# This file is the result of combining several RDB files, specifically # T0356.t04.dssp-ebghstl.rdb (weight 1.53986) # T0356.t04.stride-ebghtl.rdb (weight 1.24869) # T0356.t04.str2.rdb (weight 1.54758) # T0356.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 T0356.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.3343 # # ============================================ # Comments from T0356.t04.stride-ebghtl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.3343 # # ============================================ # Comments from T0356.t04.str2.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.3343 # # ============================================ # Comments from T0356.t04.alpha.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.3343 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.1274 0.0257 0.8468 2 W 0.2053 0.0559 0.7388 3 G 0.3870 0.0403 0.5728 4 L 0.7800 0.0158 0.2042 5 T 0.8650 0.0098 0.1253 6 V 0.8761 0.0099 0.1140 7 T 0.8275 0.0114 0.1611 8 R 0.6702 0.0231 0.3067 9 G 0.2471 0.0154 0.7375 10 P 0.0631 0.0841 0.8528 11 H 0.0529 0.0801 0.8670 12 K 0.0545 0.1025 0.8430 13 E 0.0923 0.0887 0.8190 14 R 0.3624 0.0658 0.5718 15 Q 0.5690 0.0684 0.3626 16 N 0.5557 0.0798 0.3645 17 L 0.4511 0.1742 0.3747 18 G 0.5014 0.1802 0.3184 19 I 0.5706 0.2306 0.1988 20 Y 0.5055 0.3015 0.1930 21 R 0.5141 0.2972 0.1887 22 Q 0.5708 0.2648 0.1643 23 Q 0.5907 0.2637 0.1456 24 L 0.6015 0.2030 0.1955 25 I 0.3865 0.2075 0.4060 26 G 0.1784 0.0457 0.7759 27 K 0.0339 0.0807 0.8855 28 N 0.1228 0.0538 0.8235 29 K 0.7107 0.0318 0.2575 30 L 0.8880 0.0091 0.1029 31 I 0.9154 0.0099 0.0747 32 M 0.9134 0.0087 0.0779 33 R 0.8886 0.0117 0.0998 34 W 0.8537 0.0199 0.1265 35 L 0.6577 0.0368 0.3055 36 S 0.3905 0.1025 0.5071 37 H 0.1620 0.1504 0.6877 38 R 0.0899 0.1565 0.7536 39 G 0.0621 0.1505 0.7874 40 G 0.1007 0.2572 0.6421 41 A 0.1172 0.5445 0.3383 42 L 0.1057 0.6529 0.2414 43 D 0.1082 0.7003 0.1915 44 Y 0.0293 0.8964 0.0743 45 Q 0.0193 0.9231 0.0576 46 E 0.0199 0.9230 0.0571 47 W 0.0164 0.9203 0.0633 48 C 0.0218 0.8885 0.0897 49 A 0.0302 0.7946 0.1751 50 A 0.0370 0.6035 0.3595 51 H 0.0691 0.0719 0.8590 52 P 0.0205 0.0842 0.8954 53 G 0.0161 0.0425 0.9414 54 E 0.1126 0.0343 0.8532 55 R 0.2520 0.0152 0.7328 56 F 0.3517 0.0094 0.6388 57 P 0.4045 0.0060 0.5895 58 V 0.8751 0.0048 0.1200 59 S 0.9162 0.0044 0.0794 60 V 0.9290 0.0046 0.0664 61 A 0.9103 0.0072 0.0825 62 L 0.7576 0.0282 0.2141 63 G 0.2440 0.0272 0.7289 64 A 0.0810 0.0357 0.8833 65 D 0.1092 0.0283 0.8624 66 P 0.0101 0.8719 0.1179 67 A 0.0298 0.8684 0.1018 68 T 0.0787 0.8332 0.0881 69 I 0.1591 0.7615 0.0793 70 L 0.1229 0.7728 0.1042 71 G 0.2152 0.6616 0.1232 72 A 0.2385 0.5794 0.1821 73 V 0.2074 0.3912 0.4014 74 T 0.1689 0.0368 0.7944 75 P 0.1339 0.0262 0.8399 76 V 0.1151 0.0171 0.8678 77 P 0.0725 0.0413 0.8862 78 D 0.0367 0.1112 0.8520 79 T 0.0602 0.0908 0.8490 80 L 0.1025 0.0990 0.7984 81 S 0.0836 0.1804 0.7360 82 E 0.0414 0.8506 0.1080 83 Y 0.0786 0.8317 0.0897 84 A 0.0772 0.8495 0.0734 85 F 0.0588 0.8560 0.0852 86 A 0.0321 0.8840 0.0839 87 G 0.0477 0.8524 0.0999 88 L 0.0492 0.8153 0.1355 89 L 0.0464 0.7286 0.2250 90 R 0.0644 0.2627 0.6729 91 G 0.0273 0.0592 0.9136 92 T 0.0910 0.0277 0.8813 93 K 0.2450 0.0253 0.7297 94 T 0.4859 0.0144 0.4996 95 E 0.7558 0.0074 0.2368 96 V 0.8766 0.0050 0.1184 97 V 0.8429 0.0124 0.1447 98 K 0.8120 0.0102 0.1778 99 C 0.6514 0.0205 0.3281 100 I 0.4833 0.0537 0.4629 101 S 0.3375 0.0679 0.5946 102 N 0.1736 0.0615 0.7649 103 D 0.1455 0.0560 0.7984 104 L 0.2309 0.0455 0.7236 105 E 0.3282 0.0390 0.6328 106 V 0.3017 0.0235 0.6748 107 P 0.2095 0.0269 0.7636 108 A 0.1652 0.1344 0.7004 109 S 0.2371 0.0879 0.6750 110 A 0.4054 0.1036 0.4910 111 E 0.7025 0.0388 0.2587 112 I 0.9117 0.0059 0.0824 113 V 0.9243 0.0039 0.0718 114 L 0.9139 0.0059 0.0802 115 E 0.8628 0.0158 0.1214 116 G 0.8320 0.0117 0.1563 117 Y 0.8719 0.0085 0.1196 118 I 0.7637 0.0097 0.2266 119 E 0.3193 0.0139 0.6668 120 Q 0.0382 0.1029 0.8589 121 G 0.0238 0.0720 0.9043 122 E 0.1475 0.0783 0.7742 123 T 0.3362 0.0270 0.6368 124 A 0.2150 0.0242 0.7609 125 P 0.1649 0.0415 0.7937 126 E 0.1989 0.0543 0.7467 127 G 0.1380 0.0227 0.8393 128 P 0.1540 0.0541 0.7919 129 Y 0.2093 0.0723 0.7184 130 G 0.2168 0.0722 0.7110 131 D 0.2559 0.1021 0.6419 132 H 0.3646 0.0944 0.5410 133 T 0.3720 0.0888 0.5391 134 G 0.4213 0.0675 0.5112 135 Y 0.6032 0.0484 0.3484 136 Y 0.5464 0.0540 0.3996 137 N 0.3158 0.0416 0.6426 138 E 0.1738 0.1220 0.7041 139 V 0.1566 0.1735 0.6699 140 D 0.1459 0.1259 0.7282 141 S 0.1472 0.0911 0.7618 142 F 0.2070 0.0199 0.7731 143 P 0.3562 0.0160 0.6278 144 V 0.8281 0.0126 0.1592 145 F 0.9034 0.0051 0.0915 146 T 0.9097 0.0049 0.0855 147 V 0.8909 0.0084 0.1007 148 T 0.7562 0.0349 0.2089 149 H 0.7942 0.0173 0.1885 150 I 0.7852 0.0183 0.1965 151 T 0.7466 0.0257 0.2277 152 Q 0.5228 0.0410 0.4362 153 R 0.2728 0.0726 0.6546 154 E 0.1537 0.1096 0.7366 155 D 0.1495 0.0584 0.7921 156 A 0.1446 0.1646 0.6909 157 I 0.3313 0.1469 0.5217 158 Y 0.4558 0.1247 0.4195 159 H 0.4330 0.1328 0.4342 160 S 0.4658 0.1183 0.4159 161 T 0.4884 0.0938 0.4179 162 Y 0.4105 0.0651 0.5243 163 T 0.2708 0.0481 0.6811 164 G 0.1272 0.0386 0.8342 165 R 0.1238 0.0197 0.8566 166 P 0.0894 0.0195 0.8911 167 P 0.0445 0.0908 0.8647 168 D 0.0458 0.1035 0.8507 169 E 0.0566 0.2437 0.6997 170 P 0.0543 0.4039 0.5418 171 A 0.1041 0.5696 0.3263 172 V 0.1429 0.5916 0.2654 173 L 0.1062 0.6039 0.2899 174 G 0.0922 0.5601 0.3477 175 V 0.0976 0.6540 0.2484 176 A 0.1012 0.7140 0.1848 177 L 0.0658 0.7631 0.1711 178 N 0.0813 0.6854 0.2333 179 E 0.0727 0.6333 0.2940 180 V 0.0783 0.4648 0.4569 181 F 0.0635 0.1220 0.8146