# This file is the result of combining several RDB files, specifically # T0634.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0634.t2k.stride-ebghtl.rdb (weight 1.24869) # T0634.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 T0634.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0634 # 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 T0634.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 1163 # # ============================================ # Comments from T0634.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0634 # 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 T0634.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 1163 # # ============================================ # Comments from T0634.t2k.str.rdb # ============================================ # TARGET T0634 # 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 T0634.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 1163 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0191 0.0079 0.9730 2 S 0.0833 0.0159 0.9008 3 L 0.1178 0.0207 0.8614 4 K 0.5510 0.0138 0.4352 5 K 0.9207 0.0025 0.0768 6 I 0.9722 0.0024 0.0254 7 L 0.9722 0.0024 0.0254 8 I 0.9147 0.0025 0.0828 9 I 0.4853 0.0039 0.5109 10 D 0.0696 0.0083 0.9221 11 Q 0.0121 0.1293 0.8585 12 Q 0.0046 0.8164 0.1790 13 D 0.0041 0.9067 0.0892 14 F 0.0041 0.9507 0.0452 15 S 0.0038 0.9680 0.0282 16 R 0.0038 0.9684 0.0278 17 I 0.0043 0.9690 0.0267 18 E 0.0049 0.9653 0.0297 19 L 0.0044 0.9657 0.0299 20 K 0.0038 0.9611 0.0351 21 N 0.0038 0.9522 0.0440 22 F 0.0045 0.9154 0.0801 23 L 0.0068 0.8621 0.1312 24 D 0.0114 0.6709 0.3177 25 S 0.0056 0.2860 0.7084 26 E 0.0126 0.0097 0.9778 27 Y 0.2223 0.0075 0.7702 28 L 0.7991 0.0061 0.1948 29 V 0.9398 0.0049 0.0553 30 I 0.9402 0.0071 0.0527 31 E 0.9081 0.0050 0.0870 32 S 0.6516 0.0088 0.3396 33 K 0.1507 0.0183 0.8310 34 N 0.0350 0.0202 0.9448 35 E 0.0107 0.6946 0.2947 36 K 0.0037 0.9553 0.0409 37 E 0.0037 0.9690 0.0273 38 A 0.0037 0.9737 0.0225 39 L 0.0037 0.9752 0.0211 40 E 0.0037 0.9728 0.0235 41 Q 0.0037 0.9707 0.0256 42 I 0.0037 0.9679 0.0284 43 D 0.0037 0.9408 0.0554 44 H 0.0039 0.7733 0.2228 45 H 0.0093 0.5153 0.4753 46 H 0.0228 0.0310 0.9462 47 P 0.0221 0.0190 0.9589 48 D 0.0963 0.0184 0.8853 49 L 0.9368 0.0091 0.0541 50 V 0.9766 0.0063 0.0171 51 I 0.9770 0.0052 0.0178 52 L 0.9540 0.0067 0.0393 53 D 0.6617 0.0235 0.3148 54 M 0.3260 0.0859 0.5881 55 D 0.2254 0.1170 0.6576 56 I 0.0880 0.0726 0.8394 57 I 0.0399 0.0967 0.8634 58 G 0.0228 0.0627 0.9145 59 E 0.0308 0.0547 0.9145 60 N 0.0436 0.0557 0.9007 61 S 0.0125 0.8194 0.1681 62 P 0.0041 0.9669 0.0290 63 N 0.0041 0.9730 0.0229 64 L 0.0044 0.9720 0.0236 65 C 0.0048 0.9702 0.0250 66 L 0.0048 0.9695 0.0257 67 K 0.0048 0.9581 0.0371 68 L 0.0073 0.9376 0.0551 69 K 0.0102 0.8491 0.1408 70 R 0.0097 0.6327 0.3576 71 S 0.0154 0.1496 0.8350 72 K 0.0098 0.2539 0.7363 73 G 0.0094 0.2262 0.7645 74 L 0.0258 0.3679 0.6062 75 K 0.0312 0.1449 0.8238 76 N 0.0442 0.0838 0.8721 77 V 0.1773 0.0160 0.8067 78 P 0.3875 0.0072 0.6054 79 L 0.9577 0.0031 0.0391 80 I 0.9743 0.0033 0.0224 81 L 0.9703 0.0045 0.0252 82 L 0.9133 0.0087 0.0781 83 F 0.6755 0.0185 0.3060 84 S 0.3211 0.0641 0.6148 85 S 0.1121 0.1093 0.7786 86 E 0.0463 0.1615 0.7923 87 H 0.0409 0.3161 0.6430 88 K 0.0179 0.8494 0.1327 89 E 0.0139 0.9065 0.0796 90 A 0.0143 0.9160 0.0698 91 I 0.0156 0.9405 0.0439 92 V 0.0264 0.9151 0.0585 93 N 0.0215 0.8934 0.0851 94 G 0.0176 0.8699 0.1125 95 L 0.0290 0.8500 0.1210 96 H 0.0447 0.7438 0.2115 97 S 0.0339 0.4825 0.4835 98 G 0.0535 0.0784 0.8681 99 A 0.1006 0.0705 0.8289 100 D 0.1078 0.1021 0.7901 101 D 0.3674 0.1500 0.4826 102 Y 0.5492 0.0983 0.3524 103 L 0.6218 0.0691 0.3091 104 T 0.4307 0.0390 0.5303 105 K 0.1543 0.0172 0.8285 106 P 0.1179 0.0196 0.8625 107 F 0.0894 0.0207 0.8899 108 N 0.0280 0.0373 0.9347 109 R 0.0038 0.9331 0.0631 110 N 0.0037 0.9690 0.0272 111 D 0.0037 0.9736 0.0227 112 L 0.0037 0.9766 0.0197 113 L 0.0037 0.9759 0.0204 114 S 0.0037 0.9759 0.0204 115 R 0.0037 0.9759 0.0204 116 I 0.0037 0.9762 0.0200 117 E 0.0037 0.9766 0.0197 118 I 0.0037 0.9759 0.0204 119 H 0.0037 0.9749 0.0214 120 L 0.0038 0.9699 0.0264 121 R 0.0039 0.9450 0.0510 122 T 0.0041 0.9147 0.0812 123 Q 0.0042 0.8949 0.1009 124 N 0.0052 0.8304 0.1644 125 Y 0.0052 0.8314 0.1634 126 Y 0.0052 0.8629 0.1319 127 S 0.0051 0.8807 0.1142 128 D 0.0059 0.8782 0.1160 129 L 0.0094 0.8509 0.1397 130 R 0.0119 0.8302 0.1579 131 K 0.0111 0.7470 0.2419 132 N 0.0114 0.5191 0.4695 133 E 0.0212 0.3952 0.5836 134 G 0.0463 0.3010 0.6527 135 H 0.0973 0.2976 0.6050 136 H 0.1161 0.2373 0.6466 137 H 0.1380 0.1625 0.6995 138 H 0.1510 0.1183 0.7307 139 H 0.1268 0.0657 0.8075 140 H 0.0123 0.0122 0.9755