# This file is the result of combining several RDB files, specifically # T0403.t06.str2.rdb (weight 1.54425) # T0403.t06.str4.rdb (weight 0.924988) # T0403.t06.pb.rdb (weight 0.789901) # T0403.t06.bys.rdb (weight 0.748322) # T0403.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 T0403.t06.str2.rdb # ============================================ # TARGET T0403 # 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 T0403.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 1378 # # ============================================ # Comments from T0403.t06.str4.rdb # ============================================ # TARGET T0403 # 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 T0403.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 1378 # # ============================================ # Comments from T0403.t06.pb.rdb # ============================================ # TARGET T0403 # 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 T0403.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 1378 # # ============================================ # Comments from T0403.t06.bys.rdb # ============================================ # TARGET T0403 # 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 T0403.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 1378 # # ============================================ # Comments from T0403.t06.alpha.rdb # ============================================ # TARGET T0403 # 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 T0403.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 1378 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2213 0.1792 0.5995 2 G 0.2107 0.1768 0.6124 3 R 0.1965 0.3004 0.5031 4 D 0.2214 0.2619 0.5167 5 L 0.2874 0.1908 0.5218 6 Q 0.4407 0.0777 0.4817 7 V 0.6648 0.0308 0.3044 8 T 0.7173 0.0274 0.2552 9 L 0.6885 0.0366 0.2749 10 Y 0.4898 0.0948 0.4154 11 G 0.4161 0.0632 0.5207 12 T 0.5227 0.0811 0.3961 13 I 0.4541 0.1486 0.3972 14 K 0.3412 0.1666 0.4922 15 A 0.2844 0.1655 0.5501 16 G 0.3604 0.1040 0.5355 17 V 0.5753 0.0470 0.3778 18 E 0.6143 0.0507 0.3350 19 V 0.5975 0.0693 0.3333 20 S 0.4942 0.1030 0.4028 21 R 0.4505 0.1108 0.4387 22 V 0.3674 0.1471 0.4855 23 K 0.2983 0.1809 0.5208 24 D 0.2639 0.1513 0.5848 25 A 0.1963 0.2462 0.5575 26 G 0.2155 0.2329 0.5516 27 T 0.3246 0.1902 0.4852 28 Y 0.2895 0.1686 0.5419 29 K 0.2300 0.1663 0.6038 30 A 0.1941 0.1719 0.6340 31 Q 0.1337 0.1600 0.7063 32 G 0.1251 0.1065 0.7683 33 G 0.2041 0.1176 0.6784 34 K 0.3108 0.1689 0.5203 35 S 0.3875 0.1827 0.4299 36 K 0.4078 0.1711 0.4210 37 T 0.3973 0.1678 0.4349 38 A 0.2837 0.2242 0.4921 39 T 0.2734 0.1947 0.5319 40 Q 0.2562 0.2098 0.5340 41 I 0.3437 0.1942 0.4621 42 A 0.3345 0.1905 0.4750 43 D 0.2331 0.1693 0.5975 44 F 0.1416 0.2502 0.6082 45 G 0.1455 0.2070 0.6476 46 S 0.2137 0.2175 0.5688 47 K 0.2360 0.2583 0.5057 48 I 0.3056 0.1674 0.5270 49 G 0.3733 0.0913 0.5354 50 F 0.4579 0.0515 0.4906 51 K 0.4670 0.0505 0.4825 52 G 0.4636 0.0701 0.4663 53 Q 0.3423 0.2105 0.4472 54 E 0.3140 0.2787 0.4072 55 D 0.2404 0.2516 0.5080 56 L 0.1479 0.2346 0.6175 57 G 0.1103 0.1661 0.7236 58 N 0.1165 0.1557 0.7278 59 G 0.1968 0.0843 0.7189 60 M 0.4922 0.0396 0.4682 61 K 0.7094 0.0218 0.2688 62 A 0.8107 0.0093 0.1800 63 I 0.7990 0.0128 0.1881 64 W 0.8184 0.0082 0.1735 65 Q 0.8039 0.0126 0.1835 66 L 0.7399 0.0343 0.2258 67 E 0.6132 0.0968 0.2900 68 Q 0.4659 0.1149 0.4192 69 K 0.4686 0.0779 0.4534 70 A 0.5960 0.0272 0.3768 71 S 0.5561 0.0322 0.4117 72 I 0.3943 0.1393 0.4664 73 A 0.2354 0.1538 0.6109 74 G 0.2070 0.0975 0.6955 75 T 0.2349 0.1186 0.6465 76 N 0.1851 0.1326 0.6823 77 S 0.1576 0.1607 0.6817 78 G 0.1580 0.1981 0.6439 79 W 0.1800 0.2089 0.6111 80 G 0.1826 0.1526 0.6648 81 N 0.2286 0.1786 0.5928 82 R 0.2514 0.3732 0.3754 83 Q 0.3748 0.2974 0.3277 84 S 0.5408 0.2086 0.2506 85 F 0.6214 0.1411 0.2375 86 I 0.6310 0.1102 0.2588 87 G 0.5712 0.0966 0.3322 88 L 0.5258 0.0826 0.3916 89 K 0.4126 0.0820 0.5054 90 G 0.2702 0.0708 0.6590 91 G 0.2031 0.1367 0.6602 92 F 0.3114 0.0970 0.5916 93 G 0.5157 0.0441 0.4402 94 T 0.7377 0.0168 0.2456 95 V 0.7545 0.0113 0.2342 96 R 0.7287 0.0230 0.2483 97 A 0.5972 0.0511 0.3518 98 G 0.4051 0.0640 0.5309 99 N 0.4125 0.1071 0.4803 100 L 0.3986 0.1424 0.4590 101 N 0.3005 0.1830 0.5166 102 T 0.3128 0.1803 0.5070 103 V 0.2405 0.3869 0.3726 104 L 0.2155 0.4598 0.3247 105 K 0.1906 0.5000 0.3094 106 D 0.1753 0.4171 0.4076 107 S 0.1629 0.3610 0.4761 108 G 0.1564 0.2897 0.5539 109 D 0.1712 0.2393 0.5895 110 N 0.1784 0.2160 0.6055 111 V 0.2687 0.1206 0.6106 112 N 0.2238 0.0527 0.7235 113 A 0.0647 0.5082 0.4272 114 W 0.0830 0.4368 0.4802 115 E 0.1106 0.4075 0.4819 116 S 0.1336 0.2492 0.6172 117 G 0.1213 0.1704 0.7083 118 S 0.1583 0.1978 0.6439 119 N 0.1717 0.1995 0.6288 120 T 0.1871 0.2102 0.6027 121 E 0.1951 0.2357 0.5692 122 D 0.2183 0.2053 0.5764 123 V 0.1355 0.4350 0.4294 124 L 0.1496 0.3396 0.5108 125 G 0.1553 0.2569 0.5878 126 L 0.1705 0.2431 0.5864 127 G 0.1536 0.2196 0.6268 128 T 0.1864 0.2092 0.6043 129 I 0.2162 0.1949 0.5889 130 G 0.2214 0.1576 0.6210 131 R 0.2500 0.1458 0.6042 132 V 0.2413 0.1772 0.5816 133 E 0.2392 0.2178 0.5430 134 S 0.2718 0.1860 0.5422 135 R 0.2540 0.2147 0.5313 136 E 0.2455 0.1734 0.5810 137 I 0.3664 0.0906 0.5430 138 S 0.6535 0.0274 0.3191 139 V 0.7374 0.0130 0.2497 140 R 0.7630 0.0135 0.2236 141 Y 0.6699 0.0172 0.3129 142 D 0.4541 0.0537 0.4921 143 S 0.3519 0.0516 0.5965 144 P 0.1920 0.2501 0.5579 145 V 0.1978 0.2758 0.5264 146 F 0.2404 0.2095 0.5500 147 A 0.1795 0.1762 0.6442 148 G 0.2086 0.1039 0.6876 149 F 0.4843 0.0471 0.4686 150 S 0.6385 0.0354 0.3261 151 G 0.7179 0.0322 0.2499 152 S 0.7435 0.0273 0.2292 153 V 0.7682 0.0237 0.2081 154 Q 0.7442 0.0244 0.2314 155 Y 0.7260 0.0190 0.2550 156 V 0.5505 0.0228 0.4268 157 P 0.3143 0.0756 0.6101 158 R 0.1501 0.2043 0.6456 159 D 0.1208 0.2063 0.6729 160 N 0.1464 0.1891 0.6645 161 A 0.1350 0.2513 0.6136 162 N 0.1353 0.2020 0.6627 163 D 0.1841 0.1779 0.6380 164 V 0.1896 0.2472 0.5632 165 D 0.1931 0.2171 0.5899 166 K 0.1668 0.2957 0.5375 167 Y 0.1838 0.2694 0.5469 168 K 0.1763 0.2844 0.5393 169 H 0.2167 0.2416 0.5417 170 T 0.2408 0.2345 0.5248 171 K 0.2445 0.2164 0.5391 172 S 0.2099 0.1880 0.6021 173 S 0.1479 0.2109 0.6412 174 R 0.1424 0.2042 0.6534 175 E 0.2398 0.1810 0.5792 176 S 0.4417 0.1220 0.4364 177 Y 0.5806 0.0816 0.3378 178 H 0.6728 0.0537 0.2735 179 A 0.7009 0.0632 0.2359 180 G 0.7242 0.0576 0.2182 181 L 0.7583 0.0361 0.2057 182 K 0.7542 0.0313 0.2145 183 Y 0.6544 0.0667 0.2789 184 E 0.4314 0.1574 0.4111 185 N 0.2711 0.1367 0.5923 186 A 0.1667 0.1453 0.6880 187 G 0.1482 0.1677 0.6841 188 F 0.2847 0.1847 0.5305 189 F 0.3879 0.1935 0.4186 190 G 0.3741 0.2644 0.3614 191 Q 0.3542 0.2771 0.3688 192 Y 0.3212 0.4009 0.2779 193 A 0.2957 0.4691 0.2352 194 G 0.3600 0.4583 0.1816 195 S 0.2850 0.5320 0.1831 196 F 0.2430 0.5693 0.1877 197 A 0.1791 0.5842 0.2367 198 K 0.1370 0.5059 0.3571 199 Y 0.1530 0.3741 0.4729 200 A 0.1157 0.3659 0.5185 201 D 0.1357 0.2544 0.6099 202 L 0.1341 0.3081 0.5578 203 N 0.1492 0.2289 0.6219 204 T 0.1442 0.3263 0.5295 205 D 0.1452 0.3330 0.5218 206 A 0.1119 0.4667 0.4214 207 E 0.1139 0.4403 0.4458 208 R 0.1483 0.4123 0.4395 209 V 0.2076 0.3710 0.4214 210 A 0.2300 0.3224 0.4475 211 V 0.2504 0.2622 0.4874 212 N 0.2044 0.2118 0.5839 213 T 0.1663 0.2610 0.5727 214 A 0.1429 0.3256 0.5315 215 N 0.1692 0.2535 0.5774 216 A 0.1936 0.2021 0.6043 217 H 0.2850 0.0933 0.6216 218 P 0.2278 0.1155 0.6567 219 V 0.1552 0.3606 0.4842 220 K 0.1054 0.4232 0.4714 221 D 0.1264 0.3872 0.4864 222 Y 0.1819 0.4340 0.3841 223 Q 0.2955 0.3502 0.3543 224 V 0.4846 0.2641 0.2513 225 H 0.5456 0.2173 0.2371 226 R 0.6613 0.1321 0.2066 227 V 0.7039 0.0968 0.1993 228 V 0.7239 0.0622 0.2139 229 A 0.7066 0.0557 0.2377 230 G 0.6492 0.0633 0.2875 231 Y 0.5933 0.0567 0.3500 232 D 0.4439 0.0703 0.4858 233 A 0.2145 0.2016 0.5839 234 N 0.1557 0.1751 0.6692 235 D 0.2754 0.1308 0.5938 236 L 0.5650 0.0745 0.3606 237 Y 0.6975 0.0574 0.2451 238 V 0.7577 0.0517 0.1906 239 S 0.7639 0.0460 0.1901 240 V 0.7594 0.0448 0.1958 241 A 0.6967 0.0694 0.2339 242 G 0.6091 0.1212 0.2697 243 Q 0.4359 0.2290 0.3351 244 Y 0.3330 0.3108 0.3562 245 E 0.2510 0.3883 0.3607 246 A 0.1860 0.4354 0.3786 247 A 0.1644 0.3650 0.4707 248 K 0.1429 0.2926 0.5645 249 N 0.1705 0.1990 0.6305 250 N 0.1457 0.2579 0.5964 251 E 0.1694 0.2625 0.5681 252 V 0.2134 0.2332 0.5533 253 G 0.2110 0.2436 0.5454 254 S 0.2200 0.2698 0.5102 255 I 0.1895 0.3015 0.5090 256 K 0.1310 0.2619 0.6071 257 G 0.1153 0.1993 0.6854 258 K 0.1702 0.2287 0.6011 259 K 0.1835 0.2960 0.5205 260 H 0.1835 0.2926 0.5240 261 E 0.1814 0.2814 0.5372 262 Q 0.2283 0.2474 0.5243 263 T 0.3033 0.1896 0.5071 264 Q 0.5484 0.0996 0.3520 265 V 0.7059 0.0440 0.2500 266 A 0.7502 0.0303 0.2195 267 A 0.7805 0.0241 0.1954 268 T 0.7901 0.0167 0.1931 269 A 0.7921 0.0186 0.1893 270 A 0.7720 0.0209 0.2071 271 Y 0.7577 0.0201 0.2222 272 R 0.5980 0.0426 0.3594 273 F 0.3391 0.0685 0.5924 274 G 0.1844 0.0944 0.7212 275 N 0.1955 0.1519 0.6526 276 V 0.3313 0.1222 0.5466 277 T 0.4450 0.0527 0.5023 278 P 0.4710 0.1090 0.4199 279 R 0.5798 0.1157 0.3045 280 V 0.7082 0.0698 0.2220 281 S 0.6861 0.0793 0.2346 282 Y 0.6974 0.0824 0.2202 283 A 0.5510 0.1477 0.3013 284 H 0.4211 0.1687 0.4102 285 G 0.2716 0.1965 0.5319 286 F 0.2027 0.3050 0.4923 287 K 0.1670 0.3980 0.4351 288 A 0.1413 0.4745 0.3842 289 K 0.1487 0.4416 0.4097 290 V 0.1787 0.3493 0.4720 291 N 0.1396 0.2374 0.6230 292 G 0.1369 0.1681 0.6950 293 V 0.2199 0.1482 0.6319 294 K 0.2063 0.1741 0.6196 295 D 0.1746 0.1660 0.6595 296 A 0.1290 0.2689 0.6020 297 N 0.1779 0.1840 0.6381 298 Y 0.2160 0.1614 0.6226 299 Q 0.2577 0.1305 0.6118 300 Y 0.3092 0.1606 0.5302 301 D 0.3628 0.1236 0.5136 302 Q 0.7073 0.0406 0.2522 303 V 0.7407 0.0191 0.2403 304 I 0.7710 0.0172 0.2118 305 V 0.7239 0.0294 0.2467 306 G 0.6634 0.0340 0.3026 307 A 0.6512 0.0450 0.3038 308 D 0.5717 0.0746 0.3537 309 Y 0.5297 0.0876 0.3827 310 D 0.3594 0.1255 0.5151 311 F 0.3224 0.1591 0.5184 312 S 0.2506 0.0988 0.6506 313 K 0.0861 0.3601 0.5538 314 R 0.1411 0.2651 0.5938 315 T 0.3635 0.1709 0.4656 316 S 0.5570 0.1503 0.2927 317 A 0.7081 0.0932 0.1987 318 L 0.7318 0.0876 0.1806 319 V 0.7272 0.0953 0.1775 320 S 0.7157 0.0895 0.1947 321 A 0.6487 0.1517 0.1995 322 G 0.5479 0.2447 0.2074 323 W 0.4895 0.3104 0.2001 324 L 0.3741 0.3732 0.2527 325 K 0.2621 0.3508 0.3871 326 Q 0.1559 0.2300 0.6141 327 G 0.1188 0.1587 0.7226 328 K 0.1214 0.1674 0.7112 329 G 0.1230 0.1405 0.7365 330 A 0.1722 0.1564 0.6714 331 G 0.1913 0.1315 0.6771 332 K 0.3397 0.1313 0.5291 333 V 0.4351 0.1070 0.4579 334 E 0.4684 0.1025 0.4290 335 Q 0.5010 0.0798 0.4192 336 T 0.4836 0.0707 0.4457 337 A 0.4550 0.0779 0.4671 338 S 0.3775 0.0862 0.5363 339 M 0.2798 0.1182 0.6020