Figure 4

Homology models of Pf-GyrA and Tg-GyrA by I-TASSER. (A) Alignment of Pf-GyrA with Ec-ParC (1ZVU [21]). One monomer of ParC is dark grey, the other is cyan for ParC with the β-pinwheel (497-740) colored purple. One monomer of Pf-GyrA is light grey and the other colored according to the results of the Pfam prediction as follows: N-terminal residues 196-667 are in dark blue, and the predicted β-pinwheel blades (538-840) are orange and in stick representation. The remaining sequences, which are not predicted to have any secondary structure, are red. Right hand side is the same alignment as A but rotated 90° around the y axis. (B) Alignment of the CTD (671-1222) of Pf-GyrA with Ec-ParC (1ZVU). Part of the model aligns with the a-helical bundle of the template, but is likely due to a-helices being predicted in that region of Pf-GyrA, rather than specific homology to the region in the template. (C) Alignment of Tg-GyrA with Ec-ParC. One monomer of ParC is dark grey, the other monomer is cyan for ParC with the β-pinwheel (497-740) colored purple. One monomer of Pf-GyrA is light grey and the other is colored according to the results of the Pfam prediction as follows: N-terminal residues 297-770 are dark blue, and the predicted β-pinwheel blades (1052-1086, 1323-1371, 1405-1446 and 1523-1564) are orange and in stick representation. The likely GyrA-box of Tg-GyrA is shown as green spheres. The remaining sequences that are not predicted to have any secondary structure are red. Right hand side is the same alignment as C but rotated 90° around the y axis. (D) Alignment of the CTD (775-1594) of Tg-GyrA with the template (3L6V). As for Pf-GyrA, a-helices are also predicted N-terminal to the b-pinwheel motifs.