What's New in the UM-BBD?

December 13, 2007
UM-BBD software and hardware upgrade is complete. During the upgrade, some pages and functions were redirected to port 81. These are now back to the usual port 80. Response should be faster and more stable. The pathway for 2-chloro-N-isopropylacetanilide (Propachlor), (US) or (UK), and the BTEX metapathway, have been updated. 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 (bt0357) and second (bt0358) steps in cleavage of hydroquinones. Predictions for this class of compounds are better and faster. Try these super rules using homogentisate, Oc1ccc(O)c(CC([O-])=O)c1, which is cleaved to 4-maleylacetoacteate using the first super rule. The latter is cleaved to fumarate and acetoacetate using the second. Prediction of dehalogenation has also been improved.

November 21, 2007
The new pathway for 4-hydroxypyridine, (US) or (UK), has been added. This pathway was contributed by a student in the 2007 BioC/MicE 5309 class. A new Path Search allows you to search for paths between BBD compounds. Enter the cnumbers for any two BBD compounds, and it will display known paths between them with 10 or fewer reactions. A demo is available. Try it! A list of all BBD compounds is available. There is a link to the Path Search on the main Search page. In the Pathway Predictive System (PPS), when a compound does not trigger any btrules with very likely, likely, or neutral aerobic likelihood, but does trigger some aerobically unlikely or very unlikely rules, and the system is set to show only compounds predicted using "Aerobic" rules (the default), it now switches to "All", and shows the other compounds. Try this by pasting the SMILES string for nitroglycerin,
[O-][N+](=O)OCC(CO[N+]([O-])=O)O[N+]([O-])=O into the PPS.

October 31, 2007
UM-BBD software and hardware is being upgraded. This has caused two scheduled, and several unscheduled, outages in the past month. The upgrade is not yet complete. We apologize for any inconvenience the past outages have caused, and for any outages and broken links or functionality in the next few weeks. During the upgrade, some pages and functions are being redirected to port 81, rather than the usual port 80. This may cause some firewall problems, which will cease once the upgrade is complete.

The pathways for benz[a]pyrene, (US) or (UK), and 2,4-D, (US) or (UK), have been updated. 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 (bt0351) and second (bt0352) steps in extradiol cleavage of aromatic rings, including biphenyls. Predictions for these classes of compounds are better and faster. Try out these super rules using 4-chlorobiphenyl, a model compound for PCB biodegradation, Clc1ccc(cc1)-c2ccccc2, which cleaves off a carboxylate using the first, and pyruvate using the second, extradiol super rule. On the Links page, a link was updated to OSHA Chemical Sampling Information, and a link was removed to the EPA's PCB Identifiers.

September 28, 2007
A pathway for 4-(1-ethyl-1,4-dimethyl-pentyl)phenol, a model 4-nonylphenol, (US) or (UK), has been added, and the pathway for atrazine, (US) or (UK), has been updated. UM-BBD links to the BRENDA comprehensive enzyme information system have been updated. They are found on enzyme pages when the enzyme has a full 4-digit EC code, such as the page for haloalkane dehalogenase, EC 3.8.1.5. A list of all enzyme pages, including their EC codes, is available. Two additional super rules, rules that include two or more continguous btrules that form a small pathway of their own, have been added to the Pathway Prediction System (PPS). These are dioxygenation of aromatic rings to form catechol derivatives (bt0005), and intradiol ring cleavage in the lower catechol pathway (bt0348). Predictions for these classes of compounds are better and faster. Try out these super rules using phenanthrene, c1ccc2c(c1)ccc3ccccc23, which has three instead of six compounds in its first step using the dioxygenase super rule, all three of them known UM-BBD compounds, or cis,cis-muconate,
[O-]C(=O)\C=C/C=C\C([O-])=O, which goes to succinate in one step using the intradiol lower catechol pathway super rule. On the Links page, a link was updated to the BRENDA comprehensive enzyme information system, and links were added to the EPA's Office of Pollution Prevention and Toxics and its Pesticide Fact Sheets and PCB Identifiers, and to EzCatDB: Enzyme Catalytic Mechanism Database, from AIST, Japan.

August 24, 2007
The pathways for phenanthrene, (US) or (UK), and biphenyl, (US) or (UK), have been updated. Super rules have been added to the Pathway Prediction System (PPS). These are btrules which include several contiguous btrules that form a small pathway of their own. The first two super rules are for beta-oxidation of fatty acids (bt0337) and the upper naphthalene pathway for cleavage of fused aromatic rings (bt0340). Predictions for these classes of compounds are better and faster. Try super rules out using octanoate, CCCCCCCC(=O)[O-], which goes to butyrate in two steps using the beta oxidation super rule, or 1,2-dihydroxynaphthalene, Oc1ccc2ccccc2c1O, which undergoes ring cleavage in two steps using the upper naphthalene pathway super rule. On the Links page, links were updated to the National Safety Council's Chemical Backgrounders, the Australian Safety and Compensation Council's Hazardous Substances Information System, and the University of Edinburgh's Microbial World, and a link was deleted to the EMP Database.

July 26, 2007
A pathway for hexadecyltrimethylammonium chloride, (US) or (UK), has been added. This pathway was started by a student in the 2007 BioC/MicE 5309 class. In the Pathway Prediction System (PPS), a statement of PPS purpose and scope has been developed.
"The PPS predicts plausible pathways for microbial degradation of chemical compounds. Predictions use biotransformation rules, based on reactions found in the UM-BBD database or in the scientific literature. A list of all rules is available. PPS predictions are most accurate for compounds that are:

similar to compounds whose biodegradation pathways are reported in the scientific literature;
in environments exposed to air, in moist soil or water, at moderate temperatures and pH, with no competing chemicals or toxins; and
the sole source of energy, carbon, nitrogen, or other essential element for the microbes in these environments, rather than present in trace amounts.

Biodegradation of some types of compounds should not be predicted. More information is available."
On the Links page, a link was added to the UK Pesticides Safety Directorate.

June 27, 2007
Links to Medline primary references on reaction pages and in Biochemical Periodic Table element pages now use the PubMed AbstractPlus format. For example, see the link to the Medline reference in the Atrazine to Hydroxyatrazine reaction page. A list of all reactions is available. In the Biochemical Periodic Tables, the element page for Sulfur has been updated. In the Pathway Prediction System (PPS), relative reasoning has been implemented. This allows rules for biotransformation to have relative likelihoods among themselves in addition to their absolute aerobic likelihood. Relative likelihood is based on metabolic logic and the study of the biotransformations of all UM-BBD compounds, comparing those a compound can undergo to those it is known to undergo in the UM-BBD. As implemented in the PPS, biotransformations with lower relative likelihood are removed from the list of choices. To demonstrate this feature, two relative rules, "ring cleavage > ring di- and mono- oxygenation" and "hydroxyaromatic ring vic-monooxygenation > ring dioxygenation and other ring monooxygenation," have been implemented. PPS predictions for aromatic compounds have increased specificity, with no loss in sensitivity. Try it using the PPS demo compound, benzyl alcohol. s-Triazines are an important class of pesticide chemicals. The UM-BBD has focused on these compounds since its very beginning; a pathway map for the s-triazine atrazine was one of the first four in the original, February 1995, UM-BBD. It has been updated several times since then. In 1999, the s-Triazine Metapathway Map was developed, to emphasize the similar biodegradation pathways found for several commercially important s-triazines. Most recently, PPS predictions for this class of compounds have been improved. To help publicize this project, a web page for Agricultural s-Triazines was developed. Try it! A click on the SMILES string of one of the compounds, sends that string to the PPS, where you can generate a PPS-predicted biodegradation pathway for it. On the Links page, links were added to Alan Wood's Compendium of Pesticide Common Names, and the IUPAC Goldbook: Compendium of Chemical Terminology.

May 30, 2007
A pathway for isooctane, (US) or (UK), has been added and the pathway for Bisphenol A, (US) or (UK), has been updated. The isooctane pathway was started by a student in the 2006 BioC/MicE 5309 class. Links to EXTOXNET and EXTOXNET searches on compound pages have been updated. A list of all compounds is available. A mechanism graphic for methane monooxygenase was contributed by Professor John Lipscomb, and added to the methane -> methanol reaction page. This is the 34th enzyme mechanism graphic in the UM-BBD; a complete list is available. In the Biochemical Periodic Tables, the element pages for Selenium and Technetium have been updated. In the Pathway Prediction System, the default is now "aerobic", meaning that only biotransformations with very likely, likely and neutral aerobic likelihood ratings will be seen. This is easily changed to "All" at any time in the prediction process. If the "aerobic" button is selected, all very likely and some likely biotransformations now occur automatically whenever possible. Aerobic pathways will grow more quickly. This feature is described in more detail on the About the PPS web page. On the Links page, the link to BIOREP abstracts was removed. This is the 150th Progress Report, an important milestone. The UM-BBD began in February 1995, and the email list for Progress Reports was started from the BBD guestbook soon after. It grew to 152 members by November of that year. Some current subscribers have been with us from the beginning.

April 16, 2007
A pathway for 2-mercaptobenzothiazole, (US) or (UK), has been added. This pathway was started by a student in the 2006 BioC/MicE 5309 class. In the Pathway Prediction System (PPS), the results page now includes a navigation bar, for easy navigation back to previous prediction steps, the PPS Home or the UM-BBD Home. This feature is described in more detail in About the PPS. A small molecule filter was added, so prediction results no longer contain acetate, CO₂ and similar small molecules whose degradation should not be predicted. If you see other similar compounds on results pages and think they also should not be shown, let us know. The UM-BBD now has over 400 microorganism entries, a major milestone. The complete list is available; this can be searched by organism name. Organism names are linked to ATCC or DSMZ culture collections, if possible.

March 26, 2007
Pathways for testosterone, (US) or (UK), and isoniazid, (US) or (UK), have been added. The testosterone pathway was started by a student in the 2006 BioC/MicE 5309 class. In the Pathway Prediction System (PPS), the results page uses .png format graphics, rather than Java Applets, to show results. PPS results appear more rapidly, and their display is more stable. The Applets, which allow resizing the compound window for better visualization of larger compounds, are available from a click on the compound .png graphic. This feature is described in more detail in About the PPS. PPS documentation has been improved. Introduction to Rule Prioritization has been updated and reformatted, and a new page has been developed on Compounds whose Biodegradation Should Not be Predicted. They are linked to in About the PPS.

February 16, 2007
Pathways for bacterial caffeine, (US) or (UK), and fungal caffeine, (US) or (UK), have been added. The bacterial pathway was developed by a student in the 2006 BioC/MicE 5309 class. Links to the ATCC on the Microorganism List and on text pathway maps work again.

January 19, 2007
An pathway for anaerobic menthol, (US) or (UK), has been added. This pathway was developed by a student in the 2006 BioC/MicE 5309 class. Links to the ATCC on the Microorganism List and on text pathway maps are broken. We are working with ATCC to fix this. On the Links page, links for the USDA Agricultural Research Service (ARS) Pesticide Properties Database and the NLM Chemical Information Page were updated. The Whats New page restarts; 2006 activities have been archived.

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