Pathway Prediction System | PredictBT Workshops | Biochemical Periodic Tables

About the University of Minnesota Biocatalysis/Biodegradation Database

Return to Top Introduction

This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology.

The reactions covered are studied for basic understanding of nature, biocatalysis leading to specialty chemical manufacture, and biodegradation of environmental pollutants. Individual reactions and metabolic pathways are presented with information on the starting and intermediate chemical compounds, the organisms that transform the compounds, the enzymes, and the genes. The present database has been sucessfully used to teach enzymology and use of biochemical Internet information resources to advanced undergraduate and graduate students, and is being expanded primarily with the help of such students.

In addition to reactions and pathways, this database also contains Biochemical Periodic Tables (see About the Periodic Tables) and a Pathway Prediction System (see About the PPS).

Return to Top How to Use This Database

This "About the UM-BBD" page describes the general structure of information in the UM-BBD. There is also a list of Frequently Asked Questions (FAQs) and their answers. General information is found on the UM-BBD home page and its associated pages, such as this page, What's New, and Useful Internet Resources pages. These are accessible from links at the left side of the top-level UM-BBD web pages.

Distinct from that is the information on biodegradation pathways, reactions and compounds. This can be accessed from the body of the UM-BBD home page or from search page, which also contains links to indexes and is discussed below. This "About the UM-BBD" page also describes the format of the UM-BBD pathway, reaction and compound pages. If you are new to the database, read this page, look at the FAQs, and then go to the Home Page and follow your interests.

If you have a specific compound or enzyme name, chemical formula, CAS Registry Number, chemical structure or substructure, or EC code or partial code in mind, use our Search option. Since chemical and enzyme nomenclature may vary, if you don't find what you want from a name search, use synonyms or partial names. For example, a search for the name 5-sulfosalicylic acid returned no match on April 21, 1998, but one for 5-sulfosalicylate returned one compound and three reactions on that same date. You might also try searching for a CAS Registry Number, structure, substructure, or a chemical formula. CAS Registry Number searches are more specific than formula searches, but formulas are available for all compounds, while CAS Numbers are incomplete. Structure and substructure searches require that the structure desired be entered either as a SMILES string or drawn using a Java applet. Not all browser and computer combinations support the Java applet.

If you prefer to browse, the Search page also has links to lists of pathways, compounds, enzymes, reactions, microorganisms, and graphics. There is a search option on most of these list pages.

Return to Top How Accurate is UM-BBD Information?

The UM-BBD strives to collect and distribute accurate, relevant information. This includes making judgments as to which pathways and reactions to include, based on the scientific literature and the expertise of our staff, and to correctly transcribe this information onto the Web.

Taking the second part first, our goal is correct information but errors do creep in. We offer links to other Internet resources and urge users to compare information from multiple sites. In this manner inconsistencies in numeric values, such as molecular weights or CAS Registry Numbers, can be uncovered. We would appreciate being informed of any inconsistencies thus found.

We also link to dynamic searches of the PubMed bibliographic database. We may have misread citations or more recent entries may contradict older literature upon which UM-BBD pathways were based. We would appreciate being informed of these types of inconsistencies as well.

This leads directly to our first concern: basing the UM-BBD on credible scientific evidence. When appropriate citations exist which pass our scientific review, we create UM-BBD pathway, reaction, and compound pages and give a citation for each reaction. When the evidence is not as firm, we either delay installing a pathway or indicate less certain reactions or pathway parts in several ways.

If a compound is a plausible, but not certain, intermediate, we put brackets ([ ]) around it in pathways. We may also specifically mention less certain parts of a pathway in its introductory paragraphs. For an example, see the mention of uncertainty and bracketting of the compounds benzoyl acetate and benzoyl acetyl-CoA in the anerobic Ethylbenzene Pathway. In a second example, 5,6-dichloro-1,3-cyclohexadiene is bracketted in both the beta-Hexachlorocyclohexane Pathway and its reaction B.

We use multiple arrows ( -> -> ) and/or words in the introductory paragraphs to indicate unknown intermediates. For an example of the former, see the Trichloroethylene Pathway and its reaction E2. For an example of the latter, see the introduction to the Phenylboronic Acid Pathway.

Return to Top Format of a Pathway Map Page

Here is an excerpt from a pathway map, with 15 numbered, annotated sections.

1. Glyphosate Pathway Map

2. [Compounds and Reactions] [BBD Main Menu]
3. This pathway was started by Robyn Wiersema and completed by Michael Burns and Doug Hershberger, University of Minnesota.

4. Glyphosate, also known by the tradename Roundup, is a broad-spectrum herbicide widely used in the United States and elsewhere. It is moderately biodegradable, largely due to soil microorganisms. It is representative of a broad class of compounds, known as phosphonic acids, which contain a direct carbon-to-phosphorus (C-P) bond. Although the C-P bond is chemically very stable, many bacteria, even enteric bacteria such as Escherichia coli, have the ability to enzymatically cleave the bond to liberate inorganic phosphate.

In almost all studies of glyphosate metabolism it was the sole source of phosphorous, however the organisms investigated were not capable of using it as a source of carbon or nitrogen. Because the pathway utilizing the intermediate aminomethylphosphonic acid (AMPA) (pathway shown on the right below) has been found in organisms archived prior to the introduction of glyphosate, it has been postulated that the ability to degrade glyphosate is naturally present in the environment (Kertesz et al., 1994). However, the prevalence of the sarcosine intermediate pathway (shown on the left below) in isolates from glyphosate-enriched sources (Dick and Quinn, 1995) suggests that this pathway is selected for in these environments, possibly because the pathway is more favorable to the organisms.

Glyphosate kills plants and bacteria by inhibiting the bacterial and plant enzyme enolpyruvylshikimate-phosphate synthase (EPSPS). Monsanto has developed a way to introduce a bacterial gene for a glyphosate-resistant EPSPS into plants, so that glyphosate can be used for weed control on otherwise glyphosate-susceptible crops.

5. The following is a text-format glyphosate pathway map. Follow the links for more information on compounds or reactions. This map is also available in graphic (3k) format. 


6.               Glyphosate                        Glyphosate
7.        Agrobacterium radiobacter    Geobacillus caldoxylosilyticus T20
           Enterobacter aerogenes              Flavobacterium sp.
                     |                                 |
8.                   | C-P lyase                       | glyphosate
                     |                                 | dehydrogenase
                     |                                 |
                     v                                 v
9.               Sarcosine                           AMPA
                     |                                 |
                     |                                 |
                     |                                 | C-P lyase
                     |                                 |
                     v                                 v
10.            Intermediary                       Methylamine 
                Metabolism                             |
                  (KEGG)                               |
                                                       | methylamine
                                                       | dehydrogenase
                                                       |
                                                       v
                                                  Formaldehyde
11. [Compounds and Reactions] [BBD Main Menu]

12. Page Author(s): Robyn Wiersema, Michael A. Burns, and Doug Hershberger

13. April 25, 2008 Contact Us 

14. © 2009, University of Minnesota.
    All rights reserved.

15. http://umbbd.msi.umn.edu/gly/gly_map.html

A brief annotation of each of these sections:

  1. The title of the pathway (name of starting compound).
  2. Links to a list of all compounds and reactions in the pathway and to the UM-BBD home page.
  3. The names of the people who contributed the pathway to the UM-BBD, and their affiliations at the time they made the contribution.
  4. A paragraph on the significance of the pathway.
  5. Introduction to the text pathway map. When a graphical pathway map exists, a link to it is put here.
  6. Link to the page for the starting compound.
  7. Names of microbes known to initiate this pathway. Other organisms may also carry out later steps. If both genus and species names are known, as here, the organism name links to a search of a microbial database for organismal information.
  8. Link to the page for the first reaction.
  9. Link to the page for the next compound. The pathway continues with arrows, possibly cofactors, and links to compounds and reactions.
  10. Link to an intermediary metabolism pathway in the KEGG database. The compound which links the UM-BBD to KEGG is shown as a red circle in the KEGG pathway graphic. Since KEGG does not link to the UM-BBD on its pathway pages, use your browser's BACK function to return to the UM-BBD if you visit it.
  11. See 2.
  12. The names of the page author(s), earliest author first.
  13. Date Last Modified, and a link to a contact page. Questions sent from there will be directed to the person best able to answer them.
  14. © notice.
  15. Page URL.
You can examine the complete pathway map from which this example was taken.

Return to Top Format of a Reaction Page

The format of a reaction page is a bit more complex. At a minimum it includes a balanced reaction in text and graphic form. Here is an excerpt from a reaction page, with 11 numbered, annotated links:

From 1,2-Dichloroethane to 2-Chloroethanol

1. Graphic (3k) of the reaction.

2. Medline reference
Verschueren KH, Seljee F, Rozeboom HJ, Kalk KH, Dijkstra BW Nature (1993) 363(6431): 693-8.

3. Search Medline titles for haloalkane dehalogenase.
23 citations on Oct. 27, 1997.

4.     1,2-Dichloroethane
               |
               |  H2O
    haloalkane | /
  dehalogenase |/
5., 6. 3.8.1.5 | Search GenBank, 4 hits on Oct. 22, 1997
7.       Kyoto |\
8.      ExPASy | \
               |  HCl
               v
9.      2-Chloroethanol
10. Generate a pathway starting from this reaction.

11. UM-BBD Biotransformation rules in accord with this reaction:
Alkyl halide -----> Alcohol (bt0022)
12. [1,2-Dichloroethane] [BBD Main Menu]
A brief description of each of these links:
  1. A graphic (size in parentheses) of the reaction, in GIF format and balanced where possible, with the reacting atoms and bonds highlighted in a red, bold-face font. A link to a graphic for a mechanism of the reaction may also appear here.
  2. Usually an Entrez Medline reference. If no reference exists in Medline, the citation which is available is entered in its place.
  3. A search of a subset of Medline, or Medline titles, for the enzyme name or a varient of this name, where possible. If the name is not specific enough for a search, an EC code may be used instead. The basis for including a reaction in this database is at least one citation in the peer-reviewed, scientific literature, OR original unpublished work that has been accepted after review by one or more members of the UM-BBD Scientific Advisory Board. Those reactions with more than this minimum in the Medline search, especially those with larger numbers of citations spanning several years, are better validated.
  4. The substrate's UM-BBD compound page (format described below).
  5. The enzyme's UM-BBD enzyme page (format described below).
  6. A search of GenBank, when one or more hits are found.
  7. An enzyme page in the Ligand Chemical Database at Kyoto University, when a 4-digit EC code exists.
  8. An enzyme page or enzyme subclass page in the ENZYME database on the ExPASy server, when 4- or 3-digit EC codes, respectively, exist. The enzyme subclass page may contain the 4-digit code if it was assigned after the UM-BBD page was last modified. If the exact enzyme is not found, the other enzymes in the same class may provide useful information.
  9. The product's compound page (format described below).
  10. A dynamically generated catabolic pathway map starting from this reaction and continuing to intermediary metabolism or as far as UM-BBD reactions can take it. The generated pathway maps include all possible reactions, aerobic and anaerobic, from all microbes found in the UM-BBD. The static UM-BBD pathway maps are more restrictive and state their constraints.
  11. Links to one or more btrule pages in accord with this reaction, if they exist (format described below).
  12. Links to each of the static UM-BBD pathway maps in which the reaction appears and a link to the UM-BBD Main Menu (home page).

You can examine the complete reaction page from which this example was taken.

Return to Top Format of a BioTransformation Rule Page

Here is a excerpt from a btrule page, with 7 numbered, annotated sections.

Rule bt0022

1. [Pathway Prediction Engine] [All Rules List] [BBD Main Menu]
2.   Pattern 118 image
3. organoHalide -> Alcohol

4. Aerobic Likelihood:              Neutral

5. UM-BBD Reaction(s):
Atrazine -----> Hydroxyatrazine (reacID# r0113)
Carbon Tetrachloride -----> Formate (reacID# r0677)
1-Chloro-2,2-bis(4'-chlorophenyl)ethane (DDMS) -----> 2,2-bis(4'-Chlorophenyl)ethanol (DDOH) (reacID# r0519)
Chloroacetate -----> Glycolate (reacID# r0004)
Chloroacetate -----> Glycolate (reacID# r0090)
4-Chlorobenzoyl-CoA -----> 4-Hydroxybenzoyl-CoA (reacID# r0140)
4-Chlorophenylacetate -----> 3,4-Dihydroxyphenylacetate (reacID# r0308)
Deisopropylatrazine -----> Deisopropylhydroxyatrazine (reacID# r0119)
1,2-Dichloroethane -----> 2-Chloroethanol (reacID# r0001)
2,5-Dichlorohydroquinone -----> 5-Chloro-1,2,4-trihydroxybenzene (reacID# r0361)
cis-1,3-Dichloropropene -----> cis-3-Chloro-2-propene-1-ol (reacID# r0687)
trans-1,3-Dichloropropene -----> trans-3-Chloro-2-propene-1-ol (reacID# r0686)
Fluoroacetate -----> Glycolate (reacID# r1028)
Methyl fluoride -----> Formaldehyde (reacID# r0344)
Pentachlorophenol -----> 2,3,5,6-Tetrachlorohydroquinone (TeCH) (reacID# r0313)
1,3(R),4,6(R)-Tetrachloro-1,4-cyclohexadiene -----> 2,4,5-Trichloro-2,5-cyclohexadiene-1-ol (reacID# r0551)
1,2,3-Tribromopropane -----> 2,3-Dibromo-1-propanol (reacID# r0702)
2,4,5-Trichloro-2,5-cyclohexadiene-1-ol -----> 2,5-Dichloro-2,5-cyclohexadiene-1,4-diol (reacID# r0552)
2,4,5-Trichlorophenol -----> 2,5-Dichlorohydroquinone (reacID# r0360)
2,4,6-Trichlorophenol (2,4,6-TCP) -----> 2,6-Dichlorohydroquinone (DiCH) (reacID# r0317)

6. Comments:
Hydrolytic dehalogenation

7. Similarities:
bt0029: organoHalide -> RH

8. Contact Us if you have any comments on rule bt0022.
A brief description of each of these sections:
  1. Links to the Pathway Prediction Engine, a List of All BTrules, and the UM-BBD Main Menu.
  2. One rule pattern for this rule. If there are multiple patterns, this image is followed by an "All patterns" link to a page containing all patterns.
  3. One or more descriptions of the type(s) of reaction handled by the rule. These descriptions can be searched from the UM-BBD Search or All Rules List pages.
  4. Likelihood that the reaction will occur under aerobic conditions, in soil (moderate moisture) or water, at neutral pH, 25°C, with no competing or toxic other compounds. Rules are assigned aerobic likelihood by two or more biodegradation experts. More information on the process is found at Introduction to Biotransformation Rule Priorization.
  5. List of the UM-BBD reactions that exemplify the rule.
  6. UM-BBD Staff Comments, if any, on the rule.
  7. Other UM-BBD btrules similar in some way to this btrule, if any.
  8. A way for the user to give UM-BBD Staff comments on a rule.
You can examine the complete btrule page from which this example was taken.

Return to Top Format of an Enzyme Page

Here is a excerpt from an enzyme page, with 13 numbered, annotated links.

haloalkane dehalogenase

13. [1,2-Dichloroethane] [1,3-Dichloropropene] [1,2,3-Tribromopropane] [BBD Main Menu]
A brief description of each of these links:
  1. Official alternative enzyme name(s), if any.
  2. The enzyme's EC number.
  3. An enzyme page in the Ligand Chemical Database at Kyoto University, when a 4-digit EC code exists.
  4. An enzyme page or enzyme subclass page in the ENZYME database on the ExPASy server, when 4- or 3-digit EC codes, respectively, exist. The enzyme subclass page may contain the 4-digit code if it was assigned after the UM-BBD page was last modified. If the exact enzyme is not found, the other enzymes in the same class may provide useful information.
  5. An enzyme page in the BRENDA Enzyme Database at the University of Cologne, when a 4-digit EC code exists.
  6. An enzyme page in the IUBMB Enzyme Nomenclature Database, when a 4-digit EC code exists.
  7. An enzyme page in the European Bioinformatics Institute's Integrated relational Enzyme database, when a 4-digit EC code exists.
  8. An enzyme page in the Enzyme Database, Trinity College, Dublin, when a 4-digit EC code exists.
  9. A search of GenBank (DNA sequences), when one or more hits are found.
  10. Where possible, a search of GenPept (protein sequences).
  11. Where possible, a search of Structure (protein .pdf files).
  12. UM-BBD reactions which are catalyzed by this enzyme.
  13. Links to each of the static UM-BBD pathway maps in which one or more reactions catalyzed by the enzyme appear and a link to the UM-BBD Main Menu (home page).
You can examine the complete enzyme page from which this example was taken.

Return to Top Format of a Compound Page

Here is a excerpt from a compound page, with 10 numbered, annotated links.

1,2-Dichloroethane

  • 1. 1,2-dichloroethane (4k)

  • 2. Formula: C2H4Cl2

  • 3. MW: 98.959

  • 4. Smiles String: ClCCCl

  • 5. Synonyms: Ethylene dichloride; Ethylene chloride; glycol dichloride; Freon 150; Dutch liquid; Dutch oil; EDC; 1,2-Ethylidene dichloride; sym-dichloroethane; Brocide; Ethane dichloride; 1,2-Ethylene dichloride; alpha, beta-dichloroethane; 1,2-DCE; borer sol; destruxol borer-sol; dichloremulsion; di-chlor-mulsion; 2-Dichloroethane

  • 6. CAS Reg. 107-06-2i

  • 7. PubChem Substance Entry

  • 8. National Toxicology Program

  • 9. UM-BBD reactions whose substrate is 1,2-Dichloroethane
10. [1,2-Dichloroethane] [BBD Main Menu]
A brief description of each of these links:
  1. A graphic image (in GIF format) of the compound. If the image is clicked, a version suitable for downloading is obtained.
  2. The compound's chemical formula.
  3. The molecular weight.
  4. The compound's representation in SMILES format. SMILES format is described on the SMILES Home Page from Daylight Chemical Information Systems, Inc.
  5. Synonyms of the primary compound name.
  6. The CAS Registry Number, when available.
  7. A link to the PubChem Substance entry for this compound.
  8. Links to selected other resources, such as information from the National Toxicology Program, are added when available.
  9. UM-BBD reactions which use or produce this compound.
  10. Links to each of the static UM-BBD pathway maps in which the compound appears and a link to the UM-BBD Main Menu (home page).
You can examine the complete compound page from which this example was taken.

Return to Top For Further Information or To Make Comments

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