Table 4.
Substitutions in predicted T cell epitopes in PvMsp-5 among isolates from Thailand, Indonesia, Brazil and Colombia that alter HLA-binding
| Domain | HLA Supertype |
Predicted epitope* | Predicted score** |
Geographic distribution (n) |
|||
|---|---|---|---|---|---|---|---|
| Thailand | Indonesia | Brazil | Colombia | ||||
| Exon I | A1 | KTDNAAAGK | 0.80 | 18 | 8 | - | 1 |
| ETDNAAAGK | 0.78 | 7 | 2 | 8 | 4 | ||
| KTGNAAAGK | 0.44 | 4 | 2 | - | - | ||
| ETKKEATGK | 0.40 | 16 | 4 | 3 | 3 | ||
| GKDNAAAGK | 0.39 | 67 | 7 | 10 | 8 | ||
| GKDNADAGK | 0.38 | 5 | 1 | - | - | ||
| GKDKAAAGK | 0.38 | 2 | - | - | - | ||
| ETKKEAAGK | 0.36 | 1 | - | 1 | - | ||
| GKNNAAAGK | 0.35 | 6 | 1 | 1 | - | ||
| A3 | GSAGESGSK | 1.07 | 43 | 11 | 6 | 4 | |
| GSDGESGSK | 0.67 | 6 | - | 3 | 1 | ||
| GSDGESGEK | 0.49 | 12 | 6 | 5 | 5 | ||
| GSEGESGEK | 0.43 | 65 | 8 | 10 | 6 | ||
| A3 | RLKPLDSEK | 1.10 | 8 | - | 1 | - | |
| KMKTLDSEK | 1.07 | 3 | - | - | - | ||
| RLKTLISGE | 0.18 | 45 | 3 | - | - | ||
| RLKTLNSRE | 0.18 | - | - | 5 | - | ||
| RLKTLNSGE | 0.14 | 16 | 1 | - | 4 | ||
| RLKTLNSEE | 0.13 | 2 | 2 | 3 | 1 | ||
| RLKPLNSGE | 0.13 | 9 | - | - | - | ||
| KMKTLGSGE | 0.10 | 13 | 1 | 1 | - | ||
| KMKTLNSEE | 0.10 | - | - | 5 | - | ||
| KMKTLGSEE | 0.10 | - | 1 | - | - | ||
| QMKTLDSGD | 0.05 | - | - | - | 3 | ||
| RLKTLDSGE | 0.04 | - | - | - | 2 | ||
| RLKPLDSGE | 0.04 | 3 | 2 | 1 | 1 | ||
| QMKTLGSGD | 0.03 | - | 1 | 8 | 3 | ||
| KMKTLGSGD | 0.03 | - | - | - | 1 | ||
| KMKTLDSGD | 0.02 | 9 | 3 | - | - | ||
| KMKTLDSGE | 0.02 | - | 1 | - | - | ||
| QMKTLGSGE | 0.01 | 18 | 10 | - | 1 | ||
| B7 | RAKDKQASV | 0.86 | 11 | 2 | 1 | 1 | |
| RAKEENASV | 0.75 | 1 | 1 | - | - | ||
| RAKNEQASV | 0.75 | 6 | 2 | - | - | ||
| RAKDENASV | 0.72 | 13 | 9 | 8 | 5 | ||
| RAKEEQASV | 0.70 | 59 | 3 | - | - | ||
| RAKDEQASV | 0.67 | 24 | 6 | 14 | 7 | ||
| RAEGENASV | 0.54 | 12 | 2 | 1 | 3 | ||
| B8 | NLKKTDNAA | 1.14 | 18 | 9 | - | 1 | |
| NLKKTGNAA | 1.26 | 4 | 2 | - | - | ||
| NLKETDNAA | 0.76 | 7 | 2 | 8 | 4 | ||
| NLEGKNNAA | 0.48 | 6 | 1 | 1 | - | ||
| NLEGKDNAA | 0.47 | 68 | 6 | 9 | 8 | ||
| NLEGKDKAA | 0.43 | 2 | - | - | - | ||
| NLEETKKEA | 0.27 | 16 | 4 | 4 | 3 | ||
| NLEGKDNAD | 0.13 | 5 | 1 | - | - | ||
| B39 | SEEEQMKTL | 1.03 | 18 | 10 | - | 1 | |
| SEEDRLKTL | 0.86 | 2 | 3 | 8 | 7 | ||
| PEEDKMKTL | 0.56 | - | - | - | 1 | ||
| PEEEQMKTL | 0.55 | - | 1 | 8 | 6 | ||
| PEEEKMKTL | 0.53 | 13 | 2 | 6 | - | ||
| PEEDRLKTL | 0.50 | 61 | 4 | - | - | ||
| SEKDRLKPL | 0.49 | 20 | 1 | 1 | - | ||
| PEEKKMKTL | 0.47 | 3 | 2 | - | - | ||
| PEKEKMKTL | 0.36 | 9 | 2 | - | - | ||
| B58 | STSGEHTNL | 0.94 | - | 1 | - | - | |
| STSEEAPNL | 0.84 | 1 | 1 | - | - | ||
| STSGEDTNL | 0.78 | 30 | 10 | 14 | 9 | ||
| STSGKDTNL | 0.56 | 2 | 4 | - | - | ||
| SRSGEHTNL | 0.28 | 2 | 1 | - | - | ||
| PQTEGDTNL | 0.21 | 68 | 4 | 5 | 4 | ||
| PPSGEDTNL | 0.20 | 12 | 1 | 5 | - | ||
| PPSEEAPNL | 0.20 | 1 | 3 | - | 3 | ||
| B62 | KQSGDVHPA | 0.98 | 1 | - | - | - | |
| KQAEEVNST | 0.91 | 20 | 4 | 1 | - | ||
| KQAEGVDST | 0.80 | 5 | - | - | - | ||
| KQSGDVEPT | 0.71 | - | 1 | - | - | ||
| KQAEEVDPT | 0.70 | 2 | 1 | - | - | ||
| KQAEQVDPA | 0.67 | - | 1 | - | - | ||
| KQAEEVDST | 0.63 | - | 2 | 9 | 4 | ||
| KQSGDVDPA | 0.62 | 2 | 2 | 8 | 5 | ||
| KQAEKVDST | 0.60 | 9 | - | 4 | - | ||
| KQSGYVDPT | 0.59 | 2 | 2 | - | - | ||
| KQAKEVDST | 0.41 | - | - | - | 3 | ||
| KKAEQIDPA | 0.10 | 9 | - | - | - | ||
| KKSGDVDPA | 0.09 | 11 | 7 | - | - | ||
| KKAEQVDPA | 0.08 | 4 | - | 2 | 3 | ||
| KNAEEVDST | 0.07 | 1 | - | - | - | ||
| KKAEEVDST | 0.06 | 59 | 5 | - | - | ||
| KKAEQVDPT | 0.05 | 1 | - | - | - | ||
| Exon II | A2 | YLFGDKCIL | 1.14 | 1 | - | - | - |
| HLFGGKCIL | 0.68 | 60 | 24 | 5 | 2 | ||
| HLFGDKCIL | 0.67 | 67 | 1 | 19 | 14 | ||
*
Underlined residues were positively selected sites based on the model M8 estimated using the BEB method implemented in PAML package (Yang et al, 2005).
**
Threshold for epitope identification was set at ≥ 0.75 using weight on C terminal cleavage at ≥ 0.15 and weight on transporter associated with antigen processing transport efficiency at ≥ 0.05 (Larsen et al, 2005).