# This file is the result of combining several RDB files, specifically # T0316.t06.dssp-ebghstl.rdb (weight 1.53986) # T0316.t06.stride-ebghtl.rdb (weight 1.24869) # T0316.t06.str2.rdb (weight 1.54758) # T0316.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 T0316.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 2446 # # ============================================ # Comments from T0316.t06.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 2446 # # ============================================ # Comments from T0316.t06.str2.rdb # ============================================ # TARGET T0316 # 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 T0316.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 2446 # # ============================================ # Comments from T0316.t06.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 2446 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0619 0.0117 0.9264 2 S 0.0911 0.0347 0.8742 3 D 0.0702 0.1081 0.8217 4 N 0.0515 0.1503 0.7982 5 S 0.0467 0.1817 0.7716 6 K 0.0706 0.0701 0.8593 7 T 0.1851 0.0224 0.7925 8 R 0.6641 0.0051 0.3307 9 V 0.9114 0.0035 0.0851 10 V 0.9332 0.0032 0.0636 11 V 0.9317 0.0033 0.0649 12 G 0.9244 0.0041 0.0715 13 M 0.8774 0.0077 0.1150 14 S 0.5334 0.0190 0.4477 15 G 0.1199 0.0312 0.8489 16 G 0.0734 0.0687 0.8579 17 V 0.0534 0.3770 0.5696 18 D 0.0285 0.6161 0.3553 19 S 0.0060 0.9208 0.0732 20 S 0.0050 0.9553 0.0397 21 V 0.0047 0.9598 0.0355 22 T 0.0049 0.9604 0.0347 23 A 0.0047 0.9608 0.0345 24 L 0.0047 0.9608 0.0346 25 L 0.0046 0.9608 0.0345 26 L 0.0047 0.9601 0.0353 27 K 0.0048 0.9544 0.0408 28 E 0.0058 0.9135 0.0807 29 Q 0.0424 0.3772 0.5804 30 G 0.0352 0.0183 0.9465 31 Y 0.0700 0.0090 0.9211 32 D 0.4334 0.0091 0.5575 33 V 0.8449 0.0034 0.1517 34 I 0.8963 0.0053 0.0984 35 G 0.9281 0.0036 0.0683 36 I 0.9298 0.0033 0.0669 37 F 0.9203 0.0037 0.0759 38 M 0.8299 0.0061 0.1640 39 K 0.4813 0.0260 0.4927 40 N 0.2523 0.0284 0.7193 41 W 0.1194 0.0970 0.7836 42 D 0.1407 0.1353 0.7241 43 D 0.1565 0.1671 0.6764 44 T 0.1530 0.1729 0.6740 45 D 0.0774 0.1424 0.7802 46 E 0.0311 0.1892 0.7798 47 N 0.0546 0.0913 0.8541 48 G 0.0671 0.0650 0.8678 49 V 0.1791 0.0627 0.7582 50 C 0.3264 0.0579 0.6157 51 T 0.1507 0.0705 0.7788 52 A 0.0867 0.1426 0.7706 53 T 0.0267 0.6502 0.3230 54 E 0.0237 0.7427 0.2336 55 D 0.0294 0.7427 0.2279 56 Y 0.0061 0.9235 0.0704 57 K 0.0049 0.9426 0.0525 58 D 0.0048 0.9475 0.0477 59 V 0.0047 0.9571 0.0382 60 V 0.0046 0.9609 0.0345 61 A 0.0046 0.9605 0.0349 62 V 0.0046 0.9609 0.0344 63 A 0.0047 0.9601 0.0352 64 D 0.0048 0.9535 0.0418 65 Q 0.0054 0.9315 0.0630 66 I 0.0445 0.4813 0.4742 67 G 0.0431 0.0144 0.9425 68 I 0.0630 0.0077 0.9293 69 P 0.2687 0.0144 0.7170 70 Y 0.8496 0.0062 0.1442 71 Y 0.9127 0.0048 0.0825 72 S 0.9225 0.0039 0.0736 73 V 0.8689 0.0076 0.1236 74 N 0.5851 0.0065 0.4084 75 F 0.1404 0.1238 0.7359 76 E 0.0468 0.2708 0.6823 77 K 0.0088 0.8122 0.1789 78 E 0.0091 0.8639 0.1270 79 Y 0.0088 0.8794 0.1119 80 W 0.0077 0.9102 0.0821 81 D 0.0069 0.9175 0.0756 82 R 0.0074 0.9172 0.0754 83 V 0.0088 0.9172 0.0740 84 F 0.0100 0.9235 0.0665 85 E 0.0069 0.9399 0.0532 86 Y 0.0073 0.9394 0.0533 87 F 0.0077 0.9311 0.0612 88 L 0.0083 0.9276 0.0641 89 A 0.0064 0.9358 0.0577 90 E 0.0075 0.9287 0.0638 91 Y 0.0130 0.9041 0.0830 92 R 0.0188 0.8360 0.1453 93 A 0.0395 0.4597 0.5008 94 G 0.0281 0.0828 0.8891 95 R 0.0719 0.0456 0.8825 96 T 0.1094 0.0190 0.8716 97 P 0.1033 0.0446 0.8522 98 N 0.1164 0.0311 0.8525 99 P 0.0605 0.2324 0.7071 100 D 0.0974 0.3176 0.5850 101 V 0.1053 0.5021 0.3925 102 M 0.1123 0.4411 0.4465 103 C 0.0789 0.4820 0.4390 104 N 0.0409 0.4560 0.5031 105 K 0.0167 0.7389 0.2444 106 E 0.0179 0.8741 0.1080 107 I 0.0271 0.8968 0.0761 108 K 0.0179 0.9180 0.0641 109 F 0.0081 0.9442 0.0476 110 K 0.0057 0.9525 0.0418 111 A 0.0048 0.9563 0.0389 112 F 0.0048 0.9573 0.0379 113 L 0.0047 0.9607 0.0346 114 D 0.0047 0.9601 0.0352 115 Y 0.0047 0.9596 0.0357 116 A 0.0047 0.9597 0.0357 117 I 0.0048 0.9521 0.0431 118 T 0.0052 0.9284 0.0664 119 L 0.0438 0.4743 0.4820 120 G 0.0539 0.0116 0.9345 121 A 0.0850 0.0070 0.9080 122 D 0.1084 0.0497 0.8419 123 Y 0.8915 0.0054 0.1031 124 V 0.9277 0.0043 0.0680 125 A 0.9165 0.0074 0.0761 126 T 0.8354 0.0164 0.1482 127 G 0.4894 0.0271 0.4835 128 H 0.3397 0.0780 0.5822 129 Y 0.2629 0.1353 0.6017 130 A 0.3303 0.1514 0.5182 131 R 0.4307 0.1360 0.4333 132 V 0.3688 0.1230 0.5083 133 A 0.1630 0.1001 0.7369 134 R 0.1617 0.1546 0.6837 135 D 0.1279 0.2916 0.5805 136 E 0.0903 0.3918 0.5179 137 D 0.0984 0.3307 0.5709 138 G 0.1199 0.2238 0.6563 139 T 0.2967 0.2104 0.4929 140 V 0.3413 0.3147 0.3440 141 H 0.3074 0.3338 0.3588 142 M 0.2596 0.3591 0.3813 143 L 0.2091 0.3114 0.4796 144 R 0.1173 0.2036 0.6792 145 G 0.0889 0.1691 0.7419 146 V 0.1247 0.2004 0.6749 147 D 0.0806 0.2652 0.6542 148 N 0.0547 0.2877 0.6576 149 G 0.0567 0.3362 0.6071 150 K 0.0657 0.3870 0.5473 151 D 0.0925 0.3588 0.5487 152 Q 0.1384 0.3686 0.4930 153 T 0.1629 0.4416 0.3954 154 Y 0.1472 0.5734 0.2795 155 F 0.1515 0.5820 0.2665 156 L 0.1218 0.5541 0.3241 157 S 0.0900 0.4567 0.4533 158 Q 0.0910 0.4553 0.4537 159 L 0.1022 0.3462 0.5515 160 S 0.0769 0.3232 0.5999 161 Q 0.0159 0.7777 0.2064 162 E 0.0193 0.7742 0.2065 163 Q 0.0213 0.7742 0.2044 164 L 0.0549 0.6537 0.2913 165 Q 0.1228 0.5089 0.3682 166 K 0.2122 0.4080 0.3797 167 T 0.3806 0.3130 0.3064 168 M 0.5018 0.1853 0.3130 169 F 0.4080 0.1577 0.4343 170 P 0.2799 0.2058 0.5143 171 L 0.0895 0.4562 0.4544 172 G 0.0514 0.4135 0.5351 173 H 0.0470 0.3273 0.6257 174 L 0.1101 0.0456 0.8443 175 E 0.0600 0.0275 0.9125 176 K 0.0063 0.9328 0.0609 177 P 0.0047 0.9573 0.0380 178 E 0.0047 0.9603 0.0351 179 V 0.0047 0.9608 0.0345 180 R 0.0046 0.9610 0.0343 181 R 0.0046 0.9611 0.0343 182 L 0.0046 0.9615 0.0339 183 A 0.0047 0.9610 0.0344 184 E 0.0048 0.9556 0.0397 185 E 0.0056 0.9339 0.0605 186 A 0.0431 0.4599 0.4970 187 G 0.0431 0.0152 0.9417 188 L 0.0644 0.0084 0.9272 189 S 0.1072 0.0470 0.8458 190 T 0.3337 0.1058 0.5606 191 A 0.2878 0.1390 0.5733 192 K 0.3041 0.1533 0.5427 193 K 0.2568 0.0806 0.6626 194 K 0.1565 0.0802 0.7633 195 D 0.1150 0.0625 0.8225 196 S 0.1013 0.0874 0.8113 197 T 0.0806 0.1393 0.7801 198 G 0.1363 0.1134 0.7503 199 I 0.2474 0.1236 0.6290 200 C 0.3666 0.1100 0.5234 201 F 0.4261 0.1076 0.4663 202 I 0.3255 0.0881 0.5864 203 G 0.1875 0.0754 0.7371 204 E 0.0928 0.0846 0.8226 205 K 0.0574 0.0413 0.9013