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. 2012 Mar 27;7(3):e33863. doi: 10.1371/journal.pone.0033863

Figure 1. Phylogenetic tree of CRAL_TRIO and BCH domains from the Sec14 superfamily.

Figure 1

This bootstrapped Neighbor Joining tree includes 175 BCH domains and 98 CRAL_TRIO/BCH-like domains from multiple organisms. The tree is displayed in a circular mode and different groups are marked by colored stripes. The clades with branch length <0.05 are collapsed and the number against each collapsed clade gives the number of collapsed branches. Branch lengths are ignored in order to maintain clarity. Against each branch the domain architectures of individual protein are shown as identified by the Pfam database (release 25) with a cut-off e-value ≤0.1. The Pfam database does not differentiate between CRAL_TRIO and BCH domains and thus both are indicated by yellow colored rectangles. However, if no such domain was identified by the Pfam database, we marked the annotations for BCH domains as determined by our analyses and they are indicated by an orange colored rectangle. The protein length is scaled. Eexcept when there is more than one protein from one genus (for these NCBI accessions are also given with name initials) only the generic names are given. The accession codes for remaining species/branches can be found in the Table S1. The abbreviations used are as follows; Dr: Danio rerio, Tn: Tetraodon nigroviridis, Ci: Ciona intestinalis, Dd: Dictyostelium discoideum, At: Arabidopsis thaliana, Rc: Ricinus communis, Pt: Populus trichocarpa, Gm: Glycine max, Mt: Medicago truncatula, Ps: Picea sitchensis, Zm: Zea mays, Os: Oryza sativa. This phylogenetic tree shows the distinct clustering of BCH domains from CRAL_TRIO domains. The three BCH subgroups are group I, group II and group III respectively and distinct groups within the CRAL_TRIO domain are also marked accordingly. Each cluster represents a distinct domain architecture. Pfam does not recognize the complete domain in BCH groups. The CRAL_TRIO_N domain, which is characteristically associated with CRAL_TRIO domains, is also missing in BCH and BCH-like (NF1 and RhoGEF) proteins. Similar to NF1 protein, Dictyostelium discoideum has an ancestral BCH sequence, which is associated with a RasGAP domain.