# This file is the result of combining several RDB files, specifically # T0247.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0247.t2k.stride-ebghtl.rdb (weight 1.24869) # T0247.t2k.str2.rdb (weight 1.54758) # T0247.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 T0247.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0247 # 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 T0247.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 294 # # ============================================ # Comments from T0247.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0247 # 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 T0247.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 294 # # ============================================ # Comments from T0247.t2k.str2.rdb # ============================================ # TARGET T0247 # 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 T0247.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 294 # # ============================================ # Comments from T0247.t2k.alpha.rdb # ============================================ # TARGET T0247 # 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 T0247.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 294 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0728 0.0417 0.8855 2 A 0.1575 0.0817 0.7608 3 Q 0.2414 0.0857 0.6728 4 Q 0.2114 0.1323 0.6563 5 T 0.1333 0.0948 0.7719 6 P 0.0874 0.3482 0.5644 7 L 0.0296 0.5742 0.3962 8 Y 0.0156 0.7573 0.2271 9 E 0.0107 0.8958 0.0934 10 Q 0.0075 0.9305 0.0620 11 H 0.0098 0.9380 0.0522 12 T 0.0078 0.9337 0.0585 13 L 0.0081 0.9005 0.0914 14 C 0.0437 0.3270 0.6293 15 G 0.0451 0.0202 0.9348 16 A 0.1296 0.0122 0.8582 17 R 0.6724 0.0139 0.3137 18 M 0.8573 0.0073 0.1354 19 V 0.8274 0.0106 0.1619 20 D 0.7683 0.0231 0.2086 21 F 0.4797 0.0468 0.4734 22 H 0.1742 0.0589 0.7670 23 G 0.1146 0.0909 0.7945 24 W 0.1857 0.1249 0.6894 25 M 0.2370 0.1319 0.6311 26 M 0.2268 0.0952 0.6780 27 P 0.2178 0.1338 0.6484 28 L 0.2544 0.2221 0.5235 29 H 0.3098 0.1791 0.5112 30 Y 0.1665 0.1207 0.7128 31 G 0.0518 0.1549 0.7933 32 S 0.0445 0.2167 0.7387 33 Q 0.0219 0.7388 0.2393 34 I 0.0183 0.8407 0.1411 35 D 0.0259 0.8721 0.1021 36 E 0.0156 0.9165 0.0679 37 H 0.0110 0.9257 0.0633 38 H 0.0134 0.9220 0.0646 39 A 0.0242 0.8897 0.0861 40 V 0.0354 0.8474 0.1172 41 R 0.0495 0.7595 0.1910 42 T 0.0336 0.5330 0.4334 43 D 0.0516 0.3146 0.6338 44 A 0.1794 0.1351 0.6855 45 G 0.4696 0.0734 0.4570 46 M 0.7785 0.0454 0.1761 47 F 0.7955 0.0356 0.1689 48 D 0.7143 0.0214 0.2643 49 V 0.3134 0.1567 0.5299 50 S 0.1534 0.2233 0.6233 51 H 0.1129 0.2680 0.6192 52 M 0.1843 0.1109 0.7048 53 T 0.4035 0.0674 0.5291 54 I 0.7596 0.0178 0.2226 55 V 0.8465 0.0132 0.1403 56 D 0.8799 0.0068 0.1133 57 L 0.7895 0.0108 0.1998 58 R 0.5265 0.0254 0.4481 59 G 0.1413 0.0386 0.8201 60 S 0.0235 0.3668 0.6097 61 R 0.0435 0.4132 0.5433 62 T 0.0052 0.9232 0.0716 63 R 0.0049 0.9411 0.0540 64 E 0.0050 0.9437 0.0514 65 F 0.0052 0.9431 0.0517 66 L 0.0057 0.9289 0.0654 67 R 0.0057 0.8939 0.1004 68 Y 0.0066 0.8376 0.1558 69 L 0.0179 0.7196 0.2626 70 L 0.0528 0.4888 0.4584 71 A 0.0380 0.4308 0.5313 72 N 0.0497 0.3798 0.5705 73 D 0.0737 0.4015 0.5248 74 V 0.0190 0.7713 0.2097 75 A 0.0140 0.7624 0.2236 76 K 0.0214 0.6932 0.2855 77 L 0.0610 0.4005 0.5385 78 T 0.0571 0.1689 0.7740 79 K 0.0663 0.1295 0.8043 80 S 0.0719 0.1413 0.7868 81 G 0.1100 0.0837 0.8063 82 K 0.3788 0.0404 0.5808 83 A 0.7684 0.0114 0.2202 84 L 0.8629 0.0124 0.1247 85 Y 0.9019 0.0062 0.0919 86 S 0.8768 0.0088 0.1145 87 G 0.8798 0.0098 0.1105 88 M 0.8612 0.0084 0.1304 89 L 0.8079 0.0080 0.1841 90 N 0.2501 0.0155 0.7344 91 A 0.0175 0.1231 0.8594 92 S 0.0491 0.0284 0.9225 93 G 0.1177 0.0509 0.8315 94 G 0.4347 0.0218 0.5434 95 V 0.8040 0.0107 0.1854 96 I 0.7691 0.0205 0.2104 97 D 0.6773 0.0198 0.3029 98 D 0.7331 0.0179 0.2490 99 L 0.8980 0.0049 0.0971 100 I 0.9223 0.0039 0.0738 101 V 0.9298 0.0030 0.0672 102 Y 0.9074 0.0056 0.0870 103 Y 0.8950 0.0045 0.1005 104 F 0.7185 0.0248 0.2567 105 T 0.2766 0.0360 0.6874 106 E 0.0310 0.0859 0.8831 107 D 0.0445 0.0554 0.9002 108 F 0.6219 0.0158 0.3623 109 F 0.8915 0.0037 0.1047 110 R 0.9241 0.0038 0.0721 111 L 0.9218 0.0037 0.0745 112 V 0.8598 0.0071 0.1331 113 V 0.5806 0.0138 0.4056 114 N 0.1762 0.0241 0.7998 115 S 0.0262 0.3623 0.6114 116 A 0.0183 0.5022 0.4795 117 T 0.0209 0.5507 0.4284 118 R 0.0112 0.7495 0.2393 119 E 0.0062 0.9130 0.0807 120 K 0.0055 0.9343 0.0603 121 D 0.0051 0.9477 0.0472 122 L 0.0047 0.9565 0.0388 123 S 0.0047 0.9554 0.0399 124 W 0.0048 0.9507 0.0445 125 I 0.0048 0.9469 0.0483 126 T 0.0050 0.9358 0.0593 127 Q 0.0066 0.9021 0.0913 128 H 0.0129 0.8369 0.1502 129 A 0.0393 0.6444 0.3163 130 E 0.0259 0.4306 0.5436 131 P 0.0274 0.2460 0.7266 132 F 0.0618 0.1397 0.7984 133 G 0.1961 0.0598 0.7441 134 I 0.5888 0.0106 0.4007 135 E 0.7565 0.0062 0.2373 136 I 0.7766 0.0077 0.2157 137 T 0.5558 0.0158 0.4284 138 V 0.2145 0.0975 0.6881 139 R 0.1304 0.0884 0.7812 140 D 0.0497 0.3289 0.6214 141 D 0.0765 0.3993 0.5242 142 L 0.3210 0.3562 0.3229 143 S 0.4772 0.3382 0.1845 144 M 0.6152 0.2789 0.1059 145 I 0.5798 0.3277 0.0925 146 A 0.5155 0.3726 0.1119 147 V 0.4315 0.3709 0.1976 148 Q 0.2210 0.2656 0.5134 149 G 0.0677 0.1626 0.7697 150 P 0.0135 0.7210 0.2655 151 N 0.0126 0.7816 0.2058 152 A 0.0068 0.8916 0.1015 153 Q 0.0049 0.9431 0.0520 154 A 0.0053 0.9427 0.0520 155 K 0.0052 0.9409 0.0539 156 A 0.0057 0.9260 0.0682 157 A 0.0058 0.9037 0.0905 158 T 0.0073 0.8697 0.1229 159 L 0.0170 0.7426 0.2405 160 F 0.0553 0.3733 0.5714 161 N 0.0416 0.1980 0.7604 162 D 0.0435 0.1848 0.7718 163 A 0.0787 0.1608 0.7605 164 Q 0.0168 0.7382 0.2450 165 R 0.0112 0.6855 0.3033 166 Q 0.0208 0.5931 0.3861 167 A 0.0878 0.1675 0.7447 168 V 0.0909 0.1384 0.7706 169 E 0.2045 0.1970 0.5986 170 G 0.2954 0.1910 0.5136 171 M 0.4547 0.1141 0.4312 172 K 0.6086 0.0691 0.3222 173 P 0.6892 0.0536 0.2573 174 F 0.7601 0.0376 0.2023 175 F 0.7527 0.0294 0.2179 176 G 0.7089 0.0296 0.2615 177 V 0.5328 0.0528 0.4143 178 Q 0.1505 0.0649 0.7846 179 A 0.1164 0.0471 0.8365 180 G 0.3708 0.0180 0.6112 181 D 0.6512 0.0128 0.3359 182 L 0.8790 0.0062 0.1149 183 F 0.9167 0.0042 0.0790 184 I 0.9111 0.0051 0.0838 185 A 0.8683 0.0079 0.1238 186 T 0.7599 0.0102 0.2299 187 T 0.4033 0.0240 0.5727 188 G 0.2019 0.0505 0.7476 189 Y 0.2024 0.0903 0.7073 190 T 0.2184 0.0995 0.6821 191 G 0.1668 0.0713 0.7619 192 E 0.1472 0.0999 0.7529 193 A 0.1872 0.0799 0.7329 194 G 0.3888 0.0501 0.5611 195 Y 0.7447 0.0152 0.2401 196 E 0.8786 0.0096 0.1119 197 I 0.8864 0.0079 0.1057 198 A 0.8409 0.0095 0.1496 199 L 0.6104 0.0104 0.3792 200 P 0.2679 0.0158 0.7163 201 N 0.0103 0.7094 0.2803 202 E 0.0072 0.7521 0.2407 203 K 0.0073 0.8063 0.1864 204 A 0.0056 0.8920 0.1024 205 A 0.0052 0.9376 0.0571 206 D 0.0048 0.9487 0.0465 207 F 0.0048 0.9538 0.0414 208 W 0.0047 0.9561 0.0392 209 R 0.0048 0.9555 0.0397 210 A 0.0048 0.9547 0.0405 211 L 0.0049 0.9491 0.0460 212 V 0.0052 0.9221 0.0727 213 E 0.0060 0.8437 0.1503 214 A 0.0415 0.3816 0.5769 215 G 0.0366 0.0542 0.9091 216 V 0.0925 0.0272 0.8803 217 K 0.2600 0.0436 0.6964 218 P 0.3526 0.0842 0.5632 219 C 0.2179 0.1005 0.6816 220 G 0.1106 0.1403 0.7490 221 L 0.0161 0.7817 0.2022 222 G 0.0111 0.8212 0.1677 223 A 0.0073 0.9171 0.0756 224 R 0.0067 0.9287 0.0646 225 D 0.0080 0.9258 0.0661 226 T 0.0078 0.9273 0.0649 227 L 0.0198 0.8877 0.0924 228 R 0.0340 0.8684 0.0976 229 L 0.0266 0.8654 0.1080 230 E 0.0207 0.8576 0.1217 231 A 0.0408 0.6162 0.3430 232 G 0.0386 0.2637 0.6976 233 M 0.1150 0.2129 0.6721 234 N 0.2274 0.2173 0.5553 235 L 0.1484 0.2780 0.5736 236 Y 0.1460 0.2221 0.6319 237 G 0.1210 0.1704 0.7086 238 Q 0.1712 0.1836 0.6453 239 E 0.2014 0.1550 0.6436 240 M 0.1459 0.1186 0.7355 241 D 0.0921 0.0692 0.8387 242 E 0.0381 0.1492 0.8127 243 T 0.0729 0.1166 0.8105 244 I 0.2187 0.0930 0.6883 245 S 0.1793 0.0832 0.7375 246 P 0.1001 0.5749 0.3250 247 L 0.0845 0.6758 0.2397 248 A 0.1231 0.6727 0.2042 249 A 0.1203 0.5820 0.2978 250 N 0.1117 0.3650 0.5233 251 M 0.1294 0.4061 0.4645 252 G 0.1498 0.4394 0.4108 253 W 0.2505 0.4266 0.3229 254 T 0.3805 0.3327 0.2868 255 I 0.4140 0.2502 0.3359 256 A 0.3965 0.1923 0.4111 257 W 0.2621 0.2563 0.4817 258 E 0.2284 0.1819 0.5898 259 P 0.1240 0.1876 0.6885 260 A 0.0732 0.1072 0.8196 261 D 0.0436 0.1585 0.7979 262 R 0.0485 0.1303 0.8212 263 D 0.0725 0.1314 0.7960 264 F 0.1299 0.1941 0.6760 265 I 0.0819 0.3991 0.5190 266 G 0.0529 0.5955 0.3515 267 R 0.0086 0.9339 0.0575 268 E 0.0089 0.9465 0.0446 269 A 0.0078 0.9509 0.0413 270 L 0.0086 0.9481 0.0433 271 E 0.0077 0.9489 0.0434 272 V 0.0064 0.9455 0.0480 273 Q 0.0067 0.9258 0.0675 274 R 0.0096 0.8839 0.1065 275 E 0.0145 0.7593 0.2261 276 H 0.0440 0.2906 0.6655 277 G 0.0405 0.0408 0.9187 278 T 0.0931 0.0257 0.8812 279 E 0.3539 0.0146 0.6316 280 K 0.6952 0.0080 0.2968 281 L 0.8478 0.0064 0.1458 282 V 0.8641 0.0102 0.1257 283 G 0.8705 0.0066 0.1229 284 L 0.8599 0.0053 0.1348 285 V 0.8296 0.0060 0.1644 286 M 0.6879 0.0139 0.2982 287 T 0.3048 0.0479 0.6473 288 E 0.1024 0.0606 0.8370 289 K 0.0740 0.0689 0.8571 290 G 0.1195 0.0406 0.8399 291 V 0.1811 0.0379 0.7810 292 L 0.1904 0.0724 0.7372 293 R 0.1454 0.0990 0.7557 294 N 0.0884 0.1324 0.7792 295 E 0.1008 0.0837 0.8156 296 L 0.2529 0.0517 0.6955 297 P 0.5443 0.0412 0.4145 298 V 0.5583 0.0519 0.3898 299 R 0.5073 0.0498 0.4429 300 F 0.3481 0.0694 0.5825 301 T 0.2104 0.1007 0.6889 302 D 0.2271 0.1327 0.6402 303 A 0.1462 0.1573 0.6965 304 Q 0.0683 0.1863 0.7454 305 G 0.0513 0.1198 0.8289 306 N 0.0775 0.0621 0.8604 307 Q 0.3099 0.0152 0.6749 308 H 0.6557 0.0068 0.3375 309 E 0.7884 0.0154 0.1962 310 G 0.8236 0.0100 0.1664 311 I 0.8925 0.0056 0.1019 312 I 0.8761 0.0096 0.1144 313 T 0.8009 0.0144 0.1847 314 S 0.5559 0.0311 0.4130 315 G 0.3363 0.0572 0.6066 316 T 0.3232 0.0740 0.6028 317 F 0.3086 0.0760 0.6153 318 S 0.2192 0.0708 0.7100 319 P 0.0936 0.1743 0.7321 320 T 0.0811 0.1444 0.7745 321 L 0.0646 0.1108 0.8247 322 G 0.0666 0.0618 0.8716 323 Y 0.2242 0.0307 0.7451 324 S 0.5872 0.0192 0.3935 325 I 0.7735 0.0199 0.2066 326 A 0.8732 0.0097 0.1172 327 L 0.8941 0.0087 0.0972 328 A 0.8932 0.0073 0.0995 329 R 0.8975 0.0059 0.0966 330 V 0.8502 0.0075 0.1423 331 P 0.7412 0.0165 0.2423 332 E 0.2328 0.1412 0.6260 333 G 0.0808 0.1641 0.7552 334 I 0.1036 0.1168 0.7796 335 G 0.0753 0.0440 0.8807 336 E 0.2445 0.0159 0.7395 337 T 0.7923 0.0051 0.2026 338 A 0.9044 0.0042 0.0914 339 I 0.9251 0.0035 0.0714 340 V 0.9171 0.0038 0.0791 341 Q 0.9137 0.0037 0.0825 342 I 0.8313 0.0108 0.1579 343 R 0.1710 0.0374 0.7916 344 N 0.0920 0.0382 0.8698 345 R 0.6068 0.0151 0.3781 346 E 0.8056 0.0072 0.1872 347 M 0.8280 0.0070 0.1650 348 P 0.8217 0.0061 0.1722 349 V 0.8426 0.0054 0.1520 350 K 0.8928 0.0045 0.1027 351 V 0.8948 0.0034 0.1018 352 T 0.7488 0.0123 0.2388 353 K 0.5148 0.0086 0.4766 354 P 0.1832 0.0129 0.8039 355 V 0.1460 0.0193 0.8348 356 F 0.1954 0.0335 0.7711 357 V 0.3191 0.0179 0.6629 358 R 0.1288 0.0259 0.8453 359 N 0.0418 0.2062 0.7519 360 G 0.0308 0.1634 0.8058 361 K 0.0578 0.1054 0.8368 362 A 0.1965 0.0326 0.7709 363 V 0.3273 0.0225 0.6503 364 A 0.0664 0.0180 0.9156