MPW Pathway Database
The MPW database is the largest collection of metabolic diagrams curated since the 1980s. The collection keeps growing, and currently includes diagrams representing different variants of metabolic and membrane transport networks of microorganisms, higher plants, and animals. The pathway encoding is based on a precise unequivocal pathway nomenclature which includes initial substrates, end products, coenzymes, intracellular localization, and other specific details as necessary.
The MPW nomenclature defines a 'pathway' as a chain of reactions between metabolic crossroads. In most cases, such a definition eliminates the need for selecting the best fit from a set of partially overlapping pathways.
The database presently contains 9672 pathways, with a total number of 14378 instances of 6764 unique reactions over 6202 chemical compounds. 529 reactions involve one of 53 unique prosthetic groups; 440 reactions use one of 37 unique co-enzymes. 6690 reaction instances are attributed to one of 167 unique subcellular localizations. For 1881 reactions, regulatory mechanisms are encoded.
MPW provides both detailed compartmentalization data for each component of each reaction, and a collection of molecular transporters and multicomponent transport mechanisms. The reconstructions we produce will contain details on the processes performed in different compartments, and mechanisms for material exchanges between compartments and between cytoplasm and the extracellular matrix.
The fundamental advantage of MPW is that its pathway diagrams are encoded as a plain ASCII text that can be converted into any standard hyperlinked graphics. The quasi-graphics allows quick encoding, editing, parsing, indexing and hyperlinking the database content, as well as creating software capable of automatic assembly of metabolic models from sequenced genomes. Another advantage is the fact that an expensive and time consuming 100% coverage of genome sequencing is not required for building comprehensive reconstructions.
Detailed organism or tissue-specific metabolic reconstructions, automatically generated with the help of MPW, can be used not only for visualizing metabolic networks, but also as an effective research tool for predicting new functions, making important discoveries and working on metabolic designs.
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