# This file is the result of combining several RDB files, specifically # T0380.t06.dssp-ebghstl.rdb (weight 1.53986) # T0380.t06.stride-ebghtl.rdb (weight 1.24869) # T0380.t06.str2.rdb (weight 1.54758) # T0380.t06.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 T0380.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0380 # 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 T0380.t06-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 1013 # # ============================================ # Comments from T0380.t06.stride-ebghtl.rdb # ============================================ # TARGET T0380 # Using neural net t06-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 T0380.t06-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 1013 # # ============================================ # Comments from T0380.t06.str2.rdb # ============================================ # TARGET T0380 # 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 T0380.t06-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 1013 # # ============================================ # Comments from T0380.t06.alpha.rdb # ============================================ # TARGET T0380 # Using neural net t06-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 T0380.t06-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 1013 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0362 0.0934 0.8705 2 I 0.0552 0.1658 0.7789 3 D 0.0465 0.2984 0.6551 4 E 0.0170 0.6558 0.3271 5 K 0.0194 0.7242 0.2565 6 F 0.0301 0.7180 0.2519 7 L 0.0179 0.7704 0.2117 8 I 0.0063 0.9309 0.0628 9 E 0.0068 0.9220 0.0712 10 S 0.0059 0.9288 0.0653 11 N 0.0059 0.9239 0.0701 12 E 0.0065 0.8945 0.0990 13 L 0.0065 0.8700 0.1236 14 V 0.0148 0.8091 0.1761 15 E 0.0130 0.6589 0.3281 16 S 0.0251 0.2822 0.6927 17 S 0.0894 0.0494 0.8612 18 K 0.1179 0.0609 0.8213 19 I 0.8117 0.0051 0.1832 20 V 0.9128 0.0037 0.0835 21 M 0.9305 0.0032 0.0663 22 V 0.9202 0.0052 0.0746 23 G 0.9004 0.0050 0.0946 24 T 0.8582 0.0057 0.1362 25 N 0.7095 0.0161 0.2744 26 G 0.1540 0.0160 0.8300 27 E 0.0176 0.1062 0.8762 28 N 0.0439 0.0321 0.9239 29 G 0.0597 0.0355 0.9048 30 Y 0.1872 0.0170 0.7957 31 P 0.5609 0.0175 0.4216 32 N 0.6454 0.0180 0.3366 33 I 0.7749 0.0153 0.2098 34 K 0.8109 0.0155 0.1736 35 A 0.8578 0.0097 0.1325 36 M 0.8367 0.0160 0.1474 37 M 0.8465 0.0113 0.1423 38 R 0.8457 0.0149 0.1394 39 L 0.8567 0.0138 0.1295 40 K 0.8591 0.0127 0.1282 41 H 0.7195 0.0291 0.2514 42 D 0.2109 0.0713 0.7178 43 G 0.0606 0.0810 0.8585 44 L 0.1149 0.0335 0.8516 45 K 0.2125 0.0400 0.7475 46 K 0.7697 0.0061 0.2242 47 F 0.9226 0.0033 0.0741 48 W 0.9273 0.0036 0.0691 49 L 0.9196 0.0040 0.0765 50 S 0.8596 0.0075 0.1329 51 T 0.5588 0.0153 0.4259 52 N 0.1643 0.0399 0.7958 53 T 0.0257 0.1613 0.8130 54 S 0.0272 0.2113 0.7614 55 T 0.0418 0.4592 0.4991 56 R 0.0373 0.7678 0.1949 57 M 0.0312 0.8749 0.0940 58 V 0.0107 0.9298 0.0594 59 E 0.0063 0.9471 0.0466 60 R 0.0061 0.9456 0.0483 61 L 0.0074 0.9273 0.0653 62 K 0.0096 0.8482 0.1421 63 K 0.0167 0.5407 0.4426 64 N 0.0712 0.0409 0.8879 65 N 0.0530 0.0851 0.8619 66 K 0.2399 0.0596 0.7004 67 I 0.8171 0.0080 0.1749 68 C 0.9155 0.0037 0.0807 69 L 0.9293 0.0032 0.0675 70 Y 0.9240 0.0037 0.0723 71 F 0.9055 0.0048 0.0897 72 V 0.7828 0.0100 0.2071 73 D 0.4448 0.0130 0.5423 74 D 0.0651 0.1327 0.8022 75 N 0.0397 0.1478 0.8125 76 K 0.1069 0.1723 0.7207 77 F 0.3097 0.0737 0.6165 78 A 0.5545 0.0350 0.4105 79 G 0.8371 0.0079 0.1551 80 L 0.9190 0.0035 0.0775 81 M 0.9288 0.0034 0.0678 82 L 0.9280 0.0032 0.0688 83 V 0.8747 0.0158 0.1095 84 G 0.8725 0.0061 0.1214 85 T 0.9005 0.0039 0.0956 86 I 0.9065 0.0037 0.0898 87 E 0.8845 0.0063 0.1092 88 I 0.8926 0.0051 0.1024 89 L 0.5267 0.0272 0.4461 90 H 0.2432 0.0245 0.7323 91 D 0.1033 0.0496 0.8471 92 R 0.0086 0.8259 0.1655 93 A 0.0088 0.8860 0.1052 94 S 0.0072 0.9180 0.0748 95 K 0.0062 0.9344 0.0594 96 E 0.0066 0.9291 0.0643 97 M 0.0066 0.9074 0.0860 98 L 0.0083 0.8809 0.1108 99 W 0.0185 0.8170 0.1645 100 T 0.0183 0.7409 0.2409 101 D 0.0291 0.6030 0.3679 102 G 0.0286 0.4998 0.4716 103 C 0.0415 0.5440 0.4145 104 E 0.0417 0.6515 0.3068 105 I 0.0579 0.5998 0.3424 106 Y 0.1000 0.4329 0.4671 107 Y 0.1216 0.0973 0.7811 108 P 0.0807 0.1505 0.7689 109 L 0.0762 0.1323 0.7915 110 G 0.0991 0.0645 0.8364 111 I 0.1230 0.0511 0.8259 112 D 0.1524 0.0354 0.8122 113 D 0.1087 0.0284 0.8629 114 P 0.0291 0.1315 0.8394 115 D 0.0791 0.0719 0.8491 116 Y 0.4973 0.0217 0.4810 117 T 0.8172 0.0072 0.1756 118 A 0.9237 0.0034 0.0729 119 L 0.9238 0.0036 0.0727 120 C 0.9247 0.0035 0.0719 121 F 0.9091 0.0041 0.0869 122 T 0.8190 0.0066 0.1744 123 A 0.6899 0.0249 0.2852 124 E 0.5788 0.0682 0.3530 125 W 0.8067 0.0438 0.1494 126 G 0.8375 0.0335 0.1291 127 N 0.8418 0.0423 0.1158 128 Y 0.8025 0.0680 0.1295 129 Y 0.6778 0.1076 0.2145 130 R 0.4723 0.1594 0.3682 131 H 0.2715 0.1937 0.5347 132 L 0.1712 0.2257 0.6031 133 K 0.0745 0.2668 0.6587 134 N 0.0939 0.2387 0.6674 135 I 0.1460 0.2975 0.5565 136 T 0.2043 0.3266 0.4692 137 F 0.2555 0.3376 0.4069 138 K 0.3153 0.3395 0.3451 139 I 0.1432 0.6605 0.1963 140 D 0.1153 0.7140 0.1706 141 E 0.1432 0.7085 0.1483 142 I 0.1400 0.6824 0.1776 143 Y 0.1451 0.5448 0.3101 144 N 0.0917 0.2600 0.6483 145 Y 0.0380 0.0545 0.9074