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Table 2 Aligning sequences according to MASIA motif analysis improves the correlation between structures.

From: Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases

  1. The segmental RMSD between homologous motifs from huAPE1 (from PDB file 1DE9), DNase 1 (1DNK) and synaptojanin (I9Z) are shown first ungapped, from a simple alignment, and then gapped to match conserved residues (Motifs 1 and 2) and allow insertions in the secondary structure elements. Motif 12 is shown as an example of the RMSD where the molegos are spelled in a similar fashion in all three proteins.