# This file is the result of combining several RDB files, specifically # T0138.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0138.t2k.stride-ebghtl.rdb (weight 1.24869) # T0138.t2k.str.rdb (weight 1.53983) # T0138.t2k.alpha.rdb (weight 0.659012) # 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 T0138.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0138 # 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 T0138.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 3 # # ============================================ # Comments from T0138.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0138 # 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 T0138.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 3 # # ============================================ # Comments from T0138.t2k.str.rdb # ============================================ # TARGET T0138 # 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 T0138.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 3 # # ============================================ # Comments from T0138.t2k.alpha.rdb # ============================================ # TARGET T0138 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0138.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 3 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0578 0.0343 0.9079 2 L 0.1141 0.0488 0.8371 3 S 0.1503 0.0492 0.8005 4 Q 0.2356 0.1508 0.6135 5 I 0.4666 0.1124 0.4210 6 A 0.6359 0.1045 0.2596 7 I 0.7163 0.0955 0.1882 8 C 0.7277 0.0988 0.1735 9 I 0.6771 0.1247 0.1982 10 W 0.6035 0.1164 0.2801 11 V 0.4286 0.1013 0.4701 12 E 0.2050 0.0625 0.7326 13 S 0.0822 0.2186 0.6992 14 T 0.0133 0.7598 0.2269 15 A 0.0157 0.8406 0.1437 16 I 0.0153 0.8785 0.1062 17 L 0.0126 0.9013 0.0861 18 Q 0.0148 0.8964 0.0888 19 D 0.0138 0.9005 0.0857 20 C 0.0168 0.9018 0.0813 21 Q 0.0153 0.9012 0.0836 22 R 0.0181 0.8661 0.1158 23 A 0.0235 0.8136 0.1629 24 L 0.0482 0.6723 0.2795 25 S 0.0475 0.5417 0.4107 26 A 0.0480 0.4271 0.5249 27 D 0.0711 0.3159 0.6130 28 R 0.0213 0.7195 0.2593 29 Y 0.0248 0.7105 0.2647 30 Q 0.0441 0.7414 0.2145 31 L 0.1258 0.6501 0.2241 32 Q 0.1645 0.6024 0.2331 33 V 0.1747 0.6093 0.2160 34 C 0.1400 0.5837 0.2763 35 E 0.0976 0.5715 0.3309 36 S 0.0693 0.5682 0.3625 37 G 0.0137 0.8266 0.1597 38 E 0.0089 0.8999 0.0912 39 M 0.0068 0.9126 0.0806 40 L 0.0060 0.9298 0.0643 41 L 0.0055 0.9383 0.0562 42 E 0.0054 0.9285 0.0661 43 Y 0.0054 0.9157 0.0789 44 A 0.0098 0.8874 0.1028 45 Q 0.0087 0.8054 0.1859 46 T 0.0164 0.6242 0.3594 47 H 0.0529 0.2996 0.6475 48 R 0.0192 0.4775 0.5033 49 D 0.0219 0.3846 0.5935 50 Q 0.0778 0.3925 0.5297 51 I 0.3389 0.0823 0.5788 52 D 0.5031 0.0742 0.4227 53 C 0.8726 0.0174 0.1100 54 L 0.8917 0.0151 0.0932 55 I 0.9019 0.0164 0.0816 56 L 0.8736 0.0206 0.1058 57 V 0.7454 0.0264 0.2283 58 A 0.4430 0.0615 0.4955 59 A 0.1632 0.0732 0.7636 60 N 0.0712 0.1507 0.7781 61 P 0.0361 0.2386 0.7253 62 S 0.0575 0.2998 0.6428 63 F 0.0160 0.7559 0.2281 64 R 0.0053 0.9200 0.0747 65 A 0.0048 0.9380 0.0572 66 V 0.0044 0.9509 0.0447 67 V 0.0045 0.9523 0.0433 68 Q 0.0048 0.9499 0.0453 69 Q 0.0050 0.9355 0.0594 70 L 0.0071 0.9147 0.0783 71 C 0.0117 0.8454 0.1429 72 F 0.0156 0.6717 0.3127 73 E 0.0415 0.3074 0.6511 74 G 0.0942 0.0937 0.8122 75 V 0.2972 0.0587 0.6441 76 V 0.6773 0.0347 0.2880 77 V 0.7261 0.0220 0.2519 78 P 0.7960 0.0157 0.1883 79 A 0.8927 0.0075 0.0998 80 I 0.9054 0.0050 0.0896 81 V 0.8962 0.0053 0.0985 82 V 0.8074 0.0140 0.1786 83 G 0.5201 0.0157 0.4642 84 D 0.1773 0.0394 0.7833 85 R 0.0854 0.0648 0.8498 86 D 0.0469 0.1684 0.7847 87 S 0.0506 0.1601 0.7893 88 E 0.0605 0.1215 0.8180 89 D 0.0829 0.0676 0.8496 90 P 0.0949 0.0822 0.8230 91 D 0.0983 0.0764 0.8253 92 E 0.0880 0.0590 0.8530 93 P 0.0783 0.0787 0.8430 94 A 0.0873 0.0855 0.8272 95 K 0.0830 0.1234 0.7937 96 E 0.1106 0.0886 0.8008 97 Q 0.2389 0.0665 0.6947 98 L 0.4670 0.0484 0.4846 99 Y 0.6692 0.0278 0.3030 100 H 0.7212 0.0266 0.2522 101 S 0.7486 0.0264 0.2249 102 A 0.7956 0.0239 0.1804 103 E 0.8610 0.0160 0.1230 104 L 0.8602 0.0160 0.1238 105 H 0.8378 0.0149 0.1473 106 L 0.5885 0.0171 0.3944 107 G 0.2414 0.0351 0.7235 108 I 0.0240 0.6444 0.3316 109 H 0.0148 0.7135 0.2718 110 Q 0.0129 0.7919 0.1952 111 L 0.0075 0.8571 0.1354 112 E 0.0070 0.8203 0.1727 113 Q 0.0100 0.7407 0.2493 114 L 0.0306 0.5900 0.3793 115 P 0.0111 0.8029 0.1860 116 Y 0.0076 0.8952 0.0972 117 Q 0.0076 0.9248 0.0676 118 V 0.0050 0.9496 0.0454 119 D 0.0045 0.9552 0.0404 120 A 0.0045 0.9561 0.0394 121 A 0.0046 0.9518 0.0436 122 L 0.0046 0.9476 0.0478 123 A 0.0049 0.9465 0.0486 124 E 0.0055 0.9238 0.0707 125 F 0.0064 0.9095 0.0841 126 L 0.0159 0.8522 0.1319 127 R 0.0200 0.7485 0.2314 128 L 0.0393 0.6341 0.3265 129 A 0.0704 0.3082 0.6214 130 P 0.0810 0.3284 0.5906 131 V 0.1139 0.4230 0.4631 132 E 0.1330 0.3755 0.4915 133 T 0.1522 0.2766 0.5712 134 M 0.1188 0.1335 0.7477 135 A 0.0415 0.0422 0.9163