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. 2018 Sep 18;16(9):341. doi: 10.3390/md16090341

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© 2018 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

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Sequence alignment, 3D modeling and phylogenetic analysis of putative zinc metalloproteinases from A. coerulea. (A) Three putative sequences TRINITY_DN45838_c0_g1|m.27904, TRINITY_DN44124_c13_g11|m.23323, and TRINITY_DN35212_c0_g1|m.10040 in mucus-enriched proteins are aligned with a model metalloproteinase (pdb ID: 3LQB). At the bottom of columns, asterisks (*) show conserved positions, colons (:) show conserved substitutions and points (.) show non-conserved substitutions. Grey line, green bend, blue banded arrowhead and red solenoid represent coil, turn, sheet and helix, respectively. Different fragments are framed by red lines. (B) 3D modeling was simulated using the template metalloproteinase (pdb ID: 3LQB) by SWISS-MODEL and viewed by Discovery Studio 4.5. The colors grey, green, blue and red represent coils, turns, sheets and helices, respectively. Different fragments are indicated by red arrows. (C) Phylogenetic tree constructed using three putative zinc metalloproteinases and 11 other sequences from different species using MEGA 7 with the Neighbor-Joining method.