ИСТИНА

Alignment of amino acid sequences by means of dynamic programming is one of the popular sequence comparison methods. This work is focused on the finding microbial rhodopsin family-specific scoring functions for global similarity matrix-based sequence alignment. We constructed a set of substitution matrices based on sequence (RHOD1, RHOD2) and structure (RHODS) alignment of microbial rhodopsins using methods described elsewhere [1]. We examined performance of developed substitution matrices along with several popular (BLOSUM, VTML) and rare (JTT, PHAT, PFASUM) substitution matrices for pairwise amino acid alignment of microbial rhodopsins in two kind of tests. First, we compared alignments obtained with the particular matrix with a reference alignment obtained from structural superposition of corresponding proteins. We found that all matrices demonstrate similar performance which was slightly better for family-specific matrices RHOD1, RHOD2, RHODS. Second, we checked an ability of matrices under consideration to detect similarity between type-1 rhodopsins and novel heliorhodopsin discovered recently [2]. To this end we tried to find probable heliorhodopsin homologues in SwissProt and PDB databases. In this test matrices showed very different performance. While BLOSUM and VTML matrices were able to detect similarity with halorhodopsin in both databases, PFASUM matrices did it only in PDB and the rest matrices (RHOD1, RHOD2, RHODS, JTT, PHAT) failed the test. The research is carried out using the equipment of the shared research facilities of HPC computing resources at Lomonosov Moscow State University [3]. The work is ongoing with the support of RFBR grant 17-00-00167K (KOMFI 17-00-00166). [1] I.B. Kuznetsov, BMC Res. Notes 4 (2011). [2] A. Pushkarev, K. Inoue, S. Larom, J. Flores-Uribe, M. Singh, M. Konno, S. Tomida, S. Ito, R. Nakamura, S.P. Tsunoda, A. Philosof, I. Sharon, N. Yutin, E. V. Koonin, H. Kandori, O. Béjà, Nature 558 (2018) 595. [3] V. Sadovnichy, A. Tikhonravov, V. Voevodin, V. Opanasenko, in:, Contemp. High Perform. Comput. From Petascale Towar. Exascale (Chapman Hall/CRC Comput. Sci., CRC Press, Boca Raton, USA, 2013, pp. 283–307.