# This file is the result of combining several RDB files, specifically # T0413.t06.str2.rdb (weight 1.54425) # T0413.t06.str4.rdb (weight 0.924988) # T0413.t06.pb.rdb (weight 0.789901) # T0413.t06.bys.rdb (weight 0.748322) # T0413.t06.alpha.rdb (weight 0.678173) # 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 T0413.t06.str2.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0413.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17884 # # ============================================ # Comments from T0413.t06.str4.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0413.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17884 # # ============================================ # Comments from T0413.t06.pb.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0413.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17884 # # ============================================ # Comments from T0413.t06.bys.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0413.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17884 # # ============================================ # Comments from T0413.t06.alpha.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0413.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17884 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1763 0.1900 0.6337 2 N 0.1804 0.1636 0.6560 3 A 0.1679 0.1985 0.6335 4 M 0.1962 0.1418 0.6620 5 K 0.2401 0.0462 0.7137 6 P 0.2058 0.0952 0.6990 7 A 0.1763 0.2250 0.5987 8 D 0.1792 0.1975 0.6233 9 L 0.1366 0.3062 0.5572 10 T 0.1494 0.2770 0.5735 11 N 0.1355 0.3055 0.5590 12 A 0.1087 0.4315 0.4598 13 D 0.1150 0.4920 0.3929 14 R 0.1294 0.5406 0.3300 15 I 0.1329 0.5498 0.3173 16 A 0.1369 0.5376 0.3255 17 L 0.1398 0.4979 0.3623 18 E 0.1509 0.4015 0.4477 19 L 0.1667 0.2614 0.5718 20 G 0.1639 0.1788 0.6573 21 H 0.2261 0.1480 0.6258 22 A 0.2210 0.1495 0.6295 23 G 0.2540 0.1168 0.6292 24 R 0.4024 0.1023 0.4954 25 N 0.5200 0.0678 0.4122 26 A 0.5600 0.0475 0.3924 27 I 0.4987 0.0272 0.4741 28 P 0.3983 0.0678 0.5339 29 Y 0.4117 0.0807 0.5076 30 L 0.3505 0.1063 0.5432 31 D 0.2901 0.1418 0.5681 32 D 0.2837 0.1714 0.5450 33 D 0.2482 0.1819 0.5700 34 R 0.2232 0.1751 0.6017 35 N 0.1457 0.1850 0.6693 36 A 0.1501 0.1328 0.7171 37 D 0.1461 0.0853 0.7686 38 R 0.3877 0.0297 0.5826 39 P 0.5767 0.0267 0.3966 40 F 0.7140 0.0210 0.2650 41 T 0.7643 0.0134 0.2223 42 L 0.7866 0.0108 0.2026 43 N 0.7714 0.0156 0.2130 44 T 0.7774 0.0165 0.2061 45 Y 0.7201 0.0253 0.2546 46 R 0.6136 0.0160 0.3704 47 P 0.4173 0.0505 0.5322 48 Y 0.1838 0.1801 0.6360 49 G 0.1172 0.1319 0.7508 50 Y 0.2014 0.1125 0.6861 51 T 0.2211 0.0544 0.7244 52 P 0.1307 0.1915 0.6777 53 D 0.1391 0.1183 0.7426 54 R 0.2910 0.0335 0.6754 55 P 0.3678 0.0266 0.6056 56 V 0.7834 0.0071 0.2094 57 V 0.8169 0.0046 0.1784 58 V 0.8102 0.0048 0.1851 59 V 0.8027 0.0058 0.1916 60 Q 0.7211 0.0160 0.2630 61 H 0.4775 0.0385 0.4841 62 G 0.2528 0.0667 0.6805 63 V 0.2243 0.1332 0.6424 64 L 0.1865 0.1704 0.6432 65 R 0.1668 0.1775 0.6557 66 N 0.1550 0.1448 0.7002 67 G 0.0869 0.3209 0.5922 68 A 0.0676 0.4818 0.4506 69 D 0.0923 0.4827 0.4250 70 Y 0.0716 0.6071 0.3213 71 R 0.0483 0.6943 0.2574 72 D 0.0372 0.7050 0.2578 73 F 0.0421 0.6910 0.2668 74 W 0.0512 0.6894 0.2595 75 I 0.0426 0.7631 0.1942 76 P 0.0188 0.8425 0.1386 77 A 0.0174 0.8384 0.1442 78 A 0.0224 0.7916 0.1860 79 D 0.0229 0.6996 0.2774 80 R 0.0373 0.5464 0.4162 81 H 0.0904 0.1953 0.7143 82 K 0.1378 0.0812 0.7810 83 L 0.4730 0.0097 0.5173 84 L 0.7045 0.0115 0.2840 85 I 0.8044 0.0050 0.1906 86 V 0.7934 0.0069 0.1997 87 A 0.7117 0.0071 0.2812 88 P 0.4285 0.0449 0.5265 89 T 0.2703 0.0689 0.6608 90 F 0.1798 0.1048 0.7154 91 S 0.1657 0.1443 0.6900 92 D 0.1561 0.1767 0.6672 93 E 0.1616 0.2231 0.6154 94 I 0.1950 0.1783 0.6266 95 W 0.2344 0.0771 0.6885 96 P 0.1657 0.1496 0.6847 97 G 0.1537 0.1616 0.6847 98 V 0.1823 0.2298 0.5878 99 E 0.1807 0.2763 0.5430 100 S 0.1774 0.2946 0.5280 101 Y 0.1409 0.3090 0.5500 102 N 0.1280 0.2868 0.5852 103 N 0.1107 0.2481 0.6411 104 G 0.1028 0.2468 0.6504 105 R 0.1580 0.2880 0.5539 106 A 0.1816 0.3444 0.4740 107 F 0.1974 0.3488 0.4538 108 T 0.1811 0.3455 0.4734 109 A 0.1333 0.3837 0.4830 110 A 0.1096 0.2744 0.6161 111 G 0.0953 0.1741 0.7306 112 N 0.1885 0.0738 0.7377 113 P 0.1342 0.2349 0.6309 114 R 0.1474 0.2473 0.6054 115 H 0.1598 0.2072 0.6330 116 V 0.1404 0.2500 0.6096 117 D 0.1100 0.2354 0.6547 118 G 0.0738 0.3998 0.5264 119 W 0.0971 0.5040 0.3989 120 T 0.1043 0.5594 0.3362 121 Y 0.0159 0.8162 0.1679 122 A 0.0088 0.8931 0.0981 123 L 0.0083 0.9231 0.0686 124 V 0.0083 0.9233 0.0684 125 A 0.0083 0.9225 0.0692 126 R 0.0083 0.9246 0.0671 127 V 0.0083 0.9236 0.0681 128 L 0.0083 0.9236 0.0681 129 A 0.0083 0.9207 0.0710 130 N 0.0084 0.9204 0.0712 131 I 0.0087 0.9138 0.0775 132 R 0.0093 0.8995 0.0912 133 A 0.0134 0.8246 0.1620 134 A 0.0409 0.6285 0.3305 135 E 0.0637 0.3642 0.5722 136 I 0.0939 0.2320 0.6740 137 A 0.1849 0.1210 0.6941 138 D 0.1746 0.0537 0.7717 139 C 0.0752 0.4385 0.4863 140 E 0.1357 0.3049 0.5593 141 Q 0.4877 0.0872 0.4251 142 V 0.7305 0.0154 0.2541 143 Y 0.7862 0.0127 0.2012 144 L 0.7919 0.0106 0.1976 145 F 0.7456 0.0220 0.2324 146 G 0.5834 0.0370 0.3796 147 H 0.3017 0.1290 0.5693 148 S 0.1882 0.2579 0.5540 149 A 0.0345 0.6565 0.3090 150 G 0.0215 0.7913 0.1872 151 G 0.0107 0.8980 0.0913 152 Q 0.0085 0.9169 0.0746 153 F 0.0084 0.9225 0.0692 154 V 0.0083 0.9244 0.0674 155 H 0.0083 0.9238 0.0680 156 R 0.0083 0.9226 0.0691 157 L 0.0087 0.9109 0.0804 158 M 0.0107 0.8600 0.1292 159 S 0.0150 0.7365 0.2484 160 S 0.0341 0.4620 0.5039 161 Q 0.1346 0.1507 0.7146 162 P 0.0629 0.3509 0.5862 163 H 0.0692 0.1971 0.7337 164 A 0.1780 0.0768 0.7452 165 P 0.1982 0.1139 0.6879 166 F 0.3126 0.1262 0.5612 167 H 0.4411 0.0857 0.4732 168 A 0.7724 0.0279 0.1997 169 V 0.7710 0.0140 0.2150 170 T 0.8029 0.0143 0.1828 171 A 0.7339 0.0261 0.2399 172 A 0.5757 0.0487 0.3756 173 N 0.3656 0.0258 0.6086 174 P 0.1699 0.1800 0.6502 175 G 0.1498 0.2238 0.6264 176 W 0.1766 0.2332 0.5902 177 Y 0.1894 0.1918 0.6188 178 T 0.2248 0.1548 0.6204 179 L 0.2296 0.0995 0.6709 180 P 0.1607 0.2288 0.6105 181 T 0.1660 0.2700 0.5640 182 F 0.1560 0.3247 0.5193 183 E 0.1330 0.3499 0.5171 184 H 0.1607 0.2695 0.5698 185 R 0.1902 0.1864 0.6234 186 F 0.2120 0.0672 0.7208 187 P 0.1364 0.2429 0.6208 188 E 0.0977 0.2535 0.6489 189 G 0.0967 0.2052 0.6981 190 L 0.1478 0.3363 0.5159 191 D 0.1163 0.3375 0.5463 192 G 0.1030 0.3062 0.5908 193 V 0.1666 0.1750 0.6584 194 G 0.1546 0.1239 0.7215 195 L 0.2080 0.0943 0.6976 196 T 0.1817 0.0531 0.7652 197 E 0.0229 0.6797 0.2974 198 D 0.0179 0.7986 0.1835 199 H 0.0206 0.8471 0.1322 200 L 0.0267 0.8327 0.1406 201 A 0.0271 0.8126 0.1603 202 R 0.0213 0.7308 0.2479 203 L 0.0362 0.5849 0.3788 204 L 0.1360 0.2643 0.5997 205 A 0.1451 0.1393 0.7155 206 Y 0.2796 0.0580 0.6625 207 P 0.3335 0.0850 0.5814 208 M 0.7494 0.0272 0.2234 209 T 0.7958 0.0123 0.1919 210 I 0.8041 0.0083 0.1876 211 L 0.7701 0.0159 0.2139 212 A 0.6729 0.0264 0.3007 213 G 0.3386 0.0490 0.6123 214 D 0.1977 0.1736 0.6287 215 Q 0.1532 0.2705 0.5764 216 D 0.1644 0.2561 0.5795 217 I 0.1053 0.3703 0.5244 218 A 0.1670 0.2733 0.5597 219 T 0.2599 0.1017 0.6384 220 D 0.2192 0.0664 0.7144 221 D 0.1431 0.1660 0.6908 222 P 0.0340 0.4792 0.4868 223 N 0.0607 0.3593 0.5800 224 L 0.1285 0.2461 0.6254 225 P 0.0666 0.4168 0.5166 226 S 0.0878 0.4052 0.5070 227 E 0.0692 0.4859 0.4449 228 P 0.0166 0.8395 0.1440 229 A 0.0107 0.8861 0.1032 230 A 0.0138 0.8498 0.1364 231 L 0.0473 0.7390 0.2137 232 R 0.0423 0.6082 0.3495 233 Q 0.0719 0.4578 0.4703 234 G 0.1151 0.2158 0.6691 235 P 0.0922 0.3464 0.5614 236 H 0.1072 0.2869 0.6059 237 R 0.1711 0.3517 0.4771 238 Y 0.2106 0.3522 0.4372 239 A 0.2140 0.3269 0.4591 240 R 0.2264 0.2849 0.4886 241 A 0.1791 0.3474 0.4735 242 R 0.1705 0.3709 0.4586 243 H 0.1617 0.3812 0.4571 244 Y 0.1523 0.4149 0.4328 245 Y 0.1466 0.4285 0.4250 246 E 0.1310 0.4576 0.4113 247 A 0.1440 0.4414 0.4146 248 G 0.1425 0.4367 0.4208 249 Q 0.1729 0.4887 0.3385 250 R 0.1943 0.5185 0.2872 251 A 0.1895 0.5372 0.2733 252 A 0.1891 0.4924 0.3185 253 A 0.1324 0.4888 0.3788 254 Q 0.1038 0.3984 0.4977 255 R 0.1164 0.2644 0.6193 256 G 0.1143 0.1738 0.7119 257 L 0.2130 0.0687 0.7183 258 P 0.2127 0.0862 0.7011 259 F 0.2779 0.0716 0.6504 260 G 0.3420 0.0512 0.6068 261 W 0.5489 0.0144 0.4366 262 Q 0.6986 0.0115 0.2899 263 L 0.7601 0.0068 0.2331 264 Q 0.7712 0.0101 0.2187 265 V 0.7290 0.0080 0.2631 266 V 0.5147 0.0157 0.4696 267 P 0.2171 0.0910 0.6919 268 G 0.0942 0.1244 0.7813 269 I 0.1802 0.1298 0.6900 270 G 0.1722 0.1341 0.6937 271 H 0.1865 0.1818 0.6317 272 D 0.1336 0.1869 0.6795 273 G 0.0675 0.4298 0.5027 274 Q 0.0726 0.5946 0.3328 275 A 0.0659 0.6752 0.2589 276 M 0.0232 0.8156 0.1612 277 S 0.0098 0.8947 0.0954 278 Q 0.0086 0.9150 0.0764 279 V 0.0091 0.9150 0.0759 280 C 0.0093 0.9146 0.0761 281 A 0.0089 0.9098 0.0813 282 S 0.0128 0.8826 0.1046 283 L 0.0247 0.8218 0.1535 284 W 0.0399 0.7333 0.2268 285 F 0.0672 0.5794 0.3534 286 D 0.0648 0.3790 0.5563 287 G 0.0660 0.2364 0.6976 288 R 0.1254 0.1873 0.6873 289 M 0.1583 0.1269 0.7148 290 P 0.0571 0.4665 0.4763 291 D 0.0480 0.5937 0.3583 292 A 0.0191 0.8144 0.1665 293 A 0.0108 0.8922 0.0970 294 E 0.0100 0.9115 0.0785 295 L 0.0097 0.9137 0.0766 296 A 0.0091 0.9077 0.0832 297 R 0.0107 0.8953 0.0940 298 L 0.0233 0.7881 0.1887 299 A 0.0514 0.5282 0.4204 300 G 0.0513 0.2797 0.6690 301 S 0.1129 0.2748 0.6123 302 Q 0.1527 0.2319 0.6154 303 S 0.1716 0.1851 0.6433 304 A 0.1488 0.2120 0.6392