# This file is the result of combining several RDB files, specifically # T0368.t04.dssp-ebghstl.rdb (weight 1.53986) # T0368.t04.stride-ebghtl.rdb (weight 1.24869) # T0368.t04.str2.rdb (weight 1.54758) # T0368.t04.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 T0368.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0368 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0368.t04-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 3.53726 # # ============================================ # Comments from T0368.t04.stride-ebghtl.rdb # ============================================ # TARGET T0368 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0368.t04-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 3.53726 # # ============================================ # Comments from T0368.t04.str2.rdb # ============================================ # TARGET T0368 # Using neural net t04-2621-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 T0368.t04-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 3.53726 # # ============================================ # Comments from T0368.t04.alpha.rdb # ============================================ # TARGET T0368 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0368.t04-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 3.53726 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0615 0.0479 0.8906 2 K 0.1036 0.0630 0.8334 3 P 0.1207 0.1758 0.7035 4 L 0.0239 0.8059 0.1702 5 K 0.0115 0.9233 0.0652 6 E 0.0102 0.9359 0.0538 7 V 0.0066 0.9407 0.0527 8 V 0.0059 0.9469 0.0472 9 G 0.0051 0.9497 0.0452 10 A 0.0050 0.9490 0.0460 11 Y 0.0051 0.9475 0.0473 12 L 0.0054 0.9364 0.0581 13 A 0.0068 0.8993 0.0939 14 L 0.0092 0.8658 0.1250 15 S 0.0179 0.8409 0.1412 16 D 0.0058 0.8992 0.0951 17 A 0.0062 0.9241 0.0697 18 Q 0.0059 0.9335 0.0606 19 R 0.0065 0.9350 0.0585 20 Q 0.0069 0.9273 0.0658 21 L 0.0099 0.8911 0.0989 22 V 0.0127 0.8114 0.1759 23 A 0.0189 0.6531 0.3280 24 G 0.0222 0.4362 0.5416 25 E 0.0324 0.4893 0.4783 26 Y 0.0152 0.8149 0.1698 27 D 0.0059 0.9292 0.0648 28 E 0.0055 0.9387 0.0558 29 A 0.0049 0.9407 0.0544 30 A 0.0048 0.9407 0.0545 31 A 0.0049 0.9146 0.0805 32 N 0.0062 0.8390 0.1548 33 C 0.0087 0.8091 0.1822 34 R 0.0140 0.8322 0.1538 35 R 0.0180 0.8342 0.1478 36 A 0.0213 0.8631 0.1156 37 M 0.0482 0.8007 0.1511 38 E 0.0706 0.7305 0.1989 39 I 0.0880 0.6781 0.2339 40 S 0.1014 0.5100 0.3886 41 H 0.1350 0.2486 0.6163 42 T 0.1877 0.0986 0.7136 43 M 0.1516 0.0167 0.8317 44 P 0.0824 0.0097 0.9079 45 P 0.0156 0.6287 0.3557 46 E 0.0162 0.6977 0.2861 47 E 0.0316 0.7445 0.2239 48 A 0.1345 0.5583 0.3073 49 F 0.1673 0.4099 0.4229 50 D 0.1313 0.2991 0.5696 51 H 0.0468 0.3356 0.6176 52 A 0.0349 0.2693 0.6958 53 G 0.0506 0.2890 0.6604 54 F 0.0607 0.4120 0.5273 55 D 0.0405 0.5933 0.3661 56 A 0.0711 0.8369 0.0921 57 F 0.0567 0.8907 0.0526 58 C 0.0547 0.8795 0.0659 59 H 0.0497 0.8679 0.0824 60 A 0.0507 0.8418 0.1075 61 G 0.0274 0.8210 0.1516 62 L 0.0099 0.8735 0.1165 63 A 0.0063 0.9264 0.0673 64 E 0.0050 0.9301 0.0649 65 A 0.0059 0.9280 0.0661 66 L 0.0085 0.8989 0.0926 67 A 0.0100 0.7781 0.2119 68 G 0.0125 0.5826 0.4049 69 L 0.0288 0.4849 0.4863 70 R 0.0246 0.4484 0.5269 71 S 0.0430 0.4841 0.4729 72 F 0.0129 0.8179 0.1693 73 D 0.0055 0.9184 0.0761 74 E 0.0062 0.9289 0.0649 75 A 0.0064 0.9278 0.0658 76 L 0.0079 0.9135 0.0786 77 H 0.0066 0.8839 0.1095 78 S 0.0083 0.8666 0.1251 79 A 0.0052 0.9321 0.0628 80 D 0.0049 0.9464 0.0487 81 K 0.0051 0.9369 0.0580 82 A 0.0050 0.9237 0.0713 83 L 0.0070 0.9060 0.0871 84 H 0.0085 0.8561 0.1353 85 Y 0.0118 0.8479 0.1403 86 F 0.0438 0.7109 0.2453 87 N 0.0517 0.4602 0.4881 88 R 0.0593 0.3666 0.5741 89 R 0.0914 0.2364 0.6722 90 G 0.1007 0.1372 0.7622 91 E 0.2336 0.1594 0.6071 92 L 0.3388 0.1727 0.4886 93 N 0.2397 0.1205 0.6397 94 Q 0.0744 0.2657 0.6600 95 D 0.0697 0.2841 0.6462 96 E 0.0605 0.2016 0.7378 97 G 0.0658 0.1572 0.7769 98 K 0.2079 0.3058 0.4863 99 L 0.5130 0.3489 0.1380 100 W 0.5249 0.4069 0.0682 101 I 0.4756 0.4704 0.0540 102 S 0.3857 0.5659 0.0484 103 A 0.3777 0.5714 0.0510 104 V 0.2345 0.7043 0.0612 105 Y 0.1552 0.7701 0.0748 106 S 0.0597 0.8403 0.1000 107 R 0.0255 0.8661 0.1084 108 A 0.0178 0.8911 0.0911 109 L 0.0220 0.8787 0.0994 110 A 0.0208 0.8666 0.1126 111 L 0.0299 0.8143 0.1557 112 D 0.0167 0.7112 0.2721 113 G 0.0199 0.4926 0.4874 114 L 0.0563 0.2448 0.6989 115 G 0.0515 0.0736 0.8748 116 R 0.0622 0.1024 0.8354 117 G 0.0581 0.2337 0.7082 118 A 0.0111 0.7224 0.2665 119 E 0.0132 0.7389 0.2479 120 A 0.0147 0.7482 0.2371 121 M 0.0159 0.7383 0.2458 122 P 0.0054 0.8694 0.1252 123 E 0.0063 0.8667 0.1271 124 F 0.0063 0.9065 0.0871 125 K 0.0055 0.9195 0.0750 126 K 0.0059 0.9205 0.0736 127 V 0.0063 0.9328 0.0609 128 V 0.0062 0.9457 0.0481 129 E 0.0075 0.9391 0.0534 130 M 0.0066 0.9399 0.0535 131 I 0.0083 0.9358 0.0560 132 E 0.0105 0.9219 0.0677 133 E 0.0128 0.8885 0.0988 134 R 0.0218 0.7982 0.1801 135 K 0.0460 0.4367 0.5173 136 G 0.0344 0.1190 0.8466 137 E 0.0704 0.0704 0.8591 138 T 0.0789 0.0485 0.8726 139 P 0.0386 0.1473 0.8142 140 G 0.0354 0.3147 0.6499 141 K 0.0224 0.8348 0.1428 142 E 0.0096 0.9247 0.0657 143 R 0.0075 0.9405 0.0520 144 M 0.0057 0.9488 0.0456 145 M 0.0050 0.9582 0.0368 146 E 0.0047 0.9607 0.0347 147 V 0.0047 0.9601 0.0352 148 A 0.0047 0.9589 0.0364 149 I 0.0047 0.9584 0.0369 150 D 0.0048 0.9548 0.0404 151 R 0.0048 0.9494 0.0458 152 I 0.0050 0.9472 0.0478 153 A 0.0058 0.9280 0.0662 154 Q 0.0069 0.8903 0.1028 155 L 0.0309 0.7229 0.2462 156 G 0.0337 0.4242 0.5421 157 A 0.0407 0.3554 0.6040 158 S 0.0512 0.3248 0.6240 159 N 0.0583 0.2391 0.7026 160 Q 0.0468 0.3217 0.6315 161 Q 0.0641 0.2576 0.6783 162 K 0.1137 0.1509 0.7353 163 K 0.0950 0.0357 0.8693 164 P 0.0465 0.0952 0.8583 165 G 0.0764 0.0563 0.8673 166 Y 0.3919 0.0327 0.5754 167 K 0.6863 0.0238 0.2899 168 A 0.8539 0.0178 0.1283 169 W 0.8725 0.0275 0.1000 170 W 0.8650 0.0376 0.0974 171 E 0.8418 0.0496 0.1087 172 F 0.6943 0.0615 0.2442 173 W 0.4409 0.0598 0.4993 174 S 0.1847 0.0426 0.7727