# This file is the result of combining several RDB files, specifically # T0561.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0561.t2k.stride-ebghtl.rdb (weight 1.24869) # T0561.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 T0561.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0561 # 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 T0561.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 4 # # ============================================ # Comments from T0561.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0561 # 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 T0561.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 4 # # ============================================ # Comments from T0561.t2k.str.rdb # ============================================ # TARGET T0561 # 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 T0561.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 4 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.0222 0.0359 0.9420 2 E 0.0694 0.1304 0.8003 3 K 0.0622 0.3082 0.6295 4 K 0.0532 0.4275 0.5193 5 K 0.0586 0.4900 0.4514 6 Y 0.0627 0.4903 0.4469 7 L 0.0672 0.4786 0.4542 8 D 0.0483 0.5034 0.4483 9 S 0.0160 0.7739 0.2100 10 E 0.0093 0.8010 0.1897 11 F 0.0082 0.7933 0.1985 12 L 0.0074 0.8265 0.1661 13 L 0.0051 0.8206 0.1743 14 H 0.0052 0.7861 0.2087 15 C 0.0089 0.6961 0.2950 16 I 0.0143 0.5845 0.4012 17 S 0.0109 0.5035 0.4856 18 A 0.0040 0.9171 0.0789 19 Q 0.0039 0.9402 0.0559 20 L 0.0038 0.9597 0.0365 21 L 0.0037 0.9665 0.0298 22 D 0.0038 0.9603 0.0360 23 M 0.0039 0.9559 0.0402 24 W 0.0037 0.9653 0.0309 25 K 0.0037 0.9614 0.0349 26 Q 0.0037 0.9477 0.0486 27 A 0.0037 0.9407 0.0555 28 R 0.0038 0.9448 0.0514 29 A 0.0037 0.9572 0.0391 30 R 0.0038 0.9485 0.0477 31 W 0.0038 0.9594 0.0369 32 L 0.0044 0.9634 0.0322 33 E 0.0050 0.9588 0.0361 34 L 0.0058 0.9354 0.0589 35 V 0.0098 0.9119 0.0783 36 G 0.0090 0.9073 0.0837 37 K 0.0050 0.9277 0.0673 38 E 0.0059 0.9334 0.0607 39 W 0.0061 0.9395 0.0544 40 A 0.0047 0.9455 0.0498 41 H 0.0044 0.9349 0.0606 42 M 0.0050 0.9054 0.0896 43 L 0.0088 0.8620 0.1292 44 A 0.0131 0.7055 0.2814 45 L 0.0174 0.4934 0.4892 46 N 0.0177 0.0499 0.9324 47 P 0.0166 0.2090 0.7744 48 E 0.0300 0.2399 0.7301 49 R 0.0857 0.2587 0.6556 50 K 0.1579 0.1151 0.7270 51 D 0.2496 0.0899 0.6604 52 F 0.4741 0.0635 0.4624 53 L 0.5360 0.0456 0.4184 54 W 0.4977 0.0730 0.4293 55 K 0.3266 0.0868 0.5867 56 N 0.1692 0.0895 0.7413 57 Q 0.0836 0.1294 0.7870 58 S 0.0688 0.2069 0.7244 59 E 0.0707 0.3502 0.5791 60 M 0.0610 0.4778 0.4613 61 N 0.0532 0.5937 0.3531 62 S 0.0729 0.6629 0.2642 63 A 0.0554 0.7339 0.2107 64 F 0.0627 0.7905 0.1467 65 F 0.0686 0.7886 0.1428 66 D 0.0687 0.7628 0.1685 67 L 0.0182 0.8421 0.1397 68 C 0.0095 0.8875 0.1030 69 E 0.0057 0.9158 0.0785 70 V 0.0047 0.9504 0.0449 71 G 0.0038 0.9539 0.0422 72 K 0.0064 0.9513 0.0423 73 Q 0.0127 0.9424 0.0449 74 V 0.0087 0.9388 0.0524 75 M 0.0272 0.8899 0.0828 76 L 0.0223 0.8404 0.1373 77 G 0.0306 0.7240 0.2454 78 L 0.0480 0.5587 0.3933 79 L 0.0650 0.3512 0.5838 80 G 0.0423 0.1146 0.8431 81 K 0.0486 0.1418 0.8096 82 E 0.1224 0.1361 0.7415 83 V 0.1293 0.0871 0.7836 84 A 0.0826 0.0571 0.8602 85 L 0.0285 0.0494 0.9221 86 P 0.0106 0.4798 0.5097 87 K 0.0066 0.7389 0.2546 88 E 0.0075 0.7639 0.2287 89 E 0.0075 0.7870 0.2055 90 Q 0.0076 0.8243 0.1681 91 A 0.0092 0.8675 0.1233 92 F 0.0070 0.9343 0.0586 93 W 0.0041 0.9698 0.0261 94 I 0.0041 0.9744 0.0215 95 M 0.0037 0.9748 0.0215 96 Y 0.0037 0.9720 0.0243 97 A 0.0037 0.9676 0.0286 98 V 0.0038 0.9528 0.0434 99 H 0.0051 0.9023 0.0927 100 L 0.0086 0.8592 0.1323 101 S 0.0070 0.8112 0.1818 102 A 0.0040 0.8543 0.1417 103 A 0.0060 0.8261 0.1679 104 C 0.0095 0.8086 0.1819 105 A 0.0081 0.8446 0.1473 106 E 0.0082 0.7957 0.1961 107 E 0.0115 0.7195 0.2691 108 L 0.0135 0.4819 0.5047 109 H 0.0186 0.1892 0.7922 110 M 0.0147 0.1041 0.8812 111 E 0.0251 0.2144 0.7605 112 V 0.0213 0.2642 0.7146 113 A 0.0435 0.2785 0.6780 114 M 0.0728 0.2269 0.7003 115 S 0.1475 0.1688 0.6837 116 L 0.2382 0.3059 0.4559 117 R 0.3349 0.3030 0.3621 118 K 0.4699 0.2751 0.2550 119 L 0.4469 0.2261 0.3270 120 N 0.5432 0.0811 0.3758 121 V 0.6085 0.0589 0.3326 122 K 0.6486 0.0484 0.3030 123 L 0.5646 0.0685 0.3669 124 K 0.3353 0.0871 0.5776 125 D 0.1775 0.0837 0.7389 126 F 0.1756 0.0958 0.7286 127 N 0.1944 0.0725 0.7332 128 F 0.1333 0.0824 0.7843 129 G 0.0995 0.0972 0.8032 130 G 0.1728 0.1540 0.6732 131 T 0.2579 0.1598 0.5822 132 R 0.3902 0.2430 0.3668 133 Y 0.3764 0.2726 0.3509 134 F 0.2136 0.2871 0.4993 135 K 0.0820 0.1971 0.7209 136 D 0.0482 0.1063 0.8454 137 M 0.0349 0.0471 0.9179 138 P 0.0160 0.0685 0.9155 139 P 0.0059 0.6296 0.3645 140 E 0.0050 0.8040 0.1910 141 E 0.0047 0.8078 0.1875 142 K 0.0055 0.8426 0.1519 143 K 0.0069 0.8648 0.1284 144 R 0.0048 0.8634 0.1318 145 R 0.0047 0.8686 0.1267 146 M 0.0045 0.8840 0.1115 147 E 0.0045 0.8869 0.1086 148 R 0.0043 0.8871 0.1086 149 K 0.0043 0.9104 0.0853 150 Q 0.0042 0.9212 0.0746 151 R 0.0044 0.9167 0.0789 152 I 0.0039 0.9499 0.0463 153 E 0.0038 0.9530 0.0431 154 E 0.0042 0.9456 0.0501 155 A 0.0039 0.9349 0.0612 156 R 0.0047 0.9066 0.0886 157 R 0.0049 0.8318 0.1633 158 H 0.0054 0.5902 0.4045 159 G 0.0130 0.2181 0.7689 160 M 0.0166 0.0443 0.9391 161 P 0.0094 0.0049 0.9858