FIG. 7.
Multiple amino acid alignments of three coronavirus pp1a and pp1ab sequences around the PCP1 cleavage site. The gap-free alignments (blocks) shown in uppercase letters were generated by use of the MACAW program (27) with a Gibbs sampler (21) and the Blossum62 scoring table (11). The statistical significance (19) of the alignments was assessed with a searching space comprised of the MHV A59, HCV 229E, and TGEV pp1a sequences. Fragments of the sequences not aligned by the program are shown in lowercase type. Roman bold type indicates residues conserved in any two sequences; italic bold type indicates a positive residue occupying the P5 position relative to the (putative) PCP1 cleavage site, whose position is indicated in the MHV A59 and HCV 229E sequences with ><. The positions of the fragments aligned within the pp1a and pp1ab sequences and sequence database accession numbers are indicated on the left and right sides of the alignments, respectively (GB, GenBank; SP, Swissprot). (A) Alignment constrained by the need to have the P5 and P1 residues of the PCP1 cleavage sites of MHV A59 and HCV 229E in equivalent positions. The statistical significances of the similarities in block AI and block AII were 1.0e+0 (statistically nonsignificant) and 1.2e−3, respectively. (B) Alignment including the statistically most favorable block encompassing the PCP1 cleavage sites in MHV A59 and HCV 229E. The statistical significances of the similarities in block BI and block BII were 1.0e+0 (statistically nonsignificant) and 4.4e−5, respectively.