Metabolic Pathway Service
Vera Povolna, Metaphorics, LLC
Mug 2003, Santa Fe, NM
a Fedora server for exploration of metabolism and as an index to data from other sources
a computer model of the paper-based metabolic pathway
chart by Gerhard Michal
data is organized into 9 data types:
Landmarks point general area of a particular metabolism,
i.e. Histidine metabolism
Compounds are reactants and products of steps, include structures with stereochemistry, i.e.
Cofactors are additional reactants and products; usually drive the step energetically, i.e.
Enzymes are primary catalysts; most steps enzymatic, some nonenzymatic, EC numbers included, i.e. Histidine ammonia lyase
Agents are nonenzymatic catalysts; usually metal ions, i.e.
Regulators are substances that enhance or supress a step; fast or slow action on enzyme, i.e. AMP
Diseases are associated with steps, i.e. Histidinemia
Steps are metabolic reactions; include all the above; differentiated on the basis of direction (unidirectional vs reversible), catabolism vs anabolism, and on the basis of species (monocellular organisms, animals, plants or across all species)
Pathways are sequences of life essential steps and/or across all species; terminal/excretory products; i.e. Hidantoin propionate in Histidine degradation pathway
- object locations are indicated by hotspots (pale gray or yellow
- clicking on the image redraws the chart centered at the selected
location with a description of the nearest object (i.e.
- clicking on similar searches Empath for like structures
- clicking on related searches other databases that are connected to Empath for like
- zoom in/out, location, abbreviations, preferences, help, show stoichiometry
- uses modern communication rather than paper
- http-based application
- live reactions with live objects
- integrates similarity searches (name, structure, EC number) within
Empath and connected databases
- it does not replace the chart - it IS the chart
- add known EC numbers and diseases
- add new information as it is discovered