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. Author manuscript; available in PMC: 2020 Oct 15.
Published in final edited form as: Biochemistry. 2019 Oct 4;58(41):4169–4182. doi: 10.1021/acs.biochem.9b00735

Figure 2. Determining the value for the minimum alignment score threshold for generating the initial SSN (SSN120) by EFI-EST.

Figure 2.

Panel A, “Sequences as a Function of Length Histogram”. Panel B, “Alignment Length vs Alignment Score Box Plot”. Panel C, “Percent Identity vs Alignment Score Box Plot”. The use of the histogram and box plots for determining the minimum alignment score threshold for the initial SSN is described in the text: Panel A is used to determine the “full-length” of single domain proteins (>650 residues; blue arrow). Panel B is used to determine the lower limit of the alignment score threshold (y-axis) that for “full-length” single domain proteins (x-axis), i.e., the alignment score is chosen at length that corresponds to >650 residues; green arrows). Panel C is used to associate percent identity (y-axis) with alignment score (x-axis), with 35 to 40% the recommended value for generating the initial SSN, i.e., an alignment score ≥120 (red arrows).