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Table 1 The optimized property weights and gap penalties for the four default amino acid properties

From: PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids

Pair-wise sequence identity Weight for hydrophobicity Weight for size Weight for coil propensity Weight for thiol group Gap initiation penalty Gap extension penalty N pairs
0-10% 0.7 0.15 0.1 0.05 0.8 0.2 1,282
10-20% 0.3 0.2 0.15 0.35 0.6 0.1 2,023
20-30% 0.3 0.2 0.15 0.35 0.7 0.1 1,674
30-40% 0.25 0.2 0.15 0.4 0.7 0.1 1,100
Above 40% 0.2 0.2 0.25 0.35 0.6 0.1 705
  1. The four default amino acid properties are hydrophobicity [29], size [30], coil propensity [31] and the presence of the thiol group. By default, PR2ALIGN uses the combination of property weights and gap penalties optimized for aligning sequences with pair-wise sequence identity between 30 and 40 percent (highlighted in boldface type).the column “N pairs” shows the total number of sequence pairs in each benchmark dataset.