# This file is the result of combining several RDB files, specifically # T0175.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0175.t2k.stride-ebghtl.rdb (weight 1.24869) # T0175.t2k.str.rdb (weight 1.53983) # T0175.t2k.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 T0175.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0175 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0175.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 561 # # ============================================ # Comments from T0175.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0175 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0175.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 561 # # ============================================ # Comments from T0175.t2k.str.rdb # ============================================ # TARGET T0175 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0175.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 561 # # ============================================ # Comments from T0175.t2k.alpha.rdb # ============================================ # TARGET T0175 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0175.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 561 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0591 0.0613 0.8795 2 D 0.1039 0.1288 0.7673 3 I 0.1071 0.2256 0.6673 4 P 0.1042 0.3015 0.5943 5 R 0.1068 0.3407 0.5525 6 I 0.1068 0.3351 0.5581 7 F 0.0993 0.3598 0.5409 8 T 0.0881 0.3906 0.5213 9 I 0.0943 0.3664 0.5394 10 S 0.0734 0.3987 0.5280 11 E 0.0633 0.3789 0.5578 12 S 0.0573 0.3287 0.6140 13 E 0.0400 0.3620 0.5980 14 H 0.0461 0.3108 0.6431 15 R 0.0649 0.3003 0.6348 16 I 0.0655 0.2929 0.6416 17 H 0.0515 0.3435 0.6050 18 N 0.0452 0.4156 0.5392 19 P 0.0193 0.6770 0.3037 20 F 0.0190 0.6746 0.3064 21 T 0.0151 0.7606 0.2243 22 E 0.0074 0.8971 0.0954 23 E 0.0073 0.9145 0.0782 24 K 0.0054 0.9330 0.0616 25 Y 0.0047 0.9491 0.0461 26 A 0.0046 0.9536 0.0418 27 T 0.0045 0.9526 0.0429 28 L 0.0045 0.9523 0.0432 29 G 0.0047 0.9456 0.0497 30 R 0.0055 0.9169 0.0777 31 V 0.0087 0.8491 0.1422 32 L 0.0565 0.4987 0.4448 33 R 0.0536 0.0890 0.8574 34 M 0.0676 0.0307 0.9017 35 K 0.0548 0.0286 0.9165 36 P 0.0290 0.1124 0.8587 37 G 0.0374 0.0655 0.8971 38 T 0.2731 0.0271 0.6999 39 R 0.7850 0.0060 0.2091 40 I 0.8821 0.0125 0.1055 41 L 0.8774 0.0128 0.1097 42 D 0.8524 0.0112 0.1363 43 L 0.5241 0.0503 0.4256 44 G 0.2763 0.0475 0.6761 45 S 0.1246 0.0905 0.7850 46 G 0.0736 0.1528 0.7736 47 S 0.0410 0.3703 0.5888 48 G 0.0198 0.6003 0.3799 49 E 0.0075 0.9360 0.0565 50 M 0.0047 0.9532 0.0421 51 L 0.0044 0.9579 0.0377 52 C 0.0044 0.9593 0.0363 53 T 0.0044 0.9585 0.0371 54 W 0.0044 0.9551 0.0405 55 A 0.0045 0.9463 0.0492 56 R 0.0053 0.9074 0.0873 57 D 0.0086 0.8025 0.1889 58 H 0.0483 0.3723 0.5794 59 G 0.0445 0.0303 0.9252 60 I 0.1519 0.0142 0.8339 61 T 0.6531 0.0100 0.3369 62 G 0.8947 0.0044 0.1008 63 T 0.8823 0.0201 0.0976 64 G 0.8987 0.0087 0.0926 65 I 0.8371 0.0098 0.1531 66 D 0.5235 0.0097 0.4667 67 M 0.1169 0.0267 0.8565 68 S 0.0676 0.0234 0.9090 69 S 0.0050 0.9085 0.0864 70 L 0.0046 0.9433 0.0521 71 F 0.0046 0.9526 0.0429 72 T 0.0044 0.9602 0.0354 73 A 0.0044 0.9596 0.0360 74 Q 0.0044 0.9586 0.0370 75 A 0.0045 0.9550 0.0405 76 K 0.0046 0.9564 0.0390 77 R 0.0048 0.9520 0.0432 78 R 0.0049 0.9485 0.0466 79 A 0.0049 0.9454 0.0497 80 E 0.0048 0.9350 0.0602 81 E 0.0059 0.8877 0.1064 82 L 0.0438 0.4594 0.4968 83 G 0.0420 0.0518 0.9063 84 V 0.0789 0.0602 0.8608 85 S 0.1102 0.1166 0.7732 86 E 0.0577 0.2114 0.7309 87 R 0.1756 0.0980 0.7265 88 V 0.6300 0.0138 0.3563 89 H 0.8699 0.0075 0.1226 90 F 0.9028 0.0066 0.0906 91 I 0.8681 0.0126 0.1193 92 H 0.7833 0.0286 0.1881 93 N 0.4152 0.0570 0.5279 94 D 0.2466 0.0621 0.6913 95 A 0.0585 0.5168 0.4247 96 A 0.0442 0.5275 0.4283 97 G 0.0542 0.4834 0.4625 98 Y 0.0867 0.1375 0.7758 99 V 0.0788 0.1306 0.7907 100 A 0.0784 0.1652 0.7565 101 N 0.0468 0.2522 0.7009 102 E 0.0530 0.1862 0.7608 103 K 0.0782 0.1061 0.8157 104 C 0.1656 0.0185 0.8159 105 D 0.2296 0.0462 0.7243 106 V 0.9078 0.0063 0.0859 107 A 0.9286 0.0058 0.0657 108 A 0.9204 0.0086 0.0710 109 C 0.8479 0.0132 0.1389 110 V 0.3515 0.0881 0.5603 111 G 0.1586 0.3174 0.5241 112 A 0.1106 0.5336 0.3558 113 T 0.0834 0.6711 0.2455 114 W 0.0842 0.6185 0.2973 115 I 0.0761 0.3917 0.5322 116 A 0.0850 0.1054 0.8096 117 G 0.0355 0.1547 0.8098 118 G 0.0758 0.0999 0.8243 119 F 0.0105 0.8263 0.1632 120 A 0.0052 0.9233 0.0715 121 G 0.0049 0.9454 0.0496 122 A 0.0045 0.9529 0.0426 123 E 0.0044 0.9578 0.0378 124 E 0.0044 0.9575 0.0381 125 L 0.0045 0.9547 0.0408 126 L 0.0045 0.9493 0.0462 127 A 0.0046 0.9380 0.0574 128 Q 0.0055 0.8719 0.1226 129 S 0.0175 0.6263 0.3562 130 L 0.1436 0.2338 0.6226 131 K 0.1333 0.0322 0.8346 132 P 0.2333 0.0734 0.6933 133 G 0.2324 0.0335 0.7341 134 G 0.5441 0.0099 0.4459 135 I 0.8640 0.0042 0.1318 136 M 0.9252 0.0036 0.0712 137 L 0.9193 0.0041 0.0767 138 I 0.9025 0.0045 0.0930 139 G 0.7768 0.0146 0.2085 140 E 0.5532 0.0221 0.4247 141 P 0.2932 0.0536 0.6532 142 Y 0.1927 0.0696 0.7377 143 W 0.1219 0.1560 0.7221 144 R 0.0806 0.2062 0.7132 145 Q 0.0757 0.2314 0.6929 146 L 0.0729 0.2458 0.6813 147 P 0.0725 0.2802 0.6473 148 A 0.0641 0.3591 0.5768 149 T 0.0592 0.4032 0.5376 150 E 0.0644 0.4613 0.4743 151 E 0.0787 0.4905 0.4308 152 I 0.0984 0.5213 0.3803 153 A 0.1228 0.5492 0.3280 154 Q 0.1415 0.5641 0.2944 155 A 0.1457 0.5627 0.2916 156 C 0.1344 0.5277 0.3378 157 G 0.1504 0.4031 0.4465 158 V 0.1672 0.2780 0.5548 159 S 0.1453 0.1943 0.6604 160 S 0.1019 0.1953 0.7028 161 T 0.0786 0.2192 0.7022 162 S 0.0633 0.2378 0.6989 163 D 0.0808 0.2044 0.7148 164 F 0.1145 0.0921 0.7934 165 L 0.1022 0.0649 0.8329 166 T 0.0787 0.0503 0.8710 167 L 0.0072 0.9004 0.0924 168 P 0.0047 0.9397 0.0556 169 G 0.0045 0.9508 0.0447 170 L 0.0044 0.9564 0.0392 171 V 0.0044 0.9583 0.0373 172 G 0.0044 0.9562 0.0394 173 A 0.0044 0.9564 0.0392 174 F 0.0044 0.9519 0.0437 175 D 0.0046 0.9316 0.0637 176 D 0.0052 0.8287 0.1660 177 L 0.0409 0.3317 0.6274 178 G 0.0398 0.0225 0.9377 179 Y 0.1431 0.0133 0.8436 180 D 0.5881 0.0184 0.3935 181 V 0.7981 0.0155 0.1865 182 V 0.8300 0.0185 0.1515 183 E 0.8086 0.0151 0.1763 184 M 0.7656 0.0241 0.2102 185 V 0.6667 0.0334 0.3000 186 L 0.5393 0.0488 0.4119 187 A 0.3180 0.1032 0.5788 188 D 0.2228 0.1152 0.6620 189 Q 0.1154 0.2865 0.5981 190 E 0.0761 0.2973 0.6267 191 G 0.0633 0.3024 0.6343 192 W 0.0426 0.4818 0.4757 193 D 0.0253 0.5610 0.4137 194 R 0.0294 0.5496 0.4209 195 Y 0.0343 0.5433 0.4224 196 E 0.0316 0.5820 0.3864 197 A 0.0242 0.6987 0.2771 198 A 0.0217 0.7503 0.2280 199 K 0.0179 0.8044 0.1778 200 W 0.0135 0.8517 0.1349 201 L 0.0121 0.8455 0.1424 202 T 0.0097 0.8651 0.1252 203 M 0.0059 0.9192 0.0750 204 R 0.0052 0.9370 0.0578 205 R 0.0050 0.9391 0.0559 206 W 0.0053 0.9318 0.0630 207 L 0.0052 0.9178 0.0769 208 E 0.0063 0.8477 0.1460 209 A 0.0112 0.6976 0.2912 210 N 0.0246 0.5611 0.4144 211 P 0.0135 0.6319 0.3545 212 D 0.0144 0.6684 0.3172 213 D 0.0192 0.6819 0.2989 214 D 0.0165 0.7998 0.1837 215 F 0.0147 0.8419 0.1434 216 A 0.0126 0.8922 0.0952 217 A 0.0124 0.9074 0.0802 218 E 0.0118 0.9033 0.0849 219 V 0.0106 0.9046 0.0847 220 R 0.0090 0.8940 0.0970 221 A 0.0096 0.8709 0.1195 222 E 0.0094 0.8454 0.1452 223 L 0.0155 0.7845 0.2001 224 N 0.0120 0.7044 0.2836 225 I 0.0189 0.6110 0.3701 226 A 0.0407 0.4732 0.4860 227 P 0.0182 0.6151 0.3667 228 K 0.0105 0.7989 0.1906 229 R 0.0108 0.8461 0.1431 230 Y 0.0166 0.8834 0.1000 231 V 0.0116 0.9238 0.0647 232 T 0.0090 0.9336 0.0573 233 Y 0.0066 0.9440 0.0494 234 A 0.0055 0.9499 0.0447 235 R 0.0050 0.9520 0.0431 236 E 0.0047 0.9524 0.0429 237 C 0.0048 0.9473 0.0479 238 F 0.0049 0.9426 0.0525 239 G 0.0047 0.9437 0.0516 240 W 0.0050 0.9377 0.0573 241 G 0.0056 0.9381 0.0564 242 V 0.0062 0.9267 0.0672 243 F 0.0071 0.8957 0.0971 244 A 0.0092 0.8538 0.1371 245 L 0.0236 0.7726 0.2038 246 I 0.0489 0.5794 0.3717 247 A 0.0524 0.3359 0.6117 248 R 0.0309 0.0603 0.9088