{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Analyse the active site of an enzymatic domain" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This example is adapted from the method used by [AntiSMASH](https://antismash.secondarymetabolites.org/#!/about) to annotate biosynthetic gene clusters. AntiSMASH uses profile HMMs to annotate enzymatic domains in protein sequences. By matching the amino acids in the alignment, it can then predict the product specificity of the enzyme. \n", "\n", "In this notebook, we show how to reproduce this kind of analysis, using a PKSI Acyltransferase domain built by the AntiSMASH authors (the HMM in HMMER2 format can be downloaded from [their git repository](https://github.com/antismash/antismash/blob/master/antismash/modules/active_site_finder/data/PKSI-AT.hmm2)).\n", "\n", "