# This file is the result of combining several RDB files, specifically # T0517.t04.dssp-ebghstl.rdb (weight 1.53986) # T0517.t04.stride-ebghtl.rdb (weight 1.24869) # T0517.t04.str2.rdb (weight 1.54758) # T0517.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 T0517.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0517 # Using neural net t04-2621-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 T0517.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 156.387 # # ============================================ # Comments from T0517.t04.stride-ebghtl.rdb # ============================================ # TARGET T0517 # 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 T0517.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 156.387 # # ============================================ # Comments from T0517.t04.str2.rdb # ============================================ # TARGET T0517 # 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 T0517.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 156.387 # # ============================================ # Comments from T0517.t04.alpha.rdb # ============================================ # TARGET T0517 # 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 T0517.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 156.387 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0633 0.0637 0.8730 2 E 0.0774 0.1457 0.7769 3 N 0.0666 0.1502 0.7832 4 K 0.1139 0.0644 0.8217 5 K 0.3534 0.0155 0.6311 6 M 0.8028 0.0037 0.1935 7 N 0.9123 0.0034 0.0843 8 L 0.9322 0.0032 0.0646 9 L 0.9310 0.0033 0.0657 10 L 0.9146 0.0038 0.0816 11 F 0.7546 0.0107 0.2347 12 S 0.2457 0.0261 0.7282 13 G 0.0606 0.0329 0.9065 14 D 0.1012 0.0583 0.8405 15 Y 0.0232 0.7001 0.2768 16 D 0.0114 0.8050 0.1836 17 K 0.0119 0.8192 0.1688 18 A 0.0130 0.8541 0.1329 19 L 0.0070 0.9205 0.0726 20 A 0.0047 0.9518 0.0435 21 S 0.0047 0.9600 0.0353 22 L 0.0047 0.9607 0.0347 23 I 0.0047 0.9610 0.0344 24 I 0.0047 0.9607 0.0347 25 A 0.0046 0.9600 0.0353 26 N 0.0047 0.9572 0.0382 27 A 0.0047 0.9545 0.0408 28 A 0.0048 0.9438 0.0514 29 R 0.0061 0.9073 0.0866 30 E 0.0079 0.8516 0.1405 31 M 0.0500 0.3948 0.5552 32 E 0.0406 0.0546 0.9048 33 I 0.1104 0.0294 0.8603 34 E 0.4109 0.0242 0.5649 35 V 0.8332 0.0098 0.1571 36 T 0.8887 0.0125 0.0988 37 I 0.9183 0.0117 0.0700 38 F 0.8974 0.0264 0.0761 39 C 0.8330 0.0518 0.1152 40 A 0.5297 0.1823 0.2880 41 F 0.2487 0.3329 0.4184 42 W 0.1282 0.5493 0.3225 43 G 0.0542 0.7923 0.1536 44 L 0.0437 0.8604 0.0958 45 L 0.0648 0.8346 0.1006 46 L 0.0615 0.7850 0.1534 47 L 0.1096 0.5497 0.3407 48 R 0.0984 0.3111 0.5905 49 D 0.0722 0.0915 0.8364 50 P 0.0151 0.3707 0.6143 51 E 0.0353 0.3638 0.6008 52 K 0.0626 0.4078 0.5295 53 A 0.0573 0.3895 0.5532 54 S 0.0752 0.3542 0.5706 55 Q 0.0757 0.3080 0.6163 56 E 0.0682 0.3228 0.6090 57 D 0.0735 0.3185 0.6080 58 K 0.0561 0.4810 0.4629 59 S 0.0481 0.5979 0.3540 60 L 0.0361 0.6892 0.2747 61 Y 0.0335 0.7106 0.2559 62 E 0.0279 0.7428 0.2293 63 Q 0.0156 0.7570 0.2274 64 A 0.0210 0.7138 0.2652 65 F 0.0461 0.6266 0.3273 66 S 0.0290 0.5900 0.3810 67 S 0.0378 0.4516 0.5106 68 L 0.0632 0.2595 0.6774 69 T 0.0790 0.0597 0.8613 70 P 0.0493 0.1652 0.7856 71 R 0.0291 0.3766 0.5943 72 E 0.0369 0.4091 0.5540 73 A 0.0247 0.6665 0.3088 74 E 0.0237 0.5771 0.3992 75 E 0.0353 0.4681 0.4966 76 L 0.0928 0.0934 0.8138 77 P 0.0637 0.1429 0.7934 78 L 0.0613 0.3671 0.5716 79 S 0.0718 0.4219 0.5063 80 K 0.0629 0.5029 0.4342 81 M 0.1168 0.3730 0.5102 82 N 0.1070 0.2587 0.6342 83 L 0.0687 0.2986 0.6327 84 G 0.0429 0.3592 0.5979 85 G 0.0328 0.5356 0.4316 86 I 0.0250 0.7278 0.2472 87 G 0.0134 0.8369 0.1497 88 K 0.0053 0.9462 0.0485 89 K 0.0049 0.9566 0.0385 90 M 0.0047 0.9579 0.0374 91 L 0.0048 0.9559 0.0394 92 L 0.0047 0.9596 0.0357 93 E 0.0047 0.9592 0.0361 94 M 0.0048 0.9588 0.0364 95 M 0.0050 0.9515 0.0435 96 K 0.0056 0.9394 0.0550 97 E 0.0073 0.8778 0.1148 98 E 0.0296 0.5146 0.4558 99 K 0.0258 0.0989 0.8753 100 A 0.0601 0.0228 0.9171 101 P 0.0627 0.0374 0.8999 102 K 0.1169 0.0518 0.8313 103 L 0.0050 0.9392 0.0558 104 S 0.0047 0.9547 0.0405 105 D 0.0047 0.9567 0.0386 106 L 0.0047 0.9570 0.0383 107 L 0.0047 0.9584 0.0369 108 S 0.0047 0.9552 0.0401 109 G 0.0047 0.9528 0.0425 110 A 0.0051 0.9468 0.0481 111 R 0.0049 0.9271 0.0680 112 K 0.0064 0.8581 0.1354 113 K 0.0441 0.3382 0.6177 114 E 0.0504 0.0163 0.9333 115 V 0.1673 0.0076 0.8251 116 K 0.7932 0.0103 0.1965 117 F 0.9135 0.0088 0.0776 118 Y 0.8871 0.0244 0.0885 119 A 0.8278 0.0288 0.1434 120 C 0.4950 0.1153 0.3896 121 Q 0.1284 0.5612 0.3104 122 L 0.0376 0.7576 0.2049 123 S 0.0170 0.8926 0.0903 124 V 0.0110 0.9281 0.0609 125 E 0.0075 0.9401 0.0524 126 I 0.0070 0.9089 0.0841 127 M 0.0457 0.4620 0.4923 128 G 0.0352 0.0356 0.9292 129 F 0.0983 0.0130 0.8888 130 K 0.1059 0.0176 0.8765 131 K 0.0077 0.8543 0.1380 132 E 0.0101 0.8727 0.1172 133 E 0.0126 0.8395 0.1479 134 L 0.1119 0.5098 0.3782 135 F 0.0790 0.2616 0.6595 136 P 0.0827 0.3277 0.5896 137 E 0.1806 0.1840 0.6354 138 V 0.5136 0.0621 0.4243 139 Q 0.5622 0.0794 0.3585 140 I 0.6938 0.0488 0.2574 141 M 0.4543 0.0744 0.4713 142 D 0.2170 0.0487 0.7343 143 V 0.0075 0.8949 0.0976 144 K 0.0052 0.9555 0.0393 145 E 0.0052 0.9563 0.0386 146 Y 0.0066 0.9519 0.0415 147 L 0.0055 0.9534 0.0412 148 K 0.0048 0.9443 0.0509 149 N 0.0052 0.9088 0.0860 150 A 0.0091 0.8260 0.1649 151 L 0.0119 0.6858 0.3024 152 E 0.0171 0.4171 0.5658 153 S 0.0616 0.1200 0.8185 154 D 0.0942 0.0402 0.8657 155 L 0.5933 0.0093 0.3974 156 Q 0.8855 0.0039 0.1106 157 L 0.9157 0.0033 0.0809 158 F 0.8880 0.0041 0.1079 159 I 0.7123 0.0082 0.2795