# This file is the result of combining several RDB files, specifically # T0557.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0557.t2k.stride-ebghtl.rdb (weight 1.24869) # T0557.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 T0557.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0557 # 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 T0557.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 155 # # ============================================ # Comments from T0557.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0557 # 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 T0557.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 155 # # ============================================ # Comments from T0557.t2k.str.rdb # ============================================ # TARGET T0557 # 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 T0557.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 155 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0224 0.0918 0.8858 2 R 0.0558 0.2750 0.6692 3 S 0.0412 0.5633 0.3955 4 A 0.0075 0.8943 0.0983 5 T 0.0054 0.9384 0.0562 6 D 0.0044 0.9530 0.0426 7 L 0.0041 0.9633 0.0326 8 L 0.0041 0.9673 0.0286 9 D 0.0041 0.9648 0.0312 10 E 0.0038 0.9570 0.0392 11 L 0.0039 0.9424 0.0537 12 N 0.0044 0.8839 0.1117 13 A 0.0072 0.6535 0.3394 14 V 0.0110 0.3146 0.6745 15 D 0.0193 0.0928 0.8879 16 E 0.0617 0.0987 0.8396 17 S 0.1560 0.1207 0.7234 18 A 0.2888 0.1238 0.5874 19 R 0.4719 0.1288 0.3993 20 I 0.6408 0.1896 0.1695 21 E 0.6867 0.1761 0.1372 22 A 0.6735 0.1746 0.1518 23 K 0.6109 0.1939 0.1952 24 R 0.3952 0.2070 0.3979 25 A 0.1175 0.1542 0.7283 26 S 0.0291 0.0932 0.8777 27 D 0.0248 0.0761 0.8990 28 M 0.0400 0.0499 0.9102 29 G 0.0273 0.1121 0.8606 30 K 0.0128 0.5340 0.4532 31 S 0.0316 0.5869 0.3815 32 V 0.0281 0.8286 0.1433 33 M 0.0861 0.7736 0.1403 34 E 0.0639 0.8063 0.1298 35 T 0.1193 0.7893 0.0914 36 V 0.1063 0.8081 0.0856 37 I 0.1156 0.8009 0.0835 38 A 0.1237 0.7811 0.0953 39 F 0.1898 0.6659 0.1443 40 A 0.1456 0.5402 0.3142 41 N 0.1048 0.2108 0.6844 42 E 0.0554 0.0726 0.8720 43 P 0.0258 0.1102 0.8641 44 G 0.0275 0.0890 0.8835 45 L 0.0645 0.0900 0.8455 46 D 0.0803 0.0396 0.8801 47 G 0.1399 0.0325 0.8275 48 G 0.3851 0.0102 0.6047 49 Y 0.8580 0.0030 0.1390 50 L 0.9625 0.0025 0.0350 51 L 0.9703 0.0024 0.0273 52 L 0.9568 0.0026 0.0406 53 G 0.9140 0.0031 0.0829 54 V 0.8587 0.0046 0.1367 55 D 0.7068 0.0081 0.2851 56 W 0.3042 0.0586 0.6372 57 A 0.0739 0.0704 0.8556 58 I 0.0309 0.0552 0.9139 59 N 0.0885 0.0348 0.8767 60 D 0.5696 0.0136 0.4168 61 K 0.8131 0.0053 0.1816 62 G 0.7791 0.0088 0.2121 63 D 0.6623 0.0183 0.3194 64 T 0.5503 0.0267 0.4229 65 V 0.4223 0.0459 0.5318 66 Y 0.2989 0.0583 0.6427 67 R 0.1633 0.0803 0.7564 68 P 0.0765 0.1270 0.7965 69 V 0.0377 0.1286 0.8337 70 G 0.0305 0.1457 0.8238 71 L 0.0208 0.4787 0.5005 72 P 0.0196 0.5621 0.4183 73 D 0.0187 0.6392 0.3421 74 P 0.0068 0.8831 0.1100 75 D 0.0055 0.9274 0.0671 76 K 0.0042 0.9472 0.0486 77 V 0.0038 0.9526 0.0436 78 Q 0.0038 0.9542 0.0420 79 R 0.0039 0.9354 0.0608 80 D 0.0040 0.9060 0.0900 81 L 0.0053 0.8663 0.1284 82 A 0.0057 0.7723 0.2219 83 S 0.0075 0.6623 0.3302 84 Q 0.0098 0.6710 0.3192 85 C 0.0174 0.6882 0.2944 86 A 0.0245 0.6769 0.2985 87 S 0.0337 0.5933 0.3731 88 M 0.0628 0.4083 0.5288 89 L 0.0928 0.2115 0.6957 90 N 0.0829 0.0601 0.8570 91 V 0.0928 0.0670 0.8401 92 A 0.1306 0.0535 0.8159 93 L 0.1913 0.0453 0.7634 94 R 0.2030 0.0313 0.7657 95 P 0.2455 0.0490 0.7055 96 E 0.4106 0.0348 0.5546 97 M 0.7325 0.0088 0.2587 98 Q 0.9136 0.0030 0.0834 99 L 0.9404 0.0028 0.0567 100 E 0.9539 0.0029 0.0432 101 Q 0.8590 0.0034 0.1376 102 V 0.6507 0.0157 0.3336 103 G 0.0404 0.0273 0.9323 104 G 0.0250 0.0288 0.9462 105 K 0.4322 0.0101 0.5577 106 T 0.8984 0.0027 0.0989 107 L 0.9693 0.0024 0.0283 108 L 0.9799 0.0024 0.0178 109 V 0.9804 0.0024 0.0172 110 V 0.9727 0.0024 0.0250 111 Y 0.9019 0.0026 0.0955 112 V 0.5765 0.0040 0.4196 113 P 0.1811 0.0109 0.8079 114 E 0.0722 0.0496 0.8782 115 A 0.0749 0.0373 0.8878 116 D 0.0509 0.0377 0.9114 117 V 0.0199 0.3327 0.6474 118 T 0.0251 0.3073 0.6677 119 H 0.0585 0.2308 0.7107 120 K 0.1328 0.0219 0.8453 121 P 0.2303 0.0135 0.7562 122 I 0.8104 0.0087 0.1809 123 Y 0.8987 0.0075 0.0938 124 K 0.8298 0.0094 0.1608 125 K 0.6215 0.0130 0.3655 126 A 0.2574 0.0237 0.7190 127 T 0.1220 0.0299 0.8481 128 G 0.1163 0.0460 0.8377 129 L 0.1361 0.0599 0.8040 130 P 0.1651 0.0642 0.7707 131 G 0.1751 0.0443 0.7806 132 G 0.3340 0.0285 0.6375 133 A 0.6996 0.0112 0.2892 134 Y 0.9043 0.0071 0.0886 135 R 0.9136 0.0071 0.0793 136 R 0.8418 0.0075 0.1507 137 I 0.5065 0.0155 0.4779 138 G 0.1220 0.0273 0.8507 139 S 0.0434 0.0445 0.9121 140 S 0.0744 0.0580 0.8677 141 D 0.1520 0.0696 0.7785 142 Q 0.2970 0.0776 0.6255 143 R 0.3614 0.0757 0.5629 144 C 0.1594 0.0404 0.8001 145 V 0.0128 0.0054 0.9817