# This file is the result of combining several RDB files, specifically # T0244.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0244.t2k.stride-ebghtl.rdb (weight 1.24869) # T0244.t2k.str2.rdb (weight 1.54758) # T0244.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 T0244.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0244 # 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 T0244.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 876 # # ============================================ # Comments from T0244.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0244 # 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 T0244.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 876 # # ============================================ # Comments from T0244.t2k.str2.rdb # ============================================ # TARGET T0244 # 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 T0244.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 876 # # ============================================ # Comments from T0244.t2k.alpha.rdb # ============================================ # TARGET T0244 # 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 T0244.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 876 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.3438 0.1874 0.4687 2 A 0.4187 0.2024 0.3789 3 I 0.3874 0.2362 0.3764 4 N 0.4128 0.1704 0.4168 5 T 0.3263 0.1300 0.5437 6 K 0.3446 0.1356 0.5198 7 V 0.5593 0.0701 0.3707 8 K 0.6269 0.0468 0.3263 9 K 0.8059 0.0285 0.1656 10 A 0.9013 0.0214 0.0773 11 V 0.9007 0.0273 0.0720 12 I 0.8843 0.0315 0.0842 13 P 0.7549 0.0753 0.1698 14 V 0.3782 0.1160 0.5057 15 A 0.1892 0.0957 0.7151 16 G 0.1224 0.0938 0.7839 17 L 0.0970 0.1825 0.7205 18 G 0.0939 0.2570 0.6491 19 T 0.1236 0.2932 0.5831 20 R 0.1602 0.2706 0.5692 21 M 0.1624 0.2255 0.6121 22 L 0.1255 0.1878 0.6867 23 P 0.1246 0.2747 0.6007 24 A 0.1047 0.3126 0.5826 25 T 0.1204 0.2288 0.6508 26 K 0.0697 0.2689 0.6614 27 A 0.0793 0.2129 0.7078 28 I 0.1093 0.0963 0.7944 29 P 0.1150 0.0731 0.8119 30 K 0.1265 0.2244 0.6491 31 E 0.1222 0.2885 0.5893 32 M 0.1509 0.3321 0.5170 33 L 0.2920 0.1561 0.5519 34 P 0.2401 0.1263 0.6336 35 L 0.1553 0.1177 0.7270 36 V 0.0718 0.0764 0.8518 37 D 0.0317 0.0501 0.9182 38 K 0.1100 0.0709 0.8192 39 P 0.2719 0.2133 0.5148 40 L 0.2213 0.5512 0.2275 41 I 0.1869 0.6619 0.1512 42 Q 0.0835 0.7899 0.1266 43 Y 0.0519 0.8463 0.1018 44 V 0.0223 0.9217 0.0560 45 V 0.0057 0.9514 0.0428 46 N 0.0052 0.9544 0.0404 47 E 0.0049 0.9555 0.0396 48 C 0.0049 0.9493 0.0458 49 I 0.0051 0.9374 0.0574 50 A 0.0066 0.8014 0.1920 51 A 0.0409 0.2117 0.7473 52 G 0.0493 0.0162 0.9345 53 I 0.1104 0.0086 0.8810 54 T 0.3170 0.0384 0.6446 55 E 0.8798 0.0056 0.1146 56 I 0.9325 0.0032 0.0642 57 V 0.9327 0.0033 0.0640 58 L 0.9285 0.0034 0.0681 59 V 0.8661 0.0093 0.1246 60 T 0.5272 0.0193 0.4535 61 H 0.1756 0.0241 0.8004 62 S 0.0563 0.1089 0.8348 63 S 0.0516 0.1229 0.8255 64 K 0.0151 0.7525 0.2325 65 N 0.0086 0.8813 0.1101 66 S 0.0108 0.9143 0.0749 67 I 0.0124 0.9283 0.0593 68 E 0.0159 0.9258 0.0583 69 N 0.0152 0.9192 0.0656 70 H 0.0098 0.8980 0.0922 71 F 0.0184 0.8527 0.1289 72 D 0.0115 0.7810 0.2075 73 T 0.0165 0.6499 0.3336 74 S 0.0504 0.4983 0.4513 75 F 0.0274 0.6570 0.3156 76 E 0.0237 0.7110 0.2653 77 L 0.0249 0.7209 0.2542 78 E 0.0254 0.7364 0.2382 79 A 0.0363 0.7447 0.2190 80 M 0.0375 0.7562 0.2063 81 L 0.0348 0.7419 0.2234 82 E 0.0282 0.7462 0.2257 83 K 0.0271 0.7126 0.2604 84 R 0.0405 0.5304 0.4291 85 V 0.0500 0.3975 0.5525 86 K 0.0801 0.4879 0.4320 87 R 0.0815 0.6518 0.2666 88 Q 0.0737 0.6708 0.2555 89 L 0.0552 0.7069 0.2379 90 L 0.0297 0.7765 0.1937 91 D 0.0285 0.8148 0.1567 92 E 0.0311 0.7946 0.1743 93 V 0.0528 0.6888 0.2584 94 Q 0.0580 0.5855 0.3565 95 S 0.0537 0.4597 0.4866 96 I 0.0518 0.3395 0.6086 97 C 0.0700 0.2175 0.7125 98 P 0.0699 0.2332 0.6968 99 P 0.0804 0.1733 0.7463 100 H 0.1107 0.0713 0.8180 101 V 0.3264 0.0185 0.6551 102 T 0.6204 0.0104 0.3691 103 I 0.8665 0.0041 0.1295 104 M 0.8899 0.0058 0.1043 105 Q 0.8935 0.0045 0.1020 106 V 0.8378 0.0069 0.1553 107 R 0.6749 0.0190 0.3061 108 Q 0.4244 0.0366 0.5389 109 G 0.2830 0.0791 0.6379 110 L 0.1773 0.0750 0.7477 111 A 0.1107 0.1370 0.7523 112 K 0.0709 0.1695 0.7597 113 G 0.0613 0.1911 0.7476 114 L 0.0568 0.4328 0.5104 115 G 0.0186 0.8625 0.1189 116 H 0.0150 0.9108 0.0742 117 A 0.0111 0.9396 0.0493 118 V 0.0140 0.9429 0.0431 119 L 0.0199 0.9266 0.0535 120 C 0.0171 0.8973 0.0856 121 A 0.0180 0.8819 0.1001 122 H 0.0152 0.8953 0.0895 123 P 0.0155 0.8469 0.1376 124 V 0.0218 0.7608 0.2175 125 V 0.0794 0.3802 0.5404 126 G 0.0413 0.1008 0.8580 127 D 0.0375 0.0663 0.8962 128 E 0.1223 0.0223 0.8554 129 P 0.4504 0.0148 0.5348 130 V 0.8963 0.0044 0.0993 131 A 0.9271 0.0032 0.0697 132 V 0.9216 0.0038 0.0746 133 I 0.8693 0.0108 0.1199 134 L 0.5945 0.0187 0.3868 135 P 0.2680 0.0655 0.6664 136 D 0.1731 0.1072 0.7197 137 V 0.2655 0.1213 0.6132 138 I 0.3328 0.1393 0.5279 139 L 0.3095 0.1586 0.5319 140 D 0.2384 0.1718 0.5898 141 E 0.1344 0.1547 0.7109 142 Y 0.0641 0.2671 0.6689 143 E 0.0602 0.2725 0.6673 144 S 0.0565 0.2320 0.7116 145 D 0.0669 0.1499 0.7832 146 L 0.0431 0.3109 0.6460 147 S 0.0537 0.2494 0.6969 148 Q 0.0690 0.2830 0.6479 149 D 0.0815 0.2950 0.6235 150 N 0.0059 0.9010 0.0931 151 L 0.0048 0.9465 0.0487 152 A 0.0048 0.9537 0.0416 153 E 0.0047 0.9556 0.0397 154 M 0.0048 0.9508 0.0445 155 I 0.0048 0.9429 0.0522 156 R 0.0051 0.9318 0.0632 157 R 0.0072 0.9008 0.0919 158 F 0.0096 0.8369 0.1535 159 D 0.0146 0.6897 0.2957 160 E 0.0379 0.3196 0.6425 161 T 0.0448 0.0574 0.8977 162 G 0.0941 0.0296 0.8763 163 H 0.2688 0.0226 0.7086 164 S 0.7608 0.0083 0.2309 165 Q 0.9042 0.0038 0.0920 166 I 0.9209 0.0034 0.0757 167 M 0.9145 0.0035 0.0819 168 V 0.8864 0.0049 0.1087 169 E 0.8142 0.0068 0.1790 170 P 0.7583 0.0083 0.2333 171 V 0.4126 0.0136 0.5738 172 A 0.1728 0.0420 0.7852 173 D 0.1251 0.0280 0.8468 174 V 0.0962 0.1697 0.7341 175 T 0.0859 0.2022 0.7120 176 A 0.1329 0.2562 0.6109 177 Y 0.2825 0.0837 0.6339 178 G 0.4763 0.0422 0.4815 179 V 0.8067 0.0127 0.1806 180 V 0.8452 0.0138 0.1410 181 D 0.8247 0.0106 0.1647 182 C 0.6332 0.0297 0.3371 183 K 0.3448 0.0648 0.5904 184 G 0.2346 0.1324 0.6331 185 V 0.2324 0.2179 0.5496 186 E 0.3099 0.2304 0.4597 187 L 0.2875 0.2738 0.4387 188 A 0.2273 0.2180 0.5547 189 P 0.1477 0.1717 0.6805 190 G 0.0854 0.1056 0.8090 191 E 0.1258 0.0961 0.7781 192 S 0.2742 0.0559 0.6699 193 V 0.4465 0.0252 0.5283 194 P 0.7174 0.0100 0.2726 195 M 0.8658 0.0045 0.1297 196 V 0.8424 0.0206 0.1370 197 G 0.8614 0.0090 0.1296 198 V 0.8506 0.0127 0.1367 199 V 0.8306 0.0147 0.1547 200 E 0.6994 0.0189 0.2816 201 K 0.4594 0.0192 0.5214 202 P 0.2912 0.0267 0.6822 203 K 0.1282 0.0428 0.8290 204 A 0.0416 0.2770 0.6813 205 D 0.0346 0.2732 0.6922 206 V 0.0540 0.1743 0.7718 207 A 0.0733 0.1217 0.8049 208 P 0.1034 0.1819 0.7147 209 S 0.1109 0.2139 0.6752 210 N 0.1553 0.1721 0.6726 211 L 0.4597 0.1059 0.4345 212 A 0.6245 0.0883 0.2872 213 I 0.7189 0.0790 0.2021 214 V 0.6567 0.0834 0.2599 215 G 0.6585 0.0839 0.2576 216 R 0.7156 0.0965 0.1879 217 Y 0.7658 0.0602 0.1741 218 V 0.7091 0.0653 0.2256 219 L 0.4679 0.0497 0.4824 220 S 0.1299 0.0328 0.8373 221 A 0.0082 0.7666 0.2252 222 D 0.0085 0.8283 0.1632 223 I 0.0065 0.8923 0.1012 224 W 0.0058 0.9061 0.0882 225 P 0.0070 0.8599 0.1331 226 L 0.0084 0.8572 0.1344 227 L 0.0181 0.8352 0.1467 228 A 0.0125 0.7588 0.2288 229 K 0.0219 0.6035 0.3746 230 T 0.0820 0.2824 0.6356 231 P 0.0866 0.1048 0.8086 232 P 0.0493 0.1454 0.8053 233 G 0.0440 0.1158 0.8402 234 A 0.0412 0.1520 0.8069 235 G 0.0524 0.1287 0.8189 236 D 0.0648 0.1532 0.7820 237 E 0.1719 0.2336 0.5945 238 I 0.3001 0.2707 0.4292 239 Q 0.2714 0.2938 0.4349 240 L 0.1016 0.4403 0.4582 241 T 0.0467 0.5765 0.3768 242 D 0.0361 0.7514 0.2125 243 A 0.0083 0.8936 0.0981 244 I 0.0058 0.9400 0.0542 245 D 0.0051 0.9514 0.0435 246 M 0.0049 0.9549 0.0402 247 L 0.0049 0.9526 0.0425 248 I 0.0058 0.9280 0.0662 249 E 0.0069 0.8198 0.1733 250 K 0.0441 0.2771 0.6789 251 E 0.0328 0.0302 0.9370 252 T 0.1330 0.0261 0.8409 253 V 0.6743 0.0079 0.3178 254 E 0.8473 0.0111 0.1415 255 A 0.8961 0.0048 0.0991 256 Y 0.8922 0.0042 0.1036 257 H 0.8495 0.0049 0.1456 258 M 0.6289 0.0144 0.3567 259 K 0.1497 0.0429 0.8074 260 G 0.0888 0.0485 0.8626 261 K 0.4616 0.0372 0.5012 262 S 0.6353 0.0388 0.3259 263 H 0.5679 0.0504 0.3817 264 D 0.3917 0.0524 0.5560 265 C 0.1429 0.0748 0.7823 266 G 0.0785 0.0411 0.8803 267 N 0.0766 0.0395 0.8839 268 K 0.0106 0.8734 0.1160 269 L 0.0061 0.9161 0.0778 270 G 0.0053 0.9336 0.0611 271 Y 0.0047 0.9551 0.0402 272 M 0.0047 0.9564 0.0389 273 Q 0.0047 0.9548 0.0405 274 A 0.0047 0.9544 0.0409 275 F 0.0050 0.9558 0.0392 276 V 0.0052 0.9544 0.0405 277 E 0.0048 0.9500 0.0452 278 Y 0.0053 0.9332 0.0615 279 G 0.0069 0.8954 0.0977 280 I 0.0114 0.7981 0.1906 281 R 0.0256 0.6496 0.3249 282 H 0.0480 0.3940 0.5579 283 N 0.0130 0.5889 0.3980 284 T 0.0161 0.5531 0.4308 285 L 0.0453 0.4585 0.4961 286 G 0.0449 0.3252 0.6299 287 T 0.0159 0.8282 0.1558 288 E 0.0083 0.8785 0.1132 289 F 0.0061 0.9243 0.0696 290 K 0.0047 0.9440 0.0513 291 A 0.0047 0.9545 0.0408 292 W 0.0047 0.9563 0.0390 293 L 0.0047 0.9571 0.0382 294 E 0.0047 0.9525 0.0427 295 E 0.0052 0.9323 0.0625 296 E 0.0061 0.8919 0.1020 297 M 0.0474 0.6164 0.3361 298 G 0.0268 0.3310 0.6422 299 I 0.0621 0.2740 0.6639 300 K 0.1039 0.1427 0.7534 301 K 0.0391 0.0739 0.8870