Exploring new features of α-amylases from different source organisms by an in silico approach

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.