# This file is the result of combining several RDB files, specifically # T0347.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0347.t2k.stride-ebghtl.rdb (weight 1.24869) # T0347.t2k.str2.rdb (weight 1.54758) # T0347.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 T0347.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0347 # 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 T0347.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 32 # # ============================================ # Comments from T0347.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0347 # 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 T0347.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 32 # # ============================================ # Comments from T0347.t2k.str2.rdb # ============================================ # TARGET T0347 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0347.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 32 # # ============================================ # Comments from T0347.t2k.alpha.rdb # ============================================ # TARGET T0347 # 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 T0347.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 32 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0619 0.0440 0.8941 2 T 0.1150 0.0724 0.8126 3 H 0.1151 0.0859 0.7989 4 I 0.0592 0.1442 0.7966 5 Y 0.0717 0.1264 0.8019 6 E 0.0914 0.1192 0.7894 7 P 0.0988 0.1187 0.7825 8 R 0.2058 0.1115 0.6827 9 L 0.4345 0.0714 0.4941 10 S 0.6152 0.0597 0.3251 11 R 0.7689 0.0284 0.2027 12 I 0.6757 0.0191 0.3052 13 A 0.5265 0.0278 0.4457 14 I 0.0373 0.7603 0.2024 15 D 0.0166 0.7865 0.1969 16 K 0.0271 0.7593 0.2136 17 L 0.0864 0.4111 0.5026 18 R 0.1115 0.1482 0.7403 19 P 0.0611 0.4051 0.5338 20 T 0.1530 0.4608 0.3862 21 Q 0.2266 0.5031 0.2703 22 I 0.2568 0.5435 0.1997 23 A 0.2424 0.5461 0.2115 24 V 0.1784 0.5774 0.2443 25 G 0.1146 0.5482 0.3372 26 F 0.0119 0.9300 0.0581 27 R 0.0068 0.9455 0.0477 28 E 0.0063 0.9474 0.0464 29 V 0.0071 0.9444 0.0486 30 E 0.0067 0.9331 0.0602 31 L 0.0071 0.9026 0.0903 32 K 0.0070 0.8983 0.0947 33 R 0.0072 0.9228 0.0700 34 K 0.0069 0.9141 0.0790 35 E 0.0075 0.8877 0.1048 36 W 0.0083 0.8505 0.1413 37 R 0.0088 0.7660 0.2252 38 E 0.0130 0.5164 0.4706 39 T 0.0356 0.2641 0.7004 40 R 0.0508 0.1169 0.8323 41 K 0.0076 0.8839 0.1085 42 K 0.0061 0.9222 0.0717 43 D 0.0063 0.9347 0.0590 44 G 0.0053 0.9475 0.0472 45 D 0.0055 0.9466 0.0479 46 D 0.0053 0.9407 0.0540 47 F 0.0058 0.9214 0.0728 48 L 0.0082 0.8762 0.1156 49 G 0.0102 0.7467 0.2431 50 N 0.0306 0.4455 0.5239 51 H 0.0670 0.1172 0.8159 52 I 0.0835 0.0259 0.8905 53 V 0.2149 0.0125 0.7726 54 P 0.4697 0.0091 0.5212 55 V 0.7915 0.0072 0.2013 56 V 0.8370 0.0059 0.1571 57 A 0.7242 0.0091 0.2667 58 G 0.2048 0.0175 0.7776 59 P 0.0228 0.0952 0.8820 60 K 0.0426 0.0238 0.9336 61 D 0.0599 0.0334 0.9067 62 R 0.3714 0.0107 0.6178 63 A 0.8687 0.0045 0.1268 64 Y 0.9075 0.0057 0.0868 65 L 0.9051 0.0059 0.0891 66 I 0.7592 0.0251 0.2157 67 D 0.4674 0.0331 0.4996 68 H 0.1062 0.2051 0.6887 69 H 0.0621 0.3614 0.5765 70 H 0.0487 0.6488 0.3025 71 L 0.0193 0.8457 0.1350 72 V 0.0262 0.8829 0.0909 73 L 0.0280 0.8886 0.0833 74 A 0.0324 0.8942 0.0735 75 L 0.0340 0.8868 0.0792 76 S 0.0441 0.8437 0.1123 77 K 0.0437 0.7048 0.2515 78 E 0.0524 0.3684 0.5792 79 G 0.0541 0.0610 0.8849 80 V 0.0718 0.0831 0.8451 81 E 0.0955 0.0917 0.8127 82 H 0.3885 0.0618 0.5497 83 V 0.7373 0.0133 0.2494 84 L 0.8202 0.0125 0.1672 85 T 0.8700 0.0087 0.1214 86 S 0.8818 0.0085 0.1097 87 E 0.8844 0.0114 0.1042 88 V 0.8599 0.0163 0.1239 89 A 0.7093 0.0512 0.2394 90 K 0.5487 0.0479 0.4034 91 F 0.2218 0.1873 0.5909 92 S 0.1025 0.2522 0.6453 93 H 0.0711 0.2562 0.6726 94 L 0.0665 0.1227 0.8108 95 G 0.0808 0.0645 0.8547 96 K 0.0105 0.7955 0.1940 97 D 0.0068 0.9043 0.0889 98 E 0.0065 0.9319 0.0616 99 F 0.0058 0.9460 0.0482 100 W 0.0060 0.9538 0.0402 101 S 0.0051 0.9562 0.0386 102 V 0.0050 0.9543 0.0406 103 M 0.0062 0.9456 0.0482 104 D 0.0059 0.9127 0.0814 105 H 0.0103 0.7433 0.2464 106 R 0.0444 0.2902 0.6654 107 N 0.0448 0.0410 0.9142 108 L 0.2428 0.0343 0.7229 109 I 0.5809 0.0216 0.3976 110 Y 0.6073 0.0135 0.3792 111 P 0.5318 0.0316 0.4366 112 F 0.4879 0.0387 0.4734 113 D 0.1245 0.0298 0.8458 114 A 0.0152 0.1311 0.8537 115 Q 0.0497 0.0277 0.9226 116 G 0.0427 0.0301 0.9272 117 L 0.1132 0.0132 0.8736 118 R 0.5515 0.0127 0.4358 119 R 0.2718 0.0202 0.7081 120 Q 0.1544 0.0401 0.8055 121 S 0.0175 0.7571 0.2254 122 G 0.0101 0.7382 0.2516 123 D 0.0230 0.6777 0.2993 124 I 0.0658 0.1934 0.7408 125 P 0.0606 0.3480 0.5914 126 K 0.0254 0.5999 0.3747 127 N 0.0381 0.6613 0.3006 128 I 0.0303 0.6976 0.2720 129 H 0.0400 0.5641 0.3959 130 D 0.0399 0.3845 0.5755 131 L 0.0749 0.2387 0.6864 132 E 0.0464 0.2710 0.6826 133 D 0.0480 0.2205 0.7314 134 D 0.0990 0.1037 0.7972 135 P 0.0103 0.5395 0.4502 136 F 0.0145 0.6272 0.3583 137 R 0.0202 0.7791 0.2007 138 S 0.0320 0.8535 0.1145 139 L 0.0165 0.9275 0.0560 140 A 0.0106 0.9444 0.0450 141 G 0.0125 0.9414 0.0462 142 A 0.0204 0.9358 0.0438 143 L 0.0290 0.9166 0.0544 144 R 0.0184 0.9039 0.0777 145 M 0.0155 0.8410 0.1436 146 A 0.0418 0.3839 0.5743 147 G 0.0414 0.0626 0.8960 148 G 0.0828 0.0967 0.8205 149 Y 0.1977 0.0979 0.7044 150 A 0.1393 0.0735 0.7872 151 K 0.0889 0.1169 0.7942 152 V 0.0920 0.0803 0.8277 153 I 0.1170 0.0673 0.8157 154 I 0.1154 0.0475 0.8372 155 P 0.1097 0.1578 0.7325 156 F 0.1099 0.3978 0.4923 157 S 0.0922 0.5820 0.3258 158 E 0.1150 0.6453 0.2397 159 F 0.1332 0.6701 0.1967 160 G 0.1169 0.6525 0.2306 161 W 0.0370 0.8218 0.1412 162 A 0.0121 0.8926 0.0952 163 D 0.0073 0.9159 0.0769 164 F 0.0067 0.9111 0.0822 165 L 0.0119 0.8792 0.1089 166 R 0.0208 0.7704 0.2088 167 R 0.0270 0.6166 0.3565 168 R 0.0573 0.3831 0.5596 169 I 0.0769 0.2170 0.7061 170 D 0.0639 0.1334 0.8027 171 R 0.0336 0.4513 0.5152 172 D 0.0209 0.5130 0.4661 173 L 0.0287 0.5333 0.4380 174 L 0.0489 0.4133 0.5378 175 S 0.0559 0.3880 0.5560 176 D 0.0218 0.4870 0.4912 177 S 0.0387 0.3635 0.5978 178 F 0.0183 0.5529 0.4288 179 D 0.0119 0.8112 0.1768 180 D 0.0065 0.8932 0.1003 181 A 0.0069 0.9106 0.0825 182 L 0.0068 0.9335 0.0596 183 A 0.0055 0.9451 0.0494 184 E 0.0059 0.9463 0.0479 185 A 0.0052 0.9440 0.0508 186 M 0.0052 0.9379 0.0569 187 K 0.0051 0.8995 0.0954 188 L 0.0059 0.8109 0.1832 189 A 0.0232 0.6067 0.3701 190 K 0.0291 0.4238 0.5471 191 S 0.0518 0.2644 0.6838 192 R 0.0104 0.7332 0.2564 193 E 0.0117 0.7842 0.2042 194 A 0.0203 0.8063 0.1734 195 R 0.0174 0.6691 0.3136 196 H 0.0283 0.4055 0.5662 197 L 0.0740 0.1223 0.8036 198 P 0.0521 0.1384 0.8095 199 G 0.0750 0.1584 0.7666 200 W 0.1788 0.2173 0.6039 201 C 0.2067 0.1256 0.6678 202 G 0.1499 0.0847 0.7653 203 V 0.1268 0.0698 0.8034 204 E 0.0703 0.0389 0.8907 205 E 0.0440 0.0326 0.9234