NrdBik phylogeny

Maximum likelihood phylogeny of NrdBk and NrdBi class I ribonucleotide reductase radical generating subunits. Sequences from NCBI's RefSeq database (Haft et al. 2018; https://doi.org/10.1093/nar/gkx1068Opens in a new tab), downloaded July 2018, was searched with subclass specific HMMER (Eddy 2011; https://doi.org/10.1371/journal.pcbi.1002195Opens in a new tab) profiles from RNRdb (http://rnrdb.pfitmap.orgOpens in a new tab) representing the NrdBk and NrdBi subclasses plus an outgroup consisting of NrdBe and NrdBn. The choice of outgroup was made by analysis of the full NrdB phylogeny presented in Grinberg et al. 2018 (https://doi.org/10.7554/eLife.31529Opens in a new tab). The resulting sequences were clustered at 70% identity with UCLUST (Edgar 2010; https://doi.org/10.1093/bioinformatics/btq461Opens in a new tab) to create a representative set of sequences. After manual inspection of sequences, 144 out of 7725 original sequences remained. The sequences were aligned with ProbCons (Do et al. 2005; https://doi.org/10.1101/gr.2821705Opens in a new tab) and 158 reliably aligned positions were selected with BMGE (Criscuolo & Gribaldo 2010; https://doi.org/10.1186/1471-2148-10-210Opens in a new tab) using the BLOSUM30 matrix. The alignment file is NrdBik_with_NrdBen.uc0.70.c.pb.BLOSUM30.bmge.alnfaa. A maximum likelihood phylogeny was estimated using RAxML v. 8.2.4 (Stamatakis 2014; https://doi.org/10.1093/bioinformatics/btu033Opens in a new tab) with the PROTGAMMAAUTO model using the rapid bootstopping algorithm and subsequent maximum likelihood search. The phylogeny, in Dendroscope (Huson et al. 2007; https://doi.org/10.1186/1471-2105-8-460Opens in a new tab) nexml format, is NrdBik_with_NrdBen.uc0.70.c.pb.BLOSUM30.bmge.PROTGAMMAAUTO.raxml.bipartitions.nexml.