# This file is the result of combining several RDB files, specifically # T0290.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0290.t2k.stride-ebghtl.rdb (weight 1.24869) # T0290.t2k.str2.rdb (weight 1.54758) # T0290.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 T0290.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0290 # 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 T0290.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 1354 # # ============================================ # Comments from T0290.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0290 # 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 T0290.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 1354 # # ============================================ # Comments from T0290.t2k.str2.rdb # ============================================ # TARGET T0290 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0290.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 100.106 # # ============================================ # Comments from T0290.t2k.alpha.rdb # ============================================ # TARGET T0290 # 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 T0290.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 1354 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 R 0.0799 0.0231 0.8970 2 P 0.1155 0.0164 0.8681 3 R 0.6283 0.0135 0.3582 4 C 0.8663 0.0073 0.1264 5 F 0.8639 0.0135 0.1226 6 F 0.8382 0.0115 0.1503 7 D 0.7596 0.0192 0.2213 8 I 0.6911 0.0282 0.2808 9 A 0.6478 0.0457 0.3065 10 I 0.5956 0.0571 0.3473 11 N 0.4428 0.0463 0.5109 12 N 0.3029 0.0436 0.6536 13 Q 0.3377 0.0196 0.6427 14 P 0.4293 0.0381 0.5326 15 A 0.3979 0.0535 0.5486 16 G 0.5284 0.0227 0.4490 17 R 0.8190 0.0059 0.1751 18 V 0.9053 0.0035 0.0912 19 V 0.9222 0.0041 0.0737 20 F 0.9226 0.0038 0.0737 21 E 0.9126 0.0045 0.0829 22 L 0.8313 0.0101 0.1586 23 F 0.5370 0.0295 0.4336 24 S 0.1790 0.2431 0.5779 25 D 0.0734 0.2570 0.6696 26 V 0.1008 0.2552 0.6440 27 C 0.0874 0.1071 0.8054 28 P 0.0502 0.5648 0.3850 29 K 0.0481 0.7469 0.2051 30 T 0.0420 0.8470 0.1110 31 C 0.0060 0.9495 0.0444 32 E 0.0052 0.9550 0.0398 33 N 0.0055 0.9522 0.0423 34 F 0.0048 0.9534 0.0418 35 R 0.0053 0.9515 0.0431 36 C 0.0058 0.9355 0.0587 37 L 0.0084 0.9032 0.0884 38 C 0.0282 0.7524 0.2194 39 T 0.0318 0.5419 0.4263 40 G 0.0583 0.3037 0.6380 41 E 0.0625 0.1915 0.7459 42 K 0.0795 0.1902 0.7303 43 G 0.0875 0.2021 0.7104 44 T 0.1375 0.1727 0.6898 45 G 0.1755 0.1381 0.6864 46 K 0.1458 0.1584 0.6958 47 S 0.1341 0.1660 0.6998 48 T 0.1257 0.1113 0.7630 49 Q 0.1540 0.0727 0.7733 50 K 0.2406 0.0513 0.7081 51 P 0.3234 0.0656 0.6110 52 L 0.3715 0.0842 0.5443 53 H 0.4241 0.0663 0.5096 54 Y 0.3880 0.0647 0.5473 55 K 0.2363 0.0842 0.6794 56 S 0.2038 0.0589 0.7373 57 C 0.4023 0.0384 0.5593 58 L 0.6164 0.0503 0.3333 59 F 0.7172 0.0696 0.2131 60 H 0.7584 0.0633 0.1783 61 R 0.7766 0.0578 0.1656 62 V 0.7358 0.0526 0.2116 63 V 0.5301 0.0319 0.4380 64 K 0.0960 0.0882 0.8159 65 D 0.0611 0.0606 0.8784 66 F 0.4528 0.0401 0.5071 67 M 0.7966 0.0169 0.1865 68 V 0.8512 0.0097 0.1390 69 Q 0.7405 0.0220 0.2375 70 G 0.4425 0.0304 0.5272 71 G 0.2653 0.0304 0.7042 72 D 0.1609 0.0351 0.8040 73 F 0.1022 0.0908 0.8070 74 S 0.0936 0.0930 0.8134 75 E 0.0864 0.0833 0.8303 76 G 0.0872 0.0835 0.8294 77 N 0.1079 0.0916 0.8005 78 G 0.0831 0.0771 0.8398 79 R 0.1030 0.0770 0.8200 80 G 0.1192 0.0803 0.8005 81 G 0.1430 0.1295 0.7275 82 E 0.2378 0.1465 0.6157 83 S 0.3032 0.1493 0.5475 84 I 0.2595 0.1898 0.5507 85 Y 0.1695 0.1608 0.6698 86 G 0.1094 0.1235 0.7671 87 G 0.1103 0.1286 0.7611 88 F 0.1562 0.1403 0.7035 89 F 0.1448 0.1440 0.7113 90 E 0.0988 0.2074 0.6937 91 D 0.0664 0.3499 0.5837 92 E 0.0743 0.3457 0.5800 93 S 0.1151 0.2359 0.6490 94 F 0.1192 0.2104 0.6703 95 A 0.1640 0.2014 0.6346 96 V 0.2137 0.2024 0.5839 97 K 0.1934 0.1911 0.6155 98 H 0.1659 0.1411 0.6930 99 N 0.1252 0.0811 0.7938 100 A 0.1212 0.1022 0.7767 101 A 0.1915 0.1659 0.6426 102 F 0.4624 0.1403 0.3973 103 L 0.6636 0.1459 0.1905 104 L 0.7327 0.1265 0.1408 105 S 0.6639 0.1748 0.1614 106 M 0.5558 0.2220 0.2222 107 A 0.4108 0.2245 0.3647 108 N 0.2656 0.1603 0.5741 109 R 0.2303 0.0706 0.6991 110 G 0.1463 0.0313 0.8224 111 K 0.1574 0.0897 0.7528 112 D 0.1041 0.0812 0.8147 113 T 0.0852 0.0938 0.8209 114 N 0.0869 0.0705 0.8425 115 G 0.1117 0.0781 0.8102 116 S 0.3566 0.0286 0.6148 117 Q 0.7535 0.0176 0.2288 118 F 0.8770 0.0074 0.1156 119 F 0.8935 0.0073 0.0992 120 I 0.8915 0.0069 0.1016 121 T 0.8452 0.0083 0.1465 122 T 0.6641 0.0249 0.3111 123 K 0.3322 0.0214 0.6464 124 P 0.1940 0.0426 0.7635 125 T 0.1823 0.0534 0.7643 126 P 0.1265 0.2201 0.6534 127 H 0.1500 0.2302 0.6198 128 L 0.1597 0.1481 0.6922 129 D 0.1197 0.0662 0.8141 130 G 0.0548 0.0771 0.8681 131 H 0.1745 0.0532 0.7723 132 H 0.7099 0.0139 0.2761 133 V 0.8708 0.0053 0.1239 134 V 0.8923 0.0072 0.1004 135 F 0.8352 0.0207 0.1441 136 G 0.7642 0.0199 0.2160 137 Q 0.7728 0.0202 0.2070 138 V 0.7054 0.0472 0.2474 139 I 0.4023 0.1183 0.4794 140 S 0.1372 0.1670 0.6958 141 G 0.0603 0.2642 0.6755 142 Q 0.0338 0.7838 0.1825 143 E 0.0418 0.8499 0.1083 144 V 0.0092 0.9387 0.0521 145 V 0.0079 0.9508 0.0412 146 R 0.0096 0.9487 0.0417 147 E 0.0081 0.9436 0.0483 148 I 0.0101 0.9287 0.0612 149 E 0.0114 0.8741 0.1145 150 N 0.0213 0.6719 0.3069 151 Q 0.0776 0.2866 0.6359 152 K 0.0995 0.0927 0.8078 153 T 0.1586 0.0681 0.7733 154 D 0.0792 0.0858 0.8350 155 A 0.0354 0.1460 0.8186 156 A 0.0460 0.0830 0.8710 157 S 0.0574 0.0473 0.8953 158 K 0.1265 0.0130 0.8605 159 P 0.2829 0.0165 0.7006 160 F 0.3099 0.0393 0.6508 161 A 0.3354 0.0237 0.6409 162 E 0.4876 0.0163 0.4961 163 V 0.7675 0.0052 0.2273 164 R 0.8785 0.0048 0.1166 165 I 0.8947 0.0035 0.1018 166 L 0.7967 0.0204 0.1829 167 S 0.6986 0.0110 0.2904 168 C 0.6142 0.0189 0.3670 169 G 0.7070 0.0170 0.2760 170 E 0.7200 0.0146 0.2654 171 L 0.4874 0.0262 0.4864 172 I 0.2288 0.0191 0.7521 173 P 0.0630 0.0247 0.9123