Fig. 5

Conservation of HIV pseudoknot stems P1 and P2. Nucleotide sequence alignment of the pseudoknot and TAR start in LAI and other HIV-1 isolates. Colors mark base-paired nucleotides in pseudoknot stems P1 (red) and P2 (blue), in the stem of the TATA box loop (nucleotides 27–40 in Fig. 4A) (magenta) and in TAR (green). Grey boxes denote nucleotide differences that prevent base pairing; cyan boxes denote nucleotide differences that do not abolish base pairing. Black boxes denote bulged nucleotides. HIV-1 group M isolate sequences (region 9481–9547) corresponding to different subtypes were retrieved from http://www.hiv.lanl.gov/ (year 2017). Representative examples from a deeper conservation analysis are shown. For subtypes with more than 150 entries, the 1st, 50th, 100th and 150th isolates are presented (subtype B and C); for subtypes occurring less than 150 times, the 1st, 10th and 20th isolate are presented (A1, D, F1 and G); and for subtypes occurring less than 20 times, the 1st and 5th isolate are presented (H and J). In case of sequence uncertainty or incompleteness, the next complete isolate was selected