Alignment-Free Methods for the Detection and Specificity Prediction of Adenylation Domains

Methods in Molecular Biology
Guillermín Agüero-ChapinAgostinho Antunes

Abstract

Identifying adenylation domains (A-domains) and their substrate specificity can aid the detection of nonribosomal peptide synthetases (NRPS) at genome/proteome level and allow inferring the structure of oligopeptides with relevant biological activities. However, that is challenging task due to the high sequence diversity of A-domains (~10-40 % of amino acid identity) and their selectivity for 50 different natural/unnatural amino acids. Altogether these characteristics make their detection and the prediction of their substrate specificity a real challenge when using traditional sequence alignment methods, e.g., BLAST searches. In this chapter we describe two workflows based on alignment-free methods intended for the identification and substrate specificity prediction of A-domains. To identify A-domains we introduce a graphical-numerical method, implemented in TI2BioP version 2.0 (topological indices to biopolymers), which in a first step uses protein four-color maps to represent A-domains. In a second step, simple topological indices (TIs), called spectral moments, are derived from the graphical representations of known A-domains (positive dataset) and of unrelated but well-characterized sequences (negative set). Spectral moment...Continue Reading

Citations

Jun 9, 2017·Metallomics : Integrated Biometal Science·Zachary L ReitzAlison Butler
Sep 13, 2017·Applied Microbiology and Biotechnology·Yang LiuHuitu Zhang
Sep 14, 2019·Biotechnology Advances·Antoine VassauxValérie Leclère

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