Discriminating the reaction types of plant type III polyketide synthases.

ABSTRACT:

Motivation

Functional prediction of paralogs is challenging in bioinformatics because of rapid functional diversification after gene duplication events combined with parallel acquisitions of similar functions by different paralogs. Plant type III polyketide synthases (PKSs), producing various secondary metabolites, represent a paralogous family that has undergone gene duplication and functional alteration. Currently, there is no computational method available for the functional prediction of type III PKSs.

Results

We developed a plant type III PKS reaction predictor, pPAP, based on the recently proposed classification of type III PKSs. pPAP combines two kinds of similarity measures: one calculated by profile hidden Markov models (pHMMs) built from functionally and structural

SUBMITTER: Shimizu Y 

PROVIDER: S-EPMC5870536 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature