Conserved peptides recognition by ensemble of neural networks for mining protein data – LPMO case study

Mining protein data is a recent promising area of modern bioinformatics. In this work, we suggested a novel approach for mining protein data – conserved peptides recognition by ensemble of neural networks (CPRENN). This approach was applied for mining lytic polysaccharide monooxygenases (LPMOs) in 19 ascomycete, 18 basidiomycete, and 18 bacterial proteomes. LPMOs are recently discovered enzymes and their mining is of high relevance for biotechnology of lignocellulosic materials. CPRENN was compared with two conventional bioinformatic methods for mining protein data – profile hidden Markov models (HMMs) search (HMMER program) and peptide pattern recognition (PPR program combined with Hotpep application). The maximum number of hypothetical LPMO amino acid sequences was discovered by HMMER. Profile HMMs search proved to be the more sensitive method for mining LPMOs than conserved peptides recognition. Totally, CPRENN found 76 %, 67 %, and 65 % of hypothetical ascomycete, basidiomycete, and bacterial LPMOs discovered by HMMER, respectively. For AA9, AA10, and AA11 families which contain the major part of all LPMOs in the carbohydrate-active enzymes database (CAZy), CPRENN and PPR + Hotpep found 69–98 % and 62–95 % of amino acid sequences discovered by HMMER, respectively. In contrast with PPR + Hotpep, CPRENN possessed perfect precision and provided more complete mining of basidiomycete and bacterial LPMOs.