# This file is the result of combining several RDB files, specifically # T0389.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0389.t2k.stride-ebghtl.rdb (weight 1.24869) # T0389.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 T0389.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0389 # 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 T0389.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 408 # # ============================================ # Comments from T0389.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0389 # 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 T0389.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 408 # # ============================================ # Comments from T0389.t2k.str.rdb # ============================================ # TARGET T0389 # 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 T0389.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 408 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0283 0.0184 0.9533 2 I 0.1401 0.1416 0.7183 3 G 0.1135 0.2667 0.6198 4 T 0.0785 0.3761 0.5454 5 Q 0.1018 0.3992 0.4990 6 I 0.1155 0.4579 0.4266 7 V 0.0787 0.4752 0.4461 8 T 0.0170 0.8657 0.1174 9 E 0.0092 0.9115 0.0793 10 R 0.0079 0.9243 0.0679 11 L 0.0068 0.9277 0.0655 12 V 0.0077 0.9302 0.0620 13 A 0.0084 0.9106 0.0811 14 L 0.0072 0.9015 0.0913 15 L 0.0099 0.8565 0.1337 16 E 0.0102 0.7901 0.1997 17 S 0.0102 0.6015 0.3883 18 G 0.0165 0.2134 0.7701 19 T 0.0242 0.1013 0.8745 20 E 0.0327 0.0537 0.9136 21 K 0.1377 0.0225 0.8398 22 V 0.7405 0.0035 0.2561 23 L 0.9621 0.0025 0.0353 24 L 0.9730 0.0025 0.0246 25 I 0.9572 0.0027 0.0401 26 D 0.8871 0.0034 0.1095 27 S 0.4971 0.0082 0.4946 28 R 0.1477 0.0107 0.8416 29 P 0.0429 0.0347 0.9224 30 F 0.0167 0.5912 0.3920 31 V 0.0144 0.7681 0.2175 32 E 0.0128 0.8155 0.1717 33 Y 0.0175 0.8118 0.1707 34 N 0.0294 0.7047 0.2659 35 T 0.0206 0.5165 0.4630 36 S 0.0338 0.2813 0.6849 37 H 0.0858 0.1666 0.7476 38 I 0.1116 0.1127 0.7757 39 L 0.0597 0.2026 0.7377 40 E 0.0650 0.1709 0.7641 41 A 0.2549 0.1094 0.6358 42 I 0.5907 0.0683 0.3410 43 N 0.6190 0.0523 0.3288 44 I 0.3944 0.0373 0.5683 45 N 0.1351 0.0350 0.8299 46 C 0.0159 0.5259 0.4582 47 S 0.0059 0.7376 0.2565 48 K 0.0058 0.8345 0.1596 49 L 0.0096 0.8627 0.1278 50 M 0.0156 0.8264 0.1581 51 K 0.0196 0.7706 0.2099 52 R 0.0206 0.6945 0.2849 53 R 0.0211 0.6758 0.3031 54 L 0.0198 0.5984 0.3817 55 Q 0.0195 0.5271 0.4534 56 Q 0.0198 0.3886 0.5916 57 D 0.0218 0.3126 0.6656 58 K 0.0313 0.4406 0.5280 59 V 0.0736 0.4743 0.4521 60 L 0.1321 0.5048 0.3632 61 I 0.1982 0.5491 0.2528 62 T 0.2385 0.5344 0.2271 63 E 0.2845 0.4952 0.2203 64 L 0.2815 0.4198 0.2987 65 I 0.2216 0.3135 0.4649 66 Q 0.0922 0.2937 0.6141 67 H 0.0329 0.4789 0.4882 68 S 0.0243 0.5284 0.4473 69 A 0.0372 0.5767 0.3861 70 K 0.0611 0.5686 0.3704 71 H 0.0860 0.5217 0.3924 72 K 0.1009 0.4893 0.4098 73 V 0.1042 0.4470 0.4488 74 D 0.1052 0.3340 0.5608 75 I 0.0769 0.2719 0.6513 76 D 0.0610 0.1887 0.7503 77 C 0.0491 0.1362 0.8146 78 S 0.0640 0.0573 0.8788 79 Q 0.2314 0.0173 0.7513 80 K 0.6593 0.0044 0.3364 81 V 0.9424 0.0025 0.0551 82 V 0.9731 0.0024 0.0245 83 V 0.9647 0.0024 0.0329 84 Y 0.9192 0.0026 0.0782 85 D 0.5039 0.0110 0.4851 86 Q 0.0537 0.0430 0.9034 87 S 0.0231 0.0595 0.9173 88 S 0.0360 0.0992 0.8649 89 Q 0.0537 0.1441 0.8022 90 D 0.1115 0.2066 0.6819 91 V 0.0678 0.3429 0.5893 92 A 0.0435 0.3825 0.5740 93 S 0.0310 0.5045 0.4644 94 L 0.0308 0.5089 0.4603 95 S 0.0198 0.5120 0.4682 96 S 0.0108 0.6410 0.3482 97 D 0.0101 0.6674 0.3225 98 C 0.0110 0.7838 0.2052 99 F 0.0061 0.9225 0.0713 100 L 0.0056 0.9419 0.0525 101 T 0.0054 0.9549 0.0396 102 V 0.0057 0.9611 0.0333 103 L 0.0062 0.9590 0.0348 104 L 0.0056 0.9594 0.0350 105 G 0.0053 0.9510 0.0437 106 K 0.0048 0.9399 0.0553 107 L 0.0062 0.9004 0.0934 108 E 0.0084 0.7849 0.2067 109 K 0.0100 0.3692 0.6208 110 S 0.0180 0.0702 0.9117 111 F 0.0592 0.0340 0.9068 112 N 0.1353 0.0365 0.8283 113 S 0.3820 0.0384 0.5796 114 V 0.8375 0.0150 0.1475 115 H 0.9351 0.0092 0.0557 116 L 0.9347 0.0116 0.0537 117 L 0.7947 0.0232 0.1820 118 A 0.3761 0.0713 0.5526 119 G 0.0725 0.1239 0.8036 120 G 0.0579 0.2468 0.6953 121 F 0.0179 0.7898 0.1923 122 A 0.0046 0.9422 0.0532 123 E 0.0044 0.9581 0.0375 124 F 0.0044 0.9600 0.0356 125 S 0.0044 0.9551 0.0405 126 R 0.0045 0.9071 0.0884 127 C 0.0058 0.8140 0.1802 128 F 0.0207 0.3432 0.6361 129 P 0.0124 0.4920 0.4956 130 G 0.0120 0.5337 0.4543 131 L 0.0423 0.5564 0.4013 132 C 0.1255 0.3149 0.5596 133 E 0.1225 0.1832 0.6944 134 G 0.0739 0.0903 0.8359 135 K 0.0782 0.0503 0.8715 136 S 0.1409 0.0431 0.8160 137 T 0.1838 0.0468 0.7694 138 L 0.1495 0.0445 0.8059 139 V 0.1290 0.0639 0.8071 140 P 0.1001 0.0613 0.8386 141 T 0.0815 0.0677 0.8507 142 C 0.0790 0.0832 0.8378 143 I 0.0663 0.0764 0.8573 144 S 0.0636 0.0644 0.8720 145 Q 0.0534 0.0559 0.8907 146 P 0.0487 0.0608 0.8905 147 A 0.0358 0.0892 0.8750 148 H 0.0506 0.0999 0.8495 149 H 0.0555 0.0797 0.8648 150 H 0.0786 0.0770 0.8444 151 H 0.0964 0.0613 0.8423 152 H 0.0751 0.0435 0.8814 153 H 0.0112 0.0080 0.9809