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RD Finn, A Bateman, J Clements, P Coggill, RY Eberhardt, SR Eddy, A Heger, K Hethe-rington, L Holm, J Mistry, ELL Sonnhammer, J Tate, M Punta (2014)
Pfam: The protein families databaseNucleic Acid Res., 42
JD Thompson, DG Higgins, TJ Gibson, W Clustal (1994)
Improving the sensitivity of progressive multiple sequence aligment through sequence weighting, position specific gap penalties and weight matrix choiceNucleic Acid Res., 22
M Kolbe, H Besir, LO Essen, D Oesterhelt (2000)
Structure of the light-driven chloride pump halorho-dopsin at 1.8 Å resolutionScience, 288
F Keul, M Hess, M Goesele, K Hamacher (2017)
PFASUM: A substitution matrix from Pfam structural alignmentsBMC Bioinf., 18
TF Smith, MS Waterman (1981)
Identification of common molecular subsequencesJ. Mol. Biol., 147
M Stamm, R Staritzbichler, K Khafizov, LR Forrest (2014)
AlignMe—a membrane protein sequence alignment web serverNucleic Acid Res., 42
V Sadovnichy, A Tikhonravov, V Voevodin, VI Opanasenko (2013)
Contemporary High Performance Computing: From Petascale toward Exascale
WR Pearson (1990)
Rapid and sensitive sequence comparison with FASTP and FASTAMethods Enzymol., 183
SB Needleman, CD Wunsch (1970)
A general method applicable to the search for similarities in the amino acid sequence of two proteinsJ. Mol. Biol., 48
I Gushchin, A Reshetnyak, V Borshchevskiy, A Ishchenko, E Round, S Grudinin, M Engelhard, G Büldt, V Gordeliy (2011)
Active state of sensory rho-dopsin II: Structural determinants for signal transfer and proton pumpingJ. Mol. Biol., 412
FI Khan, DQ Wei, KR Gu, MI Hassan, S Tabrez (2016)
Current updates on computer aided protein modeling and designingInt. J. Biol. Macromol., 85
(2018)
UniProt: The universal protein knowledgebaseNucleic Acids Res., 46
HE Kato, K Inoue, R Abe-Yoshizumi (2015)
Structural basis for Na+ transport mechanism by a light-driven Na+ pumpNature, 521
EG Govorunova, OA Sineshchekov, H Li, JL Spudich (2017)
Microbial rhodopsins: Diversity, mechanisms, and optogenetic applicationsAnnu. Rev. Bio-chem., 86
IB Kuznetsov (2011)
Protein sequence alignment with family-specific amino acid similarity matricesBMC Res. Notes, 4
F Sievers, DG Higgins (2018)
Clustal Omega for making accurate alignments of many protein sequencesProtein Sci., 27
A Pushkarev, K Inoue, S Larom (2018)
A distinct abundant group of microbial rhodopsins discovered using functional metagenomicsNature, 558
T Kouyama, S Kanada, Y Takeguchi, A Narusawa, M Murakami, K Ihara (2010)
Crystal structure of the light-driven chloride pump halorhodopsin from Natronomonas pharaonisJ. Mol. Biol., 396
HM Berman, J Westbrook, Z Feng, G Gilliland, TN Bhat, H Weissig, IN Shindyalov, PE Bourne (2000)
The protein data bankNucleic Acid Res., 28
J Zhang, K Mizuno, Y Murata, H Koide, M Murakami, K Ihara, T Kouyama (2013)
Crystal structure of deltarhodopsin-3 from Haloterrigena ther-motoleransProteins: Struct., Funct., Bioinf., 81
S Henikoff, JG Henikoff (1992)
Amino acid substitution matrices from protein blocksProc. Natl. Acad. Sci. U.S.A., 89
T Müller, R Spang, M Vingron (2002)
Estimating amino acid substitution models: A comparison of Day-hoff’s estimator, the resolvent approach and a maximum likelihood methodMol. Biol. Evol., 19
A Löytynoja (2012)
Alignment methods: Strategies, challenges, benchmarking, and comparative overviewEvolutionary Genomics. Methods in Molecular Biology (Methods and Protocols), 855
RC Edgar (2004)
MUSCLE: Multiple sequence alignment with high accuracy and high throughputNucleic Acid Res., 32
Pairwise alignment of amino acid sequences is the basic tool of bioinformatics, which is widely used both independently and within numerous more complex methods. The effectiveness of this tool critically depends on the scoring function used, which consists of a substitution matrix and gap penalties. In this work, amino acid substitution matrices for the superfamily of microbial rhodopsins (RHOD) were constructed and analyzed and then compared with a set of general-purpose matrices (BLOSUM, VTML, PFASUM). It was shown that all matrices allow constructing alignments of microbial rhodopsin sequences of almost the same quality, but only BLOSUM and VTML matrices and their linear combinations with RHOD matrices allow revealing homology between microbial rhodopsins and heliorhodopsin.
Moscow University Biological Sciences Bulletin – Springer Journals
Published: May 24, 2019
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