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. 2017 Aug 4;11(12):2754–2766. doi: 10.1038/ismej.2017.125

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Copyright © 2017 The Author(s)

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/4.0/

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The phylogenetic tree of representative PDOs whose genes are physically linked to sqr in bacterial genomes. 69 representative PDOs were used for phylogenetic tree construction with reference sequences. PDOs belong to the metallo-beta-lactamase superfamily, and several related proteins, such as glyoxalase II (GloB) proteins, were also included as references. The representative proteins were labeled with their GenBank accession numbers and bacterial genera. These sequences were aligned by using ClustalW, and the tree was built by using MEGA6. Reference proteins with accession number were given below. Type I PDOs: SaPdoI (YP_003957083.1), CpPdoI (YP_297536.1), MxPdoI (YP_633997.1), HsPdoI (NP_055112.2), CaPdoI (YP_007162862.1), BvPdoI (ZP_00420127.1), AtPdoI (NP_974018.3), AcPdoI (AEK59246.1). Type II PDOs: XfPdoII (NP_298058.1), SmPdoII (NP_435818.1), CpPdoII (YP_297791.1), PaPdoII (NP_251605.1), BxPdoII (YP_554628.1), AfaPdoII (AAK89929.1), AfePdoII (ZP_11421028.1), AfrPdoII (YP_002424776.1). Type III PDOs: ZpPdoIII (ADF52140.1), SaPdoIII (WP_000465474.1), BcPdoIII (EEK49737.1). Glyoxalase II and related proteins: aGLX2-5 (NP_850166.1), AtGloB1 (NP_356997.2), BcII (AAA22276.1), CphA (CAA40386.1), EcGloB1 (NP_414748.1), EcGloB2 (NP_415447.1), hGLX2 (CAA62483.1), HiGloB1 (ADO96205.1), PaGloB2 (NP_249523.1), PpGloB2 (ABQ76961.1), YcbL (CAD05397.1) and ytGLO2 (CAA71335.1).