The Use of ClusterMine360 for the Analysis of Polyketide and Nonribosomal Peptide Biosynthetic Pathways

Methods Mol Biol. 2016;1401:233-52. doi: 10.1007/978-1-4939-3375-4_15.

Abstract

Polyketides and nonribosomal peptides constitute two large families of microbial natural products. Over the past 20 years a broad range of microbial polyketide and nonribosomal peptide biosynthetic pathways have been characterized leading to a surfeit of genetic data on polyketide and nonribosomal peptide biosynthesis. We developed the ClusterMine360 database, which stores the antiSMASH-based annotation of gene clusters in the NCBI database, linking the structure of the natural product to the biosynthetic gene cluster. This database is searchable and enables the user to access multiple sequence files for phylogenetic analysis of polyketide and nonribosomal peptide biosynthetic genes. Herein we describe how to add compound families and gene clusters to the database and search it using key words or structures to identify specific gene clusters. We also describe how to download multiple sequence files for specific catalytic domains from polyketide and nonribosomal peptide biosynthesis.

Keywords: Biosynthesis; Database; Gene cluster; Genome; Natural product; Nonribosomal peptide; Polyketide.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / genetics*
  • Bacteria / metabolism
  • Biological Products / chemistry
  • Biological Products / metabolism
  • Biosynthetic Pathways*
  • Databases, Genetic
  • Genomics / methods*
  • Multigene Family*
  • Peptide Biosynthesis, Nucleic Acid-Independent*
  • Peptides / chemistry
  • Peptides / metabolism
  • Polyketides / chemistry
  • Polyketides / metabolism*

Substances

  • Biological Products
  • Peptides
  • Polyketides