Multiple sequence alignment of deduced amino acids of HIV-1 reverse transcriptase (RT) gene from mother-infant pair B involved in vertical transmission. In the alignment, the top sequence is the consensus RT sequence of subtype or clade B (CON B) to which mother-infant pair-B RT sequences are aligned. In mother-infant pair B sequences, each line refers to a clone identified by a clone number with M referring to mothers and I referring to infants. 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 activity are shown by spanning arrowheads indicated above the alignment.