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. 2014 Jun 13;15:473. doi: 10.1186/1471-2164-15-473

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© Gorriti et al.; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Phylogenetic relationships among microbial rhodopsins. The evolutionary history was inferred using the Neighbor-Joining method [89]. The optimal tree with the sum of branch length = 12.05461219 is shown. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the JTT matrix-based method [90] and are in the units of the number of amino acid differences per site. The rate variation among sites was modeled with a gamma distribution (shape parameter = 2.4). The analysis involved 38 amino acid sequences. All positions containing gaps and missing data were eliminated. PR, proteorhodopsin (blue); XR, xanthorhodopsin (pink); NQ, NQ rhodopsin; BR, bacteriorhodopsin; ActR, actinorhodopsin.