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Sequence-based classification of type II polyketide synthase biosynthetic gene clusters for antiSMASH

  • Rasmus Villebro
  • Simon Shaw
  • Kai BlinEmail author
  • Tilmann WeberEmail author
Natural Products - Original Paper

Abstract

The software antiSMASH examines microbial genome data to identify and analyze biosynthetic gene clusters for a wide range of natural products. So far, type II polyketide synthase (PKS) gene clusters could only be identified, but no detailed predictions for type II PKS gene clusters could be provided. In this study, an antiSMASH module for analyzing type II PKS gene clusters has been developed. The module detects genes/proteins in the type II PKS gene cluster involved with polyketide biosynthesis and is able to make predictions about the aromatic polyketide product. Predictions include the putative starter unit, the number of malonyl elongations during polyketide biosynthesis, the putative class and the molecular weight of the product. Furthermore, putative cyclization patterns are predicted. The accuracy of the predictions generated with the new PKSII antiSMASH module was evaluated using a leave-one-out cross validation. The prediction module is available in antiSMASH version 5 at https://antismash.secondarymetabolites.org.

Keywords

Type II polyketide synthases PKS Aromatic polyketides Secondary metabolite Natural product Genome mining 

Notes

Acknowledgements

This work was funded by Grants of the Novo Nordisk Foundation [NNF10CC1016517, NNF16OC0021746] to TW.

Supplementary material

10295_2018_2131_MOESM1_ESM.pdf (938 kb)
Supplementary material 1 (PDF 938 kb)

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Copyright information

© Society for Industrial Microbiology and Biotechnology 2019

Authors and Affiliations

  1. 1.The Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkKongens LyngbyDenmark

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