# This file is the result of combining several RDB files, specifically # T0308.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0308.t2k.stride-ebghtl.rdb (weight 1.24869) # T0308.t2k.str2.rdb (weight 1.54758) # T0308.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 T0308.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0308 # 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 T0308.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 2613 # # ============================================ # Comments from T0308.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0308 # 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 T0308.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 2613 # # ============================================ # Comments from T0308.t2k.str2.rdb # ============================================ # TARGET T0308 # 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 T0308.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 2613 # # ============================================ # Comments from T0308.t2k.alpha.rdb # ============================================ # TARGET T0308 # 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 T0308.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 2613 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 E 0.2464 0.0285 0.7251 2 V 0.5030 0.0094 0.4876 3 H 0.8514 0.0073 0.1414 4 V 0.9184 0.0048 0.0768 5 L 0.9252 0.0040 0.0708 6 C 0.9216 0.0035 0.0748 7 L 0.8030 0.0193 0.1777 8 G 0.4825 0.0109 0.5066 9 L 0.1158 0.0342 0.8500 10 D 0.0259 0.1343 0.8398 11 N 0.0178 0.1310 0.8511 12 S 0.0539 0.2241 0.7220 13 G 0.0501 0.2351 0.7149 14 K 0.0275 0.8089 0.1636 15 T 0.0165 0.8619 0.1216 16 T 0.0129 0.9217 0.0653 17 I 0.0141 0.9188 0.0671 18 I 0.0100 0.9339 0.0561 19 N 0.0121 0.9138 0.0741 20 K 0.0156 0.8548 0.1295 21 L 0.0371 0.6897 0.2732 22 K 0.0471 0.4713 0.4816 23 P 0.0544 0.2274 0.7181 24 S 0.0579 0.1666 0.7755 25 N 0.1425 0.1661 0.6914 26 A 0.2697 0.1056 0.6247 27 Q 0.3138 0.0841 0.6021 28 S 0.2716 0.0824 0.6460 29 Q 0.2756 0.0711 0.6533 30 N 0.3610 0.0470 0.5920 31 I 0.4743 0.0342 0.4915 32 L 0.4723 0.0265 0.5013 33 P 0.4654 0.0377 0.4970 34 T 0.4691 0.0485 0.4824 35 I 0.4932 0.0660 0.4409 36 G 0.4939 0.0393 0.4667 37 F 0.6380 0.0193 0.3427 38 S 0.7247 0.0109 0.2644 39 I 0.8488 0.0057 0.1455 40 E 0.8925 0.0046 0.1029 41 K 0.9075 0.0037 0.0887 42 F 0.8698 0.0064 0.1238 43 K 0.7424 0.0226 0.2350 44 S 0.4166 0.0512 0.5321 45 S 0.1377 0.0795 0.7828 46 S 0.2147 0.0396 0.7457 47 L 0.6396 0.0065 0.3538 48 S 0.8357 0.0035 0.1608 49 F 0.9191 0.0034 0.0774 50 T 0.9265 0.0034 0.0701 51 V 0.9186 0.0042 0.0772 52 F 0.8708 0.0076 0.1216 53 D 0.5535 0.0124 0.4341 54 M 0.1426 0.0469 0.8104 55 S 0.0537 0.0814 0.8649 56 G 0.0483 0.1189 0.8328 57 Q 0.1150 0.2529 0.6321 58 G 0.1716 0.4169 0.4115 59 R 0.1375 0.4815 0.3810 60 Y 0.0858 0.6127 0.3015 61 R 0.0657 0.6078 0.3264 62 N 0.0444 0.7119 0.2437 63 L 0.0420 0.7421 0.2159 64 W 0.0541 0.7319 0.2139 65 E 0.0193 0.8395 0.1412 66 H 0.0190 0.8222 0.1588 67 Y 0.0261 0.7637 0.2101 68 Y 0.0626 0.6095 0.3279 69 K 0.0278 0.4300 0.5422 70 E 0.0452 0.1467 0.8081 71 G 0.1458 0.0224 0.8319 72 Q 0.2571 0.0420 0.7009 73 A 0.9016 0.0041 0.0943 74 I 0.9308 0.0033 0.0659 75 I 0.9327 0.0033 0.0640 76 F 0.9264 0.0035 0.0701 77 V 0.8766 0.0052 0.1182 78 I 0.6687 0.0121 0.3192 79 D 0.4097 0.0201 0.5701 80 S 0.1141 0.1524 0.7335 81 S 0.0685 0.1384 0.7931 82 D 0.0809 0.1319 0.7872 83 R 0.0206 0.4735 0.5058 84 L 0.0321 0.5893 0.3786 85 R 0.0280 0.6848 0.2871 86 M 0.0112 0.8609 0.1278 87 V 0.0093 0.8842 0.1065 88 V 0.0088 0.8837 0.1075 89 A 0.0068 0.9176 0.0756 90 K 0.0058 0.9396 0.0545 91 E 0.0053 0.9426 0.0521 92 E 0.0056 0.9446 0.0498 93 L 0.0053 0.9474 0.0473 94 D 0.0056 0.9450 0.0493 95 T 0.0051 0.9387 0.0562 96 L 0.0064 0.9139 0.0797 97 L 0.0087 0.8329 0.1584 98 N 0.0123 0.6489 0.3388 99 H 0.0324 0.4658 0.5018 100 P 0.0436 0.3775 0.5788 101 D 0.0464 0.3403 0.6134 102 I 0.0282 0.4695 0.5022 103 K 0.0387 0.3755 0.5858 104 H 0.0486 0.3916 0.5598 105 R 0.0351 0.2364 0.7284 106 R 0.0583 0.0794 0.8623 107 I 0.1603 0.0135 0.8263 108 P 0.3364 0.0062 0.6574 109 I 0.8993 0.0038 0.0970 110 L 0.9274 0.0034 0.0692 111 F 0.9282 0.0034 0.0684 112 F 0.9072 0.0087 0.0840 113 A 0.7948 0.0170 0.1882 114 N 0.5301 0.0222 0.4478 115 K 0.1589 0.1223 0.7187 116 M 0.1466 0.1650 0.6883 117 D 0.1366 0.1688 0.6946 118 L 0.0491 0.3322 0.6187 119 R 0.0281 0.4230 0.5488 120 D 0.0334 0.5043 0.4623 121 A 0.0566 0.4849 0.4584 122 V 0.1120 0.4410 0.4470 123 T 0.1010 0.4666 0.4323 124 S 0.0523 0.6344 0.3133 125 V 0.0463 0.7204 0.2333 126 K 0.0371 0.8023 0.1606 127 V 0.0256 0.8323 0.1421 128 S 0.0196 0.8326 0.1477 129 Q 0.0121 0.8775 0.1104 130 L 0.0105 0.8829 0.1066 131 L 0.0102 0.8865 0.1033 132 C 0.0087 0.8777 0.1137 133 L 0.0076 0.9011 0.0913 134 E 0.0071 0.9098 0.0831 135 N 0.0071 0.8966 0.0963 136 I 0.0086 0.8139 0.1775 137 K 0.0097 0.6947 0.2956 138 D 0.0199 0.5842 0.3960 139 K 0.0492 0.2126 0.7382 140 P 0.0469 0.0489 0.9043 141 W 0.1679 0.0200 0.8120 142 H 0.5261 0.0188 0.4551 143 I 0.8495 0.0102 0.1403 144 C 0.8549 0.0151 0.1300 145 A 0.8504 0.0117 0.1379 146 S 0.6962 0.0389 0.2649 147 D 0.5178 0.0689 0.4133 148 A 0.2879 0.2392 0.4728 149 I 0.1901 0.2934 0.5166 150 K 0.1182 0.2356 0.6462 151 G 0.0512 0.1107 0.8382 152 E 0.0692 0.1245 0.8063 153 G 0.1233 0.1399 0.7367 154 L 0.0173 0.8055 0.1771 155 Q 0.0059 0.9322 0.0619 156 E 0.0057 0.9454 0.0489 157 G 0.0048 0.9522 0.0430 158 V 0.0047 0.9560 0.0392 159 D 0.0047 0.9560 0.0393 160 W 0.0048 0.9537 0.0415 161 L 0.0049 0.9452 0.0500 162 Q 0.0059 0.9069 0.0872 163 D 0.0071 0.7197 0.2732 164 Q 0.0131 0.5072 0.4798 165 I 0.0333 0.1508 0.8159