# This file is the result of combining several RDB files, specifically # T0393.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0393.t2k.stride-ebghtl.rdb (weight 1.24869) # T0393.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 T0393.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0393 # 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 T0393.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 640 # # ============================================ # Comments from T0393.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0393 # 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 T0393.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 640 # # ============================================ # Comments from T0393.t2k.str.rdb # ============================================ # TARGET T0393 # 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 T0393.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 640 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0395 0.0523 0.9082 2 K 0.1256 0.0807 0.7937 3 R 0.0993 0.0956 0.8051 4 S 0.0736 0.0939 0.8325 5 I 0.0237 0.4339 0.5424 6 E 0.0186 0.3499 0.6315 7 D 0.0227 0.2162 0.7611 8 T 0.1034 0.0198 0.8768 9 P 0.4055 0.0040 0.5905 10 I 0.9549 0.0024 0.0427 11 V 0.9770 0.0024 0.0206 12 L 0.9781 0.0024 0.0196 13 I 0.9463 0.0024 0.0513 14 G 0.5651 0.0066 0.4284 15 A 0.1123 0.0781 0.8096 16 G 0.0153 0.3663 0.6184 17 N 0.0038 0.9310 0.0653 18 L 0.0037 0.9579 0.0384 19 A 0.0037 0.9713 0.0250 20 T 0.0037 0.9738 0.0225 21 N 0.0037 0.9745 0.0218 22 L 0.0037 0.9752 0.0211 23 A 0.0037 0.9753 0.0210 24 K 0.0037 0.9733 0.0230 25 A 0.0037 0.9719 0.0243 26 L 0.0037 0.9720 0.0243 27 Y 0.0038 0.9626 0.0336 28 R 0.0039 0.9025 0.0936 29 K 0.0046 0.3419 0.6535 30 G 0.0092 0.0072 0.9836 31 F 0.0406 0.0056 0.9539 32 R 0.5349 0.0051 0.4600 33 I 0.9606 0.0026 0.0368 34 V 0.9778 0.0024 0.0198 35 Q 0.9767 0.0024 0.0208 36 V 0.9544 0.0030 0.0426 37 Y 0.8036 0.0046 0.1918 38 S 0.3700 0.0103 0.6197 39 R 0.0706 0.0154 0.9140 40 T 0.0395 0.0207 0.9398 41 E 0.0039 0.8902 0.1059 42 E 0.0039 0.9237 0.0724 43 S 0.0038 0.9479 0.0484 44 A 0.0037 0.9654 0.0309 45 R 0.0037 0.9638 0.0325 46 E 0.0037 0.9604 0.0359 47 L 0.0037 0.9603 0.0360 48 A 0.0037 0.9578 0.0385 49 Q 0.0038 0.9227 0.0735 50 K 0.0041 0.8457 0.1503 51 V 0.0098 0.5347 0.4555 52 E 0.0158 0.0645 0.9197 53 A 0.0523 0.0342 0.9135 54 E 0.2656 0.0517 0.6827 55 Y 0.3680 0.0752 0.5568 56 T 0.3034 0.0949 0.6017 57 T 0.1302 0.1067 0.7631 58 D 0.0742 0.1121 0.8137 59 L 0.0089 0.8272 0.1639 60 A 0.0046 0.9075 0.0879 61 E 0.0044 0.9086 0.0869 62 V 0.0044 0.9008 0.0948 63 N 0.0062 0.8295 0.1643 64 P 0.0068 0.5176 0.4756 65 Y 0.0101 0.2514 0.7385 66 A 0.0340 0.0304 0.9356 67 K 0.0762 0.0095 0.9142 68 L 0.9587 0.0026 0.0387 69 Y 0.9822 0.0024 0.0155 70 I 0.9819 0.0024 0.0157 71 V 0.9755 0.0024 0.0220 72 S 0.7658 0.0028 0.2313 73 L 0.3348 0.0055 0.6597 74 K 0.1419 0.0131 0.8451 75 D 0.0259 0.2549 0.7192 76 S 0.0110 0.5173 0.4717 77 A 0.0107 0.7127 0.2766 78 F 0.0095 0.8441 0.1464 79 A 0.0101 0.9016 0.0883 80 E 0.0094 0.9131 0.0775 81 L 0.0073 0.9277 0.0650 82 L 0.0063 0.9335 0.0602 83 Q 0.0063 0.9102 0.0835 84 G 0.0078 0.8619 0.1303 85 I 0.0136 0.7855 0.2009 86 V 0.0178 0.7515 0.2307 87 E 0.0166 0.6759 0.3076 88 G 0.0250 0.5862 0.3888 89 K 0.0807 0.3607 0.5586 90 R 0.0805 0.1970 0.7225 91 E 0.0217 0.1183 0.8600 92 E 0.0208 0.0353 0.9439 93 A 0.2883 0.0120 0.6997 94 L 0.8701 0.0026 0.1273 95 M 0.9626 0.0024 0.0350 96 V 0.9705 0.0024 0.0271 97 H 0.9421 0.0036 0.0543 98 T 0.7125 0.0170 0.2705 99 A 0.2697 0.0590 0.6712 100 G 0.1059 0.0986 0.7955 101 S 0.1132 0.0938 0.7929 102 I 0.1529 0.0611 0.7860 103 P 0.0754 0.0980 0.8265 104 M 0.0178 0.6311 0.3511 105 N 0.0167 0.7000 0.2833 106 V 0.0154 0.7573 0.2273 107 W 0.0167 0.7586 0.2247 108 E 0.0134 0.7824 0.2042 109 G 0.0124 0.7952 0.1924 110 H 0.0119 0.7972 0.1909 111 V 0.0150 0.7211 0.2639 112 P 0.0194 0.5507 0.4299 113 H 0.0261 0.3384 0.6355 114 Y 0.0312 0.0990 0.8698 115 G 0.1111 0.0517 0.8372 116 V 0.5093 0.0302 0.4605 117 F 0.7957 0.0197 0.1846 118 Y 0.8187 0.0219 0.1594 119 P 0.7528 0.0295 0.2177 120 M 0.5405 0.0413 0.4182 121 Q 0.2503 0.0433 0.7064 122 T 0.1087 0.0744 0.8169 123 F 0.0606 0.1159 0.8235 124 S 0.0443 0.1420 0.8137 125 K 0.0291 0.3028 0.6681 126 Q 0.0401 0.4755 0.4845 127 R 0.0749 0.6124 0.3127 128 E 0.0838 0.6597 0.2565 129 V 0.1009 0.6408 0.2584 130 D 0.0831 0.5740 0.3429 131 F 0.0853 0.4344 0.4803 132 K 0.0956 0.2934 0.6109 133 E 0.1138 0.2232 0.6630 134 I 0.2666 0.2040 0.5294 135 P 0.4549 0.1749 0.3702 136 F 0.6229 0.1561 0.2210 137 F 0.6169 0.1553 0.2278 138 I 0.4373 0.1852 0.3775 139 E 0.2595 0.1895 0.5510 140 A 0.1085 0.1130 0.7785 141 S 0.0390 0.0498 0.9112 142 S 0.0199 0.0585 0.9215 143 T 0.0041 0.9122 0.0837 144 E 0.0039 0.9398 0.0563 145 D 0.0038 0.9600 0.0362 146 A 0.0038 0.9701 0.0261 147 A 0.0037 0.9686 0.0277 148 F 0.0037 0.9635 0.0328 149 L 0.0038 0.9675 0.0287 150 K 0.0037 0.9722 0.0241 151 A 0.0038 0.9682 0.0280 152 I 0.0038 0.9686 0.0276 153 A 0.0038 0.9616 0.0346 154 S 0.0039 0.9281 0.0680 155 T 0.0043 0.7930 0.2027 156 L 0.0075 0.5271 0.4654 157 S 0.0185 0.0821 0.8994 158 N 0.0714 0.0485 0.8801 159 R 0.3509 0.0333 0.6157 160 V 0.7014 0.0144 0.2843 161 Y 0.8684 0.0090 0.1226 162 D 0.8503 0.0073 0.1424 163 A 0.5046 0.0085 0.4868 164 D 0.1097 0.0184 0.8719 165 S 0.0078 0.3764 0.6158 166 E 0.0075 0.4089 0.5836 167 Q 0.0207 0.5505 0.4288 168 R 0.0417 0.5953 0.3630 169 K 0.1122 0.6421 0.2457 170 S 0.2040 0.6837 0.1124 171 L 0.2115 0.7227 0.0658 172 H 0.1708 0.7885 0.0407 173 L 0.1172 0.8456 0.0372 174 A 0.0802 0.8763 0.0435 175 A 0.0399 0.8992 0.0610 176 V 0.0317 0.8219 0.1464 177 F 0.0343 0.7329 0.2327 178 T 0.0124 0.8137 0.1740 179 C 0.0042 0.9335 0.0623 180 N 0.0038 0.9571 0.0390 181 F 0.0038 0.9700 0.0262 182 T 0.0037 0.9747 0.0215 183 N 0.0037 0.9762 0.0200 184 H 0.0037 0.9762 0.0200 185 M 0.0037 0.9762 0.0200 186 Y 0.0037 0.9766 0.0197 187 A 0.0037 0.9759 0.0204 188 L 0.0037 0.9746 0.0217 189 A 0.0037 0.9749 0.0214 190 A 0.0037 0.9737 0.0226 191 E 0.0037 0.9688 0.0274 192 L 0.0037 0.9708 0.0255 193 L 0.0038 0.9692 0.0270 194 K 0.0038 0.9604 0.0358 195 K 0.0038 0.8815 0.1147 196 Y 0.0043 0.3963 0.5994 197 N 0.0093 0.0137 0.9771 198 L 0.0208 0.0073 0.9719 199 P 0.0199 0.0137 0.9664 200 F 0.0042 0.8692 0.1266 201 D 0.0042 0.9058 0.0899 202 V 0.0042 0.9202 0.0756 203 M 0.0042 0.9373 0.0585 204 L 0.0038 0.9538 0.0424 205 P 0.0038 0.9617 0.0345 206 L 0.0038 0.9636 0.0326 207 I 0.0038 0.9668 0.0295 208 D 0.0038 0.9603 0.0359 209 E 0.0039 0.9435 0.0526 210 T 0.0039 0.9340 0.0621 211 A 0.0048 0.9126 0.0826 212 R 0.0040 0.8867 0.1093 213 K 0.0048 0.7710 0.2242 214 V 0.0064 0.7922 0.2014 215 H 0.0103 0.8207 0.1690 216 E 0.0108 0.7533 0.2359 217 L 0.0159 0.6277 0.3564 218 E 0.0268 0.3095 0.6637 219 P 0.0313 0.3411 0.6276 220 K 0.0414 0.4314 0.5271 221 T 0.0423 0.4125 0.5452 222 A 0.0381 0.3624 0.5995 223 Q 0.0563 0.2641 0.6796 224 T 0.0700 0.1785 0.7516 225 G 0.0460 0.1470 0.8070 226 P 0.0758 0.2040 0.7202 227 A 0.1698 0.3241 0.5061 228 I 0.1417 0.3806 0.4776 229 R 0.0544 0.3249 0.6207 230 Y 0.0261 0.1621 0.8118 231 D 0.0180 0.2061 0.7759 232 E 0.0038 0.9392 0.0571 233 N 0.0037 0.9663 0.0300 234 V 0.0037 0.9704 0.0259 235 I 0.0037 0.9762 0.0200 236 G 0.0037 0.9762 0.0200 237 N 0.0037 0.9745 0.0218 238 H 0.0037 0.9738 0.0225 239 L 0.0037 0.9727 0.0236 240 R 0.0037 0.9620 0.0343 241 M 0.0038 0.9375 0.0588 242 L 0.0042 0.9042 0.0916 243 A 0.0041 0.7751 0.2208 244 D 0.0050 0.6144 0.3806 245 D 0.0068 0.4561 0.5371 246 P 0.0090 0.3328 0.6582 247 A 0.0048 0.7331 0.2621 248 M 0.0053 0.8068 0.1879 249 Q 0.0066 0.8644 0.1289 250 R 0.0109 0.9095 0.0797 251 L 0.0128 0.9260 0.0612 252 Y 0.0122 0.9371 0.0507 253 E 0.0181 0.9251 0.0568 254 L 0.0168 0.9151 0.0682 255 L 0.0243 0.8824 0.0932 256 S 0.0258 0.8446 0.1296 257 R 0.0383 0.8012 0.1606 258 S 0.0442 0.7382 0.2176 259 I 0.0501 0.6896 0.2603 260 H 0.0568 0.5538 0.3894 261 E 0.0468 0.4176 0.5355 262 R 0.0413 0.2035 0.7552 263 Q 0.0110 0.0369 0.9521