# This file is the result of combining several RDB files, specifically # T0386.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0386.t2k.stride-ebghtl.rdb (weight 1.24869) # T0386.t2k.str2.rdb (weight 1.54758) # T0386.t2k.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 T0386.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0386 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0386.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 244 # # ============================================ # Comments from T0386.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0386 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0386.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 244 # # ============================================ # Comments from T0386.t2k.str2.rdb # ============================================ # TARGET T0386 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0386.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 244 # # ============================================ # Comments from T0386.t2k.alpha.rdb # ============================================ # TARGET T0386 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0386.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 244 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0570 0.6230 0.3200 2 M 0.1087 0.7456 0.1457 3 I 0.1123 0.7466 0.1411 4 N 0.0902 0.7721 0.1377 5 L 0.0714 0.7580 0.1706 6 R 0.0602 0.7390 0.2008 7 E 0.0523 0.6643 0.2834 8 E 0.0602 0.5057 0.4341 9 S 0.0511 0.3296 0.6193 10 L 0.0552 0.2161 0.7288 11 P 0.0470 0.1409 0.8121 12 E 0.0673 0.0840 0.8487 13 Y 0.1487 0.0581 0.7931 14 F 0.2124 0.0246 0.7630 15 D 0.0947 0.0150 0.8903 16 T 0.0050 0.9292 0.0658 17 A 0.0047 0.9476 0.0477 18 Y 0.0048 0.9525 0.0428 19 L 0.0047 0.9574 0.0379 20 C 0.0047 0.9571 0.0382 21 H 0.0047 0.9567 0.0386 22 I 0.0047 0.9551 0.0402 23 H 0.0047 0.9535 0.0418 24 Q 0.0048 0.9460 0.0492 25 Q 0.0056 0.9202 0.0742 26 L 0.0073 0.8743 0.1183 27 F 0.0211 0.7161 0.2627 28 K 0.0224 0.5479 0.4297 29 N 0.0371 0.3730 0.5899 30 T 0.0627 0.2839 0.6535 31 F 0.0759 0.3257 0.5984 32 E 0.0499 0.3677 0.5824 33 W 0.0518 0.3379 0.6103 34 A 0.0558 0.2382 0.7061 35 G 0.0806 0.1065 0.8129 36 Y 0.2744 0.0722 0.6534 37 L 0.6008 0.0449 0.3544 38 R 0.5241 0.0607 0.4151 39 H 0.4665 0.0591 0.4744 40 I 0.3568 0.0740 0.5691 41 P 0.3506 0.0653 0.5841 42 F 0.5504 0.0574 0.3922 43 T 0.6146 0.0550 0.3304 44 F 0.5193 0.0929 0.3878 45 A 0.3053 0.1144 0.5803 46 D 0.2030 0.1251 0.6719 47 G 0.2743 0.1518 0.5740 48 T 0.3764 0.1502 0.4734 49 T 0.4044 0.1463 0.4493 50 A 0.3142 0.1347 0.5511 51 A 0.2379 0.1237 0.6384 52 M 0.1636 0.1372 0.6991 53 P 0.1446 0.2360 0.6194 54 E 0.1472 0.2982 0.5546 55 M 0.2523 0.2576 0.4901 56 K 0.3702 0.1718 0.4580 57 R 0.3502 0.1583 0.4915 58 T 0.2615 0.1405 0.5980 59 G 0.1891 0.1046 0.7063 60 W 0.1963 0.0961 0.7076 61 K 0.2373 0.1020 0.6606 62 N 0.3605 0.1030 0.5366 63 A 0.4601 0.1030 0.4369 64 F 0.5250 0.0785 0.3965 65 A 0.4763 0.0850 0.4386 66 I 0.3397 0.0767 0.5836 67 G 0.2466 0.1397 0.6136 68 D 0.2158 0.1055 0.6787 69 E 0.2120 0.1092 0.6789 70 I 0.1450 0.0663 0.7887 71 Q 0.0886 0.0494 0.8620 72 E 0.0752 0.0902 0.8346 73 G 0.0597 0.1133 0.8270 74 L 0.0186 0.6176 0.3638 75 Q 0.0106 0.6834 0.3061 76 R 0.0140 0.7472 0.2388 77 L 0.0091 0.8421 0.1488 78 D 0.0052 0.9189 0.0759 79 Q 0.0051 0.9296 0.0654 80 T 0.0049 0.9353 0.0597 81 L 0.0049 0.9417 0.0534 82 A 0.0050 0.9419 0.0532 83 E 0.0050 0.9367 0.0583 84 K 0.0050 0.9351 0.0599 85 N 0.0054 0.9268 0.0678 86 N 0.0056 0.8888 0.1056 87 L 0.0079 0.8190 0.1731 88 Q 0.0245 0.6493 0.3263 89 G 0.0258 0.3930 0.5812 90 L 0.0305 0.3353 0.6342 91 T 0.0361 0.2141 0.7498 92 R 0.0367 0.2369 0.7264 93 E 0.0349 0.3651 0.6000 94 E 0.0327 0.4873 0.4799 95 F 0.0122 0.8460 0.1418 96 N 0.0064 0.9329 0.0607 97 S 0.0058 0.9482 0.0461 98 E 0.0055 0.9530 0.0415 99 A 0.0052 0.9555 0.0392 100 I 0.0057 0.9560 0.0383 101 E 0.0065 0.9535 0.0400 102 L 0.0083 0.9457 0.0461 103 F 0.0118 0.9341 0.0540 104 N 0.0325 0.8937 0.0738 105 S 0.0483 0.8593 0.0923 106 L 0.0954 0.7923 0.1123 107 N 0.1414 0.6867 0.1719 108 Q 0.1894 0.5295 0.2811 109 L 0.2122 0.2757 0.5121 110 H 0.1749 0.0759 0.7492 111 P 0.0930 0.1444 0.7625 112 F 0.0940 0.1172 0.7888 113 R 0.0770 0.1364 0.7866 114 E 0.0407 0.1151 0.8442 115 G 0.0308 0.1462 0.8230 116 N 0.0403 0.4217 0.5380 117 G 0.0215 0.7119 0.2666 118 R 0.0175 0.9043 0.0782 119 T 0.0056 0.9479 0.0464 120 Q 0.0047 0.9561 0.0392 121 R 0.0047 0.9592 0.0361 122 L 0.0047 0.9606 0.0347 123 F 0.0047 0.9606 0.0347 124 F 0.0047 0.9603 0.0350 125 E 0.0047 0.9600 0.0354 126 N 0.0047 0.9581 0.0371 127 L 0.0047 0.9575 0.0378 128 A 0.0049 0.9507 0.0444 129 K 0.0054 0.9345 0.0601 130 A 0.0076 0.8858 0.1066 131 A 0.0434 0.3874 0.5692 132 G 0.0373 0.0339 0.9288 133 H 0.0731 0.0228 0.9041 134 Q 0.2026 0.0326 0.7649 135 L 0.2975 0.1041 0.5985 136 N 0.3957 0.1523 0.4520 137 F 0.4601 0.1774 0.3626 138 S 0.3993 0.1971 0.4036 139 L 0.2849 0.2072 0.5079 140 I 0.1567 0.2476 0.5958 141 T 0.0804 0.2858 0.6338 142 K 0.0480 0.4107 0.5413 143 E 0.0138 0.7850 0.2011 144 R 0.0098 0.9022 0.0881 145 M 0.0085 0.9249 0.0666 146 M 0.0081 0.9412 0.0507 147 V 0.0076 0.9505 0.0419 148 A 0.0075 0.9470 0.0455 149 S 0.0055 0.9473 0.0472 150 V 0.0056 0.9450 0.0494 151 A 0.0057 0.9356 0.0587 152 V 0.0063 0.9025 0.0912 153 A 0.0154 0.7607 0.2240 154 E 0.0257 0.5470 0.4273 155 N 0.0478 0.2757 0.6764 156 G 0.0276 0.1216 0.8508 157 D 0.0570 0.0973 0.8457 158 L 0.0541 0.2673 0.6786 159 E 0.0485 0.5231 0.4283 160 P 0.0248 0.8242 0.1510 161 M 0.0174 0.8859 0.0967 162 Q 0.0128 0.9218 0.0654 163 H 0.0126 0.9281 0.0593 164 L 0.0111 0.9248 0.0641 165 F 0.0120 0.9162 0.0718 166 E 0.0093 0.9146 0.0762 167 D 0.0091 0.8754 0.1155 168 I 0.0125 0.8215 0.1661 169 S 0.0171 0.7955 0.1874 170 N 0.0158 0.8246 0.1596 171 P 0.0071 0.8944 0.0985 172 E 0.0072 0.9141 0.0787 173 K 0.0070 0.9254 0.0677 174 I 0.0070 0.9290 0.0640 175 R 0.0066 0.9332 0.0602 176 L 0.0064 0.9249 0.0686 177 L 0.0059 0.9304 0.0637 178 K 0.0063 0.9332 0.0605 179 E 0.0061 0.9279 0.0660 180 F 0.0060 0.9249 0.0691 181 M 0.0064 0.9203 0.0733 182 H 0.0071 0.8866 0.1064 183 T 0.0092 0.8210 0.1698 184 M 0.0183 0.7482 0.2335 185 K 0.0209 0.7090 0.2701 186 N 0.0263 0.6315 0.3421 187 T 0.0433 0.4658 0.4908 188 G 0.0473 0.3801 0.5726 189 R 0.0449 0.4048 0.5503 190 N 0.0661 0.3147 0.6193 191 V 0.0731 0.3681 0.5588 192 N 0.0912 0.3416 0.5672 193 D 0.1152 0.2993 0.5855 194 R 0.2214 0.1929 0.5858 195 P 0.3507 0.1291 0.5202 196 V 0.6356 0.0983 0.2660 197 M 0.7524 0.0758 0.1718 198 V 0.6918 0.0800 0.2282 199 A 0.4700 0.0703 0.4597 200 K 0.2111 0.0439 0.7450 201 E 0.0503 0.0483 0.9013