October 11, 2000
A pathway for 1,2,3-tribromopropane (US) or (UK) has been added. This pathway was developed by a student in our 2000 Biocatalysis and Biodegradation class. Many enzyme pages, such as the one for haloalkane dehalogenase, now include links which search GenPept for protein sequences. These searches retrieve many, but not all, such sequences. Several enzyme pages, such as the one for haloalkane dehalogenase, now include links which search PDB for protein structures. The description of the enzyme page in About the UM-BBD has been updated to include GenPept and PDB searches. These additions to the enzyme page were suggested by UM-BBD users. The KEGG: Kyoto Encyclopedia of Genes and Genomes now includes versions of 19 UM-BBD pathways and more are planned. The KEGG metabolism page includes UM-BBD pathways, indicated by "UMBBD", under Metabolism of Other Substances. We now link to that KEGG page and a page giving use statistics for KEGG versions of UM-BBD pathways on the UM-BBD home page. On the Useful Internet Resources page, a link has been updated for the Biodegradative Strain Database at Michigan State University.
September 13, 2000
The iprodione pathway (US) or (UK) has been added and the pentachlorophenol (US) or (UK), bromoxynil (US) or (UK), aerobic DDT (US) or (UK) and anaerobic DDT (US) or (UK) pathways have been updated. The iprodione pathway was developed by a student in our 2000 Biocatalysis and Biodegradation class. Links to enzyme pages now are found on all reaction pages, even those for reactions, like the reaction of Atrazine to Deethylatrazine, which are catalyzed by enzymes which have not yet been assigned a 4-digit EC number. Entrez PubMed has a new format for links to the UM-BBD. To see an example of this, go to the UM-BBD page for the reaction from Hydroxyatrazine to N-Isopropylammelide. Click on the Medline reference. Once at the PubMed abstract page, click on "LinkOut" on the far right. The last link on the LinkOut page returns to the UM-BBD citation page for this reference. The citation page includes links to 4 UM-BBD reactions which are discussed in this citation. Our 2000 Developer Photo is now available on the UM-BBD Developer's Photo Gallery page. On the Useful Internet Resources page, a link has been added for Enzyme Nomenclature from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology and Environmental Programs at the Lawrence Livermore National Laboratory.
August 2, 2000
The Phenylacetaldoxime Pathway (US) or (UK), our 100th pathway, has been added. Its first step highlights the novel enzyme phenylacetaldoxime dehydratase, which converts phenylaldoxime to phenylactonitrile. This enzyme has great biocatalytic potential since the chemical dehydration of aldoximes usually requires harsh reaction conditions. The addition of an oxime brings to 49 the number of organic chemical functional groups whose metabolism is contained in the UM-BBD. Compound pages now include SMILES strings for each compound. For example, the SMILES string for Toluene is CC1=CC=CC=C1. SMILES strings are described in "Format of a Compound Page" in About the UM-BBD. The Boolean operators AND OR or NOT can be used in compound and enzyme name searches. Parenthetical Boolean expressions are not allowed, but can be implied. That is, aldehyde OR ketone AND methyl is interpreted as (aldehyde OR ketone) AND methyl. The search is case-insensitive. Students in our 2000 Biocatalysis and Biodegradation class, offered completely over the Internet, have examined websites on the UM-BBD Useful Internet Resources page and selected the most interesting ones. The Useful Internet Resources page now links to the list of these choices and the reason each site was selected. KEGG: Kyoto Encyclopedia of Genes and Genomes has begun to mirror UM-BBD pathways. Twelve UM-BBD pathways are now duplicated in KEGG and more are planned. UM-BBD compound and reaction pages and search functionality differ from their KEGG counterparts. The KEGG metabolism page includes UM-BBD pathways, indicated by "UMBBD", under Metabolism of Other Substances. On the Useful Internet Resources page, a link has been added for Metabolic Pathway Minimaps at Trinity College, Dublin, Ireland; a link has been updated for the Biodegradative Strain Database at Michigan State University; and links have been deleted for Sigma Chemical Company and In Situ Microbial Filters from Lawrence Livermore National Laboratory.
June 22, 2000
Searches on partial EC codes now return results ordered by EC code. For example, a search for EC code 1.2. will return 29 ordered hits. Example enzyme pages have been added to the UM-BBD Guided Tour. UM-BBD was featured in Netwatch section of Science; Cho, A. (2000) "Munching on Strange Chemicals" Netwatch, Science, 288(5471): 1543. This and other reviews and publications are found on our Publications page. On the Useful Internet Resources page, links have been updated for the Biodegradative Strain Database at Michigan State University, Publications from the Canadian Network of Toxicology Centers, and the U.S. Geological Survey Bioremediation and Toxic Substances Hydrology Program. Links have been deleted for Bioremediation Resources on the Internet at the Canadian National Water Research Institute and Bugs 'n Stuff from the National Center for Genome Resources.
May 26, 2000
The gamma-1,2,3,4,5,6-Hexachlorocyclohexane (Lindane) Pathway (US) or (UK) has been updated. The original contributor of this pathway and member of the UM-BBD email list, Dr. Jiri Dambrosky, assisted in this update. An aerobic phenol reaction has been added to the 4-Nitrobenzene Pathway (US) or (UK). This addition was suggested by a member of the UM-BBD email list. The UM-BBD now contains pathways for both aerobic and anerobic (US) or (UK) phenol biodegradation. A link to UM-BBD enzyme pages is now available from pages for reactions which are catalyzed by enzymes with a four-digit EC code. For example, on the reaction page for each one of the reactions catalyzed by haloalkane dehalogenase, EC 126.96.36.199, the EC number now links to the UM-BBD enzyme page for this enzyme. Enzymes have been added to the list of compounds and reactions linked to on each pathway map. For example, go to the 1,2-Dichloroethane Pathway and select [Compounds and Reactions] at the top or bottom of the page. You will get a list of all compounds, reactions and enzymes in this pathway. A description of the UM-BBD enzyme page has been added to the About the UM-BBD page. The results of the Fifth Annual User Survey are now available. On the Useful Internet Resources page, links have been updated for the Journal of Biological Chemistry, Nucleic Acids Research, Bioinformatics, and In Situ Bioremediation: When Does It Work? (1993) from the National Academy Press.
April 28, 2000
The 1,3-Dichloropropene Family Pathway (US) or (UK) has been added and the 3-Chloroacrylic Acid Family Pathway (US) or (UK) has been updated. The word "Family" indicates that multiple related starting compounds are found in a pathway map. The Acetylene Pathway (US) or (UK) has been updated with the addition of a strictly anaerobic organism to this formerly completely aerobic pathway. The word "an/aerobic" has been added to the pathway name to indicate this. Searching for enzyme name synonyms (alternative names) is now available. As an example, before you could search for a full or partial enzyme name; e.g., alkane 1-monooxygenase. Now you can also search for this enzyme by its full or partial official alternative names (synonyms): alkane 1-hydroxylase, omega-hydroxylase, or fatty acid omega-hydroxylase. BioC/MicE 5309, a course on Biocatalysis and Biodegradation offered completely over the Internet, opened for registration on April 11 and quickly filled. Registration has now closed. The course will next be offered in 2001; if you are interested in being placed on the waiting list for the 2001 course, please let us know. On the Useful Internet Resources page, a link has been updated for WIT from Integrated Genomics, Inc.
March 23, 2000
Searches which return only one compound or enzyme now go directly to that compound, enzyme or reaction page. Four groups were added to the list of UM-BBD organic functional groups, to make a total of 47. A graphic version of that page has been added that includes the structure of each functional group. All links to Entrez Medline references and searches and GenBank searches on UM-BBD reaction and other pages were updated to the new Entrez format. We will move to a new server over the next few weeks. We expect the move to result in faster and more stable access, however there may be unscheduled downtime during the transition. We appreciate your patience if this occurs. On the Useful Internet Resources page, a link has been added for the E. coli Index at the University of Birmingham, UK; a link has been removed for the Enzyme Structures Database; and links have been updated for Biocatalysis at the Institute for Organic Chemistry, Technical University Granz, Austria and the Entrez PubMed bibliographic database.
February 24, 2000
The UM-BBD now has use statistics for its UK mirror site, hosted by the European Bioinformatics Institute, Hinxton, Cambridge, UK. One reaction using the enzyme alkyl hydroperoxidase was added to the n-octane pathway (US) or (UK). The page which lists 73 reactions for naphthalene 1,2-dioxygenase has been reformatted. All Chemfinder links have been updated. On the Useful Internet Resources page, a link has been added for the PathDB Metabolic Pathways Database at the National Center for Genome Resources.
January 14, 2000
The UM-BBD now has a UK mirror site, hosted by the European Bioinformatics Institute, Hinxton, Cambridge, UK. It is part of their SRS6 webserver. Once there, choose "Databanks" and scroll towards the bottom of the page or choose "Start" and expand "Metabolic Pathways." The UM-BBD has five databanks under "Metabolic Pathways", UPATHWAY, UIMAGEMAP, UREACTION, UENZYME and UCOMPOUND. A link to the UK mirror has been added to the UM-BBD main menu. We will now give two URLs for each new UM-BBD pathway; the UM and UK versions. One pathway was added for adamantone (US) or (UK). This is the first tricyclic aliphatic compound in the UM-BBD. It has been added to the list of UM-BBD functional groups. We now have a page which lists 108 reactions for toluene 1,2-dioxygenase. There is a link to this page on both UM-BBD tdo reaction pages. If there are any reactions we have missed, please let us know. Recent publication: Ellis, L.B.M., Hershberger, C.D., and Wackett, L.P. (2000) "The University of Minnesota Biocatalysis/Biodegradation Database: Microorganisms, Genomics, and Prediction" Nucleic Acids Research 28: 377-379. The full text of this paper is linked to on the UM-BBD main menu and the publications page. Use this paper or its successors to cite the database. On the Useful Internet Resources page, links have been updated for the EBI Sequence Retrieval System (SRS) and the List of Designated Hazardous Substances from the Australian National Occupational Health and Safety Commission. The What's New page restarts; 1999 activities have been archived.
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