antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

Abstract

Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. In recent years, genome mining has seen broad applications in identifying and characterizing new compounds as well as in metabolic engineering. Since 2011, the 'antibiotics and secondary metabolite analysis shell-antiSMASH' (https://antismash.secondarymetabolites.org) has assisted researchers in this, both as a web server and a standalone tool. It has established itself as the most widely used tool for identifying and analysing biosynthetic gene clusters (BGCs) in bacterial and fungal genome sequences. Here, we present an entirely redesigned and extended version 5 of antiSMASH. antiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-RiPPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines. For type II polyketide synthase-encoding gene clusters, antiSMASH 5 now offers more detailed predictions. The HTML output visualization has been redesigned to improve the navigation and visual representation of annotations. We have again improved the runtime of analysis steps, making it possible to deliver comprehensive annotations for bacterial genomes within a few minutes. A new output file in the standard JavaScript object notation (JSON) format is aimed at downstream tools that process antiSMASH results programmatically.

Figure 1.

Candidate cluster types. 1,2,3,4: Grey/yellow: gene involved in protocluster A/B. (A) Chemical Hybrids. Since cluster type A and cluster type B share a CDS that defines those protoclusters, they are classified as ‘chemical hybrid’. (B) Interleaved: Since none of the protoclusters share any defining CDS with any other protocluster, it is not annotated as a chemical hybrid, even though the biosynthetic product may or may not be. The two protoclusters form an interleaved candidate clusters, since the core of A overlaps with the core of B. (C) Neighbouring: Neighbouring candidate clusters are defined if the neighbourhoods of two protoclusters but not their cores overlap. (D) Singles: If protoclusters don’t have any overlap/relation with other protoclusters, the term single candidate cluster is assigned.

Figure 2.

Screenshot of the antiSMASH 5 user interface (example: NCBI-acc: Y16952; balhimycin BGC). The new region overview now allows panning/zooming. The candidate cluster and protocluster boxes are explained in the ‘new region concept’ section above. Information about the currently selected gene are displayed at the right ‘Gene details’ panel. For PKS or NRPS regions, the detailed domain annotation is displayed; by pressing the tabs, users can select the domain overview (shown) or the ClusterBlast, KnownClusterBlast or SubClusterBlast results. At the right, the structure prediction and details of specificity predictions are displayed upon selecting the plus sign.