# This file is the result of combining several RDB files, specifically # T0313.t04.dssp-ebghstl.rdb (weight 1.53986) # T0313.t04.stride-ebghtl.rdb (weight 1.24869) # T0313.t04.str2.rdb (weight 1.54758) # T0313.t04.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 T0313.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0313 # 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 T0313.t04-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 90.7817 # # ============================================ # Comments from T0313.t04.stride-ebghtl.rdb # ============================================ # TARGET T0313 # 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 T0313.t04-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 90.7817 # # ============================================ # Comments from T0313.t04.str2.rdb # ============================================ # TARGET T0313 # 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 T0313.t04-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 90.7817 # # ============================================ # Comments from T0313.t04.alpha.rdb # ============================================ # TARGET T0313 # 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 T0313.t04-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 90.7817 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 N 0.1480 0.0142 0.8377 2 I 0.5779 0.0047 0.4174 3 R 0.8451 0.0039 0.1510 4 V 0.9222 0.0032 0.0747 5 I 0.9255 0.0036 0.0709 6 A 0.9215 0.0038 0.0746 7 R 0.9068 0.0037 0.0895 8 V 0.7781 0.0060 0.2158 9 R 0.5147 0.0085 0.4768 10 P 0.3126 0.0225 0.6649 11 V 0.1761 0.0478 0.7761 12 T 0.1300 0.0314 0.8386 13 K 0.0343 0.2837 0.6820 14 E 0.0412 0.2764 0.6824 15 D 0.0772 0.2589 0.6640 16 G 0.0759 0.1251 0.7990 17 E 0.0863 0.0841 0.8297 18 G 0.0765 0.0461 0.8774 19 P 0.0869 0.0856 0.8275 20 E 0.1609 0.1354 0.7037 21 A 0.3080 0.1101 0.5818 22 T 0.5334 0.0620 0.4047 23 N 0.7545 0.0246 0.2209 24 A 0.8381 0.0128 0.1491 25 V 0.8645 0.0091 0.1264 26 T 0.8191 0.0093 0.1717 27 F 0.5850 0.0225 0.3925 28 D 0.2685 0.0299 0.7016 29 A 0.0483 0.1224 0.8294 30 D 0.0745 0.0770 0.8485 31 D 0.2028 0.0882 0.7089 32 D 0.5106 0.0748 0.4146 33 S 0.8058 0.0392 0.1549 34 I 0.8417 0.0354 0.1230 35 I 0.7953 0.0414 0.1632 36 H 0.7026 0.0442 0.2532 37 L 0.4402 0.1205 0.4393 38 L 0.2450 0.1469 0.6081 39 H 0.1339 0.1263 0.7398 40 K 0.1012 0.0773 0.8215 41 G 0.0881 0.0375 0.8745 42 K 0.2034 0.0126 0.7840 43 P 0.3559 0.0103 0.6337 44 V 0.7030 0.0075 0.2894 45 S 0.8748 0.0057 0.1195 46 F 0.8993 0.0045 0.0962 47 E 0.8883 0.0047 0.1070 48 L 0.7892 0.0112 0.1996 49 D 0.5696 0.0561 0.3743 50 K 0.5670 0.0485 0.3846 51 V 0.6100 0.0413 0.3487 52 F 0.5013 0.0289 0.4697 53 S 0.1209 0.0204 0.8587 54 P 0.0163 0.1815 0.8023 55 Q 0.0282 0.1588 0.8130 56 A 0.0719 0.1521 0.7759 57 S 0.0863 0.1593 0.7544 58 Q 0.0193 0.8094 0.1713 59 Q 0.0057 0.9348 0.0595 60 D 0.0088 0.9371 0.0541 61 V 0.0061 0.9430 0.0509 62 F 0.0052 0.9500 0.0448 63 Q 0.0051 0.9432 0.0517 64 E 0.0057 0.9266 0.0677 65 V 0.0057 0.9274 0.0669 66 Q 0.0052 0.9368 0.0580 67 A 0.0047 0.9372 0.0581 68 L 0.0055 0.9324 0.0621 69 V 0.0053 0.9412 0.0535 70 T 0.0053 0.9350 0.0597 71 S 0.0058 0.9258 0.0684 72 C 0.0091 0.8868 0.1040 73 I 0.0206 0.7907 0.1887 74 D 0.0355 0.4383 0.5261 75 G 0.0341 0.1314 0.8346 76 F 0.1201 0.0628 0.8170 77 N 0.2542 0.0353 0.7106 78 V 0.6983 0.0214 0.2803 79 C 0.8584 0.0142 0.1274 80 I 0.9110 0.0108 0.0781 81 F 0.9048 0.0115 0.0838 82 A 0.8540 0.0134 0.1326 83 Y 0.6702 0.0360 0.2938 84 G 0.3585 0.0311 0.6104 85 Q 0.2815 0.0542 0.6643 86 T 0.1742 0.0827 0.7431 87 G 0.1129 0.0768 0.8103 88 A 0.1134 0.0416 0.8450 89 G 0.1225 0.0413 0.8362 90 K 0.3847 0.0415 0.5738 91 T 0.6631 0.0373 0.2996 92 Y 0.7261 0.0377 0.2362 93 T 0.6983 0.0404 0.2613 94 M 0.6342 0.0537 0.3121 95 E 0.5018 0.0574 0.4408 96 G 0.2533 0.0443 0.7024 97 T 0.1560 0.0430 0.8010 98 A 0.0441 0.1789 0.7769 99 E 0.0421 0.1374 0.8205 100 N 0.0673 0.0648 0.8679 101 P 0.0302 0.1487 0.8211 102 G 0.0670 0.1543 0.7787 103 I 0.1598 0.2780 0.5622 104 N 0.0862 0.3929 0.5209 105 Q 0.0081 0.9196 0.0723 106 R 0.0075 0.9388 0.0537 107 A 0.0059 0.9474 0.0467 108 L 0.0047 0.9564 0.0389 109 Q 0.0047 0.9581 0.0372 110 L 0.0048 0.9531 0.0421 111 L 0.0049 0.9466 0.0485 112 F 0.0049 0.9450 0.0501 113 S 0.0050 0.9390 0.0560 114 E 0.0054 0.9231 0.0715 115 V 0.0087 0.8757 0.1156 116 Q 0.0151 0.7843 0.2006 117 E 0.0230 0.6815 0.2954 118 K 0.0459 0.4743 0.4798 119 A 0.0740 0.1721 0.7538 120 S 0.0375 0.1365 0.8260 121 D 0.0706 0.0610 0.8684 122 W 0.2962 0.0226 0.6812 123 E 0.5647 0.0141 0.4212 124 Y 0.8861 0.0036 0.1102 125 T 0.9153 0.0040 0.0807 126 I 0.9280 0.0032 0.0688 127 T 0.9231 0.0038 0.0732 128 V 0.9009 0.0040 0.0952 129 S 0.7972 0.0204 0.1824 130 A 0.7807 0.0619 0.1574 131 A 0.7061 0.1709 0.1230 132 E 0.6833 0.2239 0.0928 133 I 0.4944 0.3815 0.1241 134 Y 0.2590 0.4849 0.2561 135 N 0.0808 0.5716 0.3475 136 E 0.0490 0.7489 0.2022 137 V 0.0650 0.8165 0.1185 138 L 0.0298 0.9030 0.0672 139 R 0.0267 0.8947 0.0787 140 D 0.0282 0.8665 0.1053 141 L 0.0206 0.7804 0.1990 142 L 0.0370 0.5079 0.4551 143 G 0.0509 0.1019 0.8472 144 K 0.0500 0.0898 0.8602 145 E 0.0691 0.0527 0.8782 146 P 0.0519 0.1658 0.7823 147 Q 0.0562 0.2777 0.6661 148 E 0.1116 0.2528 0.6356 149 K 0.2033 0.1449 0.6518 150 L 0.3952 0.0407 0.5641 151 E 0.5717 0.0177 0.4106 152 I 0.7802 0.0074 0.2124 153 R 0.8638 0.0052 0.1311 154 L 0.8681 0.0066 0.1252 155 C 0.7363 0.0064 0.2573 156 P 0.6005 0.0297 0.3698 157 D 0.1872 0.0190 0.7939 158 G 0.0531 0.0802 0.8667 159 S 0.0529 0.0419 0.9051 160 G 0.0544 0.0540 0.8916 161 Q 0.2698 0.0253 0.7049 162 L 0.7782 0.0056 0.2162 163 Y 0.7886 0.0060 0.2054 164 V 0.5643 0.0106 0.4251 165 P 0.1795 0.0475 0.7730 166 G 0.1196 0.0291 0.8513 167 L 0.4669 0.0131 0.5201 168 T 0.8014 0.0106 0.1880 169 E 0.8807 0.0098 0.1095 170 F 0.8415 0.0065 0.1520 171 Q 0.8149 0.0056 0.1794 172 V 0.5140 0.0083 0.4777 173 Q 0.2271 0.0363 0.7366 174 S 0.1005 0.0110 0.8885 175 V 0.0050 0.9363 0.0587 176 D 0.0047 0.9571 0.0382 177 D 0.0048 0.9581 0.0371 178 I 0.0047 0.9595 0.0358 179 N 0.0047 0.9593 0.0361 180 K 0.0047 0.9584 0.0369 181 V 0.0047 0.9578 0.0375 182 F 0.0048 0.9520 0.0432 183 E 0.0051 0.9282 0.0667 184 F 0.0077 0.8371 0.1551 185 G 0.0138 0.6677 0.3185 186 H 0.0224 0.5514 0.4263 187 T 0.0365 0.5312 0.4324 188 N 0.0799 0.3994 0.5206 189 R 0.1271 0.2440 0.6289 190 T 0.2516 0.1720 0.5764 191 T 0.2780 0.1879 0.5341 192 E 0.2102 0.2167 0.5731 193 F 0.1846 0.2416 0.5738 194 T 0.1764 0.2168 0.6068 195 N 0.1607 0.1872 0.6521 196 L 0.1194 0.2000 0.6806 197 N 0.1049 0.1231 0.7720 198 E 0.0483 0.2449 0.7068 199 H 0.0581 0.1758 0.7661 200 S 0.1015 0.1134 0.7850 201 S 0.1105 0.1423 0.7472 202 R 0.1231 0.2278 0.6491 203 S 0.2240 0.1618 0.6142 204 H 0.3759 0.1208 0.5034 205 A 0.7456 0.0240 0.2304 206 L 0.8720 0.0102 0.1178 207 L 0.8972 0.0083 0.0945 208 I 0.9095 0.0062 0.0842 209 V 0.9118 0.0078 0.0804 210 T 0.9126 0.0061 0.0812 211 V 0.8979 0.0056 0.0965 212 R 0.8111 0.0257 0.1632 213 G 0.8040 0.0100 0.1860 214 V 0.6623 0.0164 0.3213 215 D 0.6324 0.0135 0.3541 216 C 0.3560 0.0645 0.5795 217 S 0.2266 0.0933 0.6800 218 T 0.0952 0.0723 0.8324 219 G 0.1161 0.0448 0.8390 220 L 0.5512 0.0196 0.4292 221 R 0.7630 0.0136 0.2234 222 T 0.7978 0.0184 0.1838 223 T 0.7691 0.0230 0.2080 224 G 0.7106 0.0218 0.2676 225 K 0.8307 0.0168 0.1525 226 L 0.8775 0.0078 0.1148 227 N 0.8786 0.0112 0.1102 228 L 0.8988 0.0192 0.0820 229 V 0.8540 0.0435 0.1026 230 D 0.7647 0.0854 0.1499 231 L 0.4961 0.1262 0.3777 232 A 0.2428 0.1329 0.6242 233 G 0.1258 0.1157 0.7585 234 S 0.1499 0.2160 0.6341 235 E 0.1464 0.3874 0.4662 236 R 0.2011 0.3922 0.4068 237 V 0.1767 0.4009 0.4224 238 G 0.1247 0.3278 0.5475 239 K 0.1636 0.2737 0.5627 240 S 0.2208 0.1763 0.6029 241 G 0.0858 0.1069 0.8074 242 A 0.0946 0.1864 0.7190 243 E 0.0611 0.2022 0.7368 244 G 0.0448 0.2161 0.7391 245 S 0.1060 0.3630 0.5310 246 R 0.1974 0.4996 0.3030 247 L 0.0750 0.7427 0.1823 248 R 0.0456 0.8405 0.1139 249 E 0.0297 0.8846 0.0857 250 A 0.0107 0.9180 0.0713 251 Q 0.0066 0.9327 0.0607 252 H 0.0056 0.9262 0.0682 253 I 0.0059 0.9216 0.0725 254 N 0.0085 0.9021 0.0894 255 K 0.0075 0.8697 0.1228 256 S 0.0075 0.8816 0.1108 257 L 0.0055 0.9383 0.0562 258 S 0.0058 0.9391 0.0551 259 A 0.0052 0.9302 0.0647 260 L 0.0049 0.9388 0.0563 261 G 0.0047 0.9526 0.0427 262 D 0.0047 0.9543 0.0410 263 V 0.0047 0.9576 0.0377 264 I 0.0047 0.9596 0.0357 265 A 0.0047 0.9561 0.0392 266 A 0.0048 0.9492 0.0460 267 L 0.0051 0.9309 0.0640 268 R 0.0079 0.8464 0.1457 269 S 0.0199 0.6336 0.3465 270 R 0.0265 0.3070 0.6665 271 Q 0.0551 0.0893 0.8556 272 G 0.0428 0.0647 0.8925 273 H 0.1875 0.0362 0.7764 274 V 0.2980 0.0176 0.6844 275 P 0.2475 0.0230 0.7295 276 F 0.1474 0.1828 0.6699 277 R 0.0636 0.3198 0.6166 278 N 0.0383 0.2714 0.6903 279 S 0.0735 0.3911 0.5354 280 K 0.0262 0.8139 0.1599 281 L 0.0119 0.9171 0.0711 282 T 0.0094 0.9286 0.0621 283 Y 0.0112 0.9338 0.0550 284 L 0.0111 0.9179 0.0710 285 L 0.0114 0.8783 0.1104 286 Q 0.0156 0.8543 0.1302 287 D 0.0227 0.7753 0.2020 288 S 0.0261 0.6923 0.2816 289 L 0.0488 0.3952 0.5561 290 S 0.0662 0.1329 0.8009 291 G 0.0469 0.0991 0.8540 292 D 0.0594 0.0681 0.8724 293 S 0.1557 0.0534 0.7908 294 K 0.3226 0.0315 0.6460 295 T 0.7915 0.0063 0.2022 296 L 0.9090 0.0037 0.0873 297 M 0.9284 0.0033 0.0683 298 V 0.9297 0.0032 0.0671 299 V 0.9125 0.0042 0.0834 300 Q 0.8714 0.0045 0.1241 301 V 0.6314 0.0171 0.3515 302 S 0.2156 0.0133 0.7711 303 P 0.0413 0.2743 0.6844 304 V 0.0376 0.3428 0.6195 305 E 0.0438 0.4809 0.4753 306 K 0.0609 0.3555 0.5836 307 N 0.0982 0.2503 0.6515 308 T 0.0346 0.6214 0.3440 309 S 0.0235 0.7878 0.1887 310 E 0.0301 0.8104 0.1595 311 T 0.0208 0.8548 0.1243 312 L 0.0110 0.9139 0.0751 313 Y 0.0091 0.8991 0.0918 314 S 0.0064 0.9187 0.0749 315 L 0.0049 0.9464 0.0487 316 K 0.0055 0.9411 0.0533 317 F 0.0051 0.9371 0.0578 318 A 0.0066 0.9214 0.0720 319 E 0.0085 0.8856 0.1058 320 R 0.0120 0.7357 0.2523 321 V 0.0495 0.4639 0.4867 322 R 0.0302 0.1277 0.8421