Beta-galactosidases (βgals) (EC 3.2.1.23) have been detected in a wide range of plant organs and tissues and are described by their ability to hydrolyze terminal nonreducing β-D-galactosyl residues from β-D-galactosides. In this study, 92 βgal protein sequences from different plants, 7 animal samples including human and mouse, 3 samples from bacteria including Escherichia coli, and 4 samples from insects including Drosophila melanogaster were aligned. Sequences were analyzed by computational tools to predict the protein properties, such as molecular mass, isoelectric point, signal peptide, motifs, transmembrane domain, and secondary and spatial structure. Protein structure analysis revealed there is a high identity between plants and other organisms. The modeled βgal has a typical spatial structure with catalytic regions. The 3-dimensional model of Arabidopsis thaliana βgal (Accession Number: NP_001154292) was further checked by PROCHECK algorithm, and showed the majority of the amino acid residues were located in the most-favored regions in a Ramachandran plot. This result suggested that the simulated 3-dimensional structure was reliable. Phylogenetic analysis indicated that A. thaliana βgal has a close relationship with some plants' βgal from different families such as Malvaceae, Solanaceae, and Poaceae. According to these results, βgals should be derived from a common ancestor.

Heat shock proteins (HSPs) are found in all living organisms, from bacteria to humans, are expressed under stress. In this study, characterization of two families of HSP including HSP60 and HSP70 protein was compared in different insect species from different orders. According to the conserved motifs analysis, none of the motifs were shared by all insects of two protein families but each family had their own common motifs. Functional and structural analyses were carried out on seven different insect species from each protein family as the representative samples. These analyses were performed via ExPASy database tools. The tertiary structure of Drosophila melanogater as the sample of each protein family were predicted by the Phyre2 and TM-score servers then their qualities were verified by SuperPose and PROCHECK. The tertiary structures were predicted through the "c4pj1E" model (PDB Accession Code: 4pj1) in HSP60 family and "c3d2fC" model (PDB Accession Code: 3d2f) in HSP70 family. The protein phylogenetic tree was constructed using the Neighbor-joining (NJ) method by Molecular Evolutionary Genetic Analysis (MEGA) 6.06. According to the results, there was a high identity of HSP60 and HSP70 families so that they should be derived from a common ancestor however they belonged to separate groups. In protein-protein interaction analysis by STRING 10.0, 10 common enriched pathways of biological process, molecular function and Kyoto Encyclopedia of Genes and Genomes (KEGG) were identified in D. melanogaster in both families. The obtained data provide a background for bioinformatic studies of the function and evolution of insects and other organisms. Communicated by Mark Joshua Valencia.

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Aspartic proteases (APs; EC: 3.4.23) are a catalytic type of protease enzymes that use an activated water molecule bound to one or more aspartate residues for catalysis of their peptide substrates. They have been extensively studied and are widely distributed among vertebrates, plants, yeast, nematodes, parasites, fungi, and viruses. In this study, bioinformatic analyses of AP enzyme were performed in seed plants protein sequences, including 33 species of 14 different families. According to the conserved motifs obtained by MEME and MAST tools, two motifs were common in all seed plants. The structural and functional analyses of six selected monocots and dicots were investigated by ProtParam, SOPMA, SignalP 4.1, TMHMM 2.0 and ProDom tools in ExPASy database. Tertiary structure of Arabidopsis thaliana as a sample of seed plants, was predicted by Phyre2 server using ''d1oewa'' model (PDB accession code: 1oew) and its quality was verified by PRO-CHECK and ProSA-web servers. The protein sequences were aligned with ClustalW algorithm by MEGA 6.06 software and phylogenetic tree was constructed using the Neighbor-joining (NJ) method. In protein-protein interactions analysis by STRING 9.1 tool, 12 and 135 significant protein interaction groups were identified in Arabidopsis thaliana and other species, respectively. According to the results, there is a high identity among APs of different species in seed plants, so that they should be derived from a common ancestor. The approaches and results reported here would be useful to prioritize candidate genes for further functional proteomic studies of this enzyme in seed plants.