# This file is the result of combining several RDB files, specifically # T0413.t2k.str2.rdb (weight 1.54425) # T0413.t2k.str4.rdb (weight 0.924988) # T0413.t2k.pb.rdb (weight 0.789901) # T0413.t2k.bys.rdb (weight 0.748322) # T0413.t2k.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.t2k.str2.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 161 # # ============================================ # Comments from T0413.t2k.str4.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 161 # # ============================================ # Comments from T0413.t2k.pb.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 161 # # ============================================ # Comments from T0413.t2k.bys.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 161 # # ============================================ # Comments from T0413.t2k.alpha.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 161 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1844 0.2133 0.6023 2 N 0.2014 0.2086 0.5900 3 A 0.3476 0.1623 0.4901 4 M 0.4725 0.0912 0.4363 5 K 0.3740 0.0507 0.5753 6 P 0.2889 0.1873 0.5238 7 A 0.2286 0.2926 0.4788 8 D 0.1666 0.3807 0.4526 9 L 0.1200 0.4365 0.4435 10 T 0.1087 0.4260 0.4652 11 N 0.0890 0.4480 0.4630 12 A 0.0648 0.6321 0.3031 13 D 0.0609 0.6780 0.2612 14 R 0.0731 0.6971 0.2298 15 I 0.0853 0.6920 0.2227 16 A 0.0761 0.7033 0.2206 17 L 0.0629 0.7207 0.2165 18 E 0.0695 0.6304 0.3002 19 L 0.0977 0.4616 0.4407 20 G 0.1003 0.3130 0.5867 21 H 0.1418 0.2538 0.6044 22 A 0.1407 0.2058 0.6535 23 G 0.1274 0.1795 0.6931 24 R 0.1544 0.1926 0.6529 25 N 0.1843 0.1486 0.6671 26 A 0.3303 0.1025 0.5671 27 I 0.4661 0.0364 0.4975 28 P 0.5038 0.0440 0.4522 29 Y 0.5405 0.0508 0.4087 30 L 0.4528 0.0646 0.4826 31 D 0.3122 0.1092 0.5786 32 D 0.1936 0.2127 0.5937 33 D 0.1602 0.2262 0.6135 34 R 0.1364 0.2221 0.6415 35 N 0.1516 0.1546 0.6938 36 A 0.1475 0.1889 0.6636 37 D 0.1631 0.1478 0.6891 38 R 0.3577 0.0405 0.6018 39 P 0.4751 0.0362 0.4887 40 F 0.6347 0.0301 0.3351 41 T 0.7282 0.0176 0.2541 42 L 0.7307 0.0245 0.2447 43 N 0.7022 0.0233 0.2746 44 T 0.6524 0.0302 0.3175 45 Y 0.5069 0.0379 0.4552 46 R 0.3842 0.0304 0.5855 47 P 0.2708 0.1156 0.6136 48 Y 0.1749 0.1699 0.6552 49 G 0.1328 0.1256 0.7416 50 Y 0.1940 0.0942 0.7117 51 T 0.1882 0.0371 0.7747 52 P 0.0845 0.2635 0.6520 53 D 0.1178 0.1628 0.7194 54 R 0.3139 0.0350 0.6511 55 P 0.4800 0.0228 0.4971 56 V 0.7740 0.0069 0.2191 57 V 0.8176 0.0048 0.1776 58 V 0.8106 0.0047 0.1847 59 V 0.8015 0.0072 0.1913 60 Q 0.7227 0.0192 0.2580 61 H 0.4922 0.0555 0.4523 62 G 0.2573 0.1046 0.6381 63 V 0.2093 0.2395 0.5512 64 L 0.1763 0.2479 0.5758 65 R 0.1696 0.2247 0.6057 66 N 0.1501 0.1486 0.7012 67 G 0.0661 0.4779 0.4560 68 A 0.0360 0.6559 0.3081 69 D 0.0518 0.6318 0.3165 70 Y 0.0513 0.6845 0.2642 71 R 0.0427 0.6935 0.2637 72 D 0.0346 0.6800 0.2855 73 F 0.0398 0.6412 0.3189 74 W 0.0658 0.5735 0.3607 75 I 0.0682 0.6055 0.3262 76 P 0.0279 0.7903 0.1818 77 A 0.0330 0.7520 0.2150 78 A 0.0397 0.7471 0.2133 79 D 0.0578 0.5479 0.3943 80 R 0.1130 0.3720 0.5150 81 H 0.1147 0.1668 0.7185 82 K 0.2659 0.0582 0.6759 83 L 0.6922 0.0073 0.3005 84 L 0.7705 0.0060 0.2235 85 I 0.8179 0.0042 0.1779 86 V 0.7899 0.0080 0.2022 87 A 0.6853 0.0085 0.3062 88 P 0.3985 0.0595 0.5421 89 T 0.2797 0.0968 0.6235 90 F 0.2497 0.0850 0.6653 91 S 0.1659 0.1809 0.6532 92 D 0.1197 0.2660 0.6144 93 E 0.1579 0.2649 0.5772 94 I 0.2019 0.1971 0.6011 95 W 0.2032 0.1068 0.6900 96 P 0.1138 0.2400 0.6462 97 G 0.0932 0.1627 0.7441 98 V 0.1851 0.1872 0.6277 99 E 0.1960 0.2834 0.5206 100 S 0.2241 0.2927 0.4832 101 Y 0.2192 0.2630 0.5178 102 N 0.1903 0.2439 0.5658 103 N 0.1353 0.2202 0.6445 104 G 0.1130 0.1804 0.7066 105 R 0.2018 0.2311 0.5671 106 A 0.2676 0.2403 0.4921 107 F 0.2930 0.2283 0.4787 108 T 0.2203 0.2220 0.5577 109 A 0.1757 0.2904 0.5340 110 A 0.1389 0.2155 0.6456 111 G 0.1189 0.1354 0.7457 112 N 0.2054 0.0601 0.7345 113 P 0.1822 0.1771 0.6407 114 R 0.2080 0.1923 0.5997 115 H 0.1924 0.1576 0.6500 116 V 0.1563 0.1823 0.6614 117 D 0.1220 0.1723 0.7057 118 G 0.0826 0.2645 0.6529 119 W 0.1220 0.3840 0.4940 120 T 0.0999 0.5626 0.3376 121 Y 0.0249 0.8149 0.1602 122 A 0.0111 0.8809 0.1079 123 L 0.0084 0.9216 0.0700 124 V 0.0083 0.9206 0.0711 125 A 0.0083 0.9238 0.0679 126 R 0.0083 0.9249 0.0668 127 V 0.0083 0.9241 0.0676 128 L 0.0083 0.9214 0.0702 129 A 0.0083 0.9215 0.0702 130 N 0.0084 0.9150 0.0766 131 I 0.0091 0.9028 0.0881 132 R 0.0099 0.8740 0.1161 133 A 0.0139 0.7918 0.1944 134 A 0.0355 0.6061 0.3584 135 E 0.0899 0.3442 0.5659 136 I 0.1405 0.1951 0.6644 137 A 0.1828 0.1395 0.6777 138 D 0.1896 0.0568 0.7536 139 C 0.0912 0.3992 0.5097 140 E 0.1312 0.3098 0.5590 141 Q 0.4247 0.1063 0.4691 142 V 0.6783 0.0196 0.3021 143 Y 0.7765 0.0118 0.2117 144 L 0.7509 0.0191 0.2300 145 F 0.6558 0.0425 0.3018 146 G 0.3854 0.0623 0.5523 147 H 0.2352 0.1427 0.6222 148 S 0.1596 0.2390 0.6013 149 A 0.0442 0.5616 0.3942 150 G 0.0249 0.7122 0.2629 151 G 0.0116 0.8585 0.1299 152 Q 0.0093 0.9108 0.0799 153 F 0.0084 0.9223 0.0693 154 V 0.0083 0.9225 0.0692 155 H 0.0083 0.9237 0.0681 156 R 0.0083 0.9239 0.0679 157 L 0.0085 0.9140 0.0774 158 M 0.0100 0.8635 0.1265 159 S 0.0176 0.7139 0.2685 160 S 0.0510 0.4184 0.5306 161 Q 0.1366 0.1452 0.7183 162 P 0.0579 0.3399 0.6022 163 H 0.0671 0.2417 0.6912 164 A 0.1735 0.1547 0.6718 165 P 0.1897 0.2816 0.5288 166 F 0.3609 0.2445 0.3946 167 H 0.6037 0.1160 0.2802 168 A 0.7324 0.0502 0.2174 169 V 0.7474 0.0321 0.2204 170 T 0.7378 0.0374 0.2248 171 A 0.6452 0.0545 0.3003 172 A 0.4190 0.0775 0.5035 173 N 0.2450 0.0470 0.7080 174 P 0.1139 0.2536 0.6325 175 G 0.1087 0.1885 0.7028 176 W 0.1919 0.2041 0.6041 177 Y 0.2554 0.1646 0.5800 178 T 0.3319 0.1248 0.5433 179 L 0.3226 0.0570 0.6204 180 P 0.2567 0.1147 0.6286 181 T 0.2159 0.1177 0.6664 182 F 0.1103 0.3959 0.4938 183 E 0.1332 0.3499 0.5169 184 H 0.2231 0.2018 0.5751 185 R 0.2152 0.1786 0.6062 186 F 0.2277 0.0891 0.6833 187 P 0.1624 0.1914 0.6461 188 E 0.1416 0.2465 0.6119 189 G 0.1160 0.2075 0.6765 190 L 0.1918 0.2355 0.5727 191 D 0.1411 0.2086 0.6503 192 G 0.1222 0.1641 0.7137 193 V 0.1483 0.1466 0.7051 194 G 0.1403 0.1343 0.7254 195 L 0.1906 0.1481 0.6613 196 T 0.1644 0.1359 0.6997 197 E 0.0304 0.6687 0.3009 198 D 0.0202 0.8030 0.1768 199 H 0.0247 0.8346 0.1408 200 L 0.0283 0.8221 0.1496 201 A 0.0266 0.8179 0.1554 202 R 0.0267 0.7532 0.2202 203 L 0.0518 0.5880 0.3602 204 L 0.1122 0.3900 0.4978 205 A 0.1404 0.2118 0.6479 206 Y 0.2667 0.0606 0.6727 207 P 0.3323 0.0765 0.5912 208 M 0.6147 0.0530 0.3323 209 T 0.7550 0.0239 0.2211 210 I 0.7822 0.0183 0.1995 211 L 0.7185 0.0306 0.2510 212 A 0.5691 0.0516 0.3793 213 G 0.2654 0.0602 0.6744 214 D 0.2009 0.1366 0.6624 215 Q 0.1625 0.2599 0.5777 216 D 0.1849 0.2248 0.5903 217 I 0.1799 0.2477 0.5724 218 A 0.1920 0.1761 0.6319 219 T 0.1751 0.2128 0.6122 220 D 0.1467 0.1691 0.6842 221 D 0.1798 0.1315 0.6887 222 P 0.0669 0.3528 0.5802 223 N 0.0951 0.2113 0.6937 224 L 0.1652 0.0872 0.7476 225 P 0.1079 0.2246 0.6675 226 S 0.1032 0.2404 0.6563 227 E 0.1531 0.2222 0.6247 228 P 0.0787 0.6105 0.3108 229 A 0.0487 0.7629 0.1883 230 A 0.0418 0.8147 0.1435 231 L 0.0455 0.7539 0.2006 232 R 0.0647 0.5973 0.3380 233 Q 0.0954 0.2808 0.6239 234 G 0.1143 0.1724 0.7132 235 P 0.0872 0.3839 0.5289 236 H 0.0757 0.5339 0.3904 237 R 0.0574 0.7122 0.2304 238 Y 0.0303 0.8160 0.1537 239 A 0.0224 0.8409 0.1367 240 R 0.0215 0.8304 0.1482 241 A 0.0165 0.8535 0.1300 242 R 0.0126 0.8781 0.1093 243 H 0.0121 0.8866 0.1013 244 Y 0.0122 0.8927 0.0951 245 Y 0.0099 0.9085 0.0816 246 E 0.0093 0.9016 0.0891 247 A 0.0096 0.8892 0.1012 248 G 0.0106 0.8784 0.1109 249 Q 0.0109 0.8876 0.1015 250 R 0.0142 0.8831 0.1027 251 A 0.0173 0.8678 0.1149 252 A 0.0191 0.8555 0.1254 253 A 0.0192 0.8012 0.1796 254 Q 0.0348 0.6581 0.3072 255 R 0.0678 0.2709 0.6613 256 G 0.0537 0.0835 0.8629 257 L 0.1820 0.0309 0.7871 258 P 0.2245 0.0660 0.7095 259 F 0.3069 0.1178 0.5753 260 G 0.3842 0.0693 0.5466 261 W 0.5622 0.0310 0.4067 262 Q 0.6863 0.0201 0.2936 263 L 0.7327 0.0151 0.2522 264 Q 0.7228 0.0179 0.2593 265 V 0.7141 0.0159 0.2700 266 V 0.5297 0.0193 0.4510 267 P 0.2918 0.0684 0.6398 268 G 0.1654 0.0668 0.7678 269 I 0.2355 0.1040 0.6605 270 G 0.2215 0.0975 0.6810 271 H 0.2236 0.1625 0.6139 272 D 0.1424 0.1921 0.6655 273 G 0.0679 0.4516 0.4806 274 Q 0.0572 0.6693 0.2735 275 A 0.0751 0.6794 0.2456 276 M 0.0774 0.7084 0.2142 277 S 0.0646 0.7521 0.1833 278 Q 0.0456 0.8037 0.1507 279 V 0.0447 0.8139 0.1414 280 C 0.0437 0.8074 0.1488 281 A 0.0428 0.8055 0.1517 282 S 0.0589 0.7695 0.1716 283 L 0.1159 0.6973 0.1868 284 W 0.1919 0.5725 0.2356 285 F 0.2631 0.4264 0.3106 286 D 0.2129 0.2847 0.5024 287 G 0.1536 0.1682 0.6782 288 R 0.1693 0.1201 0.7106 289 M 0.2128 0.0441 0.7431 290 P 0.1619 0.1439 0.6942 291 D 0.1483 0.1739 0.6779 292 A 0.0721 0.4682 0.4597 293 A 0.0626 0.5823 0.3551 294 E 0.1009 0.5044 0.3947 295 L 0.1347 0.4937 0.3716 296 A 0.1170 0.5351 0.3478 297 R 0.1136 0.5402 0.3462 298 L 0.1480 0.4403 0.4117 299 A 0.1684 0.3365 0.4951 300 G 0.1756 0.2202 0.6043 301 S 0.1969 0.1437 0.6595 302 Q 0.2058 0.1133 0.6809 303 S 0.1689 0.1410 0.6901 304 A 0.1007 0.3241 0.5751