FIG. 1.

Computer-assisted prediction of transmembrane helices (TM) in the ToRSV X2 protein. (A) Schematic representation of putative transmembrane helices within the X2 domain. The RNA1-encoded polyprotein is shown at the top of the panel with the indicated individual protein domains. Vertical lines represent the cleavage sites recognized by the ToRSV proteinase. The X2 protein domain is shown below the polyprotein diagram, with strongly and weakly predicted transmembrane helices represented by black and gray squares, respectively. The hydrophobicity plot of X2 is shown at the bottom of the panel. Hydrophobicity was calculated using the algorithm of Kyte and Doolittle with a window size of 17 amino acids (26). (B) Prediction of transmembrane helices within X2. The entire deduced amino acid sequence of X2 (GenBank accession number DQ469829) is shown at the top of the panel. Amino acids are numbered from the first amino acid of the X2 protein domain according to the previously proposed X1-X2 cleavage site (51). Predicted transmembrane domains are shown for each program (as indicated on the left of the panel). Uppercase letters indicate very high prediction scores, while lowercase letters indicate lower prediction scores. The amino acid sequences deleted in the TM1, TM2, TM3, and TM4 deletion mutants are underlined in the X2 sequence. A naturally occurring putative N-glycosylation site (NMS) is shown by the arrow.