# This file is the result of combining several RDB files, specifically # T0403.t04.str2.rdb (weight 1.54425) # T0403.t04.str4.rdb (weight 0.924988) # T0403.t04.pb.rdb (weight 0.789901) # T0403.t04.bys.rdb (weight 0.748322) # T0403.t04.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.t04.str2.rdb # ============================================ # TARGET T0403 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 1039 # # ============================================ # Comments from T0403.t04.str4.rdb # ============================================ # TARGET T0403 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 1039 # # ============================================ # Comments from T0403.t04.pb.rdb # ============================================ # TARGET T0403 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 1039 # # ============================================ # Comments from T0403.t04.bys.rdb # ============================================ # TARGET T0403 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 1039 # # ============================================ # Comments from T0403.t04.alpha.rdb # ============================================ # TARGET T0403 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 1039 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2022 0.1694 0.6285 2 G 0.1855 0.1283 0.6862 3 R 0.2027 0.2236 0.5737 4 D 0.2135 0.2095 0.5770 5 L 0.2876 0.1730 0.5393 6 Q 0.4122 0.0967 0.4912 7 V 0.5677 0.0371 0.3952 8 T 0.6243 0.0405 0.3351 9 L 0.6552 0.0665 0.2782 10 Y 0.5898 0.1087 0.3015 11 G 0.6153 0.0980 0.2867 12 T 0.6516 0.1070 0.2415 13 I 0.5619 0.1640 0.2740 14 K 0.4891 0.1662 0.3447 15 A 0.3968 0.1810 0.4222 16 G 0.4210 0.1293 0.4497 17 V 0.6431 0.0632 0.2937 18 E 0.6853 0.0531 0.2616 19 V 0.7075 0.0425 0.2500 20 S 0.6079 0.0639 0.3282 21 R 0.4651 0.0727 0.4622 22 V 0.3016 0.1543 0.5441 23 K 0.2394 0.2026 0.5579 24 D 0.2337 0.1774 0.5889 25 A 0.2029 0.2128 0.5843 26 G 0.2041 0.2204 0.5755 27 T 0.2345 0.2102 0.5553 28 Y 0.2529 0.2237 0.5234 29 K 0.2477 0.1984 0.5539 30 A 0.2219 0.2056 0.5726 31 Q 0.1703 0.1680 0.6617 32 G 0.1237 0.1106 0.7657 33 G 0.1641 0.0946 0.7413 34 K 0.2970 0.1087 0.5943 35 S 0.4686 0.1079 0.4235 36 K 0.5676 0.0959 0.3365 37 T 0.5957 0.0892 0.3151 38 A 0.5508 0.1276 0.3216 39 T 0.4570 0.1523 0.3907 40 Q 0.3810 0.1739 0.4450 41 I 0.2972 0.2281 0.4747 42 A 0.2219 0.2729 0.5052 43 D 0.1823 0.2657 0.5521 44 F 0.1755 0.2103 0.6142 45 G 0.1704 0.1655 0.6641 46 S 0.2472 0.1909 0.5619 47 K 0.3185 0.2439 0.4375 48 I 0.4146 0.1749 0.4105 49 G 0.4702 0.0980 0.4318 50 F 0.5126 0.0890 0.3984 51 K 0.4157 0.0901 0.4942 52 G 0.3087 0.1045 0.5868 53 Q 0.2690 0.2692 0.4618 54 E 0.3331 0.2972 0.3698 55 D 0.2891 0.2565 0.4544 56 L 0.1550 0.3050 0.5400 57 G 0.1241 0.1909 0.6850 58 N 0.1131 0.1568 0.7301 59 G 0.1421 0.1051 0.7528 60 M 0.4316 0.0638 0.5046 61 K 0.6181 0.0724 0.3095 62 A 0.7790 0.0149 0.2061 63 I 0.8040 0.0178 0.1782 64 W 0.8097 0.0079 0.1825 65 Q 0.7788 0.0226 0.1986 66 L 0.6924 0.0743 0.2334 67 E 0.5165 0.1806 0.3029 68 Q 0.3143 0.1521 0.5336 69 K 0.2328 0.1146 0.6525 70 A 0.4040 0.0526 0.5434 71 S 0.4182 0.0446 0.5372 72 I 0.2735 0.2150 0.5115 73 A 0.1957 0.1794 0.6248 74 G 0.1509 0.1201 0.7290 75 T 0.1667 0.1670 0.6663 76 N 0.1917 0.2139 0.5945 77 S 0.1713 0.1797 0.6490 78 G 0.1532 0.1427 0.7041 79 W 0.1789 0.1827 0.6384 80 G 0.1817 0.1583 0.6600 81 N 0.2136 0.1733 0.6132 82 R 0.2215 0.2853 0.4932 83 Q 0.3273 0.2642 0.4085 84 S 0.5107 0.1619 0.3273 85 F 0.6087 0.1127 0.2785 86 I 0.6422 0.0973 0.2605 87 G 0.6231 0.0795 0.2974 88 L 0.5342 0.1335 0.3323 89 K 0.4173 0.1007 0.4819 90 G 0.2432 0.0821 0.6747 91 G 0.1588 0.1210 0.7202 92 F 0.2684 0.0892 0.6424 93 G 0.4288 0.0498 0.5214 94 T 0.6816 0.0249 0.2936 95 V 0.7391 0.0201 0.2407 96 R 0.7026 0.0207 0.2767 97 A 0.5420 0.0737 0.3843 98 G 0.3522 0.1149 0.5329 99 N 0.3578 0.1270 0.5152 100 L 0.3010 0.1836 0.5154 101 N 0.2710 0.1814 0.5476 102 T 0.2509 0.2055 0.5436 103 V 0.2014 0.3880 0.4106 104 L 0.1803 0.4790 0.3407 105 K 0.1883 0.4831 0.3286 106 D 0.1898 0.3877 0.4226 107 S 0.1399 0.3874 0.4727 108 G 0.1318 0.2963 0.5719 109 D 0.1472 0.2590 0.5938 110 N 0.1733 0.2265 0.6002 111 V 0.2635 0.1549 0.5816 112 N 0.2293 0.0823 0.6884 113 A 0.0717 0.4686 0.4596 114 W 0.0843 0.4373 0.4784 115 E 0.1193 0.3310 0.5497 116 S 0.1429 0.2005 0.6566 117 G 0.1307 0.1792 0.6901 118 S 0.1391 0.2406 0.6204 119 N 0.1569 0.2448 0.5983 120 T 0.1879 0.2600 0.5520 121 E 0.2073 0.2841 0.5086 122 D 0.2305 0.2367 0.5328 123 V 0.1061 0.4868 0.4071 124 L 0.1242 0.4042 0.4716 125 G 0.1410 0.3235 0.5355 126 L 0.1680 0.2936 0.5384 127 G 0.1579 0.2494 0.5927 128 T 0.1612 0.2823 0.5566 129 I 0.1794 0.2729 0.5477 130 G 0.1805 0.2311 0.5884 131 R 0.2097 0.2003 0.5899 132 V 0.2245 0.2134 0.5621 133 E 0.2490 0.2041 0.5470 134 S 0.2754 0.1661 0.5586 135 R 0.2777 0.1994 0.5229 136 E 0.3037 0.1843 0.5121 137 I 0.4180 0.1215 0.4605 138 S 0.6301 0.0490 0.3209 139 V 0.7591 0.0165 0.2244 140 R 0.7584 0.0163 0.2254 141 Y 0.6440 0.0270 0.3290 142 D 0.4237 0.0666 0.5097 143 S 0.3201 0.0488 0.6311 144 P 0.1783 0.2604 0.5613 145 V 0.1797 0.2651 0.5552 146 F 0.2207 0.2070 0.5723 147 A 0.1974 0.1485 0.6541 148 G 0.2539 0.0949 0.6512 149 F 0.4610 0.0624 0.4766 150 S 0.6047 0.0490 0.3463 151 G 0.6744 0.0439 0.2817 152 S 0.7300 0.0344 0.2355 153 V 0.7764 0.0175 0.2061 154 Q 0.7602 0.0227 0.2171 155 Y 0.7165 0.0215 0.2620 156 V 0.4887 0.0274 0.4839 157 P 0.2478 0.1010 0.6513 158 R 0.1551 0.1803 0.6646 159 D 0.1244 0.2002 0.6754 160 N 0.1660 0.1744 0.6595 161 A 0.1559 0.2420 0.6021 162 N 0.1562 0.2111 0.6327 163 D 0.1994 0.1693 0.6313 164 V 0.1842 0.2672 0.5486 165 D 0.1550 0.2495 0.5955 166 K 0.1405 0.2664 0.5931 167 Y 0.2000 0.2046 0.5955 168 K 0.1899 0.2505 0.5596 169 H 0.2281 0.2028 0.5690 170 T 0.2412 0.1752 0.5837 171 K 0.2143 0.2228 0.5629 172 S 0.1848 0.2386 0.5766 173 S 0.1444 0.2091 0.6466 174 R 0.1308 0.2155 0.6536 175 E 0.2124 0.2346 0.5531 176 S 0.3872 0.1741 0.4387 177 Y 0.5028 0.1609 0.3362 178 H 0.5879 0.1397 0.2723 179 A 0.6198 0.1460 0.2342 180 G 0.6603 0.1225 0.2172 181 L 0.7081 0.0829 0.2090 182 K 0.6314 0.1212 0.2474 183 Y 0.4853 0.1720 0.3427 184 E 0.2544 0.2591 0.4865 185 N 0.1426 0.2050 0.6524 186 A 0.1373 0.1656 0.6972 187 G 0.1410 0.2032 0.6558 188 F 0.2461 0.2844 0.4695 189 F 0.3376 0.3330 0.3294 190 G 0.2881 0.4690 0.2429 191 Q 0.2596 0.5665 0.1739 192 Y 0.3034 0.5263 0.1703 193 A 0.2043 0.6304 0.1653 194 G 0.1221 0.7039 0.1740 195 S 0.0737 0.7506 0.1756 196 F 0.0899 0.6617 0.2484 197 A 0.0959 0.5766 0.3275 198 K 0.0913 0.4289 0.4798 199 Y 0.1164 0.3224 0.5612 200 A 0.1187 0.3046 0.5767 201 D 0.1383 0.2542 0.6075 202 L 0.1161 0.3437 0.5402 203 N 0.1317 0.2716 0.5967 204 T 0.1433 0.2721 0.5846 205 D 0.1519 0.2520 0.5961 206 A 0.1214 0.3858 0.4928 207 E 0.1246 0.3792 0.4962 208 R 0.1698 0.3749 0.4553 209 V 0.2578 0.2964 0.4458 210 A 0.2804 0.2675 0.4521 211 V 0.2532 0.2348 0.5120 212 N 0.1969 0.1992 0.6040 213 T 0.1690 0.1994 0.6316 214 A 0.1458 0.2431 0.6111 215 N 0.1504 0.1965 0.6531 216 A 0.1805 0.1807 0.6387 217 H 0.2361 0.1107 0.6532 218 P 0.1985 0.1913 0.6102 219 V 0.1299 0.4318 0.4382 220 K 0.0793 0.5209 0.3998 221 D 0.0917 0.4941 0.4141 222 Y 0.1470 0.5317 0.3213 223 Q 0.2000 0.5375 0.2624 224 V 0.3013 0.4591 0.2396 225 H 0.3808 0.3722 0.2469 226 R 0.5224 0.2649 0.2127 227 V 0.5523 0.2388 0.2089 228 V 0.5958 0.1616 0.2426 229 A 0.5768 0.1290 0.2942 230 G 0.4983 0.1460 0.3557 231 Y 0.4995 0.1105 0.3901 232 D 0.3538 0.0988 0.5474 233 A 0.1681 0.2199 0.6119 234 N 0.1164 0.1868 0.6968 235 D 0.2217 0.1506 0.6277 236 L 0.5037 0.0758 0.4205 237 Y 0.6470 0.0768 0.2762 238 V 0.7116 0.0836 0.2048 239 S 0.6834 0.1075 0.2091 240 V 0.6866 0.1049 0.2084 241 A 0.5678 0.1887 0.2435 242 G 0.4789 0.2310 0.2901 243 Q 0.3713 0.3229 0.3059 244 Y 0.2987 0.3661 0.3351 245 E 0.2096 0.4407 0.3497 246 A 0.1762 0.4289 0.3950 247 A 0.1712 0.3452 0.4836 248 K 0.1508 0.2996 0.5496 249 N 0.1657 0.2148 0.6195 250 N 0.1477 0.2570 0.5953 251 E 0.1561 0.2821 0.5619 252 V 0.1918 0.2348 0.5734 253 G 0.1875 0.2021 0.6104 254 S 0.2126 0.2347 0.5526 255 I 0.2064 0.2718 0.5217 256 K 0.1642 0.2011 0.6347 257 G 0.1255 0.1430 0.7316 258 K 0.1992 0.1955 0.6053 259 K 0.2209 0.2373 0.5418 260 H 0.2090 0.2612 0.5298 261 E 0.1897 0.2874 0.5229 262 Q 0.2325 0.2672 0.5003 263 T 0.2884 0.2198 0.4918 264 Q 0.5238 0.1203 0.3559 265 V 0.6960 0.0474 0.2565 266 A 0.7427 0.0379 0.2194 267 A 0.7691 0.0243 0.2066 268 T 0.7583 0.0241 0.2176 269 A 0.7620 0.0203 0.2177 270 A 0.7541 0.0260 0.2200 271 Y 0.7160 0.0288 0.2552 272 R 0.5462 0.0658 0.3880 273 F 0.2692 0.1431 0.5877 274 G 0.1200 0.1342 0.7458 275 N 0.1417 0.1544 0.7039 276 V 0.2124 0.1330 0.6546 277 T 0.2287 0.0891 0.6822 278 P 0.1694 0.3875 0.4431 279 R 0.1953 0.5239 0.2809 280 V 0.2926 0.4920 0.2155 281 S 0.2963 0.5089 0.1948 282 Y 0.2814 0.5242 0.1945 283 A 0.2626 0.4989 0.2384 284 H 0.2358 0.4693 0.2949 285 G 0.2250 0.4199 0.3552 286 F 0.2830 0.3646 0.3523 287 K 0.3504 0.3047 0.3450 288 A 0.3816 0.2562 0.3622 289 K 0.3182 0.2353 0.4465 290 V 0.2293 0.2901 0.4806 291 N 0.1284 0.1720 0.6996 292 G 0.0966 0.1164 0.7870 293 V 0.2188 0.1158 0.6654 294 K 0.2258 0.1680 0.6062 295 D 0.2024 0.1747 0.6228 296 A 0.1509 0.2537 0.5954 297 N 0.1791 0.1585 0.6625 298 Y 0.2258 0.1408 0.6334 299 Q 0.2685 0.1015 0.6300 300 Y 0.3474 0.1201 0.5325 301 D 0.3513 0.1263 0.5223 302 Q 0.6987 0.0364 0.2649 303 V 0.7448 0.0166 0.2385 304 I 0.7585 0.0124 0.2292 305 V 0.7157 0.0313 0.2530 306 G 0.6325 0.0412 0.3263 307 A 0.6260 0.0624 0.3116 308 D 0.5561 0.0812 0.3628 309 Y 0.5315 0.1094 0.3592 310 D 0.3508 0.1554 0.4939 311 F 0.2367 0.2053 0.5580 312 S 0.2036 0.1479 0.6485 313 K 0.0865 0.4139 0.4996 314 R 0.1348 0.3204 0.5448 315 T 0.2532 0.3029 0.4440 316 S 0.3212 0.3992 0.2796 317 A 0.4456 0.3646 0.1897 318 L 0.4921 0.3301 0.1777 319 V 0.5030 0.3337 0.1633 320 S 0.3349 0.4835 0.1816 321 A 0.2276 0.6037 0.1687 322 G 0.1617 0.6795 0.1589 323 W 0.1128 0.7407 0.1465 324 L 0.1116 0.7250 0.1634 325 K 0.1145 0.6330 0.2525 326 Q 0.1193 0.4227 0.4581 327 G 0.0974 0.2145 0.6881 328 K 0.0898 0.1597 0.7505 329 G 0.0923 0.1140 0.7938 330 A 0.1714 0.1480 0.6805 331 G 0.2033 0.1388 0.6579 332 K 0.3466 0.1152 0.5382 333 V 0.4663 0.1204 0.4133 334 E 0.4900 0.1479 0.3620 335 Q 0.3912 0.1853 0.4235 336 T 0.2950 0.1815 0.5235 337 A 0.2253 0.1948 0.5799 338 S 0.2080 0.1532 0.6388 339 M 0.2212 0.1693 0.6095