# This file is the result of combining several RDB files, specifically # T0204.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0204.t2k.stride-ebghtl.rdb (weight 1.24869) # T0204.t2k.str2.rdb (weight 1.54758) # T0204.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 T0204.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0204 # 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 T0204.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 114 # # ============================================ # Comments from T0204.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0204 # 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 T0204.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 114 # # ============================================ # Comments from T0204.t2k.str2.rdb # ============================================ # TARGET T0204 # 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 T0204.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 114 # # ============================================ # Comments from T0204.t2k.alpha.rdb # ============================================ # TARGET T0204 # 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 T0204.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 114 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0682 0.0357 0.8961 2 T 0.1251 0.0721 0.8028 3 S 0.0926 0.0802 0.8271 4 P 0.0737 0.2505 0.6758 5 S 0.0653 0.3470 0.5876 6 H 0.0829 0.3517 0.5654 7 A 0.1008 0.3780 0.5212 8 S 0.0920 0.3399 0.5681 9 D 0.0746 0.3261 0.5993 10 R 0.0805 0.2631 0.6564 11 G 0.0854 0.2295 0.6851 12 G 0.0896 0.1846 0.7258 13 G 0.0695 0.1712 0.7593 14 D 0.0708 0.2169 0.7123 15 G 0.0519 0.2361 0.7120 16 D 0.0669 0.1810 0.7521 17 S 0.1503 0.1165 0.7332 18 V 0.1328 0.0766 0.7907 19 E 0.0684 0.2263 0.7053 20 N 0.0617 0.1784 0.7599 21 Q 0.0815 0.1589 0.7597 22 S 0.1026 0.0756 0.8218 23 P 0.0925 0.1965 0.7110 24 E 0.2420 0.2240 0.5339 25 L 0.5020 0.1419 0.3562 26 R 0.5790 0.0839 0.3371 27 K 0.5895 0.0655 0.3451 28 D 0.2867 0.0463 0.6670 29 P 0.0258 0.2028 0.7714 30 V 0.0363 0.1526 0.8111 31 T 0.0846 0.0532 0.8622 32 N 0.0667 0.0356 0.8977 33 R 0.6299 0.0153 0.3548 34 W 0.9058 0.0039 0.0904 35 V 0.9053 0.0054 0.0893 36 I 0.9195 0.0041 0.0764 37 F 0.8363 0.0162 0.1475 38 S 0.5115 0.0122 0.4763 39 P 0.1655 0.1703 0.6642 40 A 0.0884 0.2258 0.6858 41 R 0.0606 0.3882 0.5511 42 A 0.0507 0.2373 0.7119 43 K 0.0657 0.1634 0.7709 44 R 0.0976 0.0699 0.8325 45 P 0.0767 0.2472 0.6761 46 T 0.0676 0.3183 0.6141 47 D 0.0745 0.3544 0.5711 48 F 0.0695 0.2779 0.6527 49 K 0.0748 0.2831 0.6420 50 S 0.0983 0.2441 0.6575 51 K 0.0822 0.1915 0.7263 52 S 0.0894 0.1209 0.7897 53 P 0.0771 0.2091 0.7138 54 Q 0.0685 0.2117 0.7199 55 N 0.1015 0.1659 0.7326 56 P 0.1028 0.0857 0.8115 57 N 0.0832 0.0628 0.8540 58 P 0.0869 0.0802 0.8328 59 K 0.0854 0.1291 0.7855 60 P 0.0690 0.1540 0.7769 61 S 0.0347 0.2135 0.7518 62 S 0.0716 0.1596 0.7688 63 C 0.1366 0.0546 0.8088 64 P 0.0555 0.1270 0.8176 65 F 0.1151 0.0985 0.7865 66 C 0.1379 0.0611 0.8010 67 I 0.0756 0.1229 0.8015 68 G 0.0522 0.1142 0.8336 69 R 0.0937 0.0986 0.8077 70 E 0.0868 0.1815 0.7317 71 Q 0.0957 0.1531 0.7512 72 E 0.1218 0.1155 0.7627 73 C 0.1053 0.0693 0.8254 74 A 0.0760 0.1161 0.8079 75 P 0.0738 0.4392 0.4870 76 E 0.0978 0.5299 0.3722 77 L 0.2485 0.4454 0.3061 78 F 0.4026 0.2972 0.3002 79 R 0.4611 0.2149 0.3240 80 V 0.4850 0.1458 0.3692 81 P 0.4443 0.1106 0.4451 82 D 0.3010 0.0829 0.6161 83 H 0.1635 0.1056 0.7308 84 D 0.1046 0.0491 0.8463 85 P 0.0657 0.0949 0.8394 86 N 0.0725 0.0782 0.8493 87 W 0.1748 0.0426 0.7827 88 K 0.3544 0.0225 0.6231 89 L 0.8218 0.0059 0.1723 90 R 0.8940 0.0043 0.1017 91 V 0.8867 0.0046 0.1088 92 I 0.7160 0.0082 0.2758 93 E 0.2936 0.0460 0.6604 94 N 0.1298 0.0417 0.8285 95 L 0.1253 0.0754 0.7993 96 Y 0.1525 0.0415 0.8060 97 P 0.1344 0.1455 0.7201 98 A 0.2241 0.1660 0.6099 99 L 0.2909 0.1596 0.5495 100 S 0.2516 0.1205 0.6279 101 R 0.1722 0.1535 0.6743 102 N 0.1512 0.1052 0.7436 103 L 0.1180 0.1085 0.7734 104 E 0.1012 0.1257 0.7731 105 T 0.1035 0.1312 0.7653 106 Q 0.0697 0.1760 0.7543 107 S 0.0797 0.1617 0.7587 108 T 0.0979 0.1539 0.7482 109 Q 0.0905 0.1606 0.7489 110 P 0.0607 0.2056 0.7336 111 E 0.0593 0.1883 0.7524 112 T 0.0814 0.1695 0.7492 113 G 0.1040 0.2023 0.6937 114 T 0.1503 0.2686 0.5812 115 S 0.2530 0.2230 0.5240 116 R 0.3783 0.1994 0.4222 117 T 0.4230 0.1410 0.4361 118 I 0.4641 0.0907 0.4451 119 V 0.4928 0.0750 0.4322 120 G 0.5187 0.0465 0.4348 121 F 0.4371 0.0442 0.5187 122 G 0.4785 0.0269 0.4946 123 F 0.6391 0.0206 0.3402 124 H 0.8184 0.0054 0.1761 125 D 0.9017 0.0037 0.0946 126 V 0.9184 0.0032 0.0784 127 V 0.9226 0.0034 0.0740 128 I 0.8954 0.0046 0.1000 129 E 0.7637 0.0091 0.2272 130 S 0.3006 0.0125 0.6869 131 P 0.0329 0.1406 0.8264 132 V 0.0268 0.1317 0.8415 133 H 0.0408 0.1345 0.8247 134 S 0.0530 0.1024 0.8446 135 I 0.1275 0.1203 0.7523 136 Q 0.2264 0.1255 0.6481 137 L 0.0604 0.5605 0.3792 138 S 0.0224 0.5597 0.4179 139 D 0.0324 0.4129 0.5547 140 I 0.0966 0.0466 0.8568 141 D 0.0572 0.0241 0.9188 142 P 0.0050 0.9248 0.0702 143 V 0.0048 0.9456 0.0496 144 G 0.0050 0.9469 0.0481 145 I 0.0047 0.9572 0.0381 146 G 0.0047 0.9588 0.0365 147 D 0.0047 0.9589 0.0364 148 I 0.0047 0.9602 0.0351 149 L 0.0047 0.9609 0.0345 150 I 0.0047 0.9610 0.0344 151 A 0.0047 0.9605 0.0348 152 Y 0.0047 0.9594 0.0359 153 K 0.0047 0.9584 0.0369 154 K 0.0048 0.9547 0.0405 155 R 0.0048 0.9476 0.0476 156 I 0.0049 0.9382 0.0568 157 N 0.0054 0.9268 0.0679 158 Q 0.0059 0.8898 0.1043 159 I 0.0088 0.8236 0.1676 160 A 0.0132 0.6971 0.2897 161 Q 0.0161 0.5853 0.3986 162 H 0.0588 0.2306 0.7106 163 D 0.0209 0.1530 0.8261 164 S 0.0362 0.0853 0.8785 165 I 0.2412 0.0216 0.7372 166 N 0.3962 0.0364 0.5673 167 Y 0.8660 0.0074 0.1266 168 I 0.9020 0.0056 0.0924 169 Q 0.9073 0.0051 0.0875 170 V 0.8901 0.0102 0.0997 171 F 0.8498 0.0285 0.1217 172 K 0.7323 0.0625 0.2052 173 N 0.5744 0.0623 0.3632 174 Q 0.3105 0.0943 0.5951 175 G 0.1568 0.1346 0.7086 176 A 0.0974 0.3166 0.5860 177 S 0.1049 0.3208 0.5743 178 A 0.1241 0.2305 0.6454 179 G 0.1418 0.0963 0.7620 180 A 0.1974 0.0663 0.7363 181 S 0.1506 0.0973 0.7520 182 M 0.1383 0.1054 0.7563 183 S 0.1164 0.0944 0.7892 184 H 0.1071 0.0358 0.8571 185 S 0.0859 0.0876 0.8265 186 H 0.2304 0.0643 0.7053 187 S 0.4098 0.0541 0.5361 188 Q 0.7192 0.0297 0.2510 189 M 0.8403 0.0221 0.1377 190 M 0.8145 0.0250 0.1605 191 A 0.6954 0.0290 0.2755 192 L 0.4161 0.0320 0.5518 193 P 0.2437 0.0619 0.6944 194 V 0.1826 0.0730 0.7444 195 V 0.1358 0.0415 0.8226 196 P 0.0724 0.0633 0.8643 197 P 0.0351 0.3518 0.6131 198 T 0.0191 0.6872 0.2937 199 V 0.0082 0.8713 0.1206 200 S 0.0075 0.8943 0.0983 201 S 0.0069 0.9178 0.0753 202 R 0.0064 0.9136 0.0800 203 L 0.0057 0.9268 0.0675 204 D 0.0061 0.9177 0.0762 205 G 0.0059 0.9114 0.0827 206 T 0.0061 0.9094 0.0845 207 K 0.0052 0.9338 0.0609 208 D 0.0051 0.9383 0.0566 209 Y 0.0056 0.9366 0.0578 210 F 0.0060 0.9328 0.0612 211 E 0.0069 0.9088 0.0843 212 E 0.0103 0.8467 0.1430 213 T 0.0449 0.5177 0.4374 214 G 0.0333 0.0848 0.8819 215 K 0.0661 0.0770 0.8569 216 C 0.1899 0.0858 0.7243 217 C 0.2503 0.2278 0.5219 218 L 0.2510 0.3725 0.3765 219 C 0.1775 0.5615 0.2611 220 E 0.1577 0.6015 0.2407 221 A 0.1532 0.5844 0.2624 222 K 0.1894 0.3819 0.4286 223 S 0.1133 0.1689 0.7178 224 K 0.0906 0.0724 0.8370 225 H 0.2082 0.0443 0.7475 226 F 0.5449 0.0212 0.4338 227 V 0.7964 0.0097 0.1939 228 I 0.8627 0.0074 0.1299 229 D 0.8166 0.0097 0.1737 230 E 0.6217 0.0297 0.3487 231 S 0.2400 0.0284 0.7317 232 S 0.0809 0.0862 0.8329 233 H 0.2606 0.0427 0.6968 234 F 0.7967 0.0068 0.1964 235 V 0.8877 0.0049 0.1074 236 S 0.9054 0.0048 0.0898 237 V 0.8798 0.0071 0.1131 238 A 0.7559 0.0113 0.2328 239 P 0.5901 0.0211 0.3888 240 F 0.2702 0.1333 0.5965 241 A 0.1713 0.1635 0.6653 242 A 0.1334 0.2308 0.6358 243 T 0.1441 0.1302 0.7257 244 Y 0.1511 0.0500 0.7989 245 P 0.1558 0.0904 0.7538 246 F 0.3778 0.0491 0.5732 247 E 0.7677 0.0135 0.2188 248 I 0.8797 0.0052 0.1151 249 W 0.9061 0.0044 0.0895 250 I 0.8912 0.0051 0.1037 251 I 0.7316 0.0077 0.2607 252 P 0.4527 0.0183 0.5290 253 K 0.0639 0.3065 0.6296 254 D 0.0473 0.4197 0.5329 255 H 0.0522 0.4427 0.5051 256 S 0.0624 0.3418 0.5958 257 S 0.0400 0.3379 0.6221 258 H 0.0751 0.3137 0.6113 259 F 0.0298 0.6634 0.3067 260 H 0.0169 0.6218 0.3612 261 H 0.0284 0.4424 0.5292 262 L 0.0891 0.0678 0.8432 263 D 0.0507 0.0403 0.9090 264 D 0.0054 0.9335 0.0611 265 V 0.0048 0.9480 0.0472 266 K 0.0055 0.9445 0.0500 267 A 0.0047 0.9543 0.0409 268 V 0.0049 0.9460 0.0491 269 D 0.0051 0.9334 0.0615 270 L 0.0048 0.9411 0.0541 271 G 0.0047 0.9549 0.0404 272 G 0.0047 0.9567 0.0386 273 L 0.0047 0.9585 0.0368 274 L 0.0047 0.9602 0.0352 275 K 0.0047 0.9600 0.0353 276 L 0.0047 0.9589 0.0364 277 M 0.0047 0.9574 0.0379 278 L 0.0047 0.9572 0.0381 279 Q 0.0048 0.9510 0.0442 280 K 0.0050 0.9430 0.0521 281 I 0.0054 0.9292 0.0654 282 A 0.0058 0.8948 0.0993 283 K 0.0086 0.8100 0.1814 284 Q 0.0165 0.6907 0.2929 285 L 0.0480 0.3881 0.5639 286 N 0.0385 0.1502 0.8113 287 D 0.0502 0.1112 0.8386 288 P 0.0809 0.0721 0.8470 289 P 0.1239 0.0785 0.7976 290 Y 0.4390 0.0857 0.4752 291 N 0.6246 0.0822 0.2933 292 Y 0.7507 0.0682 0.1811 293 M 0.7609 0.0746 0.1645 294 I 0.7118 0.0765 0.2116 295 H 0.4980 0.0918 0.4102 296 T 0.3376 0.0633 0.5991 297 S 0.2324 0.0347 0.7329 298 P 0.1718 0.0615 0.7667 299 L 0.0934 0.0999 0.8067 300 K 0.0754 0.0888 0.8357 301 V 0.0785 0.1400 0.7814 302 T 0.0975 0.2124 0.6901 303 E 0.0826 0.3014 0.6160 304 S 0.0531 0.2486 0.6982 305 Q 0.0583 0.1238 0.8179 306 L 0.1725 0.0498 0.7778 307 P 0.2980 0.0382 0.6638 308 Y 0.4513 0.0271 0.5215 309 T 0.5847 0.0156 0.3997 310 H 0.8071 0.0095 0.1834 311 W 0.8818 0.0057 0.1125 312 F 0.9090 0.0045 0.0865 313 L 0.9036 0.0058 0.0906 314 Q 0.8859 0.0067 0.1074 315 I 0.8284 0.0083 0.1632 316 V 0.6213 0.0112 0.3675 317 P 0.3266 0.0169 0.6564 318 Q 0.1741 0.0701 0.7558 319 L 0.1376 0.1249 0.7375 320 S 0.1135 0.1727 0.7138 321 G 0.1348 0.1675 0.6977 322 V 0.2244 0.1427 0.6328 323 G 0.3388 0.1373 0.5239 324 G 0.4380 0.1173 0.4447 325 F 0.6002 0.1225 0.2773 326 E 0.6279 0.1270 0.2451 327 I 0.4740 0.1465 0.3795 328 G 0.3291 0.1592 0.5117 329 T 0.2323 0.1596 0.6081 330 G 0.1957 0.1384 0.6659 331 C 0.3115 0.0970 0.5915 332 Y 0.3933 0.0845 0.5222 333 I 0.2780 0.1099 0.6120 334 N 0.1555 0.0688 0.7757 335 P 0.1021 0.0662 0.8317 336 V 0.1067 0.0418 0.8515 337 F 0.0688 0.0358 0.8954 338 P 0.0078 0.9164 0.0758 339 E 0.0049 0.9437 0.0514 340 D 0.0048 0.9533 0.0419 341 V 0.0048 0.9520 0.0432 342 A 0.0048 0.9493 0.0459 343 K 0.0056 0.9218 0.0726 344 V 0.0060 0.8879 0.1061 345 M 0.0175 0.8151 0.1675 346 R 0.0159 0.7121 0.2719 347 E 0.0385 0.5872 0.3743 348 V 0.1232 0.3025 0.5743 349 S 0.1910 0.1488 0.6602 350 L 0.1018 0.0795 0.8187 351 T 0.0510 0.0273 0.9217