# This file is the result of combining several RDB files, specifically # T0252.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0252.t2k.stride-ebghtl.rdb (weight 1.24869) # T0252.t2k.str2.rdb (weight 1.54758) # T0252.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 T0252.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0252 # 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 T0252.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 86 # # ============================================ # Comments from T0252.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0252 # 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 T0252.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 86 # # ============================================ # Comments from T0252.t2k.str2.rdb # ============================================ # TARGET T0252 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0252.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 86 # # ============================================ # Comments from T0252.t2k.alpha.rdb # ============================================ # TARGET T0252 # 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 T0252.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 86 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0585 0.0260 0.9155 2 L 0.0747 0.0454 0.8799 3 D 0.0912 0.0809 0.8279 4 A 0.0213 0.5100 0.4687 5 N 0.0222 0.5792 0.3986 6 K 0.0258 0.6240 0.3502 7 L 0.0130 0.8399 0.1471 8 Q 0.0077 0.9074 0.0848 9 Q 0.0068 0.9305 0.0627 10 A 0.0048 0.9470 0.0482 11 V 0.0047 0.9533 0.0419 12 D 0.0048 0.9532 0.0420 13 Q 0.0049 0.9528 0.0423 14 A 0.0049 0.9473 0.0478 15 Y 0.0058 0.9256 0.0685 16 T 0.0078 0.8661 0.1261 17 Q 0.0151 0.7664 0.2185 18 F 0.0696 0.5154 0.4150 19 H 0.0467 0.5080 0.4453 20 S 0.0601 0.4857 0.4542 21 L 0.0685 0.3371 0.5944 22 N 0.0377 0.2509 0.7114 23 G 0.0527 0.1578 0.7896 24 G 0.0739 0.1143 0.8118 25 Q 0.2207 0.1287 0.6506 26 N 0.2388 0.2709 0.4903 27 A 0.1401 0.4510 0.4089 28 D 0.1558 0.4557 0.3886 29 Y 0.1238 0.4845 0.3917 30 I 0.1250 0.4263 0.4487 31 P 0.0412 0.6640 0.2947 32 F 0.0266 0.7498 0.2236 33 L 0.0163 0.8449 0.1388 34 A 0.0221 0.7475 0.2304 35 N 0.0386 0.4546 0.5068 36 V 0.1152 0.1174 0.7674 37 P 0.1045 0.0264 0.8691 38 G 0.0117 0.3722 0.6161 39 Q 0.0153 0.3538 0.6309 40 L 0.0985 0.3822 0.5194 41 A 0.5213 0.0299 0.4488 42 A 0.8062 0.0122 0.1816 43 V 0.9122 0.0040 0.0838 44 A 0.9231 0.0036 0.0733 45 I 0.9235 0.0035 0.0730 46 V 0.9108 0.0043 0.0850 47 T 0.5930 0.0086 0.3984 48 C 0.1754 0.1073 0.7172 49 D 0.0531 0.0174 0.9295 50 G 0.0593 0.0286 0.9121 51 N 0.5205 0.0106 0.4689 52 V 0.9098 0.0037 0.0865 53 Y 0.8496 0.0094 0.1410 54 S 0.8325 0.0070 0.1604 55 A 0.5684 0.0539 0.3776 56 G 0.2971 0.0442 0.6587 57 D 0.1767 0.0570 0.7663 58 S 0.1317 0.1007 0.7677 59 D 0.1237 0.0833 0.7930 60 Y 0.1614 0.0402 0.7983 61 R 0.3411 0.0512 0.6077 62 F 0.4989 0.0479 0.4532 63 A 0.5041 0.0484 0.4475 64 L 0.3855 0.2513 0.3632 65 E 0.2349 0.3614 0.4038 66 S 0.2005 0.4037 0.3958 67 I 0.1370 0.5725 0.2905 68 S 0.1002 0.6279 0.2718 69 K 0.0758 0.7877 0.1365 70 V 0.0173 0.9382 0.0446 71 C 0.0081 0.9552 0.0367 72 T 0.0062 0.9595 0.0343 73 L 0.0056 0.9592 0.0352 74 A 0.0050 0.9594 0.0356 75 L 0.0047 0.9591 0.0362 76 A 0.0048 0.9554 0.0399 77 L 0.0049 0.9362 0.0588 78 E 0.0060 0.8818 0.1122 79 D 0.0106 0.7811 0.2083 80 V 0.0522 0.5563 0.3915 81 G 0.0493 0.2969 0.6538 82 P 0.0098 0.8299 0.1603 83 Q 0.0075 0.8944 0.0982 84 A 0.0089 0.9226 0.0685 85 V 0.0129 0.9197 0.0674 86 Q 0.0176 0.8974 0.0850 87 D 0.0192 0.8601 0.1207 88 K 0.0324 0.7561 0.2115 89 I 0.0721 0.3572 0.5707 90 G 0.0695 0.0754 0.8550 91 A 0.1641 0.0636 0.7724 92 D 0.1661 0.0477 0.7862 93 P 0.1165 0.0648 0.8187 94 T 0.0753 0.0633 0.8614 95 G 0.0584 0.0547 0.8869 96 L 0.0726 0.0754 0.8520 97 P 0.0830 0.2222 0.6947 98 F 0.1090 0.2997 0.5912 99 N 0.1159 0.3556 0.5286 100 S 0.1432 0.4218 0.4350 101 V 0.0647 0.7189 0.2164 102 I 0.0550 0.7865 0.1585 103 A 0.0676 0.7782 0.1541 104 L 0.0643 0.7891 0.1466 105 E 0.0772 0.7689 0.1539 106 L 0.0564 0.7271 0.2165 107 H 0.0673 0.4440 0.4887 108 G 0.0400 0.1278 0.8322 109 G 0.0276 0.0435 0.9290 110 K 0.0906 0.0238 0.8856 111 P 0.1371 0.0303 0.8326 112 L 0.1009 0.0681 0.8310 113 S 0.0841 0.0615 0.8544 114 P 0.0467 0.4144 0.5390 115 L 0.1431 0.4947 0.3622 116 V 0.1894 0.5852 0.2254 117 N 0.1943 0.6205 0.1852 118 A 0.1690 0.6635 0.1675 119 G 0.2092 0.6660 0.1247 120 A 0.2443 0.6841 0.0716 121 I 0.2606 0.6843 0.0550 122 A 0.2693 0.6665 0.0642 123 T 0.2458 0.6655 0.0888 124 T 0.1426 0.6852 0.1722 125 S 0.0975 0.5932 0.3093 126 L 0.0817 0.5052 0.4131 127 I 0.0975 0.2033 0.6992 128 N 0.0367 0.1535 0.8097 129 A 0.0373 0.1038 0.8589 130 E 0.0660 0.0964 0.8376 131 N 0.0707 0.1026 0.8266 132 V 0.0166 0.8139 0.1695 133 E 0.0074 0.9030 0.0896 134 Q 0.0067 0.9263 0.0670 135 R 0.0057 0.9370 0.0573 136 W 0.0050 0.9503 0.0447 137 Q 0.0048 0.9518 0.0434 138 R 0.0048 0.9538 0.0414 139 I 0.0047 0.9581 0.0372 140 L 0.0047 0.9594 0.0359 141 H 0.0047 0.9571 0.0381 142 I 0.0047 0.9576 0.0377 143 Q 0.0049 0.9535 0.0416 144 Q 0.0051 0.9432 0.0517 145 Q 0.0076 0.9104 0.0820 146 L 0.0133 0.8212 0.1655 147 A 0.0369 0.4396 0.5236 148 G 0.0291 0.0987 0.8721 149 E 0.0566 0.0751 0.8684 150 Q 0.1566 0.0760 0.7673 151 V 0.4322 0.0331 0.5347 152 A 0.4897 0.0267 0.4835 153 L 0.4896 0.0372 0.4732 154 S 0.2167 0.0472 0.7361 155 D 0.0236 0.7748 0.2016 156 E 0.0227 0.8218 0.1555 157 V 0.0461 0.8177 0.1362 158 N 0.0727 0.7354 0.1919 159 Q 0.0907 0.6509 0.2584 160 S 0.1016 0.5600 0.3384 161 E 0.0591 0.6168 0.3241 162 Q 0.0606 0.5314 0.4080 163 T 0.0631 0.4593 0.4776 164 T 0.0412 0.4535 0.5053 165 N 0.0407 0.4676 0.4918 166 F 0.0354 0.6275 0.3372 167 H 0.0142 0.8490 0.1368 168 N 0.0103 0.9171 0.0726 169 R 0.0069 0.9470 0.0461 170 A 0.0061 0.9551 0.0387 171 I 0.0047 0.9594 0.0359 172 A 0.0047 0.9599 0.0354 173 W 0.0047 0.9597 0.0357 174 L 0.0047 0.9588 0.0365 175 L 0.0049 0.9529 0.0422 176 Y 0.0056 0.9245 0.0699 177 S 0.0071 0.8214 0.1715 178 A 0.0424 0.3879 0.5697 179 G 0.0407 0.1056 0.8537 180 Y 0.1009 0.0786 0.8205 181 L 0.1338 0.0739 0.7923 182 Y 0.0581 0.1013 0.8406 183 C 0.0365 0.1112 0.8523 184 D 0.0695 0.1154 0.8151 185 A 0.0064 0.9337 0.0600 186 M 0.0049 0.9496 0.0456 187 E 0.0048 0.9543 0.0409 188 A 0.0051 0.9547 0.0402 189 C 0.0048 0.9541 0.0411 190 D 0.0049 0.9488 0.0462 191 V 0.0051 0.9438 0.0512 192 Y 0.0055 0.9371 0.0574 193 T 0.0080 0.8968 0.0951 194 R 0.0116 0.8285 0.1599 195 Q 0.0303 0.7620 0.2077 196 C 0.0647 0.7367 0.1986 197 S 0.1207 0.6621 0.2173 198 T 0.1352 0.6586 0.2061 199 L 0.2356 0.5776 0.1868 200 L 0.2042 0.5023 0.2936 201 N 0.1752 0.3790 0.4458 202 T 0.0138 0.8974 0.0887 203 I 0.0073 0.9305 0.0622 204 E 0.0057 0.9462 0.0480 205 L 0.0047 0.9536 0.0417 206 A 0.0047 0.9565 0.0388 207 T 0.0047 0.9551 0.0402 208 L 0.0047 0.9542 0.0412 209 G 0.0050 0.9530 0.0421 210 A 0.0056 0.9527 0.0418 211 T 0.0063 0.9387 0.0551 212 L 0.0071 0.9072 0.0857 213 A 0.0089 0.8353 0.1558 214 A 0.0167 0.5078 0.4755 215 G 0.0484 0.1165 0.8351 216 G 0.0656 0.0618 0.8727 217 V 0.2748 0.0392 0.6860 218 N 0.2030 0.0329 0.7640 219 P 0.0523 0.1894 0.7583 220 L 0.0437 0.1534 0.8029 221 T 0.0725 0.0817 0.8458 222 H 0.0639 0.0708 0.8653 223 K 0.2731 0.0407 0.6862 224 R 0.5607 0.0247 0.4146 225 V 0.5060 0.0256 0.4684 226 L 0.3751 0.0155 0.6094 227 Q 0.1190 0.0174 0.8636 228 A 0.0054 0.8239 0.1707 229 D 0.0050 0.8358 0.1592 230 N 0.0062 0.8900 0.1038 231 V 0.0094 0.9161 0.0745 232 P 0.0173 0.9177 0.0651 233 Y 0.0089 0.9320 0.0591 234 I 0.0084 0.9453 0.0463 235 L 0.0096 0.9424 0.0480 236 A 0.0106 0.9402 0.0492 237 E 0.0161 0.9360 0.0479 238 M 0.0163 0.9218 0.0619 239 M 0.0199 0.8890 0.0912 240 M 0.0256 0.8152 0.1592 241 E 0.0473 0.6775 0.2752 242 G 0.0459 0.4994 0.4547 243 L 0.0556 0.5526 0.3917 244 Y 0.0676 0.5474 0.3849 245 G 0.0504 0.5760 0.3736 246 R 0.0376 0.5625 0.3999 247 S 0.0603 0.5259 0.4137 248 G 0.0573 0.4799 0.4627 249 D 0.0926 0.5098 0.3975 250 W 0.2141 0.5024 0.2834 251 A 0.2782 0.4519 0.2700 252 Y 0.3865 0.3665 0.2470 253 R 0.4112 0.3157 0.2731 254 V 0.3194 0.2094 0.4712 255 G 0.2317 0.0735 0.6948 256 L 0.2664 0.0539 0.6797 257 P 0.2252 0.0719 0.7028 258 G 0.1963 0.1169 0.6868 259 K 0.1549 0.1051 0.7400 260 S 0.1138 0.0962 0.7900 261 G 0.1132 0.0729 0.8139 262 V 0.1685 0.0559 0.7756 263 G 0.1991 0.0558 0.7451 264 G 0.4659 0.0385 0.4955 265 G 0.8160 0.0201 0.1639 266 I 0.8785 0.0161 0.1054 267 L 0.8931 0.0122 0.0947 268 A 0.8730 0.0112 0.1158 269 V 0.7995 0.0209 0.1797 270 V 0.6063 0.0125 0.3812 271 P 0.1825 0.0718 0.7456 272 G 0.0687 0.0861 0.8452 273 V 0.3495 0.0594 0.5911 274 M 0.7076 0.0137 0.2787 275 G 0.8771 0.0073 0.1155 276 I 0.9157 0.0072 0.0771 277 A 0.9075 0.0089 0.0836 278 A 0.8825 0.0124 0.1051 279 F 0.7395 0.0196 0.2409 280 S 0.3994 0.0224 0.5782 281 P 0.2536 0.0726 0.6738 282 P 0.1794 0.0980 0.7226 283 L 0.1826 0.0924 0.7249 284 D 0.0866 0.0638 0.8496 285 E 0.0227 0.2438 0.7335 286 D 0.0383 0.2330 0.7287 287 G 0.0323 0.2328 0.7349 288 N 0.0660 0.3488 0.5852 289 S 0.0543 0.6305 0.3152 290 V 0.0106 0.9176 0.0718 291 R 0.0069 0.9390 0.0541 292 G 0.0049 0.9515 0.0436 293 Q 0.0047 0.9589 0.0364 294 K 0.0047 0.9584 0.0370 295 M 0.0047 0.9596 0.0357 296 V 0.0047 0.9596 0.0357 297 A 0.0047 0.9605 0.0348 298 S 0.0047 0.9600 0.0353 299 V 0.0048 0.9568 0.0385 300 A 0.0049 0.9510 0.0441 301 K 0.0057 0.9225 0.0718 302 Q 0.0094 0.8567 0.1339 303 L 0.0497 0.5572 0.3930 304 G 0.0392 0.1241 0.8367 305 Y 0.0898 0.1334 0.7768 306 N 0.1545 0.1521 0.6934 307 V 0.1406 0.3436 0.5158 308 F 0.1703 0.2407 0.5890 309 K 0.1355 0.1587 0.7058 310 G 0.0748 0.0748 0.8504