# This file is the result of combining several RDB files, specifically # T0284.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0284.t2k.stride-ebghtl.rdb (weight 1.24869) # T0284.t2k.str2.rdb (weight 1.54758) # T0284.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 T0284.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0284 # 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 T0284.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 437 # # ============================================ # Comments from T0284.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0284 # 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 T0284.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 437 # # ============================================ # Comments from T0284.t2k.str2.rdb # ============================================ # TARGET T0284 # 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 T0284.t2k-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 134.088 # # ============================================ # Comments from T0284.t2k.alpha.rdb # ============================================ # TARGET T0284 # 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 T0284.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 437 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0665 0.0812 0.8522 2 H 0.0878 0.2550 0.6572 3 R 0.0850 0.3102 0.6048 4 A 0.0516 0.3703 0.5781 5 S 0.0358 0.4444 0.5198 6 H 0.0138 0.7229 0.2633 7 H 0.0114 0.8155 0.1731 8 E 0.0125 0.8535 0.1339 9 L 0.0083 0.8810 0.1107 10 R 0.0062 0.9251 0.0687 11 A 0.0064 0.9372 0.0564 12 M 0.0051 0.9455 0.0494 13 F 0.0054 0.9458 0.0488 14 R 0.0051 0.9464 0.0485 15 A 0.0053 0.9352 0.0596 16 L 0.0064 0.9025 0.0912 17 L 0.0135 0.8128 0.1737 18 D 0.0236 0.6036 0.3728 19 S 0.0458 0.2128 0.7414 20 S 0.0348 0.0601 0.9050 21 R 0.0887 0.0331 0.8781 22 C 0.4376 0.0203 0.5421 23 Y 0.7728 0.0145 0.2127 24 H 0.8178 0.0126 0.1696 25 T 0.6866 0.0168 0.2966 26 A 0.3256 0.0829 0.5915 27 S 0.1240 0.0667 0.8094 28 V 0.1325 0.1084 0.7590 29 F 0.1191 0.0784 0.8025 30 D 0.0898 0.0587 0.8514 31 P 0.0059 0.8917 0.1023 32 M 0.0057 0.9402 0.0541 33 S 0.0049 0.9533 0.0418 34 A 0.0047 0.9599 0.0354 35 R 0.0047 0.9605 0.0348 36 I 0.0047 0.9611 0.0342 37 A 0.0047 0.9592 0.0361 38 A 0.0048 0.9533 0.0419 39 D 0.0060 0.9077 0.0863 40 L 0.0395 0.4750 0.4855 41 G 0.0329 0.0604 0.9067 42 F 0.0814 0.0354 0.8832 43 E 0.2545 0.0906 0.6549 44 C 0.8682 0.0370 0.0948 45 G 0.8972 0.0305 0.0723 46 I 0.8821 0.0406 0.0773 47 L 0.7351 0.1039 0.1610 48 G 0.3054 0.1607 0.5339 49 G 0.0656 0.4155 0.5189 50 S 0.0318 0.7188 0.2494 51 V 0.0279 0.8607 0.1113 52 A 0.0424 0.8679 0.0897 53 S 0.0397 0.8395 0.1207 54 L 0.0367 0.7568 0.2065 55 Q 0.0434 0.6418 0.3149 56 V 0.0553 0.4888 0.4559 57 L 0.0695 0.2059 0.7247 58 A 0.0730 0.0945 0.8325 59 A 0.0879 0.0578 0.8543 60 P 0.0837 0.1087 0.8076 61 D 0.0938 0.1581 0.7480 62 F 0.0495 0.4102 0.5403 63 A 0.0529 0.3258 0.6213 64 L 0.1161 0.2605 0.6235 65 I 0.2468 0.0512 0.7019 66 T 0.1153 0.0341 0.8506 67 L 0.0072 0.8675 0.1253 68 S 0.0051 0.9139 0.0809 69 E 0.0063 0.9121 0.0815 70 F 0.0053 0.9443 0.0504 71 V 0.0048 0.9552 0.0400 72 E 0.0048 0.9569 0.0383 73 Q 0.0047 0.9553 0.0400 74 A 0.0047 0.9525 0.0428 75 T 0.0047 0.9377 0.0576 76 R 0.0048 0.9192 0.0760 77 I 0.0048 0.9190 0.0762 78 G 0.0054 0.8852 0.1093 79 R 0.0091 0.8150 0.1759 80 V 0.0295 0.7482 0.2223 81 A 0.1489 0.3145 0.5366 82 R 0.1048 0.0797 0.8155 83 L 0.1225 0.0181 0.8594 84 P 0.2166 0.0151 0.7682 85 V 0.7539 0.0129 0.2332 86 I 0.8604 0.0070 0.1326 87 A 0.8401 0.0108 0.1490 88 D 0.7082 0.0178 0.2739 89 A 0.2655 0.1903 0.5442 90 D 0.1050 0.2367 0.6582 91 H 0.0873 0.2030 0.7097 92 G 0.0627 0.1082 0.8290 93 Y 0.0879 0.0852 0.8269 94 G 0.0862 0.0917 0.8222 95 N 0.0712 0.1430 0.7858 96 A 0.0111 0.8490 0.1399 97 L 0.0057 0.9090 0.0853 98 N 0.0059 0.9298 0.0643 99 V 0.0047 0.9511 0.0442 100 M 0.0047 0.9574 0.0379 101 R 0.0047 0.9587 0.0366 102 T 0.0047 0.9583 0.0370 103 V 0.0047 0.9605 0.0349 104 V 0.0047 0.9608 0.0345 105 E 0.0047 0.9610 0.0343 106 L 0.0047 0.9598 0.0355 107 E 0.0049 0.9498 0.0453 108 R 0.0050 0.9079 0.0871 109 A 0.0391 0.4989 0.4620 110 G 0.0356 0.0747 0.8896 111 I 0.1000 0.0801 0.8199 112 A 0.2619 0.0671 0.6710 113 A 0.8162 0.0308 0.1531 114 L 0.8745 0.0188 0.1067 115 T 0.8759 0.0156 0.1085 116 I 0.7833 0.0495 0.1671 117 E 0.5342 0.0928 0.3730 118 D 0.3448 0.1603 0.4949 119 T 0.2448 0.2158 0.5394 120 L 0.2137 0.1507 0.6356 121 L 0.1257 0.0707 0.8035 122 P 0.0987 0.0942 0.8071 123 A 0.1047 0.1967 0.6986 124 Q 0.1387 0.2010 0.6603 125 F 0.1318 0.1461 0.7221 126 G 0.1559 0.0947 0.7494 127 R 0.1569 0.0883 0.7548 128 K 0.1435 0.0885 0.7680 129 S 0.0542 0.0759 0.8699 130 T 0.0599 0.0466 0.8935 131 D 0.2815 0.0282 0.6904 132 L 0.6630 0.0123 0.3247 133 I 0.5875 0.0113 0.4012 134 C 0.3335 0.0212 0.6453 135 V 0.0102 0.9075 0.0823 136 E 0.0055 0.9374 0.0571 137 E 0.0048 0.9447 0.0505 138 G 0.0047 0.9492 0.0460 139 V 0.0047 0.9538 0.0415 140 G 0.0047 0.9550 0.0403 141 K 0.0047 0.9555 0.0398 142 I 0.0047 0.9583 0.0370 143 R 0.0047 0.9557 0.0396 144 A 0.0048 0.9461 0.0491 145 A 0.0048 0.9352 0.0600 146 L 0.0064 0.9073 0.0862 147 E 0.0070 0.8386 0.1544 148 A 0.0127 0.7193 0.2680 149 R 0.0285 0.5526 0.4189 150 V 0.0544 0.3760 0.5696 151 D 0.0537 0.0672 0.8791 152 P 0.0665 0.0736 0.8599 153 A 0.1094 0.0802 0.8104 154 L 0.6833 0.0217 0.2949 155 T 0.9032 0.0101 0.0867 156 I 0.9138 0.0102 0.0761 157 I 0.8958 0.0150 0.0892 158 A 0.7968 0.0331 0.1701 159 R 0.5667 0.0951 0.3382 160 T 0.2688 0.1946 0.5365 161 N 0.0894 0.4039 0.5068 162 A 0.0443 0.6079 0.3477 163 E 0.0349 0.5760 0.3891 164 L 0.0403 0.4002 0.5595 165 I 0.0562 0.2192 0.7245 166 D 0.0520 0.1640 0.7840 167 V 0.0195 0.6096 0.3709 168 D 0.0109 0.8455 0.1436 169 A 0.0073 0.8766 0.1161 170 V 0.0059 0.9097 0.0844 171 I 0.0070 0.9202 0.0728 172 Q 0.0078 0.9155 0.0768 173 R 0.0053 0.9107 0.0841 174 T 0.0071 0.9138 0.0791 175 L 0.0055 0.9297 0.0648 176 A 0.0054 0.9402 0.0544 177 Y 0.0055 0.9390 0.0556 178 Q 0.0059 0.9364 0.0577 179 E 0.0065 0.9007 0.0928 180 A 0.0407 0.4645 0.4948 181 G 0.0391 0.0663 0.8946 182 A 0.0749 0.0523 0.8728 183 D 0.1280 0.1015 0.7705 184 G 0.4252 0.0815 0.4933 185 I 0.5584 0.0687 0.3730 186 C 0.6042 0.0589 0.3369 187 L 0.4127 0.0889 0.4984 188 V 0.1791 0.1231 0.6979 189 G 0.1320 0.1357 0.7323 190 V 0.1177 0.1432 0.7391 191 R 0.0733 0.0820 0.8448 192 D 0.0702 0.0900 0.8398 193 F 0.0061 0.9174 0.0765 194 A 0.0052 0.9424 0.0524 195 H 0.0049 0.9496 0.0456 196 L 0.0047 0.9570 0.0383 197 E 0.0047 0.9565 0.0387 198 A 0.0048 0.9542 0.0411 199 I 0.0049 0.9480 0.0470 200 A 0.0056 0.9305 0.0638 201 E 0.0068 0.8351 0.1581 202 H 0.0135 0.7005 0.2860 203 L 0.0615 0.3443 0.5942 204 H 0.0435 0.1026 0.8539 205 I 0.0684 0.0437 0.8879 206 P 0.1280 0.0481 0.8239 207 L 0.3980 0.0943 0.5077 208 M 0.5429 0.0950 0.3621 209 L 0.6915 0.0916 0.2169 210 V 0.7316 0.0644 0.2040 211 T 0.6502 0.0516 0.2982 212 Y 0.3346 0.0777 0.5877 213 G 0.1505 0.0717 0.7778 214 N 0.1289 0.0800 0.7911 215 P 0.1031 0.0717 0.8252 216 Q 0.0804 0.0983 0.8213 217 L 0.1161 0.0574 0.8264 218 R 0.1157 0.0371 0.8472 219 D 0.0739 0.0237 0.9024 220 D 0.0052 0.9368 0.0580 221 A 0.0048 0.9487 0.0466 222 R 0.0048 0.9522 0.0430 223 L 0.0048 0.9509 0.0444 224 A 0.0049 0.9341 0.0610 225 R 0.0060 0.8435 0.1504 226 L 0.0316 0.4726 0.4958 227 G 0.0380 0.1758 0.7862 228 V 0.1826 0.1658 0.6516 229 R 0.5667 0.1973 0.2360 230 V 0.7332 0.1888 0.0780 231 V 0.7681 0.1518 0.0801 232 V 0.6941 0.1437 0.1622 233 N 0.3269 0.1138 0.5593 234 G 0.0612 0.2900 0.6487 235 H 0.0234 0.6425 0.3341 236 A 0.0110 0.8673 0.1217 237 A 0.0058 0.9234 0.0707 238 Y 0.0049 0.9407 0.0543 239 F 0.0058 0.9388 0.0554 240 A 0.0062 0.9386 0.0553 241 A 0.0055 0.9211 0.0734 242 I 0.0088 0.8847 0.1065 243 K 0.0078 0.8292 0.1630 244 A 0.0092 0.8257 0.1651 245 T 0.0054 0.9098 0.0848 246 Y 0.0050 0.9438 0.0513 247 D 0.0050 0.9486 0.0464 248 C 0.0048 0.9517 0.0435 249 L 0.0048 0.9501 0.0451 250 R 0.0048 0.9427 0.0524 251 E 0.0050 0.9263 0.0686 252 E 0.0067 0.9049 0.0884 253 R 0.0099 0.8443 0.1459 254 G 0.0152 0.6792 0.3056 255 A 0.0364 0.4482 0.5153 256 V 0.0381 0.2532 0.7087 257 A 0.0791 0.2977 0.6232 258 S 0.0756 0.6178 0.3066 259 D 0.0488 0.7012 0.2500 260 L 0.0599 0.6834 0.2567 261 T 0.0438 0.7031 0.2530 262 A 0.0167 0.8420 0.1412 263 S 0.0120 0.8360 0.1520 264 E 0.0107 0.8049 0.1844 265 L 0.0315 0.6747 0.2938 266 S 0.0448 0.5151 0.4401 267 K 0.0570 0.4324 0.5106 268 K 0.0199 0.7333 0.2468 269 Y 0.0349 0.7064 0.2587 270 T 0.0501 0.7260 0.2239 271 F 0.0364 0.7456 0.2180 272 P 0.0320 0.7840 0.1840 273 E 0.0347 0.8061 0.1592 274 E 0.0646 0.7389 0.1965 275 Y 0.1220 0.5533 0.3248 276 Q 0.0906 0.4187 0.4907 277 A 0.0184 0.7845 0.1971 278 W 0.0083 0.8501 0.1416 279 A 0.0098 0.8274 0.1628 280 R 0.0166 0.8320 0.1514 281 D 0.0228 0.7741 0.2031 282 Y 0.0299 0.7179 0.2522 283 M 0.0560 0.5625 0.3815 284 E 0.0772 0.4059 0.5168 285 V 0.0917 0.3085 0.5999 286 K 0.0784 0.2230 0.6986 287 E 0.0461 0.0704 0.8835