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Fig. 3 | BMC Evolutionary Biology

Fig. 3

From: Cluster expansion of apolipoprotein D (ApoD) genes in teleost fishes

Fig. 3

a Protein 3D structure modelling. Different ApoDs among species exhibit a conserved 3D structure, including a cup-like central part made up of eight antiparallel β-sheet strands and two ends connected by loops (a wide opening part formed by loops 1, 3, 5 and 7 and a narrow closed bottom formed by loops 2, 4 and 6). Unlike the very conserved cup-like central part, the loops at the two ends are highly variable. Note that most sites under positive selection are located on the loops or on the connections between the loops and the cup-like central part. b Cluster analyses based on the whole protein 3D structure. Cluster analyses can clearly segregate different ApoD duplicates, including lineage-specific duplicated genes. c Cluster analyses based on loops 1, 3, 5 and 7 at the opening side. Cluster analyses can segregate different ApoD duplicates. d Cluster analyses based on loops 2, 4 and 6 at the bottom. This cluster analyses cannot segregate different duplicates

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