The PathoLogic component of the Pathway Tools software performs prediction of metabolic pathways in sequenced and annotated genomes. This article provides a detailed presentation of the PathoLogic algorithm. The algorithm consists of two phases. The reactome inference phase infers the reactions catalyzed by the organism from the set of enzymes present in the annotated genome. The pathway inference phase infers the metabolic pathways present in the organism from the reactions catalyzed by the organism. Both phases draw on the Me-taCyc database of metabolic reactions and pathways. MetaCyc contains two data fields to support pathway inference: the expected taxonomic range of each pathway, and a list of key reactions for pathways. These fields have significantly increased the predictive accuracy of PathoLogic.
Karp, P. D., Latendresse, M., & Caspi, R. (2011). The pathway tools pathway prediction algorithm. Standards in Genomic Sciences, 5(3), 424–429. https://doi.org/10.4056/sigs.1794338