Multiple sequence alignment of deduced amino acids of HIV-1 reverse transcriptase gene from mother-infant pair F. In the alignment, the top sequence (CON B) is the consensus subtype B RT sequence and the bottom sequences are from mother-infant pair F sequences (M stands for mother sequences and I for infant sequences and the number of clones for mother and infant are indicated by clone number). The structural elements of RT are indicated above the alignment. Dots represent amino acid agreement with CON-B and substitutions are shown by single letter codes for the changed amino acid. Stop codons are shown as x and dashes represent gaps or truncated protein. Relevant amino acid motifs and domains essential for RT functions are shown by spanning arrowheads indicated above the alignment.