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. 2015 Oct 28;112(45):14096–14101. doi: 10.1073/pnas.1512865112

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Fig. S2. — Phylogenetic analysis of RCF3 homologs. RCF3-like KH domain proteins from A. thaliana. Approximate likelihood fraction (aLRT) and bootstrap values (BT) larger than 50% are shown at nodes. Black, gray, and white boxes indicate types of KH domains. The full-length RCF3 protein sequence was compared by BLASTP against the A. thaliana RefSeq protein database. All hits were analyzed for the identity of their annotated functional domains using both the National Center for Biotechnology Information (NCBI) conserved domain search engine (www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) and Pfam version 27.0 (pfam.xfam.org/search/sequence). With MEGA version 5, complete protein sequences were aligned using Muscle, and a phylogenetic tree was estimated with the Maximum Likelihood method. FASTA-formatted alignments were loaded into SeaView Version 4.5.3 for computation of trees, using the best fitted model (WAG) including the approximate likelihood fraction (aLRT) and bootstrapping (100×).