Title: Exploring new features of α-amylases from different source organisms by an in silico approach
Authors: Javad Harati; Seyed Omid Ranaei Siadat; Saeed Kaboli; Seyed Mohammad Motevalli; Ardeshir Hesampour
Addresses: National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran ' Protein Engineering Laboratory, Protein Research Center, Shahid Beheshti University, GC, Tehran, Iran; Nanobiotechnology Engineering Laboratory, Faculty of Engineering and New Technologies, Shahid Beheshti University, GC, Tehran, Iran ' Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan; Department of Biotechnology, Faculty of Biological Sciences, Shahid Beheshti University, Tehran, Iran ' Laboratory of Nanomedicine and Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, China ' Department of Biology, Islamic Azad University, Central Tehran Branch, Tehran, Iran
Abstract: A total of 78 full-length protein sequences of α-amylase from different source organisms were subjected to phylogenetic analysis, multiple sequence alignment (MSA), motif search and physiochemical properties. The phylogenetic tree was built using the maximum likelihood method in molecular evolutionary genetics analysis (MEGA) software and was pointed out in two major clusters. One of the clusters included plants and animals, whereas the other one contained fungi, archaea and bacteria. Furthermore, Firmicutes and Proteobacteria are bacterial phylum that placed in the same evolutionary cluster with plants and animals. The deviations from expected clusters were explained by motif analysis. MSA declared three conserved sequence blocks, 505-527, 725-745 and 1010-1030, that were present in all studied species. Moreover, it provided information about highly conserved residues at which three glycine and one aspartic acid residues were conserved. Motif analysis with multiple EM for the motif elicitation server revealed that Motif 4 'HDTGSTQRHWPFPSDHVMQGYAYILTHPGIPCIFYDHFFDW', Motif 6 'EGAGGPSTAFDFTTKGILQEAVKGELWRLRDPQGKPPGMIGWWPERAVTF' and Motif 11 'EQIVKLIAIRKRNGIHSRSSIRILEAEGDLYVAMIDEK VCMKIG' were present only in plants. Pearson correlation analysis to clarify relationships among different physiochemical properties showed a direct correlation between average hydropathy (GRAVY) and the aliphatic index and a reverse correlation between GRAVY and pI and instability indexes.
Keywords: α-Amylase; Aedes aegypti; bioinformatics; conserved sequence; degenerate primer; glycoside hydrolase; phylogenetic analysis; Pyrococcus furiosus; sequence analysis.
International Journal of Bioinformatics Research and Applications, 2019 Vol.15 No.2, pp.108 - 128
Received: 16 Jul 2016
Accepted: 19 Dec 2016
Published online: 06 May 2019 *