title: Configurational assignment of secondary hydroxyl groups and methyl branches in polyketide natural products through bioinformatic analysis of the ketoreductase domain.
abstract: Profile hidden Markov models (HMMs) were used to predict the configuration of secondary alcohols and α-methyl branches of modular polyketides. Based on the configurations of two chiral centers in these polyketides, 78 ketoreductases were classified into four different types of polyketide producers. The identification of positions that discriminate between these protein families was followed by fitting six profile HMMs to the data set and the corresponding subsets, to model the conserved regions of the protein types. Ultimately, the profile HMMs described herein predict protein subtypes based on the complete information-rich region; consequently, slight changes in a multiple sequence alignment do not significantly alter the outcome of this classification method. Additionally, Viterbi scores can be used to assess the reliability of the classification.
authors.affiliation: Institut für Biostatistik, Leibniz Universität Hannover, Herrenhäuserstrasse 2, 30419 Hannover, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Kitsche
authors.forename: Markus
authors.initials: M
authors.lastname: Kalesse
mesh_terms: D000429:Alcohol Oxidoreductases / Q000737:chemistry* / Q000378:metabolism; D000438:Alcohols / Q000737:chemistry* / Q000378:metabolism; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001688:Biological Products / Q000737:chemistry* / Q000378:metabolism; D019295:Computational Biology; D008969:Molecular Sequence Data; D061065:Polyketides / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D000438:Alcohols; D001426:Bacterial Proteins; D001688:Biological Products; D061065:Polyketides; D000429:Alcohol Oxidoreductases; C087192:polyketide synthase ketoreductase