Amino acid alignment of VNP- and P-Nef proteins. Nef alleles from VNPs and Ps are compared. Some conserved sequence elements in Nef, including the N-terminal myristoylation signal, the M20 and WL residues (involved in MHC-I or CD4 down-modulation, respectively), the acidic, proline-rich and diarginine motifs, a thioesterase binding site, a C-proximal adaptor-protein (AP) interaction site and a diacidic putative V1H binding site are indicated. Residues 22 and 62 are highlighted yellow. Dots specify identity with the NL4-3 Nef sequence; dashes indicate gaps introduced to optimize the alignment.