# This file is the result of combining several RDB files, specifically # T0261.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0261.t2k.stride-ebghtl.rdb (weight 1.24869) # T0261.t2k.str2.rdb (weight 1.54758) # T0261.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 T0261.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0261 # 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 T0261.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 136 # # ============================================ # Comments from T0261.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0261 # 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 T0261.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 136 # # ============================================ # Comments from T0261.t2k.str2.rdb # ============================================ # TARGET T0261 # 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 T0261.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 136 # # ============================================ # Comments from T0261.t2k.alpha.rdb # ============================================ # TARGET T0261 # 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 T0261.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 136 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0797 0.0493 0.8710 2 E 0.2580 0.0756 0.6664 3 G 0.3371 0.0909 0.5721 4 L 0.1501 0.3563 0.4936 5 E 0.0848 0.4020 0.5132 6 A 0.1214 0.3940 0.4846 7 Y 0.2241 0.1526 0.6233 8 D 0.2038 0.0643 0.7320 9 Y 0.3161 0.0922 0.5917 10 H 0.3035 0.0812 0.6153 11 L 0.2397 0.0296 0.7307 12 P 0.1223 0.0801 0.7976 13 P 0.0075 0.7822 0.2103 14 E 0.0075 0.8206 0.1719 15 Q 0.0141 0.8263 0.1596 16 I 0.0387 0.6762 0.2851 17 A 0.0584 0.4335 0.5081 18 Q 0.1075 0.2463 0.6461 19 E 0.1532 0.0369 0.8100 20 G 0.1491 0.0268 0.8241 21 V 0.1165 0.0651 0.8184 22 E 0.0737 0.0429 0.8834 23 P 0.0937 0.0770 0.8293 24 R 0.1117 0.1327 0.7557 25 D 0.1317 0.2013 0.6670 26 M 0.2496 0.2083 0.5421 27 A 0.4049 0.1407 0.4544 28 R 0.5554 0.0977 0.3468 29 L 0.7591 0.0481 0.1928 30 M 0.8440 0.0213 0.1347 31 V 0.8797 0.0100 0.1103 32 V 0.8113 0.0107 0.1780 33 Y 0.4707 0.0163 0.5130 34 R 0.0664 0.1369 0.7967 35 E 0.0282 0.1178 0.8539 36 G 0.0688 0.0708 0.8604 37 P 0.0625 0.0660 0.8715 38 F 0.1930 0.0820 0.7250 39 R 0.2730 0.0863 0.6407 40 V 0.2768 0.1377 0.5854 41 A 0.2410 0.1924 0.5666 42 H 0.1980 0.2421 0.5600 43 K 0.1882 0.2985 0.5133 44 R 0.2389 0.3323 0.4288 45 V 0.0923 0.6419 0.2659 46 R 0.0453 0.7003 0.2544 47 D 0.0501 0.6432 0.3067 48 L 0.0383 0.7297 0.2320 49 P 0.0269 0.7810 0.1921 50 E 0.0235 0.7297 0.2468 51 F 0.0403 0.4967 0.4630 52 L 0.1286 0.0545 0.8169 53 R 0.0566 0.0207 0.9228 54 P 0.0204 0.1100 0.8696 55 G 0.0253 0.0722 0.9026 56 D 0.2403 0.0564 0.7034 57 V 0.8025 0.0049 0.1926 58 L 0.9062 0.0040 0.0897 59 V 0.9187 0.0048 0.0765 60 F 0.8512 0.0195 0.1293 61 N 0.6343 0.0201 0.3456 62 E 0.2344 0.0621 0.7035 63 S 0.1522 0.0948 0.7530 64 K 0.3383 0.1073 0.5543 65 V 0.4988 0.1382 0.3631 66 I 0.5404 0.1071 0.3525 67 P 0.4930 0.1772 0.3298 68 A 0.5017 0.2520 0.2463 69 R 0.6052 0.2113 0.1835 70 L 0.6512 0.1863 0.1625 71 L 0.5730 0.1702 0.2568 72 A 0.5505 0.1000 0.3495 73 R 0.5377 0.0665 0.3958 74 K 0.4299 0.0747 0.4954 75 P 0.1914 0.1128 0.6958 76 T 0.1070 0.0774 0.8157 77 G 0.1033 0.0342 0.8625 78 G 0.3001 0.0134 0.6865 79 K 0.7866 0.0053 0.2082 80 V 0.9037 0.0043 0.0920 81 E 0.9181 0.0044 0.0775 82 I 0.9238 0.0036 0.0727 83 L 0.9152 0.0068 0.0779 84 L 0.9067 0.0077 0.0855 85 V 0.8555 0.0234 0.1211 86 R 0.8156 0.0168 0.1677 87 E 0.7440 0.0347 0.2213 88 R 0.3839 0.0426 0.5735 89 S 0.1435 0.0437 0.8128 90 P 0.0314 0.1247 0.8439 91 G 0.0781 0.1013 0.8206 92 L 0.5459 0.0714 0.3826 93 W 0.7822 0.0551 0.1626 94 E 0.8274 0.0718 0.1008 95 A 0.8289 0.0736 0.0975 96 L 0.8028 0.0633 0.1339 97 L 0.7603 0.0369 0.2028 98 G 0.5020 0.0343 0.4637 99 P 0.2504 0.1613 0.5883 100 A 0.1497 0.2868 0.5634 101 R 0.1426 0.2343 0.6231 102 K 0.2206 0.0864 0.6929 103 A 0.2618 0.0230 0.7152 104 P 0.1012 0.0182 0.8806 105 P 0.0422 0.0678 0.8900 106 G 0.0461 0.0429 0.9110 107 T 0.3369 0.0163 0.6467 108 R 0.8126 0.0054 0.1819 109 L 0.8912 0.0051 0.1037 110 L 0.8908 0.0047 0.1045 111 L 0.7264 0.0112 0.2623 112 L 0.2532 0.0408 0.7060 113 S 0.0474 0.0686 0.8840 114 P 0.0554 0.0777 0.8669 115 K 0.1872 0.1558 0.6570 116 D 0.3929 0.1988 0.4083 117 L 0.4490 0.2786 0.2724 118 A 0.4403 0.3409 0.2188 119 P 0.4055 0.4335 0.1610 120 V 0.3837 0.4746 0.1416 121 P 0.4216 0.4382 0.1402 122 G 0.4583 0.4064 0.1353 123 L 0.5121 0.3544 0.1335 124 Q 0.4188 0.4337 0.1475 125 A 0.3924 0.4411 0.1665 126 E 0.3881 0.4181 0.1938 127 V 0.3978 0.3761 0.2261 128 V 0.3256 0.3332 0.3412 129 A 0.2306 0.2294 0.5399 130 V 0.1200 0.1593 0.7206 131 E 0.1050 0.0949 0.8001 132 E 0.3041 0.0610 0.6348 133 D 0.6361 0.0336 0.3303 134 G 0.8174 0.0234 0.1592 135 V 0.8662 0.0179 0.1158 136 R 0.8327 0.0298 0.1376 137 L 0.7721 0.0349 0.1930 138 L 0.4699 0.0639 0.4662 139 R 0.1459 0.0934 0.7606 140 F 0.0674 0.0901 0.8425 141 Q 0.0509 0.1462 0.8029 142 G 0.0582 0.3331 0.6087 143 D 0.0668 0.5570 0.3762 144 L 0.0078 0.9149 0.0773 145 V 0.0049 0.9515 0.0436 146 A 0.0049 0.9560 0.0391 147 H 0.0047 0.9570 0.0382 148 L 0.0048 0.9529 0.0423 149 E 0.0051 0.9355 0.0594 150 E 0.0059 0.8966 0.0975 151 V 0.0431 0.5983 0.3586 152 G 0.0418 0.1128 0.8454 153 E 0.0732 0.0365 0.8903 154 V 0.1449 0.0216 0.8335 155 P 0.1208 0.0174 0.8618 156 L 0.1348 0.0224 0.8429 157 P 0.0958 0.0219 0.8824 158 P 0.1365 0.0894 0.7741 159 Y 0.3196 0.1151 0.5653 160 I 0.4104 0.0933 0.4963 161 K 0.2889 0.0772 0.6339 162 A 0.1638 0.0531 0.7831 163 K 0.0808 0.0799 0.8393 164 I 0.0649 0.0641 0.8709 165 P 0.0847 0.0341 0.8811 166 M 0.0375 0.3318 0.6306 167 E 0.0596 0.3808 0.5596 168 R 0.1541 0.3422 0.5036 169 Y 0.4633 0.1249 0.4117 170 Q 0.6653 0.0935 0.2412 171 T 0.7926 0.0659 0.1415 172 V 0.7455 0.1068 0.1477 173 Y 0.7685 0.0821 0.1494 174 A 0.6507 0.0856 0.2637 175 R 0.4337 0.0766 0.4897 176 R 0.2544 0.0367 0.7089 177 P 0.0686 0.0638 0.8676 178 G 0.0627 0.0656 0.8717 179 S 0.2813 0.0846 0.6341 180 V 0.4856 0.1177 0.3967 181 A 0.4640 0.1049 0.4311 182 A 0.2954 0.0866 0.6180 183 P 0.1879 0.1591 0.6530 184 T 0.1576 0.2324 0.6100 185 A 0.1456 0.2789 0.5755 186 G 0.1446 0.2698 0.5856 187 L 0.1375 0.2622 0.6003 188 H 0.2021 0.1532 0.6447 189 F 0.1706 0.0855 0.7439 190 T 0.0664 0.0789 0.8547 191 P 0.0057 0.9180 0.0762 192 E 0.0051 0.9427 0.0522 193 L 0.0052 0.9465 0.0483 194 L 0.0047 0.9568 0.0385 195 E 0.0053 0.9545 0.0402 196 R 0.0049 0.9548 0.0403 197 L 0.0051 0.9529 0.0421 198 R 0.0053 0.9400 0.0547 199 E 0.0063 0.8560 0.1378 200 M 0.0410 0.2919 0.6672 201 G 0.0347 0.0248 0.9405 202 V 0.1092 0.0126 0.8782 203 E 0.5607 0.0151 0.4243 204 L 0.8637 0.0066 0.1296 205 R 0.8850 0.0065 0.1085 206 F 0.9219 0.0035 0.0745 207 L 0.9233 0.0034 0.0733 208 T 0.9138 0.0047 0.0815 209 L 0.8758 0.0073 0.1169 210 H 0.8118 0.0125 0.1757 211 V 0.6745 0.0369 0.2885 212 G 0.4921 0.0493 0.4586 213 P 0.4096 0.0938 0.4965 214 G 0.3527 0.0823 0.5650 215 T 0.3546 0.0703 0.5752 216 F 0.3483 0.0459 0.6057 217 R 0.3128 0.0295 0.6577 218 P 0.2924 0.0322 0.6754 219 V 0.1613 0.0727 0.7659 220 K 0.1277 0.1079 0.7644 221 G 0.0893 0.1247 0.7860 222 D 0.1039 0.1078 0.7883 223 P 0.0532 0.5487 0.3980 224 E 0.0388 0.5686 0.3925 225 K 0.0753 0.4595 0.4651 226 H 0.1491 0.2632 0.5877 227 E 0.2304 0.1657 0.6039 228 M 0.3180 0.1365 0.5455 229 H 0.2615 0.0978 0.6407 230 A 0.2785 0.1989 0.5225 231 E 0.4148 0.1930 0.3921 232 P 0.5614 0.1559 0.2826 233 Y 0.6513 0.0622 0.2865 234 A 0.6859 0.0268 0.2872 235 I 0.5274 0.0143 0.4583 236 P 0.1283 0.0163 0.8554 237 E 0.0054 0.8993 0.0953 238 E 0.0048 0.9333 0.0619 239 V 0.0048 0.9533 0.0418 240 A 0.0047 0.9604 0.0349 241 E 0.0047 0.9602 0.0351 242 A 0.0047 0.9599 0.0354 243 V 0.0047 0.9598 0.0356 244 N 0.0048 0.9588 0.0364 245 R 0.0048 0.9556 0.0395 246 A 0.0050 0.9541 0.0409 247 K 0.0062 0.9427 0.0511 248 A 0.0078 0.8995 0.0927 249 E 0.0369 0.5062 0.4569 250 G 0.0398 0.0546 0.9056 251 R 0.0815 0.0192 0.8992 252 R 0.4847 0.0121 0.5032 253 V 0.8183 0.0060 0.1757 254 V 0.8495 0.0171 0.1335 255 A 0.8603 0.0103 0.1295 256 V 0.6649 0.0401 0.2950 257 G 0.3449 0.0777 0.5774 258 T 0.1481 0.4118 0.4401 259 T 0.0532 0.7196 0.2272 260 V 0.0318 0.8497 0.1185 261 V 0.0200 0.9050 0.0750 262 R 0.0223 0.9025 0.0752 263 A 0.0189 0.9076 0.0734 264 L 0.0198 0.9061 0.0741 265 E 0.0253 0.8869 0.0877 266 S 0.0295 0.8590 0.1115 267 A 0.0396 0.7579 0.2026 268 Y 0.1218 0.4651 0.4132 269 R 0.0657 0.2515 0.6828 270 E 0.0250 0.1728 0.8022 271 G 0.0482 0.0443 0.9074 272 V 0.0541 0.0443 0.9016 273 G 0.3056 0.0236 0.6708 274 V 0.6695 0.0142 0.3164 275 V 0.4745 0.0170 0.5085 276 A 0.3090 0.0774 0.6137 277 G 0.1910 0.0700 0.7390 278 E 0.1694 0.0640 0.7667 279 G 0.1765 0.0503 0.7732 280 E 0.2505 0.1060 0.6434 281 T 0.4499 0.0454 0.5047 282 R 0.5927 0.0555 0.3517 283 L 0.7939 0.0187 0.1874 284 F 0.8184 0.0147 0.1669 285 I 0.7583 0.0193 0.2224 286 R 0.3527 0.0218 0.6255 287 P 0.0478 0.0701 0.8821 288 P 0.0383 0.0587 0.9030 289 Y 0.1564 0.0555 0.7881 290 T 0.3918 0.0547 0.5535 291 F 0.6828 0.0337 0.2835 292 K 0.7556 0.0523 0.1920 293 V 0.7832 0.0597 0.1571 294 V 0.6684 0.1296 0.2020 295 D 0.5840 0.1811 0.2349 296 A 0.6039 0.1789 0.2171 297 L 0.5996 0.1898 0.2105 298 F 0.5612 0.1582 0.2806 299 T 0.3570 0.1440 0.4990 300 N 0.1615 0.0991 0.7394 301 F 0.0998 0.1208 0.7795 302 H 0.0989 0.0834 0.8177 303 L 0.0661 0.0528 0.8811 304 P 0.0559 0.1848 0.7593 305 R 0.0139 0.8118 0.1743 306 S 0.0146 0.8650 0.1204 307 T 0.0226 0.9036 0.0738 308 L 0.0236 0.9348 0.0416 309 L 0.0206 0.9402 0.0393 310 M 0.0150 0.9476 0.0374 311 L 0.0186 0.9373 0.0441 312 V 0.0150 0.9279 0.0571 313 A 0.0125 0.9190 0.0685 314 A 0.0129 0.8912 0.0959 315 F 0.0258 0.8130 0.1612 316 L 0.0516 0.6282 0.3202 317 G 0.0314 0.4850 0.4836 318 R 0.0082 0.8822 0.1096 319 E 0.0053 0.9416 0.0531 320 R 0.0051 0.9477 0.0472 321 T 0.0048 0.9535 0.0416 322 L 0.0048 0.9587 0.0365 323 E 0.0048 0.9585 0.0367 324 A 0.0048 0.9570 0.0383 325 Y 0.0047 0.9559 0.0394 326 R 0.0047 0.9570 0.0383 327 L 0.0047 0.9533 0.0420 328 A 0.0049 0.9474 0.0478 329 V 0.0053 0.9302 0.0645 330 A 0.0071 0.8644 0.1285 331 E 0.0239 0.4237 0.5525 332 G 0.0310 0.1808 0.7882 333 Y 0.1319 0.0722 0.7959 334 R 0.3945 0.0709 0.5346 335 F 0.6443 0.0702 0.2854 336 Y 0.6408 0.0621 0.2971 337 S 0.5084 0.0540 0.4375 338 L 0.2727 0.2196 0.5077 339 G 0.1459 0.2161 0.6381 340 D 0.1161 0.3106 0.5733 341 A 0.2321 0.3425 0.4254 342 M 0.3518 0.2966 0.3516 343 L 0.4316 0.2160 0.3524 344 I 0.3976 0.1261 0.4764 345 L 0.0756 0.0304 0.8941