# This file is the result of combining several RDB files, specifically # T0179.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0179.t2k.stride-ebghtl.rdb (weight 1.24869) # T0179.t2k.str.rdb (weight 1.53983) # T0179.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 T0179.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0179 # 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 T0179.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 135 # # ============================================ # Comments from T0179.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0179 # 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 T0179.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 135 # # ============================================ # Comments from T0179.t2k.str.rdb # ============================================ # TARGET T0179 # 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 T0179.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 135 # # ============================================ # Comments from T0179.t2k.alpha.rdb # ============================================ # TARGET T0179 # 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 T0179.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 135 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0582 0.0491 0.8927 2 S 0.1265 0.0641 0.8093 3 E 0.1562 0.1564 0.6875 4 L 0.2552 0.1699 0.5749 5 W 0.4813 0.1229 0.3958 6 Y 0.6087 0.1054 0.2859 7 T 0.6282 0.1069 0.2648 8 E 0.5720 0.1125 0.3156 9 K 0.4471 0.1248 0.4281 10 Q 0.3550 0.0793 0.5657 11 T 0.1678 0.0426 0.7896 12 K 0.0362 0.1087 0.8551 13 N 0.0410 0.0772 0.8818 14 F 0.3118 0.0727 0.6155 15 G 0.6813 0.0309 0.2878 16 I 0.8335 0.0306 0.1359 17 T 0.8913 0.0172 0.0916 18 M 0.8753 0.0156 0.1090 19 K 0.8653 0.0174 0.1173 20 V 0.7347 0.0892 0.1761 21 N 0.5975 0.1907 0.2118 22 K 0.5750 0.2278 0.1972 23 T 0.5546 0.2710 0.1743 24 L 0.5572 0.2566 0.1861 25 H 0.4368 0.2810 0.2822 26 T 0.3006 0.2516 0.4479 27 E 0.2254 0.1503 0.6243 28 Q 0.1684 0.0776 0.7540 29 T 0.1204 0.0317 0.8479 30 E 0.0553 0.1644 0.7803 31 F 0.1655 0.1288 0.7057 32 Q 0.4170 0.0636 0.5194 33 H 0.7187 0.0234 0.2579 34 L 0.8763 0.0072 0.1165 35 E 0.9156 0.0048 0.0796 36 M 0.9189 0.0040 0.0771 37 V 0.8921 0.0079 0.1000 38 E 0.8472 0.0064 0.1463 39 T 0.5840 0.0180 0.3980 40 E 0.1145 0.1294 0.7561 41 E 0.0679 0.1536 0.7785 42 F 0.1597 0.1005 0.7399 43 G 0.1571 0.0662 0.7768 44 N 0.5080 0.0333 0.4587 45 M 0.8678 0.0079 0.1243 46 L 0.9153 0.0046 0.0801 47 F 0.9105 0.0046 0.0849 48 L 0.8541 0.0119 0.1340 49 D 0.3984 0.0291 0.5725 50 G 0.2131 0.0671 0.7197 51 M 0.6200 0.0487 0.3313 52 V 0.7820 0.0331 0.1849 53 M 0.7632 0.0317 0.2051 54 T 0.7536 0.0314 0.2150 55 S 0.4694 0.0598 0.4708 56 E 0.2180 0.1212 0.6609 57 K 0.0756 0.2500 0.6744 58 D 0.0661 0.3109 0.6229 59 E 0.0555 0.5482 0.3963 60 F 0.0618 0.6952 0.2430 61 V 0.0638 0.7598 0.1764 62 Y 0.0523 0.8325 0.1152 63 H 0.0432 0.8651 0.0917 64 E 0.0373 0.8789 0.0837 65 M 0.0288 0.8821 0.0891 66 V 0.0373 0.8451 0.1176 67 A 0.0457 0.7748 0.1795 68 H 0.0575 0.6386 0.3039 69 V 0.0467 0.6595 0.2938 70 P 0.0406 0.6598 0.2995 71 L 0.0428 0.6623 0.2949 72 F 0.0811 0.5199 0.3990 73 T 0.0947 0.3021 0.6032 74 H 0.0802 0.1072 0.8125 75 P 0.0465 0.0987 0.8548 76 N 0.0812 0.0526 0.8662 77 P 0.1035 0.0449 0.8516 78 E 0.1335 0.0671 0.7994 79 H 0.6451 0.0122 0.3427 80 V 0.9163 0.0049 0.0788 81 L 0.9260 0.0040 0.0700 82 V 0.9249 0.0038 0.0713 83 V 0.8208 0.0283 0.1509 84 G 0.4535 0.0204 0.5261 85 G 0.1285 0.0472 0.8243 86 G 0.0673 0.1091 0.8237 87 D 0.0347 0.2970 0.6683 88 G 0.0253 0.5973 0.3774 89 G 0.0156 0.8882 0.0961 90 V 0.0102 0.9339 0.0560 91 I 0.0066 0.9492 0.0442 92 R 0.0070 0.9507 0.0423 93 E 0.0065 0.9480 0.0455 94 I 0.0067 0.9287 0.0646 95 L 0.0137 0.8670 0.1193 96 K 0.0261 0.6627 0.3112 97 H 0.0793 0.2701 0.6506 98 P 0.0686 0.0931 0.8383 99 S 0.0930 0.0875 0.8195 100 V 0.2617 0.1051 0.6332 101 K 0.4116 0.0933 0.4951 102 K 0.7665 0.0249 0.2086 103 A 0.8484 0.0062 0.1453 104 T 0.8327 0.0189 0.1484 105 L 0.8679 0.0116 0.1205 106 V 0.8474 0.0098 0.1428 107 D 0.7106 0.0133 0.2760 108 I 0.2542 0.0192 0.7266 109 D 0.0871 0.0197 0.8932 110 G 0.0050 0.8967 0.0984 111 K 0.0046 0.9422 0.0533 112 V 0.0045 0.9539 0.0416 113 I 0.0044 0.9600 0.0356 114 E 0.0044 0.9589 0.0366 115 Y 0.0045 0.9547 0.0408 116 S 0.0048 0.9467 0.0485 117 K 0.0052 0.9324 0.0625 118 K 0.0088 0.8736 0.1176 119 F 0.0169 0.7730 0.2101 120 L 0.0557 0.4029 0.5414 121 P 0.0314 0.3913 0.5772 122 S 0.0354 0.4488 0.5159 123 I 0.0515 0.3649 0.5836 124 A 0.0558 0.2807 0.6635 125 G 0.0795 0.2640 0.6565 126 K 0.0676 0.2786 0.6539 127 L 0.0722 0.2384 0.6894 128 D 0.0834 0.1664 0.7502 129 D 0.1077 0.0748 0.8175 130 P 0.0826 0.1613 0.7561 131 R 0.2909 0.1148 0.5943 132 V 0.6446 0.0380 0.3174 133 D 0.8111 0.0254 0.1634 134 V 0.8864 0.0165 0.0971 135 Q 0.8699 0.0205 0.1096 136 V 0.7401 0.0615 0.1984 137 D 0.2620 0.2138 0.5241 138 D 0.1450 0.2477 0.6073 139 G 0.0260 0.7928 0.1812 140 F 0.0179 0.8755 0.1066 141 M 0.0198 0.8802 0.1000 142 H 0.0212 0.8561 0.1227 143 I 0.0513 0.7765 0.1722 144 A 0.0488 0.7227 0.2285 145 K 0.0466 0.5552 0.3982 146 S 0.0657 0.3008 0.6335 147 E 0.0371 0.2126 0.7502 148 N 0.0436 0.1425 0.8139 149 Q 0.1116 0.0980 0.7905 150 Y 0.3188 0.0148 0.6663 151 D 0.5332 0.0171 0.4497 152 V 0.9156 0.0036 0.0808 153 I 0.9308 0.0036 0.0656 154 M 0.9269 0.0036 0.0695 155 V 0.8540 0.0061 0.1399 156 D 0.3997 0.0129 0.5874 157 S 0.1104 0.0597 0.8299 158 T 0.0749 0.0787 0.8465 159 E 0.0766 0.0603 0.8631 160 P 0.0493 0.1201 0.8306 161 V 0.0607 0.1372 0.8021 162 G 0.0577 0.1150 0.8273 163 P 0.0596 0.1668 0.7735 164 A 0.0406 0.4410 0.5183 165 V 0.0161 0.6634 0.3205 166 N 0.0180 0.6883 0.2938 167 L 0.0258 0.6344 0.3398 168 F 0.0408 0.4957 0.4635 169 T 0.0249 0.5878 0.3874 170 K 0.0052 0.9276 0.0672 171 G 0.0046 0.9452 0.0502 172 F 0.0045 0.9526 0.0430 173 Y 0.0044 0.9587 0.0369 174 A 0.0044 0.9584 0.0372 175 G 0.0044 0.9535 0.0421 176 I 0.0045 0.9502 0.0454 177 A 0.0049 0.9419 0.0532 178 K 0.0065 0.8819 0.1116 179 A 0.0156 0.6739 0.3105 180 L 0.1640 0.2843 0.5518 181 K 0.1257 0.0447 0.8296 182 E 0.1469 0.0754 0.7776 183 D 0.1785 0.0316 0.7899 184 G 0.5324 0.0097 0.4579 185 I 0.8302 0.0039 0.1659 186 F 0.9118 0.0036 0.0846 187 V 0.9018 0.0038 0.0944 188 A 0.8700 0.0051 0.1249 189 Q 0.6935 0.0158 0.2906 190 T 0.3063 0.0460 0.6477 191 D 0.0722 0.0599 0.8678 192 N 0.0971 0.0576 0.8453 193 P 0.0672 0.2122 0.7207 194 W 0.0711 0.2438 0.6851 195 F 0.0613 0.2427 0.6960 196 T 0.0515 0.3329 0.6156 197 P 0.0061 0.8949 0.0990 198 E 0.0050 0.9322 0.0629 199 L 0.0046 0.9448 0.0507 200 I 0.0047 0.9535 0.0418 201 T 0.0045 0.9561 0.0394 202 N 0.0045 0.9541 0.0414 203 V 0.0045 0.9534 0.0421 204 Q 0.0045 0.9515 0.0440 205 R 0.0048 0.9399 0.0553 206 D 0.0051 0.9208 0.0742 207 V 0.0057 0.9122 0.0821 208 K 0.0056 0.8746 0.1198 209 E 0.0074 0.7569 0.2356 210 I 0.0189 0.6060 0.3751 211 F 0.0768 0.1863 0.7369 212 P 0.0734 0.1760 0.7507 213 I 0.3828 0.1545 0.4628 214 T 0.6651 0.0523 0.2826 215 K 0.7664 0.0311 0.2025 216 L 0.7533 0.0349 0.2118 217 Y 0.6611 0.0521 0.2868 218 T 0.6490 0.0540 0.2969 219 A 0.6396 0.0403 0.3201 220 N 0.6926 0.0299 0.2775 221 I 0.6242 0.0193 0.3565 222 P 0.4748 0.0272 0.4980 223 T 0.3912 0.0415 0.5672 224 Y 0.2333 0.0457 0.7210 225 P 0.1087 0.0928 0.7985 226 S 0.0655 0.0944 0.8402 227 G 0.1157 0.0972 0.7870 228 L 0.4756 0.0655 0.4590 229 W 0.7855 0.0375 0.1770 230 T 0.8693 0.0267 0.1041 231 F 0.8945 0.0204 0.0850 232 T 0.8883 0.0214 0.0903 233 I 0.8566 0.0264 0.1170 234 G 0.7074 0.0415 0.2511 235 S 0.4255 0.0496 0.5249 236 K 0.1753 0.0959 0.7288 237 K 0.1432 0.0623 0.7946 238 Y 0.1061 0.0754 0.8185 239 D 0.1003 0.0652 0.8345 240 P 0.0391 0.4442 0.5167 241 L 0.0379 0.5013 0.4608 242 A 0.0584 0.5047 0.4369 243 V 0.0724 0.3835 0.5441 244 E 0.0808 0.2555 0.6637 245 D 0.0872 0.3114 0.6015 246 S 0.0832 0.3288 0.5880 247 R 0.0961 0.2954 0.6085 248 F 0.1021 0.3668 0.5311 249 F 0.1097 0.3287 0.5615 250 D 0.1353 0.2929 0.5718 251 I 0.1376 0.2332 0.6291 252 E 0.1636 0.1662 0.6702 253 T 0.2982 0.1309 0.5708 254 K 0.4446 0.0931 0.4623 255 Y 0.4453 0.0705 0.4842 256 Y 0.3251 0.0393 0.6356 257 T 0.1649 0.0358 0.7994 258 K 0.0126 0.5963 0.3911 259 D 0.0170 0.5809 0.4021 260 I 0.0441 0.6724 0.2835 261 H 0.0958 0.6601 0.2441 262 K 0.1453 0.6462 0.2085 263 A 0.1997 0.5991 0.2012 264 A 0.1824 0.5985 0.2190 265 F 0.2425 0.4752 0.2823 266 V 0.2370 0.2999 0.4631 267 L 0.0985 0.1140 0.7875 268 P 0.0380 0.5838 0.3782 269 K 0.0066 0.8768 0.1166 270 F 0.0050 0.9129 0.0821 271 V 0.0054 0.9181 0.0765 272 S 0.0053 0.9052 0.0895 273 D 0.0075 0.8468 0.1457 274 L 0.0081 0.7505 0.2414 275 I 0.0273 0.5296 0.4431 276 K 0.0143 0.1467 0.8391