# This file is the result of combining several RDB files, specifically # T0481.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0481.t2k.stride-ebghtl.rdb (weight 1.24869) # T0481.t2k.str.rdb (weight 1.53983) # 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 T0481.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0481 # 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 T0481.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 141 # # ============================================ # Comments from T0481.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0481 # 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 T0481.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 141 # # ============================================ # Comments from T0481.t2k.str.rdb # ============================================ # TARGET T0481 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0481.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 141 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0130 0.0222 0.9647 2 C 0.0582 0.1135 0.8283 3 Q 0.0316 0.4285 0.5399 4 S 0.0047 0.8655 0.1298 5 N 0.0043 0.8952 0.1005 6 Q 0.0041 0.9177 0.0783 7 I 0.0049 0.9248 0.0703 8 V 0.0042 0.9488 0.0470 9 S 0.0039 0.9414 0.0546 10 H 0.0041 0.9308 0.0651 11 F 0.0042 0.9326 0.0631 12 L 0.0040 0.9389 0.0571 13 S 0.0039 0.9215 0.0746 14 H 0.0039 0.9316 0.0645 15 R 0.0038 0.9447 0.0515 16 N 0.0038 0.9565 0.0397 17 V 0.0038 0.9616 0.0346 18 T 0.0038 0.9693 0.0269 19 N 0.0037 0.9753 0.0210 20 E 0.0037 0.9720 0.0243 21 L 0.0037 0.9687 0.0276 22 A 0.0037 0.9649 0.0314 23 E 0.0038 0.8704 0.1257 24 K 0.0049 0.6388 0.3563 25 I 0.0210 0.1317 0.8472 26 S 0.0191 0.0536 0.9273 27 K 0.0080 0.7168 0.2752 28 D 0.0102 0.7503 0.2395 29 H 0.0129 0.8196 0.1675 30 Y 0.0671 0.5066 0.4263 31 S 0.0961 0.2377 0.6662 32 Y 0.1310 0.1756 0.6935 33 K 0.1266 0.0701 0.8034 34 P 0.0811 0.0737 0.8452 35 A 0.0466 0.0799 0.8734 36 E 0.0168 0.1238 0.8593 37 T 0.0147 0.0980 0.8874 38 S 0.0740 0.0614 0.8646 39 M 0.1495 0.0353 0.8153 40 S 0.1128 0.0359 0.8513 41 A 0.0044 0.9412 0.0544 42 E 0.0038 0.9594 0.0369 43 E 0.0038 0.9706 0.0257 44 L 0.0037 0.9735 0.0228 45 V 0.0037 0.9726 0.0237 46 K 0.0037 0.9728 0.0235 47 H 0.0037 0.9669 0.0294 48 I 0.0037 0.9671 0.0291 49 L 0.0037 0.9628 0.0335 50 T 0.0038 0.9577 0.0386 51 S 0.0041 0.9593 0.0366 52 F 0.0038 0.9661 0.0301 53 H 0.0038 0.9697 0.0266 54 L 0.0037 0.9699 0.0264 55 F 0.0045 0.9696 0.0260 56 A 0.0055 0.9656 0.0290 57 N 0.0059 0.9495 0.0446 58 V 0.0067 0.9167 0.0766 59 I 0.0143 0.8465 0.1392 60 K 0.0177 0.6636 0.3188 61 E 0.0179 0.3685 0.6136 62 G 0.0269 0.1238 0.8494 63 N 0.0592 0.1279 0.8129 64 A 0.1092 0.1519 0.7389 65 S 0.0957 0.1413 0.7630 66 P 0.0741 0.1943 0.7316 67 F 0.0501 0.2107 0.7393 68 Q 0.0377 0.2386 0.7236 69 N 0.0333 0.2021 0.7645 70 K 0.0326 0.1262 0.8411 71 Q 0.0324 0.0976 0.8700 72 E 0.0454 0.0993 0.8553 73 E 0.0491 0.0874 0.8635 74 T 0.0334 0.0942 0.8724 75 E 0.0039 0.9427 0.0534 76 T 0.0038 0.9569 0.0393 77 D 0.0038 0.9653 0.0309 78 L 0.0038 0.9667 0.0295 79 N 0.0038 0.9670 0.0292 80 V 0.0038 0.9556 0.0406 81 L 0.0039 0.9440 0.0521 82 A 0.0039 0.9452 0.0509 83 K 0.0039 0.9388 0.0572 84 T 0.0040 0.9298 0.0662 85 Y 0.0040 0.9335 0.0624 86 T 0.0039 0.9506 0.0455 87 E 0.0038 0.9636 0.0326 88 K 0.0038 0.9651 0.0311 89 T 0.0038 0.9695 0.0267 90 V 0.0038 0.9718 0.0245 91 A 0.0038 0.9677 0.0285 92 I 0.0038 0.9605 0.0357 93 L 0.0038 0.9419 0.0543 94 E 0.0040 0.8008 0.1952 95 Q 0.0051 0.5412 0.4537 96 L 0.0187 0.1652 0.8161 97 T 0.0178 0.0625 0.9198 98 E 0.0065 0.7718 0.2217 99 E 0.0100 0.7676 0.2225 100 Q 0.0152 0.8208 0.1641 101 L 0.0450 0.7339 0.2210 102 D 0.0871 0.6025 0.3104 103 R 0.1113 0.5749 0.3138 104 E 0.2023 0.4069 0.3908 105 I 0.2674 0.3065 0.4261 106 D 0.2598 0.2465 0.4937 107 L 0.1300 0.1591 0.7109 108 T 0.0778 0.1406 0.7816 109 S 0.0444 0.1278 0.8278 110 A 0.0369 0.1361 0.8271 111 F 0.0444 0.1388 0.8168 112 G 0.0557 0.1332 0.8111 113 R 0.0936 0.1185 0.7879 114 K 0.1517 0.1037 0.7446 115 V 0.1377 0.0995 0.7628 116 T 0.0804 0.1326 0.7870 117 G 0.0041 0.9587 0.0372 118 R 0.0038 0.9691 0.0271 119 A 0.0037 0.9740 0.0223 120 L 0.0037 0.9752 0.0211 121 L 0.0037 0.9734 0.0229 122 Q 0.0037 0.9685 0.0278 123 L 0.0037 0.9586 0.0377 124 A 0.0037 0.9575 0.0388 125 M 0.0037 0.9522 0.0441 126 E 0.0037 0.9436 0.0527 127 H 0.0048 0.9132 0.0820 128 E 0.0052 0.9057 0.0892 129 I 0.0052 0.9176 0.0772 130 H 0.0070 0.8937 0.0993 131 H 0.0096 0.8742 0.1162 132 K 0.0048 0.8978 0.0974 133 G 0.0048 0.9153 0.0799 134 N 0.0048 0.9680 0.0272 135 L 0.0041 0.9759 0.0200 136 F 0.0037 0.9769 0.0193 137 V 0.0037 0.9769 0.0193 138 Y 0.0048 0.9752 0.0200 139 V 0.0062 0.9714 0.0224 140 R 0.0044 0.9655 0.0300 141 E 0.0045 0.9057 0.0898 142 M 0.0042 0.5191 0.4766 143 G 0.0158 0.0154 0.9688 144 H 0.0367 0.0059 0.9574 145 T 0.1119 0.0068 0.8813 146 E 0.0695 0.0129 0.9176 147 L 0.0903 0.0260 0.8836 148 P 0.3417 0.0731 0.5852 149 F 0.5302 0.0539 0.4159 150 Y 0.4682 0.0394 0.4924 151 Q 0.3430 0.0231 0.6339 152 Q 0.1840 0.0238 0.7922 153 R 0.0751 0.0187 0.9062 154 M 0.0104 0.0106 0.9789