# This file is the result of combining several RDB files, specifically # T0438.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0438.t2k.stride-ebghtl.rdb (weight 1.24869) # T0438.t2k.str2.rdb (weight 1.54758) # T0438.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 T0438.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0438 # 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 T0438.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 576 # # ============================================ # Comments from T0438.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0438 # 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 T0438.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 576 # # ============================================ # Comments from T0438.t2k.str2.rdb # ============================================ # TARGET T0438 # 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 T0438.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 576 # # ============================================ # Comments from T0438.t2k.alpha.rdb # ============================================ # TARGET T0438 # 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 T0438.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 576 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0509 0.2293 0.7198 2 Q 0.0858 0.4861 0.4281 3 W 0.0919 0.5060 0.4021 4 Q 0.0674 0.4546 0.4781 5 E 0.0377 0.5558 0.4064 6 L 0.0143 0.7753 0.2104 7 Y 0.0112 0.8236 0.1652 8 R 0.0131 0.8306 0.1563 9 Q 0.0146 0.7816 0.2039 10 R 0.0191 0.6377 0.3432 11 V 0.0350 0.5096 0.4554 12 C 0.1261 0.2517 0.6223 13 S 0.1524 0.1358 0.7118 14 A 0.0966 0.0681 0.8353 15 D 0.0049 0.9396 0.0555 16 E 0.0047 0.9474 0.0479 17 A 0.0048 0.9520 0.0432 18 V 0.0050 0.9495 0.0455 19 V 0.0069 0.9148 0.0783 20 D 0.0115 0.7775 0.2110 21 S 0.0340 0.6484 0.3176 22 L 0.1875 0.1726 0.6399 23 K 0.0914 0.0664 0.8423 24 P 0.0321 0.0923 0.8756 25 G 0.0371 0.0523 0.9106 26 T 0.3751 0.0204 0.6045 27 K 0.8424 0.0049 0.1527 28 V 0.8870 0.0062 0.1068 29 V 0.8711 0.0089 0.1200 30 F 0.7547 0.0222 0.2231 31 G 0.4564 0.0613 0.4823 32 H 0.2100 0.1262 0.6639 33 A 0.1350 0.1654 0.6996 34 A 0.0890 0.1654 0.7456 35 A 0.0619 0.1418 0.7963 36 A 0.0861 0.1535 0.7604 37 P 0.0747 0.4334 0.4919 38 V 0.0398 0.7200 0.2402 39 R 0.0440 0.7662 0.1899 40 F 0.0250 0.8269 0.1482 41 S 0.0076 0.9066 0.0858 42 Q 0.0061 0.9361 0.0578 43 A 0.0049 0.9502 0.0449 44 M 0.0048 0.9532 0.0420 45 Y 0.0050 0.9481 0.0468 46 R 0.0053 0.9303 0.0645 47 Q 0.0061 0.9121 0.0818 48 R 0.0067 0.8922 0.1010 49 E 0.0073 0.8375 0.1552 50 K 0.0099 0.7266 0.2634 51 L 0.0498 0.4649 0.4853 52 E 0.0333 0.2989 0.6678 53 N 0.0545 0.2972 0.6482 54 I 0.1367 0.2567 0.6066 55 T 0.2649 0.2064 0.5288 56 V 0.4812 0.1520 0.3668 57 F 0.6232 0.1392 0.2375 58 H 0.6209 0.1508 0.2283 59 M 0.5473 0.1840 0.2687 60 L 0.4027 0.2002 0.3971 61 Y 0.2820 0.1752 0.5428 62 F 0.1518 0.1248 0.7234 63 G 0.0963 0.1215 0.7822 64 D 0.0658 0.3958 0.5384 65 A 0.0583 0.5200 0.4217 66 P 0.0471 0.5882 0.3647 67 H 0.0674 0.5489 0.3837 68 L 0.0768 0.4900 0.4332 69 A 0.0816 0.3967 0.5218 70 P 0.0430 0.5053 0.4517 71 E 0.0492 0.4780 0.4728 72 M 0.0898 0.3755 0.5348 73 R 0.0838 0.2541 0.6622 74 S 0.1616 0.2149 0.6235 75 H 0.4153 0.1323 0.4524 76 V 0.6164 0.0695 0.3141 77 H 0.6805 0.0491 0.2704 78 P 0.6374 0.0646 0.2980 79 T 0.4323 0.0657 0.5020 80 L 0.2854 0.1691 0.5455 81 N 0.1926 0.1933 0.6141 82 F 0.2016 0.1561 0.6424 83 L 0.1317 0.1106 0.7577 84 E 0.0692 0.1303 0.8005 85 G 0.0209 0.7511 0.2280 86 N 0.0161 0.8450 0.1389 87 S 0.0111 0.8971 0.0918 88 R 0.0120 0.9085 0.0795 89 P 0.0140 0.8955 0.0905 90 A 0.0167 0.8655 0.1178 91 S 0.0267 0.8185 0.1548 92 R 0.0282 0.7326 0.2392 93 D 0.0428 0.4509 0.5063 94 R 0.0426 0.2241 0.7333 95 R 0.1181 0.2184 0.6635 96 V 0.2093 0.1689 0.6218 97 D 0.1955 0.1568 0.6477 98 F 0.2826 0.1326 0.5848 99 I 0.2766 0.1058 0.6175 100 P 0.3074 0.1370 0.5556 101 C 0.2692 0.2562 0.4747 102 H 0.2646 0.2717 0.4637 103 F 0.1427 0.4274 0.4298 104 H 0.0899 0.4445 0.4657 105 E 0.0606 0.4485 0.4909 106 V 0.0431 0.5099 0.4470 107 P 0.0105 0.8530 0.1366 108 E 0.0108 0.9010 0.0883 109 L 0.0091 0.9163 0.0745 110 F 0.0123 0.9102 0.0775 111 R 0.0115 0.8863 0.1022 112 Q 0.0410 0.5915 0.3675 113 G 0.0345 0.1755 0.7900 114 F 0.0511 0.0660 0.8829 115 F 0.1046 0.0377 0.8577 116 P 0.1006 0.0283 0.8711 117 L 0.1723 0.0123 0.8154 118 D 0.3021 0.0239 0.6740 119 V 0.9167 0.0034 0.0799 120 A 0.9300 0.0033 0.0666 121 V 0.9292 0.0032 0.0676 122 V 0.8957 0.0040 0.1004 123 Q 0.6925 0.0048 0.3028 124 V 0.3773 0.0100 0.6127 125 S 0.2072 0.0153 0.7775 126 T 0.1701 0.0216 0.8083 127 P 0.2530 0.0398 0.7072 128 N 0.1226 0.0432 0.8342 129 E 0.0334 0.1353 0.8313 130 E 0.0727 0.0427 0.8846 131 G 0.1243 0.0359 0.8398 132 Y 0.3321 0.0223 0.6456 133 C 0.7061 0.0123 0.2817 134 S 0.6200 0.0208 0.3591 135 F 0.4822 0.0659 0.4519 136 G 0.2990 0.0906 0.6104 137 V 0.2236 0.1376 0.6388 138 S 0.1824 0.1193 0.6983 139 C 0.0875 0.2377 0.6748 140 D 0.0695 0.1908 0.7397 141 Y 0.0887 0.2463 0.6649 142 T 0.0623 0.3093 0.6284 143 K 0.0060 0.9275 0.0665 144 A 0.0053 0.9387 0.0560 145 A 0.0051 0.9373 0.0576 146 A 0.0053 0.9287 0.0661 147 E 0.0071 0.8405 0.1523 148 C 0.0151 0.4951 0.4899 149 A 0.0881 0.0880 0.8239 150 P 0.0752 0.0897 0.8351 151 V 0.7120 0.0297 0.2583 152 V 0.9133 0.0077 0.0790 153 V 0.9234 0.0086 0.0680 154 A 0.9171 0.0064 0.0765 155 E 0.8526 0.0074 0.1400 156 V 0.5387 0.0174 0.4439 157 N 0.1761 0.0192 0.8047 158 K 0.0227 0.1235 0.8537 159 Q 0.0357 0.0968 0.8675 160 M 0.1121 0.0482 0.8397 161 P 0.1347 0.0648 0.8005 162 F 0.1781 0.1273 0.6946 163 I 0.1463 0.1617 0.6921 164 G 0.0850 0.1436 0.7714 165 G 0.0696 0.1194 0.8110 166 E 0.0721 0.1487 0.7792 167 N 0.0882 0.1380 0.7738 168 L 0.1454 0.1095 0.7451 169 I 0.2274 0.0320 0.7406 170 H 0.1394 0.0199 0.8407 171 I 0.0179 0.7056 0.2766 172 S 0.0185 0.6724 0.3091 173 K 0.0777 0.5820 0.3403 174 L 0.5237 0.0270 0.4493 175 T 0.7213 0.0410 0.2377 176 H 0.9034 0.0065 0.0902 177 I 0.9215 0.0050 0.0735 178 I 0.9050 0.0065 0.0885 179 E 0.7826 0.0112 0.2062 180 V 0.3191 0.0233 0.6576 181 D 0.0960 0.0487 0.8554 182 E 0.0894 0.0407 0.8700 183 P 0.0926 0.0894 0.8180 184 I 0.0808 0.1367 0.7825 185 A 0.0673 0.2049 0.7278 186 E 0.0724 0.1745 0.7531 187 V 0.0881 0.0873 0.8246 188 L 0.0905 0.0847 0.8247 189 P 0.1146 0.0771 0.8082 190 P 0.0850 0.0451 0.8700 191 A 0.0761 0.0231 0.9009 192 G 0.0689 0.0462 0.8849 193 S 0.0560 0.0529 0.8911 194 D 0.0090 0.9089 0.0821 195 L 0.0053 0.9405 0.0543 196 E 0.0049 0.9512 0.0439 197 L 0.0049 0.9576 0.0375 198 R 0.0050 0.9559 0.0391 199 I 0.0048 0.9539 0.0412 200 G 0.0048 0.9568 0.0385 201 Q 0.0048 0.9557 0.0395 202 N 0.0048 0.9471 0.0481 203 C 0.0048 0.9407 0.0545 204 A 0.0049 0.9265 0.0686 205 S 0.0059 0.8530 0.1411 206 L 0.0116 0.7533 0.2351 207 I 0.0869 0.3524 0.5607 208 K 0.0450 0.1928 0.7622 209 D 0.0482 0.0734 0.8784 210 G 0.0597 0.0743 0.8661 211 D 0.2937 0.0571 0.6491 212 T 0.5836 0.0687 0.3477 213 L 0.7089 0.0620 0.2290 214 Q 0.7302 0.0590 0.2108 215 L 0.5511 0.0949 0.3540 216 G 0.4165 0.0840 0.4995 217 I 0.2405 0.1712 0.5883 218 G 0.1042 0.2372 0.6587 219 G 0.0757 0.3349 0.5894 220 I 0.0316 0.6501 0.3183 221 P 0.0094 0.8396 0.1510 222 D 0.0056 0.9081 0.0863 223 A 0.0064 0.9282 0.0653 224 V 0.0067 0.9204 0.0729 225 L 0.0089 0.8797 0.1114 226 R 0.0120 0.7874 0.2005 227 A 0.0235 0.6380 0.3385 228 L 0.0693 0.2198 0.7110 229 E 0.0381 0.1709 0.7910 230 G 0.0304 0.2031 0.7666 231 H 0.0655 0.1779 0.7566 232 K 0.2336 0.0770 0.6894 233 D 0.5294 0.0356 0.4350 234 L 0.7991 0.0172 0.1837 235 G 0.8612 0.0182 0.1206 236 I 0.8619 0.0212 0.1169 237 H 0.7917 0.0369 0.1714 238 T 0.5581 0.1057 0.3362 239 E 0.3502 0.2205 0.4294 240 M 0.2444 0.3148 0.4408 241 F 0.2265 0.3933 0.3802 242 T 0.1832 0.5171 0.2997 243 D 0.1217 0.5861 0.2923 244 G 0.1056 0.6555 0.2390 245 V 0.1146 0.7201 0.1653 246 M 0.0954 0.7368 0.1678 247 R 0.0757 0.7312 0.1931 248 M 0.0631 0.7398 0.1971 249 I 0.0551 0.7219 0.2231 250 R 0.0437 0.6946 0.2617 251 K 0.0460 0.3509 0.6031 252 G 0.0439 0.0899 0.8663 253 I 0.1891 0.0994 0.7114 254 I 0.4364 0.0635 0.5001 255 N 0.2062 0.0804 0.7134 256 G 0.0561 0.4671 0.4768 257 K 0.0689 0.4825 0.4487 258 K 0.1485 0.4944 0.3570 259 K 0.2274 0.3813 0.3914 260 T 0.2601 0.2923 0.4476 261 L 0.1745 0.2608 0.5647 262 H 0.1419 0.1552 0.7029 263 P 0.1116 0.1331 0.7553 264 E 0.2074 0.0943 0.6983 265 K 0.4994 0.0564 0.4442 266 V 0.7792 0.0254 0.1954 267 V 0.8336 0.0296 0.1368 268 T 0.8072 0.0361 0.1567 269 S 0.6477 0.0491 0.3032 270 L 0.3677 0.1014 0.5309 271 I 0.1134 0.2610 0.6256 272 F 0.0564 0.2752 0.6684 273 G 0.0540 0.2426 0.7034 274 S 0.0450 0.3369 0.6181 275 K 0.0063 0.9140 0.0796 276 E 0.0067 0.9282 0.0651 277 L 0.0058 0.9377 0.0565 278 Y 0.0057 0.9416 0.0527 279 D 0.0067 0.9290 0.0643 280 F 0.0075 0.8986 0.0939 281 V 0.0185 0.8526 0.1289 282 N 0.0159 0.6606 0.3236 283 N 0.0203 0.4059 0.5738 284 N 0.0687 0.1005 0.8309 285 P 0.0311 0.2992 0.6697 286 V 0.0453 0.3765 0.5781 287 I 0.0856 0.4483 0.4661 288 E 0.1746 0.3751 0.4503 289 C 0.1911 0.2676 0.5413 290 Y 0.1607 0.1147 0.7246 291 P 0.1258 0.1145 0.7598 292 V 0.1008 0.2856 0.6136 293 D 0.0992 0.3292 0.5716 294 Y 0.1367 0.3065 0.5567 295 I 0.1461 0.1821 0.6718 296 N 0.0894 0.1261 0.7844 297 N 0.0873 0.0886 0.8241 298 P 0.0243 0.8280 0.1477 299 D 0.0156 0.8870 0.0974 300 V 0.0215 0.8992 0.0793 301 I 0.0256 0.8948 0.0796 302 G 0.0320 0.7944 0.1737 303 K 0.0317 0.5197 0.4486 304 N 0.0528 0.1827 0.7644 305 D 0.0884 0.1538 0.7578 306 R 0.1623 0.1909 0.6468 307 M 0.4219 0.1642 0.4138 308 V 0.7718 0.0657 0.1625 309 S 0.8414 0.0384 0.1202 310 I 0.8093 0.0528 0.1379 311 N 0.6106 0.0995 0.2900 312 S 0.5737 0.0946 0.3317 313 C 0.6101 0.1183 0.2716 314 L 0.7358 0.0876 0.1766 315 E 0.7598 0.0844 0.1558 316 M 0.7174 0.0926 0.1900 317 D 0.5029 0.1721 0.3250 318 L 0.1735 0.4145 0.4121 319 M 0.1186 0.2856 0.5957 320 G 0.1796 0.2090 0.6115 321 Q 0.3252 0.2126 0.4622 322 A 0.5022 0.1844 0.3134 323 A 0.4152 0.2063 0.3785 324 S 0.3378 0.2349 0.4273 325 E 0.2833 0.2108 0.5059 326 S 0.2267 0.1456 0.6278 327 I 0.1953 0.0918 0.7128 328 G 0.1017 0.0721 0.8261 329 Y 0.1477 0.0780 0.7743 330 E 0.4534 0.0564 0.4902 331 Q 0.6545 0.0465 0.2989 332 F 0.5550 0.0404 0.4046 333 S 0.3059 0.0507 0.6434 334 G 0.1513 0.0457 0.8030 335 S 0.1459 0.1837 0.6705 336 G 0.0973 0.2462 0.6565 337 G 0.0863 0.3616 0.5521 338 Q 0.0738 0.6835 0.2426 339 V 0.0593 0.8041 0.1365 340 D 0.0532 0.8164 0.1304 341 F 0.0452 0.7876 0.1673 342 L 0.0852 0.7289 0.1859 343 R 0.0653 0.4927 0.4420 344 G 0.0928 0.2749 0.6323 345 A 0.1784 0.2180 0.6037 346 K 0.2640 0.2725 0.4635 347 R 0.3236 0.1687 0.5077 348 S 0.1252 0.0599 0.8150 349 K 0.0208 0.1197 0.8595 350 G 0.0357 0.0403 0.9241 351 G 0.1512 0.0350 0.8138 352 I 0.4965 0.0134 0.4902 353 S 0.8628 0.0040 0.1333 354 I 0.9065 0.0047 0.0889 355 M 0.9049 0.0035 0.0916 356 A 0.8534 0.0051 0.1415 357 F 0.6934 0.0125 0.2941 358 P 0.5267 0.0435 0.4297 359 S 0.4336 0.0769 0.4896 360 T 0.3956 0.0932 0.5112 361 A 0.1928 0.0878 0.7194 362 K 0.0600 0.1237 0.8163 363 K 0.0447 0.0495 0.9058 364 G 0.0617 0.0355 0.9027 365 T 0.1597 0.0433 0.7970 366 E 0.2581 0.0922 0.6497 367 S 0.2311 0.1247 0.6441 368 R 0.3439 0.1144 0.5418 369 I 0.3234 0.0772 0.5994 370 V 0.2277 0.0763 0.6959 371 P 0.2808 0.1505 0.5687 372 I 0.4166 0.1557 0.4277 373 L 0.3695 0.0979 0.5326 374 K 0.2303 0.1339 0.6359 375 E 0.1710 0.1221 0.7070 376 G 0.2406 0.0714 0.6879 377 A 0.2221 0.0535 0.7244 378 C 0.2564 0.0341 0.7095 379 V 0.2957 0.0453 0.6590 380 T 0.2739 0.0547 0.6714 381 T 0.2013 0.0361 0.7626 382 G 0.1313 0.1050 0.7638 383 R 0.0753 0.2893 0.6354 384 N 0.1463 0.2380 0.6158 385 E 0.3693 0.1392 0.4915 386 V 0.5234 0.0573 0.4193 387 D 0.6030 0.0768 0.3203 388 Y 0.8618 0.0308 0.1073 389 V 0.8959 0.0206 0.0835 390 V 0.8653 0.0243 0.1104 391 T 0.7105 0.0260 0.2635 392 E 0.3976 0.0882 0.5142 393 Y 0.2668 0.1834 0.5498 394 G 0.3523 0.1981 0.4496 395 V 0.5360 0.1635 0.3005 396 A 0.5787 0.1623 0.2590 397 R 0.5858 0.1212 0.2930 398 L 0.3264 0.1435 0.5300 399 R 0.1127 0.0799 0.8074 400 G 0.0548 0.0481 0.8971 401 A 0.0789 0.0358 0.8853 402 T 0.0703 0.0286 0.9011 403 L 0.0064 0.9121 0.0815 404 R 0.0053 0.9406 0.0542 405 Q 0.0053 0.9524 0.0423 406 R 0.0048 0.9569 0.0383 407 A 0.0047 0.9567 0.0386 408 E 0.0050 0.9516 0.0434 409 A 0.0048 0.9482 0.0471 410 L 0.0048 0.9476 0.0476 411 T 0.0050 0.9321 0.0629 412 A 0.0060 0.8745 0.1195 413 I 0.0123 0.6863 0.3014 414 A 0.0560 0.2451 0.6989 415 H 0.0543 0.0973 0.8484 416 P 0.0132 0.7428 0.2439 417 D 0.0079 0.7587 0.2334 418 F 0.0161 0.7847 0.1991 419 R 0.0069 0.9314 0.0617 420 P 0.0052 0.9510 0.0438 421 A 0.0050 0.9532 0.0418 422 L 0.0048 0.9547 0.0404 423 E 0.0050 0.9569 0.0381 424 E 0.0053 0.9534 0.0413 425 E 0.0056 0.9486 0.0458 426 I 0.0056 0.9314 0.0630 427 R 0.0063 0.9044 0.0893 428 R 0.0070 0.8495 0.1434 429 R 0.0236 0.5804 0.3960 430 F 0.0373 0.2956 0.6672 431 E 0.0847 0.2144 0.7008 432 L 0.1494 0.1340 0.7166 433 E 0.0734 0.1468 0.7799 434 H 0.0257 0.2127 0.7616 435 H 0.0574 0.1591 0.7835 436 H 0.1967 0.0859 0.7173 437 H 0.2753 0.0462 0.6785 438 H 0.1604 0.0329 0.8067 439 H 0.0610 0.0183 0.9207