Phylogenetic trees of all-β protein folds with β-barrel-like architecture. Maximum parsimony was used to reconstruct a general tree of β-barrel-like folds with different β-sheet topologies and barrel mimic folds (A) and trees of β-barrel folds with Greek-key, meander, and complex β-sheet topologies (B). Barrel mimic folds include architectures such as the barrel-sandwich hybrid, with two β-sheets in the shape of a half-barrel packed in a sandwich-like arrangement, and the β-clip, with two-stranded β-sheets that fold upon themselves. Folds are described by general characteristics such as barrel architecture [closed (C), partly open (P), or open barrel (O)], number of strands (n), and shear number (S), and special features (SF) such as cross-over psi loops (p), over-side connections (oc), capping by α-helices (c), and internal pseudo-threefoil symmetry (i). Trees with lengths ranging 659–768 steps [CI = 0.833–0.941, RI = 0.729–0.904; g1 = -(0.554–0.904); PTP tests, P = 0.001] were retained after branch-and-bound or exhaustive searches.
