# This file is the result of combining several RDB files, specifically # T0403.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0403.t2k.stride-ebghtl.rdb (weight 1.24869) # T0403.t2k.str2.rdb (weight 1.54758) # T0403.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 T0403.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0403 # 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 T0403.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 1006 # # ============================================ # Comments from T0403.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0403 # 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 T0403.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 1006 # # ============================================ # Comments from T0403.t2k.str2.rdb # ============================================ # TARGET T0403 # 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 T0403.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 1006 # # ============================================ # Comments from T0403.t2k.alpha.rdb # ============================================ # TARGET T0403 # 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 T0403.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 1006 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1320 0.1372 0.7307 2 G 0.2664 0.1355 0.5982 3 R 0.2866 0.1478 0.5656 4 D 0.3204 0.0853 0.5942 5 L 0.3746 0.0554 0.5700 6 Q 0.5683 0.0309 0.4008 7 V 0.7825 0.0123 0.2053 8 T 0.8843 0.0064 0.1093 9 L 0.9059 0.0060 0.0881 10 Y 0.8538 0.0205 0.1257 11 G 0.8399 0.0129 0.1472 12 T 0.8853 0.0101 0.1046 13 I 0.8699 0.0138 0.1163 14 K 0.8000 0.0237 0.1763 15 A 0.7121 0.0388 0.2491 16 G 0.7282 0.0355 0.2364 17 V 0.8237 0.0218 0.1545 18 E 0.8184 0.0266 0.1550 19 V 0.7939 0.0247 0.1814 20 S 0.6973 0.0321 0.2706 21 R 0.4554 0.0423 0.5023 22 V 0.2597 0.0599 0.6804 23 K 0.1979 0.0895 0.7126 24 D 0.1715 0.0897 0.7388 25 A 0.1438 0.0993 0.7569 26 G 0.1290 0.1136 0.7575 27 T 0.1189 0.1134 0.7678 28 Y 0.1295 0.1073 0.7633 29 K 0.1711 0.1070 0.7219 30 A 0.2194 0.1018 0.6788 31 Q 0.1689 0.1039 0.7272 32 G 0.1600 0.0806 0.7594 33 G 0.2495 0.0822 0.6683 34 K 0.4249 0.0719 0.5031 35 S 0.6382 0.0540 0.3079 36 K 0.7277 0.0451 0.2271 37 T 0.7208 0.0430 0.2362 38 A 0.6446 0.0599 0.2955 39 T 0.5107 0.0745 0.4149 40 Q 0.3839 0.0825 0.5335 41 I 0.2560 0.1006 0.6434 42 A 0.2201 0.1093 0.6706 43 D 0.2040 0.1086 0.6875 44 F 0.1973 0.1011 0.7017 45 G 0.2071 0.1198 0.6730 46 S 0.3171 0.1075 0.5754 47 K 0.4868 0.1180 0.3952 48 I 0.4984 0.0863 0.4154 49 G 0.5003 0.0680 0.4316 50 F 0.6789 0.0422 0.2789 51 K 0.6583 0.0456 0.2960 52 G 0.6682 0.0578 0.2741 53 Q 0.6695 0.0717 0.2588 54 E 0.6537 0.0785 0.2678 55 D 0.5531 0.0652 0.3817 56 L 0.2092 0.1029 0.6879 57 G 0.0962 0.0792 0.8247 58 N 0.0695 0.0684 0.8621 59 G 0.1675 0.0599 0.7726 60 M 0.5818 0.0460 0.3722 61 K 0.8501 0.0201 0.1298 62 A 0.9201 0.0074 0.0725 63 I 0.9241 0.0067 0.0692 64 W 0.9231 0.0062 0.0706 65 Q 0.9233 0.0056 0.0711 66 L 0.8937 0.0148 0.0915 67 E 0.7717 0.0417 0.1866 68 Q 0.4709 0.0642 0.4649 69 K 0.3768 0.0492 0.5740 70 A 0.5436 0.0262 0.4302 71 S 0.4461 0.0201 0.5338 72 I 0.2564 0.1199 0.6237 73 A 0.1365 0.0983 0.7652 74 G 0.0819 0.0739 0.8443 75 T 0.0806 0.0599 0.8595 76 N 0.0968 0.0809 0.8223 77 S 0.1120 0.0907 0.7974 78 G 0.1723 0.1317 0.6959 79 W 0.2617 0.2097 0.5285 80 G 0.3069 0.1924 0.5007 81 N 0.3994 0.1280 0.4727 82 R 0.5159 0.1288 0.3554 83 Q 0.6909 0.0832 0.2259 84 S 0.7639 0.0801 0.1560 85 F 0.8211 0.0650 0.1139 86 I 0.7844 0.0771 0.1385 87 G 0.7322 0.0613 0.2065 88 L 0.6160 0.0697 0.3143 89 K 0.4216 0.0625 0.5159 90 G 0.1760 0.0421 0.7819 91 G 0.1301 0.0861 0.7839 92 F 0.3649 0.0442 0.5909 93 G 0.5851 0.0305 0.3844 94 T 0.8352 0.0114 0.1533 95 V 0.8833 0.0079 0.1089 96 R 0.8678 0.0114 0.1209 97 A 0.7664 0.0326 0.2010 98 G 0.5451 0.0501 0.4048 99 N 0.4671 0.0805 0.4523 100 L 0.4258 0.0813 0.4928 101 N 0.3035 0.0836 0.6129 102 T 0.1685 0.0908 0.7407 103 V 0.0849 0.5869 0.3282 104 L 0.0869 0.6683 0.2448 105 K 0.0981 0.6942 0.2077 106 D 0.1295 0.6275 0.2430 107 S 0.1324 0.5550 0.3126 108 G 0.1527 0.4205 0.4268 109 D 0.1629 0.2843 0.5528 110 N 0.1716 0.2279 0.6005 111 V 0.1981 0.1807 0.6212 112 N 0.1376 0.0996 0.7628 113 A 0.0526 0.3103 0.6371 114 W 0.0613 0.2789 0.6598 115 E 0.0776 0.2907 0.6316 116 S 0.1088 0.2566 0.6345 117 G 0.1351 0.2309 0.6340 118 S 0.1453 0.2107 0.6440 119 N 0.1608 0.2074 0.6318 120 T 0.1874 0.1931 0.6195 121 E 0.1925 0.2062 0.6013 122 D 0.1848 0.2057 0.6095 123 V 0.1354 0.3360 0.5286 124 L 0.1463 0.3120 0.5417 125 G 0.1605 0.3422 0.4973 126 L 0.1742 0.3185 0.5073 127 G 0.1746 0.2758 0.5496 128 T 0.1819 0.2144 0.6037 129 I 0.1702 0.1962 0.6336 130 G 0.1601 0.1660 0.6739 131 R 0.1698 0.1442 0.6860 132 V 0.2336 0.1245 0.6419 133 E 0.3463 0.1022 0.5515 134 S 0.3854 0.0835 0.5311 135 R 0.3891 0.0819 0.5290 136 E 0.2365 0.0704 0.6931 137 I 0.3048 0.0569 0.6383 138 S 0.7343 0.0174 0.2483 139 V 0.8783 0.0072 0.1145 140 R 0.8914 0.0066 0.1020 141 Y 0.8452 0.0099 0.1449 142 D 0.7321 0.0214 0.2464 143 S 0.4270 0.0198 0.5532 144 P 0.1761 0.1314 0.6924 145 V 0.2100 0.1022 0.6878 146 F 0.3026 0.1041 0.5933 147 A 0.1865 0.0779 0.7356 148 G 0.3393 0.0567 0.6040 149 F 0.7429 0.0153 0.2419 150 S 0.8623 0.0107 0.1270 151 G 0.8893 0.0131 0.0975 152 S 0.9023 0.0092 0.0885 153 V 0.9036 0.0091 0.0873 154 Q 0.9020 0.0084 0.0896 155 Y 0.8780 0.0105 0.1114 156 V 0.7766 0.0161 0.2072 157 P 0.5464 0.0517 0.4019 158 R 0.2379 0.0697 0.6924 159 D 0.1898 0.0835 0.7267 160 N 0.2134 0.0803 0.7063 161 A 0.1544 0.1139 0.7317 162 N 0.1200 0.1095 0.7704 163 D 0.1252 0.1242 0.7506 164 V 0.1380 0.1604 0.7016 165 D 0.1567 0.1469 0.6964 166 K 0.1285 0.1356 0.7359 167 Y 0.1167 0.1110 0.7722 168 K 0.1452 0.0791 0.7757 169 H 0.3155 0.0542 0.6303 170 T 0.7020 0.0210 0.2770 171 K 0.8327 0.0129 0.1545 172 S 0.8793 0.0106 0.1100 173 S 0.8848 0.0113 0.1039 174 R 0.8899 0.0098 0.1003 175 E 0.8880 0.0108 0.1012 176 S 0.8732 0.0106 0.1162 177 Y 0.8051 0.0270 0.1679 178 H 0.6020 0.0672 0.3308 179 A 0.3252 0.0639 0.6109 180 G 0.2128 0.0493 0.7379 181 L 0.3326 0.1029 0.5646 182 K 0.6804 0.0756 0.2440 183 Y 0.7932 0.0713 0.1355 184 E 0.8308 0.0708 0.0984 185 N 0.8400 0.0677 0.0923 186 A 0.8463 0.0665 0.0873 187 G 0.8288 0.0805 0.0906 188 F 0.7985 0.0997 0.1017 189 F 0.7032 0.1583 0.1385 190 G 0.5958 0.2050 0.1992 191 Q 0.4423 0.2141 0.3436 192 Y 0.2906 0.1733 0.5361 193 A 0.1965 0.1409 0.6626 194 G 0.1350 0.2404 0.6246 195 S 0.1357 0.2728 0.5914 196 F 0.1321 0.2955 0.5724 197 A 0.1409 0.3094 0.5496 198 K 0.1418 0.3515 0.5067 199 Y 0.1369 0.3233 0.5398 200 A 0.1542 0.2817 0.5641 201 D 0.1893 0.2506 0.5602 202 L 0.2050 0.2287 0.5662 203 N 0.1964 0.1995 0.6041 204 T 0.1949 0.1921 0.6130 205 D 0.1900 0.1767 0.6333 206 A 0.1664 0.1824 0.6512 207 E 0.1601 0.1774 0.6625 208 R 0.1667 0.1653 0.6680 209 V 0.1680 0.1617 0.6703 210 A 0.2038 0.1636 0.6327 211 V 0.2078 0.2077 0.5845 212 N 0.2098 0.2304 0.5599 213 T 0.1923 0.2194 0.5883 214 A 0.1780 0.2150 0.6070 215 N 0.1793 0.2368 0.5839 216 A 0.1890 0.2170 0.5941 217 H 0.1842 0.1937 0.6221 218 P 0.1590 0.2141 0.6268 219 V 0.1582 0.3101 0.5318 220 K 0.1852 0.3300 0.4849 221 D 0.3239 0.2710 0.4051 222 Y 0.4900 0.1926 0.3174 223 Q 0.6861 0.1009 0.2131 224 V 0.8236 0.0476 0.1288 225 H 0.8517 0.0344 0.1139 226 R 0.8860 0.0190 0.0951 227 V 0.8824 0.0193 0.0983 228 V 0.8702 0.0200 0.1098 229 A 0.8829 0.0163 0.1008 230 G 0.8849 0.0142 0.1010 231 Y 0.8730 0.0175 0.1095 232 D 0.8182 0.0225 0.1593 233 A 0.5883 0.0463 0.3654 234 N 0.2729 0.0583 0.6688 235 D 0.4157 0.0879 0.4964 236 L 0.8210 0.0244 0.1546 237 Y 0.8931 0.0155 0.0915 238 V 0.9121 0.0114 0.0765 239 S 0.9075 0.0127 0.0798 240 V 0.9053 0.0126 0.0821 241 A 0.9066 0.0115 0.0819 242 G 0.8975 0.0141 0.0884 243 Q 0.8480 0.0310 0.1210 244 Y 0.7972 0.0389 0.1639 245 E 0.6574 0.0710 0.2716 246 A 0.5647 0.0853 0.3500 247 A 0.4313 0.0992 0.4696 248 K 0.2933 0.1143 0.5924 249 N 0.1923 0.1076 0.7001 250 N 0.1529 0.1509 0.6962 251 E 0.1372 0.1846 0.6782 252 V 0.1282 0.1910 0.6808 253 G 0.1293 0.1901 0.6806 254 S 0.1393 0.2136 0.6471 255 I 0.1324 0.2442 0.6234 256 K 0.1268 0.2194 0.6538 257 G 0.1371 0.1759 0.6871 258 K 0.1726 0.1876 0.6398 259 K 0.2442 0.1638 0.5920 260 H 0.2677 0.1689 0.5633 261 E 0.3960 0.1188 0.4852 262 Q 0.4237 0.0755 0.5008 263 T 0.4316 0.0529 0.5154 264 Q 0.7620 0.0165 0.2215 265 V 0.8818 0.0060 0.1122 266 A 0.9098 0.0048 0.0854 267 A 0.9008 0.0066 0.0926 268 T 0.8858 0.0060 0.1082 269 A 0.8805 0.0073 0.1121 270 A 0.8823 0.0077 0.1099 271 Y 0.8605 0.0081 0.1314 272 R 0.7768 0.0127 0.2105 273 F 0.4920 0.0314 0.4766 274 G 0.1518 0.0370 0.8112 275 N 0.0500 0.2987 0.6513 276 V 0.0795 0.4129 0.5076 277 T 0.2027 0.4132 0.3842 278 P 0.3527 0.3598 0.2875 279 R 0.5133 0.2996 0.1872 280 V 0.6376 0.2161 0.1463 281 S 0.6884 0.1795 0.1321 282 Y 0.7156 0.1609 0.1236 283 A 0.7396 0.1404 0.1200 284 H 0.7492 0.1157 0.1351 285 G 0.7375 0.0902 0.1723 286 F 0.6518 0.0956 0.2527 287 K 0.4996 0.1066 0.3937 288 A 0.3163 0.1305 0.5533 289 K 0.2448 0.1219 0.6333 290 V 0.2317 0.1442 0.6241 291 N 0.2026 0.1301 0.6673 292 G 0.1747 0.1392 0.6860 293 V 0.1818 0.1281 0.6902 294 K 0.1813 0.1151 0.7036 295 D 0.1518 0.1056 0.7426 296 A 0.1292 0.1050 0.7658 297 N 0.1293 0.1029 0.7678 298 Y 0.1325 0.1229 0.7447 299 Q 0.2695 0.0675 0.6631 300 Y 0.4623 0.0359 0.5018 301 D 0.5588 0.0570 0.3842 302 Q 0.8590 0.0108 0.1302 303 V 0.9066 0.0054 0.0880 304 I 0.9161 0.0049 0.0789 305 V 0.8981 0.0101 0.0918 306 G 0.8755 0.0097 0.1148 307 A 0.8652 0.0131 0.1217 308 D 0.8499 0.0179 0.1322 309 Y 0.7784 0.0357 0.1859 310 D 0.7188 0.0477 0.2335 311 F 0.5570 0.0634 0.3796 312 S 0.2174 0.0584 0.7241 313 K 0.0744 0.2056 0.7200 314 R 0.1297 0.2387 0.6316 315 T 0.3467 0.2438 0.4095 316 S 0.5483 0.2365 0.2152 317 A 0.6830 0.2149 0.1022 318 L 0.7143 0.2072 0.0785 319 V 0.7305 0.1924 0.0770 320 S 0.7584 0.1643 0.0773 321 A 0.7160 0.1987 0.0853 322 G 0.6736 0.2396 0.0868 323 W 0.6863 0.2230 0.0907 324 L 0.5998 0.2804 0.1197 325 K 0.5380 0.2819 0.1801 326 Q 0.3434 0.2271 0.4295 327 G 0.1682 0.0944 0.7374 328 K 0.0794 0.0682 0.8525 329 G 0.0715 0.0762 0.8523 330 A 0.1428 0.0827 0.7744 331 G 0.1578 0.0603 0.7819 332 K 0.3466 0.0386 0.6148 333 V 0.5440 0.0294 0.4265 334 E 0.6193 0.0374 0.3433 335 Q 0.5348 0.0518 0.4134 336 T 0.3608 0.0899 0.5493 337 A 0.2184 0.1292 0.6524 338 S 0.2018 0.1039 0.6942 339 M 0.0671 0.0485 0.8844