# This file is the result of combining several RDB files, specifically # T0293.t06.dssp-ebghstl.rdb (weight 1.53986) # T0293.t06.stride-ebghtl.rdb (weight 1.24869) # T0293.t06.str2.rdb (weight 1.54758) # T0293.t06.alpha.rdb (weight 0.659012) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0293.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0293 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0293.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 6521 # # ============================================ # Comments from T0293.t06.stride-ebghtl.rdb # ============================================ # TARGET T0293 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0293.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 6521 # # ============================================ # Comments from T0293.t06.str2.rdb # ============================================ # TARGET T0293 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0293.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 6521 # # ============================================ # Comments from T0293.t06.alpha.rdb # ============================================ # TARGET T0293 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0293.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 6521 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.1013 0.1285 0.7702 2 I 0.1169 0.0813 0.8017 3 P 0.1096 0.1269 0.7634 4 L 0.0510 0.4642 0.4848 5 E 0.0558 0.4747 0.4695 6 R 0.1174 0.3746 0.5081 7 L 0.1744 0.1610 0.6646 8 I 0.1073 0.0681 0.8246 9 P 0.0875 0.1147 0.7978 10 T 0.1108 0.1131 0.7761 11 V 0.1149 0.0546 0.8305 12 P 0.0981 0.0986 0.8034 13 L 0.0912 0.1549 0.7539 14 R 0.0969 0.1591 0.7440 15 L 0.0679 0.2962 0.6358 16 N 0.0702 0.2824 0.6474 17 Y 0.0630 0.4170 0.5200 18 I 0.0415 0.6970 0.2615 19 H 0.0198 0.8499 0.1303 20 W 0.0165 0.8810 0.1025 21 V 0.0078 0.9374 0.0548 22 E 0.0067 0.9474 0.0459 23 D 0.0057 0.9458 0.0485 24 L 0.0066 0.9349 0.0585 25 I 0.0119 0.9100 0.0780 26 G 0.0127 0.8458 0.1416 27 H 0.0206 0.7501 0.2293 28 Q 0.0330 0.6443 0.3228 29 D 0.0533 0.3208 0.6259 30 S 0.0297 0.3116 0.6587 31 D 0.0522 0.2047 0.7432 32 K 0.0441 0.2780 0.6780 33 S 0.0521 0.2166 0.7314 34 T 0.0646 0.2124 0.7230 35 L 0.1140 0.1011 0.7849 36 R 0.2160 0.0482 0.7357 37 R 0.7141 0.0185 0.2674 38 G 0.8654 0.0116 0.1230 39 I 0.8956 0.0094 0.0950 40 D 0.8376 0.0125 0.1499 41 I 0.5097 0.0593 0.4310 42 G 0.1925 0.0501 0.7574 43 T 0.0972 0.0924 0.8104 44 G 0.0715 0.1084 0.8200 45 A 0.0596 0.2997 0.6406 46 S 0.0484 0.5495 0.4021 47 C 0.0437 0.7365 0.2198 48 I 0.0178 0.8700 0.1122 49 Y 0.0083 0.9242 0.0675 50 P 0.0058 0.9438 0.0504 51 L 0.0066 0.9437 0.0497 52 L 0.0053 0.9392 0.0555 53 G 0.0058 0.9157 0.0784 54 A 0.0095 0.8391 0.1514 55 T 0.0160 0.7190 0.2650 56 L 0.0641 0.1741 0.7618 57 N 0.0317 0.1046 0.8637 58 G 0.0432 0.0583 0.8985 59 W 0.2439 0.0210 0.7351 60 Y 0.8379 0.0071 0.1551 61 F 0.9248 0.0035 0.0717 62 L 0.9195 0.0063 0.0742 63 A 0.9085 0.0063 0.0852 64 T 0.8220 0.0102 0.1678 65 E 0.5347 0.0131 0.4522 66 V 0.0981 0.0428 0.8591 67 D 0.0801 0.0346 0.8854 68 D 0.0053 0.9000 0.0946 69 M 0.0051 0.9335 0.0614 70 C 0.0049 0.9499 0.0451 71 F 0.0047 0.9569 0.0384 72 N 0.0047 0.9591 0.0362 73 Y 0.0047 0.9593 0.0360 74 A 0.0047 0.9586 0.0367 75 K 0.0047 0.9590 0.0363 76 K 0.0049 0.9570 0.0380 77 N 0.0049 0.9544 0.0407 78 V 0.0050 0.9547 0.0404 79 E 0.0051 0.9483 0.0467 80 Q 0.0069 0.9060 0.0871 81 N 0.0469 0.4151 0.5379 82 N 0.0435 0.0376 0.9188 83 L 0.0625 0.0648 0.8727 84 S 0.0564 0.2367 0.7068 85 D 0.1126 0.2469 0.6405 86 L 0.5071 0.0937 0.3991 87 I 0.7838 0.0136 0.2026 88 K 0.8925 0.0072 0.1003 89 V 0.9184 0.0045 0.0772 90 V 0.8631 0.0117 0.1252 91 K 0.7370 0.0124 0.2506 92 V 0.2026 0.0256 0.7718 93 P 0.1074 0.0541 0.8384 94 Q 0.0129 0.8028 0.1843 95 A 0.0072 0.8892 0.1036 96 T 0.0073 0.9261 0.0666 97 L 0.0081 0.9266 0.0653 98 L 0.0079 0.9223 0.0698 99 M 0.0070 0.9233 0.0697 100 D 0.0094 0.8587 0.1319 101 A 0.0141 0.7597 0.2262 102 L 0.0346 0.5394 0.4260 103 K 0.0349 0.4388 0.5262 104 E 0.0262 0.4097 0.5641 105 E 0.0405 0.3149 0.6446 106 S 0.0457 0.2478 0.7065 107 E 0.0563 0.0935 0.8501 108 I 0.2075 0.0460 0.7464 109 I 0.5746 0.0197 0.4057 110 Y 0.7543 0.0059 0.2398 111 D 0.7783 0.0183 0.2034 112 F 0.9251 0.0037 0.0711 113 C 0.9300 0.0036 0.0664 114 M 0.9204 0.0050 0.0746 115 C 0.7904 0.0134 0.1962 116 N 0.2682 0.0149 0.7169 117 P 0.0989 0.0732 0.8279 118 P 0.0589 0.2083 0.7329 119 F 0.0715 0.2730 0.6554 120 F 0.0782 0.2555 0.6663 121 A 0.0543 0.4004 0.5453 122 N 0.0575 0.4569 0.4856 123 Q 0.0604 0.5494 0.3902 124 L 0.0552 0.6394 0.3054 125 E 0.0708 0.6645 0.2647 126 A 0.0609 0.6783 0.2608 127 K 0.0707 0.4556 0.4737 128 G 0.0710 0.2630 0.6660 129 V 0.1056 0.2866 0.6078 130 N 0.1462 0.2398 0.6141 131 S 0.1360 0.2029 0.6610 132 R 0.1409 0.1182 0.7409 133 N 0.1195 0.0529 0.8275 134 P 0.0820 0.1149 0.8030 135 R 0.0894 0.0934 0.8172 136 R 0.0782 0.0388 0.8830 137 P 0.0613 0.0230 0.9157 138 P 0.0650 0.0277 0.9072 139 P 0.0595 0.0927 0.8478 140 S 0.0326 0.5460 0.4213 141 S 0.0217 0.6834 0.2949 142 V 0.0234 0.7207 0.2559 143 N 0.0313 0.7327 0.2360 144 T 0.0260 0.7893 0.1847 145 G 0.0130 0.8453 0.1417 146 G 0.0176 0.8551 0.1273 147 I 0.0124 0.9075 0.0801 148 T 0.0101 0.9226 0.0674 149 E 0.0110 0.9103 0.0787 150 I 0.0280 0.8480 0.1241 151 M 0.0893 0.6188 0.2919 152 A 0.0928 0.2635 0.6437 153 E 0.0378 0.1535 0.8087 154 G 0.0359 0.0417 0.9224 155 G 0.2874 0.0170 0.6956 156 E 0.7731 0.0067 0.2202 157 L 0.9103 0.0041 0.0856 158 E 0.9228 0.0055 0.0717 159 F 0.9205 0.0058 0.0738 160 V 0.8680 0.0131 0.1189 161 K 0.6602 0.0279 0.3120 162 R 0.3363 0.0769 0.5868 163 I 0.2153 0.1360 0.6488 164 I 0.1687 0.2028 0.6285 165 H 0.0945 0.2936 0.6119 166 D 0.0568 0.3871 0.5561 167 S 0.0479 0.5391 0.4130 168 L 0.0359 0.6706 0.2935 169 Q 0.0384 0.7260 0.2356 170 L 0.0272 0.7906 0.1822 171 G 0.0305 0.7375 0.2321 172 K 0.0302 0.7899 0.1800 173 R 0.0484 0.8038 0.1478 174 L 0.0883 0.7399 0.1718 175 R 0.1048 0.6888 0.2064 176 W 0.1119 0.7018 0.1862 177 Y 0.1330 0.6341 0.2329 178 S 0.1982 0.4496 0.3522 179 C 0.2005 0.3586 0.4408 180 M 0.1978 0.3439 0.4582 181 L 0.1341 0.2835 0.5823 182 G 0.0994 0.1479 0.7527 183 K 0.1583 0.1893 0.6524 184 A 0.2356 0.2213 0.5431 185 C 0.1563 0.2197 0.6240 186 S 0.1223 0.1821 0.6956 187 L 0.0617 0.5074 0.4309 188 A 0.0356 0.6785 0.2859 189 P 0.0188 0.8443 0.1370 190 L 0.0098 0.9079 0.0823 191 K 0.0061 0.9392 0.0547 192 E 0.0050 0.9561 0.0389 193 E 0.0048 0.9570 0.0381 194 L 0.0056 0.9529 0.0415 195 R 0.0065 0.9416 0.0519 196 I 0.0094 0.8890 0.1016 197 Q 0.0449 0.4141 0.5410 198 G 0.0369 0.0249 0.9383 199 V 0.0728 0.0119 0.9153 200 P 0.1315 0.0561 0.8123 201 K 0.4880 0.0600 0.4520 202 V 0.7751 0.0262 0.1987 203 T 0.8594 0.0141 0.1265 204 Y 0.8677 0.0133 0.1190 205 T 0.8174 0.0212 0.1614 206 E 0.8082 0.0250 0.1668 207 F 0.5758 0.0773 0.3468 208 C 0.3466 0.1170 0.5364 209 Q 0.1065 0.0724 0.8212 210 G 0.0534 0.0480 0.8986 211 R 0.2069 0.0344 0.7587 212 T 0.5136 0.0386 0.4478 213 M 0.6865 0.0531 0.2604 214 R 0.7375 0.0569 0.2056 215 W 0.8497 0.0371 0.1131 216 A 0.8569 0.0403 0.1027 217 L 0.8418 0.0471 0.1110 218 A 0.7785 0.0744 0.1471 219 W 0.7117 0.0958 0.1925 220 S 0.6352 0.1135 0.2513 221 F 0.4519 0.1184 0.4297 222 Y 0.2484 0.0673 0.6843 223 D 0.1073 0.0241 0.8686