Figure 3 | Homology models of soluble and insoluble Toll-like Receptor 5 (TLR5) for Oncorhynchus mykiss (Rainbow Trout) and Salmo salar (Atlantic Salmon)

Figure 3 | Homology models of soluble and insoluble Toll-like Receptor 5 (TLR5) for Oncorhynchus mykiss (Rainbow Trout) and Salmo salar (Atlantic Salmon)

Amino acid (AA) coding sequences for the TLR5 genes were input into the online server Protein Homology/analogy Recognition Engine V 2.0 (Phyre2). Phyre2 generated pdb files that were then uploaded to ChimeraX, which was used for the visualization and analysis of the molecular structures shown. Results from HMMER (Figure 1) and Mixed Effects Model of Evolution (MEME) analyses were used in this modeling. The HMMER analysis provided the AA regions that contain the leucine rich repeat (LRR), Toll-interleukin-1 Receptor (TIR), and Transmembrane (TM) domains. The MEME analysis hypothesized 24 sites of positive/diversifying selection. Structural regions are colored as follows: LRR in blue, TIR domain in green, TM in orange, sites of positive selection in magenta.