# This file is the result of combining several RDB files, specifically # T0365.t06.dssp-ebghstl.rdb (weight 1.53986) # T0365.t06.stride-ebghtl.rdb (weight 1.24869) # T0365.t06.str2.rdb (weight 1.54758) # T0365.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 T0365.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0365 # Using neural net t06-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 T0365.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 170 # # ============================================ # Comments from T0365.t06.stride-ebghtl.rdb # ============================================ # TARGET T0365 # Using neural net t06-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 T0365.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 170 # # ============================================ # Comments from T0365.t06.str2.rdb # ============================================ # TARGET T0365 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.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 T0365.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 170 # # ============================================ # Comments from T0365.t06.alpha.rdb # ============================================ # TARGET T0365 # Using neural net t06-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 T0365.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 170 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0554 0.0120 0.9325 2 P 0.0973 0.0409 0.8618 3 V 0.0922 0.3850 0.5228 4 N 0.0960 0.4896 0.4144 5 S 0.1076 0.5915 0.3009 6 I 0.1234 0.5802 0.2964 7 L 0.1081 0.4983 0.3936 8 G 0.0596 0.3081 0.6324 9 V 0.0900 0.3139 0.5961 10 F 0.1140 0.2383 0.6477 11 A 0.0646 0.2349 0.7006 12 K 0.0565 0.2019 0.7416 13 S 0.0834 0.0736 0.8430 14 P 0.0420 0.2230 0.7350 15 I 0.0373 0.4340 0.5287 16 K 0.0216 0.6937 0.2847 17 P 0.0169 0.8209 0.1622 18 L 0.0056 0.9306 0.0638 19 Q 0.0051 0.9487 0.0463 20 E 0.0051 0.9476 0.0474 21 H 0.0051 0.9466 0.0483 22 M 0.0047 0.9559 0.0393 23 D 0.0047 0.9584 0.0369 24 K 0.0047 0.9564 0.0388 25 V 0.0047 0.9585 0.0368 26 Y 0.0047 0.9599 0.0354 27 D 0.0047 0.9577 0.0377 28 C 0.0047 0.9561 0.0392 29 A 0.0047 0.9568 0.0385 30 S 0.0051 0.9425 0.0525 31 L 0.0050 0.8964 0.0985 32 L 0.0054 0.9138 0.0809 33 V 0.0047 0.9548 0.0404 34 P 0.0048 0.9561 0.0391 35 F 0.0048 0.9546 0.0406 36 F 0.0048 0.9503 0.0449 37 E 0.0049 0.9464 0.0487 38 A 0.0054 0.9380 0.0566 39 T 0.0065 0.9220 0.0714 40 I 0.0134 0.8401 0.1465 41 T 0.0324 0.5799 0.3877 42 G 0.0317 0.1722 0.7961 43 N 0.0658 0.0769 0.8573 44 W 0.0147 0.6712 0.3142 45 D 0.0089 0.8201 0.1710 46 D 0.0079 0.8880 0.1041 47 A 0.0048 0.9505 0.0447 48 V 0.0047 0.9587 0.0366 49 Q 0.0047 0.9568 0.0385 50 I 0.0048 0.9554 0.0398 51 R 0.0047 0.9566 0.0386 52 K 0.0048 0.9551 0.0401 53 Q 0.0049 0.9530 0.0421 54 I 0.0058 0.9517 0.0425 55 S 0.0052 0.9539 0.0409 56 L 0.0052 0.9505 0.0442 57 A 0.0055 0.9408 0.0537 58 E 0.0055 0.9399 0.0546 59 K 0.0068 0.9205 0.0727 60 Q 0.0083 0.9047 0.0870 61 G 0.0067 0.9138 0.0795 62 D 0.0052 0.9336 0.0612 63 S 0.0050 0.9499 0.0451 64 L 0.0048 0.9538 0.0414 65 K 0.0047 0.9583 0.0370 66 R 0.0052 0.9575 0.0373 67 E 0.0060 0.9547 0.0393 68 I 0.0057 0.9492 0.0451 69 R 0.0066 0.9401 0.0533 70 L 0.0098 0.8904 0.0998 71 T 0.0176 0.7093 0.2731 72 L 0.0554 0.1674 0.7772 73 P 0.0386 0.1875 0.7739 74 S 0.0458 0.2544 0.6998 75 G 0.1189 0.2192 0.6619 76 L 0.3001 0.1034 0.5965 77 F 0.4407 0.0498 0.5096 78 M 0.3969 0.0272 0.5759 79 P 0.2373 0.0587 0.7040 80 V 0.1418 0.0871 0.7711 81 E 0.1021 0.0915 0.8063 82 R 0.0064 0.9066 0.0871 83 T 0.0054 0.9333 0.0613 84 D 0.0051 0.9453 0.0495 85 L 0.0047 0.9587 0.0366 86 L 0.0047 0.9597 0.0357 87 E 0.0047 0.9595 0.0358 88 L 0.0047 0.9573 0.0380 89 L 0.0048 0.9520 0.0433 90 T 0.0057 0.9272 0.0671 91 Q 0.0059 0.8942 0.0999 92 Q 0.0049 0.9151 0.0800 93 D 0.0049 0.9140 0.0812 94 K 0.0048 0.9315 0.0637 95 I 0.0047 0.9393 0.0560 96 A 0.0047 0.9444 0.0508 97 N 0.0047 0.9421 0.0531 98 K 0.0048 0.9431 0.0522 99 A 0.0048 0.9488 0.0464 100 K 0.0048 0.9526 0.0426 101 D 0.0051 0.9478 0.0471 102 I 0.0050 0.9399 0.0550 103 S 0.0055 0.9325 0.0620 104 G 0.0078 0.9124 0.0798 105 R 0.0206 0.9078 0.0716 106 V 0.0418 0.8788 0.0794 107 I 0.0704 0.8093 0.1202 108 G 0.0835 0.7188 0.1977 109 R 0.0958 0.5529 0.3513 110 Q 0.1497 0.3372 0.5131 111 L 0.1921 0.1880 0.6199 112 L 0.1973 0.1348 0.6679 113 I 0.1258 0.0754 0.7988 114 P 0.0789 0.1133 0.8078 115 Q 0.0254 0.5525 0.4221 116 A 0.0282 0.5850 0.3868 117 L 0.0500 0.4978 0.4521 118 Q 0.0407 0.5013 0.4579 119 V 0.0110 0.8652 0.1239 120 P 0.0092 0.9043 0.0866 121 F 0.0048 0.9521 0.0431 122 I 0.0047 0.9572 0.0380 123 A 0.0047 0.9575 0.0378 124 Y 0.0047 0.9585 0.0368 125 L 0.0047 0.9605 0.0348 126 Q 0.0046 0.9612 0.0342 127 R 0.0046 0.9606 0.0347 128 C 0.0047 0.9608 0.0345 129 I 0.0047 0.9607 0.0346 130 D 0.0046 0.9602 0.0351 131 A 0.0046 0.9594 0.0359 132 V 0.0047 0.9601 0.0352 133 G 0.0047 0.9596 0.0358 134 L 0.0047 0.9571 0.0383 135 A 0.0047 0.9597 0.0356 136 Q 0.0047 0.9594 0.0360 137 Q 0.0047 0.9551 0.0402 138 V 0.0048 0.9466 0.0486 139 I 0.0048 0.9484 0.0469 140 N 0.0050 0.9400 0.0549 141 E 0.0052 0.9094 0.0853 142 L 0.0048 0.9304 0.0648 143 D 0.0047 0.9475 0.0478 144 D 0.0047 0.9479 0.0473 145 L 0.0048 0.9423 0.0529 146 L 0.0053 0.9304 0.0643 147 E 0.0071 0.8808 0.1121 148 A 0.0444 0.6171 0.3385 149 G 0.0406 0.2004 0.7591 150 F 0.0637 0.1506 0.7857 151 R 0.0441 0.1334 0.8225 152 G 0.0321 0.1209 0.8470 153 R 0.0716 0.1331 0.7953 154 E 0.1095 0.1722 0.7184 155 V 0.0113 0.8520 0.1367 156 D 0.0055 0.9374 0.0571 157 F 0.0048 0.9529 0.0423 158 V 0.0048 0.9560 0.0392 159 A 0.0047 0.9591 0.0362 160 K 0.0047 0.9574 0.0379 161 M 0.0048 0.9539 0.0413 162 I 0.0047 0.9551 0.0402 163 N 0.0048 0.9518 0.0434 164 E 0.0049 0.9465 0.0486 165 L 0.0052 0.9481 0.0467 166 D 0.0049 0.9507 0.0444 167 I 0.0052 0.9470 0.0478 168 I 0.0056 0.9361 0.0583 169 E 0.0056 0.9298 0.0646 170 E 0.0077 0.9006 0.0918 171 D 0.0103 0.8792 0.1104 172 T 0.0068 0.9241 0.0691 173 D 0.0049 0.9268 0.0683 174 D 0.0047 0.9562 0.0392 175 L 0.0047 0.9585 0.0368 176 Q 0.0047 0.9602 0.0351 177 I 0.0046 0.9611 0.0343 178 Q 0.0047 0.9606 0.0347 179 L 0.0047 0.9590 0.0364 180 R 0.0047 0.9596 0.0357 181 R 0.0047 0.9595 0.0359 182 Q 0.0048 0.9531 0.0421 183 L 0.0049 0.9380 0.0571 184 F 0.0064 0.8901 0.1035 185 A 0.0091 0.7955 0.1955 186 L 0.0154 0.7010 0.2836 187 E 0.0287 0.5859 0.3854 188 S 0.0199 0.4202 0.5599 189 E 0.0319 0.2724 0.6957 190 L 0.0882 0.0692 0.8426 191 N 0.0776 0.0176 0.9049 192 P 0.0053 0.9331 0.0616 193 V 0.0048 0.9536 0.0416 194 D 0.0048 0.9569 0.0383 195 V 0.0052 0.9577 0.0371 196 M 0.0049 0.9584 0.0367 197 F 0.0049 0.9583 0.0368 198 L 0.0047 0.9595 0.0358 199 Y 0.0047 0.9602 0.0351 200 K 0.0047 0.9594 0.0360 201 T 0.0047 0.9596 0.0357 202 I 0.0047 0.9605 0.0348 203 E 0.0047 0.9599 0.0354 204 W 0.0047 0.9568 0.0385 205 V 0.0047 0.9551 0.0402 206 G 0.0048 0.9484 0.0467 207 G 0.0050 0.9303 0.0647 208 L 0.0052 0.9238 0.0711 209 A 0.0048 0.9316 0.0636 210 D 0.0049 0.9287 0.0664 211 L 0.0048 0.9336 0.0616 212 A 0.0048 0.9383 0.0568 213 E 0.0047 0.9443 0.0509 214 R 0.0048 0.9366 0.0586 215 V 0.0049 0.9311 0.0640 216 G 0.0048 0.9368 0.0583 217 S 0.0053 0.9326 0.0621 218 R 0.0072 0.9278 0.0650 219 L 0.0170 0.9166 0.0664 220 E 0.0507 0.8839 0.0654 221 L 0.0651 0.8817 0.0532 222 M 0.0830 0.8478 0.0692 223 L 0.1432 0.7450 0.1117 224 A 0.1985 0.5718 0.2298 225 R 0.1335 0.1795 0.6870 226 V 0.0649 0.0244 0.9107