hydroxybenzoyl-CoA. On the Links page, a link was added for the Journal of Chemical Information and Modeling and GREP: Generator of Reaction Equations and Pathways.

October 23, 2008
A pathway was added for thiamin, (US) or (UK), and the pathway for atrazine, (US) or (UK), and the metapathway for triazines, (US) or (UK), were updated. The thiamin pathway was started by a student in the 2008 Biocatalysis and Biodegradation class. One new reaction mechanism graphic has been added, for the spontaneous hydrolysis of thiamin in the first step of the thiamin pathway. This brings the number of such graphics to 35. A list of all reaction mechanism graphics is available. On the Links page, a link was added for ChemSpider, and links were removed for Bioinformatics and Educational Resources at New Mexico State University, the Bioremediation Discussion Group, and Bio Online.

September 25, 2008
A pathway was added for pyridoxine, including pyridoxamine, (US) or (UK). This pathway was started by students in the 2008 Biocatalysis and Biodegradation class. In the Pathway Prediction System (PPS), using two step prediction, the predicted pathway is shown using smaller boxes. Two step prediction is best for smaller compounds that have fewer choices at each step; those predicted compounds fit nicely in the smaller boxes. Test it by selecting "Predict: Two steps" at the PPS main menu, then click the "Demo" button. More details are found in About the PPS.

August 22, 2008
A pathway was added for dimethyl isophthalate, (US) or (UK), a model compound for phthalate esters, and the pathway for 2,4-dichlorotoluene, (US) or (UK), was updated. The dimethyl isophthalate pathway was started by a student in the 2008 Biocatalysis and Biodegradation class. In the Pathway Prediction System (PPS), prediction results have been displayed one step at a time. Now users have an option see two steps. This takes a bit more time, but not two times as long. Test it by selecting "Predict: Two steps" at the PPS main menu, then click the "Demo" button. More details are found in About the PPS. Aerobically "likely" or "neutral" rules for oxidation of aliphatic carbons, have been changed to "unlikely" when the chain contains one or more nitro groups. Test it by comparing predictions for beta oxidation (bt0337) of hexanoate (paste CCCCCC([O-])=O into the PPS) with that of 6-nitrohexanoate (paste
[O-][N+](=O)OCCCCCC([O-])=O into the PPS). Beta oxidation is predicted for both compounds, but for hexanoate it is aerobically likely, and for 6-nitrohexanoate it is aerobically unlikely. Predictions for this class of compounds are improved. On the Links page, a new link was added for MicrobesOnline.

July 11, 2008
Pathways for fungal anthracene, (US) or (UK), and bisphenol F, (US) or (UK), have been added. The fungal anthracene pathway was started by a student in the 2007 Biocatalysis and Biodegradation class, and the bisphenol F pathway was created by a student in the 2008 Biocatalysis and Biodegradation class. In the Pathway Prediction System (PPS), a super rule, bt0388, was created to degrade aromatic amines and benzoquinones to dihydroxyaromatics. Test this with p-aminophenol, Nc1ccc(O)cc1, which goes to hydroquinione in one step using the super rule bt0388. Predictions for these types of compounds are better and faster. On UM-BBD reaction pages, the number of hits from Medline searches has been updated. On UM-BBD enzyme pages, the number of hits from GenBank, GenPept, and PDB searches have been updated. Lists of all reaction and all enzyme pages are available. On the Links page, links were updated for the CBS NCCB bacteria/plasmids database, and the US Department of Energy Biological and Environmental Research (BER) Program.

June 20, 2008
A pathway for asulam, (US) or (UK), has been added, and the pathway for methyl tert-butyl ether, (US) or (UK), has been updated. The asulam pathway was created by a student in the 2008 Biocatalysis and Biodegradation class. In the Pathway Prediction System (PPS), rules for hydrolysis of organic sulfates (bt0143), and anaerobic addition of fumarate to methyl side chains on aromatic substrates (bt0270), have been updated. Predictions for these types of compounds are improved. On the Links page, a link was updated for the Environmental Writer Chemical Backgrounders, and a link was removed for the list of DSMZ organisms that degrade chemical compounds.

May 16, 2008
A pathway for furfural, (US) or (UK), has beenadded, and the pathway for 4-nitrophenol, (US) or (UK), has been updated and renamed the nitrophenol family pathway (an/aerobic). The furfural pathway was created by a student in the 2007 Biocatalysis and Biodegradation class. The nitrophenol family pathway (an/aerobic) includes aerobic pathways for 2- and 4-nitrophenol and resorcinol, and an anaerobic pathway for 3-nitrophenol degradation. In the Pathway Prediction System (PPS), hydrolysis of organic sulfates (bt0143), and anaerobic addition of fumarate to methyl side chains on aromatic substrates (bt0270), have been updated. Predictions for these types of compounds are improved. We have moved UM-BBD microorganism links to the WFCC-MIRCEN World Data Centre for Microorganisms on the list of organisms, and text pathway map pages, such as the 2-aminobenzoate pathway. On the Links page, a link was removed for the National Agricultural Library Bioremediation Bibliography.

April 18, 2008
A pathway for the aerobic Phenol Family, (US) or (UK), has been added. This includes metabolism for phenol, phenylboronic acid, and diphenyl ether. 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. 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. Due to changes in the ATCC website, our links to ATCC no longer work. We are 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. 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.

March 19, 2008
A pathway for N-nitrosodimethylamine, (US) or (UK), has been added, and the pathways for the picric acid family, (US) or (UK), and the naphthalene sulfonate family, (US) or (UK), have been updated. The pathway for N-Nitrosodimethylamine was started by a student in the 2007 BioC/MicE 5309 class. In the Pathway Prediction System (PPS), prediction of oxidation of a secondary carbon (bt0242), and addition of water to a double bond (bt0021), have been improved. Lhasa Limited is developing MEPPS, a new expert knowledge base software project for the prediction of microbial degradation in the environment. It is a stand-alone, PC-based system, combining data from the UM-BBD Pathway Prediction System with expert reasoning software from Lhasa. There are openings for sponsors for further development of MEPPS. For more information on MEPPS, or if you are interested in helping to sponsor this new and exciting project, contact Sian Ives <Sian.Ives@lhasalimited.org>. Students in our 2008 BioC/MicE 5309 Biocatalysis and Biodegradation class, offered completely over the Internet, have examined websites on the UM-BBD Links page and selected the ones of most interest to them. The Links page now links to the list of these choices and the reason each site was selected.

February 15, 2008
A pathway for endosulfan, a chlorinated pesticide, (US) or (UK), has been added, and the pathway for phthalate, (US) or (UK), has been updated. The pathway for endosulfan was started by a student in the 2007 BioC/MicE 5309 class. Structure-based variable aerobic likelihood has been added to the Pathway Prediction System (PPS). For aerobically likely aromatic ring monooxygenation, ring dioxygenation, ring cleavage, and ring decarboxylation rules, when the substrate contains one or more halogens, the aerobic likelihood for the transformation is changed to "neutral". This is the first step toward better handling of aerobic likelihood. Test it by comparing intradiol cleavage (bt0254) of catechol, Oc1c(O)cccc1, with that of tetrachlorocatechol, Oc1c(O)c(Cl)c(Cl)c(Cl)c1(Cl). The same pathway is predicted, but the one for catechol is aerobically likely and the one for tetrachlorocatechol is aerobically neutral. The International Advisory Board for the UM-BBD and PPS has been updated. Continuing members: Philip Judson, Lhasa Limited; Sol Resnick, Dow Chemicals. New members: Bob Boethling, EPA; Kathrin Fenner, EAWAG; Stefan Kramer, Technical University of Munich (TUM). On the Links page, a link was added for the Online Chemical Database, and a link was updated for ZINC, from UCSF.

January 23, 2008
The pathway for nicotine, (US) or (UK), has been updated. The scrollable list of pathways on the UM-BBD home page is now so large that it has been reformatted for better user access. 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) have also been improved. In a PPS prediction, 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. On the Links page, links were added to BDPServer: prediction of environmental fate for chemical compounds, National Center for Biotechnology, Spain, and BiocatCollection: International Collection of Biocatalysts. The link for MetaRouter was removed. The What's New page restarts; 2007 activities have been archived.

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