Figure 1

Structure and analysis of Arf/Arl GTPases. (A) Key structural features shared by Arf/Arl/Sar GTPases. In yellow are the side chains of six residues that are highly distinctive of Arf/Arl/Sar GTPases and that, within the GTP-bound state, often form the network of interactions shown. Within the Switch I region is shown a threonine residue (magenta side chain) that is conserved in the TRAFAC subclass of P-loop GTPases and that coordinates with the Mg++ ion associated with bound GTP. The structure shown is that of Arf1 bound to GTP (pdb_id: 1o3y; 1.50 Ǻ resolution) [57]. The Switch I and II regions (red and orange backbones, respectively) and the α3 helix (dark yellow backbone) are indicated. (B) Schematic representation of a contrast alignment, which reveals the sequence features distinguishing one group of proteins (termed the foreground) from related, evolutionarily-divergent proteins (termed the background). Red and gray horizontal bars represent sequences belonging to the foreground and background, respectively. Black vertical bars represent residues that are conserved in the foreground and white vertical bars represent corresponding non-conserved positions in the background. The histogram above these columns indicates the relative strengths of the selective constraints associated with evolutionary divergence of the foreground sequences from the background sequences. (C) Correspondence between a phylogenetic tree and a hyperpartition. A rooted tree is shown both as a graph and as a hyperpartition. In the hyperpartition, each column corresponds to one node in the tree such that the '+' rows in that column correspond to that node's subtree, which serves as the foreground, whereas the '-' rows in that column correspond to the rest of the parent node's subtree, which serves as the background; the remaining (non-participating) nodes in that column are labeled with an 'o'. Internal nodes (shown in blue) correspond to 'miscellaneous' subgroups, that is to sequences that are assigned to a subtree (e.g., a family), but not to a leaf node (e.g., a specific subfamily).