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Maintains heterogeneous information related to bioremediation and biodegradation. MetaRouter is a relational database where the information on chemical compounds, reactions, enzymes and organisms is stored in an integrated framework. Users can consult the database and formulate new questions with associated programs that run on top of the database. MetaRouter can assist researchers in assessing the environmental fate of compounds or mixtures and in designing biodegradative strategies for them.
A database and prediction system for the microbial biotransformation of organic environmental contaminants. enviPath provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products. User access is simplified by providing a REST API that simplifies the inclusion of enviPath into existing workflows. An RDF database is used to enable simple integration with other databases.
Stores manually curated information about proteins and genes directly implicated in the Biodegradation metabolism. When possible, Bionemo includes information on sequence, domains and structures for proteins; and sequence, regulatory elements and transcription units for genes. Bionemo has been built by manually associating sequences databases entries to biodegradation reactions, using the information extracted from published articles. Information on transcription units and their regulation was also extracted from the literature for biodegradation genes, and linked to the underlying biochemical network.
Provides a compilation of the oxygenase data as sourced from primary literature in the form of web accessible database. There are two separate search engines for searching into the database i.e. mono and dioxygenases database respectively. Each enzyme entry contains its common name and synonym, reaction in which enzyme is involved, family and subfamily, structure and gene link and literature citation. The entries are also linked to several external database including BRENDA, KEGG, ENZYME and UM-BBD providing wide background information. At present the database contains information of over 240 oxygenases including both dioxygenases and monooxygenases.
BioSurfDB / Biosurfactants and Biodegradation Database
A curated relational information system integrating data from: (i) metagenomes; (ii) organisms; (iii) biodegradation relevant genes; proteins and their metabolic pathways; (iv) bioremediation experiments results, with specific pollutants treatment efficiencies by surfactant producing organisms; and (v) a biosurfactant-curated list, grouped by producing organism, surfactant name, class and reference. The main goal of this repository is to gather information on the characterization of biological compounds and mechanisms involved in biosurfactant production and/or biodegradation and make it available in a curated way and associated with a number of computational tools to support studies of genomic and metagenomic data.
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