Figure 3

Pattern 3 variations. The DTG/ILG template's pattern 3 defines the sequence position equivalent to the β-hairpin loop called flap. A comparison among all constructed sequence logos reveals how, depending on the family, this position nucleates particular consensus motifs related but not identical to those of other families. We categorized this network into 8 variants according to the physical-chemical properties of residues and only show the entire sequence logo of the DTG/ILG template (the remaining logos are available within the database under "Results"). In this network, an alanine-asparagine variable motif predominates among LTR- and SNCAPs, instead of the canonical glycine-rich motif of HIV-1 peptidase and closer relatives.