# 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 1044 # # ============================================ # 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 1044 # # ============================================ # 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 1044 # # ============================================ # 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 1044 # # ============================================ # 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 1044 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2089 0.1283 0.6628 2 G 0.1748 0.0975 0.7277 3 R 0.1811 0.1985 0.6204 4 D 0.1929 0.1922 0.6149 5 L 0.2942 0.1605 0.5453 6 Q 0.4391 0.0883 0.4726 7 V 0.6035 0.0321 0.3644 8 T 0.6450 0.0341 0.3209 9 L 0.6677 0.0600 0.2724 10 Y 0.6045 0.1029 0.2926 11 G 0.6235 0.0929 0.2836 12 T 0.6558 0.1045 0.2397 13 I 0.5683 0.1594 0.2723 14 K 0.4913 0.1640 0.3447 15 A 0.4006 0.1798 0.4196 16 G 0.4200 0.1315 0.4485 17 V 0.6411 0.0642 0.2946 18 E 0.6816 0.0557 0.2626 19 V 0.7025 0.0452 0.2523 20 S 0.6018 0.0661 0.3322 21 R 0.4569 0.0753 0.4678 22 V 0.2991 0.1588 0.5421 23 K 0.2489 0.1961 0.5550 24 D 0.2389 0.1720 0.5891 25 A 0.1964 0.2175 0.5861 26 G 0.1918 0.2270 0.5812 27 T 0.2227 0.2214 0.5559 28 Y 0.2587 0.2129 0.5284 29 K 0.2521 0.1863 0.5616 30 A 0.2150 0.2108 0.5743 31 Q 0.1669 0.1668 0.6663 32 G 0.1260 0.1100 0.7640 33 G 0.1677 0.0964 0.7359 34 K 0.3076 0.1077 0.5847 35 S 0.4783 0.1046 0.4171 36 K 0.5751 0.0957 0.3292 37 T 0.6002 0.0886 0.3112 38 A 0.5500 0.1282 0.3218 39 T 0.4593 0.1491 0.3916 40 Q 0.3825 0.1721 0.4454 41 I 0.2964 0.2290 0.4746 42 A 0.2176 0.2752 0.5072 43 D 0.1790 0.2679 0.5531 44 F 0.1738 0.2103 0.6159 45 G 0.1702 0.1656 0.6642 46 S 0.2474 0.1921 0.5605 47 K 0.3193 0.2442 0.4365 48 I 0.4134 0.1755 0.4111 49 G 0.4689 0.0984 0.4327 50 F 0.5112 0.0890 0.3998 51 K 0.4131 0.0903 0.4966 52 G 0.3054 0.1037 0.5909 53 Q 0.2658 0.2707 0.4635 54 E 0.3301 0.2985 0.3713 55 D 0.2868 0.2585 0.4547 56 L 0.1538 0.3072 0.5390 57 G 0.1239 0.1929 0.6832 58 N 0.1136 0.1570 0.7294 59 G 0.1436 0.1049 0.7514 60 M 0.4325 0.0636 0.5038 61 K 0.6187 0.0720 0.3093 62 A 0.7795 0.0144 0.2061 63 I 0.8045 0.0175 0.1780 64 W 0.8099 0.0079 0.1822 65 Q 0.7797 0.0219 0.1984 66 L 0.6945 0.0723 0.2333 67 E 0.5190 0.1791 0.3019 68 Q 0.3168 0.1506 0.5326 69 K 0.2353 0.1136 0.6511 70 A 0.4065 0.0514 0.5421 71 S 0.4181 0.0431 0.5387 72 I 0.2699 0.2183 0.5118 73 A 0.1942 0.1800 0.6258 74 G 0.1500 0.1190 0.7310 75 T 0.1668 0.1658 0.6673 76 N 0.1939 0.2127 0.5935 77 S 0.1736 0.1785 0.6479 78 G 0.1533 0.1412 0.7055 79 W 0.1794 0.1821 0.6385 80 G 0.1825 0.1577 0.6598 81 N 0.2135 0.1721 0.6144 82 R 0.2219 0.2837 0.4945 83 Q 0.3288 0.2616 0.4097 84 S 0.5129 0.1595 0.3276 85 F 0.6107 0.1109 0.2784 86 I 0.6446 0.0957 0.2597 87 G 0.6247 0.0786 0.2966 88 L 0.5363 0.1326 0.3311 89 K 0.4185 0.1006 0.4810 90 G 0.2432 0.0819 0.6749 91 G 0.1589 0.1208 0.7202 92 F 0.2688 0.0890 0.6422 93 G 0.4298 0.0497 0.5205 94 T 0.6822 0.0244 0.2935 95 V 0.7390 0.0201 0.2409 96 R 0.7029 0.0206 0.2766 97 A 0.5427 0.0736 0.3837 98 G 0.3530 0.1146 0.5324 99 N 0.3593 0.1264 0.5142 100 L 0.3013 0.1831 0.5156 101 N 0.2708 0.1818 0.5474 102 T 0.2504 0.2068 0.5428 103 V 0.1989 0.3925 0.4086 104 L 0.1783 0.4818 0.3399 105 K 0.1875 0.4837 0.3288 106 D 0.1892 0.3873 0.4235 107 S 0.1406 0.3863 0.4731 108 G 0.1319 0.2962 0.5719 109 D 0.1491 0.2582 0.5927 110 N 0.1741 0.2263 0.5996 111 V 0.2624 0.1552 0.5824 112 N 0.2288 0.0816 0.6896 113 A 0.0717 0.4686 0.4597 114 W 0.0851 0.4331 0.4818 115 E 0.1207 0.3267 0.5526 116 S 0.1433 0.1971 0.6596 117 G 0.1305 0.1771 0.6924 118 S 0.1386 0.2365 0.6249 119 N 0.1559 0.2455 0.5986 120 T 0.1896 0.2611 0.5494 121 E 0.2138 0.2815 0.5047 122 D 0.2381 0.2331 0.5287 123 V 0.1079 0.4849 0.4072 124 L 0.1237 0.4024 0.4739 125 G 0.1401 0.3092 0.5508 126 L 0.1703 0.2831 0.5466 127 G 0.1599 0.2432 0.5969 128 T 0.1621 0.2776 0.5603 129 I 0.1775 0.2717 0.5508 130 G 0.1805 0.2303 0.5892 131 R 0.2126 0.1995 0.5879 132 V 0.2283 0.2121 0.5596 133 E 0.2528 0.2031 0.5441 134 S 0.2783 0.1671 0.5546 135 R 0.2778 0.2020 0.5203 136 E 0.3033 0.1861 0.5106 137 I 0.4164 0.1228 0.4609 138 S 0.6283 0.0496 0.3221 139 V 0.7575 0.0174 0.2251 140 R 0.7579 0.0165 0.2256 141 Y 0.6447 0.0269 0.3283 142 D 0.4259 0.0669 0.5072 143 S 0.3204 0.0485 0.6311 144 P 0.1779 0.2616 0.5604 145 V 0.1775 0.2656 0.5569 146 F 0.2181 0.2083 0.5736 147 A 0.1951 0.1486 0.6563 148 G 0.2510 0.0949 0.6540 149 F 0.4593 0.0618 0.4789 150 S 0.6052 0.0482 0.3466 151 G 0.6744 0.0434 0.2822 152 S 0.7305 0.0340 0.2355 153 V 0.7766 0.0172 0.2062 154 Q 0.7605 0.0226 0.2170 155 Y 0.7178 0.0210 0.2612 156 V 0.4915 0.0277 0.4808 157 P 0.2495 0.0996 0.6509 158 R 0.1558 0.1805 0.6637 159 D 0.1241 0.2008 0.6751 160 N 0.1643 0.1756 0.6601 161 A 0.1540 0.2433 0.6028 162 N 0.1541 0.2124 0.6335 163 D 0.1985 0.1710 0.6305 164 V 0.1855 0.2668 0.5477 165 D 0.1555 0.2503 0.5942 166 K 0.1404 0.2679 0.5917 167 Y 0.2013 0.2051 0.5936 168 K 0.1896 0.2507 0.5596 169 H 0.2260 0.2014 0.5726 170 T 0.2386 0.1744 0.5870 171 K 0.2108 0.2245 0.5647 172 S 0.1835 0.2393 0.5772 173 S 0.1449 0.2081 0.6469 174 R 0.1325 0.2118 0.6557 175 E 0.2163 0.2296 0.5540 176 S 0.3936 0.1702 0.4362 177 Y 0.5097 0.1568 0.3334 178 H 0.5938 0.1361 0.2701 179 A 0.6238 0.1429 0.2332 180 G 0.6626 0.1206 0.2168 181 L 0.7095 0.0814 0.2090 182 K 0.6332 0.1196 0.2472 183 Y 0.4879 0.1697 0.3424 184 E 0.2558 0.2562 0.4879 185 N 0.1417 0.2028 0.6555 186 A 0.1366 0.1639 0.6995 187 G 0.1423 0.2005 0.6572 188 F 0.2504 0.2795 0.4702 189 F 0.3436 0.3262 0.3301 190 G 0.2948 0.4608 0.2444 191 Q 0.2664 0.5581 0.1755 192 Y 0.3095 0.5187 0.1718 193 A 0.2093 0.6226 0.1680 194 G 0.1271 0.6934 0.1795 195 S 0.0776 0.7398 0.1826 196 F 0.0932 0.6502 0.2566 197 A 0.0994 0.5663 0.3343 198 K 0.0933 0.4260 0.4807 199 Y 0.1184 0.3279 0.5537 200 A 0.1174 0.3055 0.5770 201 D 0.1352 0.2531 0.6117 202 L 0.1167 0.3366 0.5467 203 N 0.1316 0.2710 0.5974 204 T 0.1412 0.2762 0.5826 205 D 0.1466 0.2712 0.5822 206 A 0.1169 0.4056 0.4775 207 E 0.1176 0.4144 0.4680 208 R 0.1566 0.4043 0.4391 209 V 0.2414 0.3228 0.4358 210 A 0.2600 0.2871 0.4530 211 V 0.2323 0.2496 0.5181 212 N 0.1788 0.2077 0.6135 213 T 0.1646 0.2062 0.6292 214 A 0.1467 0.2392 0.6141 215 N 0.1472 0.1939 0.6588 216 A 0.1781 0.1815 0.6403 217 H 0.2305 0.1153 0.6542 218 P 0.1950 0.2057 0.5993 219 V 0.1334 0.4306 0.4360 220 K 0.0803 0.5238 0.3959 221 D 0.0907 0.5006 0.4087 222 Y 0.1460 0.5347 0.3193 223 Q 0.2014 0.5355 0.2631 224 V 0.3030 0.4565 0.2405 225 H 0.3846 0.3677 0.2478 226 R 0.5279 0.2587 0.2134 227 V 0.5585 0.2326 0.2089 228 V 0.6023 0.1568 0.2409 229 A 0.5861 0.1237 0.2902 230 G 0.5095 0.1422 0.3484 231 Y 0.5103 0.1077 0.3820 232 D 0.3618 0.0974 0.5409 233 A 0.1706 0.2198 0.6097 234 N 0.1179 0.1857 0.6964 235 D 0.2251 0.1487 0.6262 236 L 0.5067 0.0745 0.4188 237 Y 0.6490 0.0750 0.2760 238 V 0.7132 0.0817 0.2051 239 S 0.6861 0.1047 0.2092 240 V 0.6900 0.1018 0.2083 241 A 0.5740 0.1832 0.2429 242 G 0.4850 0.2269 0.2880 243 Q 0.3727 0.3228 0.3046 244 Y 0.2983 0.3690 0.3327 245 E 0.2094 0.4433 0.3473 246 A 0.1766 0.4296 0.3938 247 A 0.1682 0.3495 0.4823 248 K 0.1476 0.3024 0.5499 249 N 0.1648 0.2158 0.6194 250 N 0.1450 0.2589 0.5961 251 E 0.1509 0.2862 0.5629 252 V 0.1878 0.2374 0.5748 253 G 0.1857 0.2016 0.6128 254 S 0.2103 0.2295 0.5601 255 I 0.2013 0.2738 0.5249 256 K 0.1677 0.2032 0.6291 257 G 0.1334 0.1481 0.7185 258 K 0.2028 0.1972 0.5999 259 K 0.2185 0.2445 0.5370 260 H 0.2073 0.2713 0.5215 261 E 0.1896 0.2941 0.5163 262 Q 0.2317 0.2704 0.4979 263 T 0.2886 0.2215 0.4899 264 Q 0.5265 0.1210 0.3525 265 V 0.6979 0.0483 0.2539 266 A 0.7426 0.0391 0.2183 267 A 0.7681 0.0254 0.2065 268 T 0.7573 0.0245 0.2182 269 A 0.7594 0.0213 0.2193 270 A 0.7518 0.0272 0.2210 271 Y 0.7132 0.0296 0.2572 272 R 0.5426 0.0674 0.3900 273 F 0.2647 0.1458 0.5894 274 G 0.1177 0.1342 0.7480 275 N 0.1457 0.1527 0.7016 276 V 0.2168 0.1319 0.6513 277 T 0.2292 0.0888 0.6820 278 P 0.1681 0.3933 0.4385 279 R 0.1920 0.5313 0.2767 280 V 0.2876 0.4990 0.2134 281 S 0.2901 0.5149 0.1950 282 Y 0.2731 0.5322 0.1947 283 A 0.2540 0.5089 0.2371 284 H 0.2287 0.4807 0.2905 285 G 0.2197 0.4355 0.3448 286 F 0.2768 0.3832 0.3400 287 K 0.3450 0.3227 0.3323 288 A 0.3741 0.2743 0.3516 289 K 0.3126 0.2511 0.4363 290 V 0.2245 0.2988 0.4766 291 N 0.1264 0.1749 0.6987 292 G 0.0954 0.1163 0.7882 293 V 0.2166 0.1152 0.6682 294 K 0.2232 0.1694 0.6074 295 D 0.2017 0.1740 0.6243 296 A 0.1529 0.2534 0.5937 297 N 0.1823 0.1568 0.6609 298 Y 0.2272 0.1396 0.6332 299 Q 0.2710 0.0989 0.6300 300 Y 0.3482 0.1180 0.5338 301 D 0.3496 0.1249 0.5255 302 Q 0.7001 0.0350 0.2648 303 V 0.7465 0.0155 0.2380 304 I 0.7597 0.0118 0.2285 305 V 0.7162 0.0308 0.2531 306 G 0.6315 0.0404 0.3281 307 A 0.6241 0.0622 0.3137 308 D 0.5517 0.0814 0.3669 309 Y 0.5242 0.1126 0.3632 310 D 0.3439 0.1587 0.4975 311 F 0.2308 0.2082 0.5610 312 S 0.2010 0.1499 0.6491 313 K 0.0854 0.4178 0.4968 314 R 0.1340 0.3263 0.5396 315 T 0.2509 0.3103 0.4388 316 S 0.3157 0.4087 0.2756 317 A 0.4383 0.3734 0.1883 318 L 0.4813 0.3428 0.1759 319 V 0.4892 0.3490 0.1618 320 S 0.3203 0.5000 0.1797 321 A 0.2162 0.6171 0.1667 322 G 0.1526 0.6916 0.1559 323 W 0.1056 0.7508 0.1436 324 L 0.1069 0.7323 0.1608 325 K 0.1105 0.6404 0.2492 326 Q 0.1176 0.4291 0.4533 327 G 0.0974 0.2129 0.6896 328 K 0.0894 0.1588 0.7517 329 G 0.0913 0.1129 0.7958 330 A 0.1722 0.1470 0.6808 331 G 0.2032 0.1395 0.6574 332 K 0.3471 0.1172 0.5357 333 V 0.4638 0.1237 0.4125 334 E 0.4833 0.1528 0.3639 335 Q 0.3836 0.1912 0.4251 336 T 0.2906 0.1877 0.5217 337 A 0.2234 0.1974 0.5792 338 S 0.2064 0.1542 0.6394 339 M 0.2205 0.1702 0.6093