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/gkx1068), downloaded July 2018, was searched with subclass specific HMMER (Eddy 2011; https://doi.org/10.1371/journal.pcbi.1002195) profiles from RNRdb (http://rnrdb.pfitmap.org) 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.31529). The resulting sequences were clustered at 70% identity with UCLUST (Edgar 2010; https://doi.org/10.1093/bioinformatics/btq461) 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.2821705) and 158 reliably aligned positions were selected with BMGE (Criscuolo & Gribaldo 2010; https://doi.org/10.1186/1471-2148-10-210) 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/btu033) 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/10.1186/1471-2105-8-460) nexml format, is NrdBik_with_NrdBen.uc0.70.c.pb.BLOSUM30.bmge.PROTGAMMAAUTO.raxml.bipartitions.nexml.本数据集针对NrdBk与NrdBi两类I型核糖核苷酸还原酶（ribonucleotide reductase）的自由基生成亚基构建最大似然系统发育树。序列数据下载自2018年7月更新的NCBI RefSeq数据库（Haft等，2018；https://doi.org/10.1093/nar/gkx1068），采用RNRdb数据库（http://rnrdb.pfitmap.org）提供的NrdBk、NrdBi亚类特异性HMMER特征谱（Eddy，2011；https://doi.org/10.1371/journal.pcbi.1002195）进行序列检索，同时纳入由NrdBe与NrdBn组成的外类群。外类群的选取依据Grinberg等2018年发表的完整NrdB系统发育分析结果（https://doi.org/10.7554/eLife.31529）。使用UCLUST工具（Edgar，2010；https://doi.org/10.1093/bioinformatics/btq461）以70%序列同一性阈值对所得序列进行聚类，获取代表性序列集。经人工序列筛选后，初始7725条序列最终保留144条。使用ProbCons工具（Do等，2005；https://doi.org/10.1101/gr.2821705）完成序列比对，再借助BMGE工具（Criscuolo & Gribaldo，2010；https://doi.org/10.1186/1471-2148-10-210）结合BLOSUM30矩阵，筛选出158个可靠比对位点。该序列比对文件名为NrdBik_with_NrdBen.uc0.70.c.pb.BLOSUM30.bmge.alnfaa。使用RAxML v. 8.2.4工具（Stamatakis，2014；https://doi.org/10.1093/bioinformatics/btu033），以PROTGAMMAAUTO模型结合快速自举停止算法及后续最大似然搜索，构建最大似然系统发育树。该系统发育树文件采用Dendroscope支持的nexml格式，文件名为NrdBik_with_NrdBen.uc0.70.c.pb.BLOSUM30.bmge.PROTGAMMAAUTO.raxml.bipartitions.nexml。