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Table 1 Structural alignment qualities between models constructed by CirPred and the actual structures of engineered CPMs

From: CirPred, the first structure modeling and linker design system for circularly permuted proteins

Target: engineered CPM (size: residues) Template: native protein (size: residues) CP site on the templatea Identityb (%) Alignment ratioc (%) RMSDc (Å)
1ajkA (212) 2ayhA (214) 84 90.2 97.6 1.441
1ajoA (212) 2ayhA (214) 129 97.2 100.0 1.026
1cpmA (214) 2ayhA (214) 59 98.6 100.0 1.001
1cpnA (208) 2ayhA (214) 59 92.5 100.0 1.050
1alqA (259) 3blmA (257) 223 98.8 100.0 0.548
1fw8A (416) 3pgkA (416) 72 72.8 98.1 3.155
1n02A (102) 2ezmA (101) 50 90.1 100.0 1.316
1un2A (186) 1a2jA (188) 100 96.3 100.0 1.156
1bd7A (176) 1blbC (187) 98 85.6 94.9 6.501
1g2bA (62) 1shgA (57) 47 86.0 100.0 1.056
1tucA (61) 1shgA (57) 20 86.0 96.7 1.609
1tudA (60) 1shgA (57) 48 89.5 100.0 0.833
1swfA (116) 1stpA (121) 51 87.9 100.0 1.256
1swgA (112) 1stpA (121) 51 86.6 100.0 0.657
1p5cA (166) 1lw9A (164) 12 98.1 100.0 1.310
  1. aNumbered according to the order of residues in the PDB file
  2. bSequence identity between the template protein and the target CPM (computed by the circularly-permuted structure alignment algorithm CPSARST [25])
  3. cThese were the structural alignment ratio and RMSD values between the model and the actual structure of target CPMs. The alignment ratio was defined as the number of aligned residues divided by the target’s size