Extended Data Fig. 10: Comparison of TnpB with IscB and IsrB, and UPGMA dendrogram of Cas12 enzymes.
From: Cryo-EM structure of the transposon-associated TnpB enzyme
(a) Structural comparison of TnpB with IscB (IscB from the human gut metagenome) (PDB ID: 7UTN) and IsrB (IsrB from Desulfovirgula thermocuniculi) (PDB ID: 8DMB). (b) UPGMA dendrogram showing similarities between different families of Type V effectors. The dendrogram was built using the UPGMA (unweighted pair group method with arithmetic mean) method and is based on the matrix of HHalign39 scores calculated for all against all pairwise alignments, with length coverage of at least 33%. The alignments for the respective families were taken from a previous report1, except for the Cas12m family for which an updated alignment (104 proteins) was used. The striped rectangle corresponds to the tree depth D between 1.5 and 2 (D = 2 roughly corresponds to the pairwise HHsearch similarity score of exp(2D) ≈ 0.02 relative to the self-score), and reflects the tree depth where the subtype assignment is uncertain and a subject for additional consideration.
