# This file is the result of combining several RDB files, specifically # T0403.t2k.str2.rdb (weight 1.54425) # T0403.t2k.str4.rdb (weight 0.924988) # T0403.t2k.pb.rdb (weight 0.789901) # T0403.t2k.bys.rdb (weight 0.748322) # T0403.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 T0403.t2k.str2.rdb # ============================================ # TARGET T0403 # 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 T0403.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 876 # # ============================================ # Comments from T0403.t2k.str4.rdb # ============================================ # TARGET T0403 # 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 T0403.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 876 # # ============================================ # Comments from T0403.t2k.pb.rdb # ============================================ # TARGET T0403 # 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 T0403.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 876 # # ============================================ # Comments from T0403.t2k.bys.rdb # ============================================ # TARGET T0403 # 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 T0403.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 876 # # ============================================ # Comments from T0403.t2k.alpha.rdb # ============================================ # TARGET T0403 # 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 T0403.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 876 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3126 0.2593 0.4281 2 G 0.2975 0.1999 0.5026 3 R 0.3038 0.2115 0.4847 4 D 0.2951 0.1568 0.5482 5 L 0.3204 0.1458 0.5339 6 Q 0.4122 0.0809 0.5068 7 V 0.5390 0.0630 0.3980 8 T 0.6077 0.0610 0.3313 9 L 0.6070 0.0787 0.3143 10 Y 0.5832 0.0902 0.3266 11 G 0.5784 0.0765 0.3451 12 T 0.6638 0.0678 0.2684 13 I 0.6219 0.0927 0.2854 14 K 0.5455 0.1050 0.3495 15 A 0.5095 0.1383 0.3522 16 G 0.5334 0.0949 0.3717 17 V 0.6636 0.0538 0.2826 18 E 0.6961 0.0478 0.2561 19 V 0.6997 0.0473 0.2530 20 S 0.5817 0.0705 0.3478 21 R 0.4508 0.0842 0.4650 22 V 0.3046 0.1177 0.5777 23 K 0.2134 0.1713 0.6154 24 D 0.1912 0.1562 0.6526 25 A 0.1684 0.1680 0.6635 26 G 0.1834 0.1479 0.6687 27 T 0.2282 0.1506 0.6212 28 Y 0.2426 0.1588 0.5986 29 K 0.2547 0.1759 0.5694 30 A 0.2413 0.1758 0.5829 31 Q 0.1947 0.1500 0.6554 32 G 0.1589 0.1183 0.7228 33 G 0.2132 0.1281 0.6587 34 K 0.3088 0.1383 0.5529 35 S 0.3823 0.1599 0.4578 36 K 0.4166 0.1576 0.4258 37 T 0.4645 0.1346 0.4009 38 A 0.4263 0.1692 0.4045 39 T 0.3965 0.1720 0.4315 40 Q 0.3393 0.1763 0.4844 41 I 0.2766 0.2509 0.4725 42 A 0.2169 0.3010 0.4821 43 D 0.2043 0.2917 0.5040 44 F 0.1794 0.2103 0.6103 45 G 0.1774 0.1628 0.6598 46 S 0.2193 0.1966 0.5841 47 K 0.2271 0.2701 0.5027 48 I 0.2469 0.2106 0.5425 49 G 0.3161 0.1275 0.5564 50 F 0.4258 0.0705 0.5037 51 K 0.4309 0.0780 0.4911 52 G 0.3835 0.0910 0.5256 53 Q 0.2823 0.3437 0.3741 54 E 0.2227 0.4449 0.3324 55 D 0.2161 0.3616 0.4223 56 L 0.1437 0.2849 0.5713 57 G 0.1199 0.1570 0.7231 58 N 0.1228 0.1448 0.7324 59 G 0.1636 0.1056 0.7308 60 M 0.4515 0.0764 0.4721 61 K 0.6475 0.0479 0.3046 62 A 0.7805 0.0203 0.1992 63 I 0.7929 0.0183 0.1888 64 W 0.8026 0.0142 0.1833 65 Q 0.7863 0.0183 0.1954 66 L 0.7060 0.0584 0.2356 67 E 0.5577 0.1396 0.3027 68 Q 0.3459 0.1039 0.5502 69 K 0.2605 0.0729 0.6666 70 A 0.4605 0.0477 0.4918 71 S 0.4774 0.0390 0.4836 72 I 0.3500 0.1504 0.4996 73 A 0.2124 0.1669 0.6208 74 G 0.1578 0.1233 0.7189 75 T 0.1574 0.1490 0.6936 76 N 0.1714 0.1687 0.6599 77 S 0.1789 0.1643 0.6568 78 G 0.1985 0.1745 0.6270 79 W 0.2295 0.2055 0.5650 80 G 0.2342 0.1931 0.5727 81 N 0.2765 0.1864 0.5371 82 R 0.3384 0.2261 0.4356 83 Q 0.4868 0.1872 0.3260 84 S 0.6361 0.1081 0.2557 85 F 0.6736 0.0759 0.2505 86 I 0.6959 0.0544 0.2497 87 G 0.6568 0.0496 0.2936 88 L 0.6208 0.0526 0.3266 89 K 0.4507 0.0719 0.4774 90 G 0.2534 0.0725 0.6741 91 G 0.2014 0.1503 0.6483 92 F 0.2871 0.1194 0.5935 93 G 0.4498 0.0621 0.4881 94 T 0.7191 0.0185 0.2624 95 V 0.7566 0.0148 0.2285 96 R 0.7289 0.0194 0.2516 97 A 0.6051 0.0632 0.3316 98 G 0.3771 0.0987 0.5242 99 N 0.3135 0.1288 0.5576 100 L 0.2372 0.2398 0.5230 101 N 0.2306 0.2293 0.5401 102 T 0.2444 0.2508 0.5048 103 V 0.1644 0.4700 0.3656 104 L 0.1464 0.5392 0.3143 105 K 0.1222 0.5803 0.2975 106 D 0.1214 0.4768 0.4018 107 S 0.1089 0.3702 0.5209 108 G 0.1012 0.2783 0.6205 109 D 0.1351 0.2518 0.6131 110 N 0.1696 0.2193 0.6111 111 V 0.2542 0.1486 0.5972 112 N 0.2235 0.0745 0.7020 113 A 0.0810 0.4608 0.4582 114 W 0.1018 0.3566 0.5416 115 E 0.1285 0.2878 0.5837 116 S 0.1384 0.2107 0.6508 117 G 0.1260 0.1832 0.6908 118 S 0.1458 0.1940 0.6602 119 N 0.1579 0.1846 0.6575 120 T 0.1761 0.2179 0.6060 121 E 0.1899 0.2753 0.5348 122 D 0.2083 0.2258 0.5659 123 V 0.1458 0.4440 0.4102 124 L 0.1465 0.3337 0.5198 125 G 0.1712 0.2609 0.5680 126 L 0.1683 0.2536 0.5781 127 G 0.1476 0.1917 0.6607 128 T 0.1982 0.2098 0.5920 129 I 0.2124 0.1893 0.5983 130 G 0.1975 0.1808 0.6217 131 R 0.2273 0.1741 0.5987 132 V 0.2354 0.2262 0.5385 133 E 0.2656 0.2193 0.5151 134 S 0.3069 0.1516 0.5415 135 R 0.2612 0.2401 0.4987 136 E 0.2819 0.1947 0.5234 137 I 0.4385 0.1115 0.4499 138 S 0.6669 0.0382 0.2949 139 V 0.7298 0.0197 0.2505 140 R 0.7532 0.0192 0.2276 141 Y 0.7023 0.0274 0.2703 142 D 0.5498 0.0513 0.3988 143 S 0.4143 0.0381 0.5476 144 P 0.2081 0.2655 0.5264 145 V 0.1898 0.2225 0.5877 146 F 0.2805 0.1677 0.5517 147 A 0.2205 0.1258 0.6537 148 G 0.2725 0.0958 0.6318 149 F 0.5701 0.0427 0.3872 150 S 0.6513 0.0322 0.3165 151 G 0.6746 0.0407 0.2847 152 S 0.7487 0.0234 0.2279 153 V 0.7548 0.0242 0.2210 154 Q 0.7457 0.0258 0.2285 155 Y 0.7247 0.0242 0.2511 156 V 0.5230 0.0214 0.4556 157 P 0.3378 0.0983 0.5639 158 R 0.1932 0.1862 0.6207 159 D 0.1521 0.1912 0.6567 160 N 0.1750 0.1680 0.6570 161 A 0.1511 0.2380 0.6109 162 N 0.1558 0.1758 0.6683 163 D 0.1869 0.1386 0.6745 164 V 0.1629 0.2768 0.5603 165 D 0.1698 0.2402 0.5900 166 K 0.1293 0.2967 0.5740 167 Y 0.1392 0.2473 0.6136 168 K 0.1554 0.2141 0.6305 169 H 0.2386 0.2003 0.5611 170 T 0.3127 0.2143 0.4730 171 K 0.3490 0.2343 0.4168 172 S 0.4137 0.2322 0.3541 173 S 0.4014 0.3142 0.2844 174 R 0.3978 0.3504 0.2518 175 E 0.3710 0.4186 0.2104 176 S 0.3288 0.4215 0.2497 177 Y 0.2345 0.4474 0.3181 178 H 0.1651 0.4017 0.4332 179 A 0.1114 0.2356 0.6529 180 G 0.1052 0.1750 0.7198 181 L 0.1366 0.3379 0.5256 182 K 0.1734 0.4326 0.3940 183 Y 0.2366 0.4728 0.2905 184 E 0.2081 0.5643 0.2276 185 N 0.2902 0.4973 0.2125 186 A 0.3223 0.4982 0.1795 187 G 0.3450 0.4845 0.1706 188 F 0.3144 0.4909 0.1947 189 F 0.2561 0.4767 0.2672 190 G 0.2121 0.4334 0.3545 191 Q 0.1659 0.4127 0.4214 192 Y 0.1519 0.2953 0.5528 193 A 0.1283 0.2180 0.6537 194 G 0.1078 0.2482 0.6440 195 S 0.1454 0.2692 0.5855 196 F 0.1882 0.3064 0.5054 197 A 0.1947 0.3514 0.4539 198 K 0.1936 0.3512 0.4552 199 Y 0.1905 0.3134 0.4961 200 A 0.1649 0.3156 0.5194 201 D 0.1657 0.2783 0.5560 202 L 0.1650 0.2564 0.5786 203 N 0.1724 0.1855 0.6421 204 T 0.1504 0.2520 0.5976 205 D 0.1474 0.2353 0.6173 206 A 0.1243 0.3455 0.5302 207 E 0.1389 0.3318 0.5292 208 R 0.1996 0.2606 0.5398 209 V 0.2422 0.2276 0.5301 210 A 0.2816 0.1894 0.5290 211 V 0.2265 0.3032 0.4703 212 N 0.2053 0.2708 0.5239 213 T 0.1828 0.2436 0.5736 214 A 0.1574 0.2341 0.6085 215 N 0.1652 0.1981 0.6367 216 A 0.2207 0.1438 0.6355 217 H 0.2769 0.0654 0.6576 218 P 0.2389 0.1300 0.6311 219 V 0.1858 0.2537 0.5605 220 K 0.1559 0.3030 0.5411 221 D 0.1924 0.2725 0.5352 222 Y 0.2666 0.2755 0.4579 223 Q 0.4106 0.2601 0.3293 224 V 0.5240 0.2179 0.2581 225 H 0.5793 0.1809 0.2398 226 R 0.6508 0.1279 0.2213 227 V 0.6815 0.0964 0.2221 228 V 0.7019 0.0677 0.2304 229 A 0.6992 0.0567 0.2441 230 G 0.6799 0.0546 0.2655 231 Y 0.6504 0.0603 0.2893 232 D 0.5220 0.0830 0.3950 233 A 0.2810 0.1863 0.5327 234 N 0.2022 0.1749 0.6228 235 D 0.2936 0.1434 0.5630 236 L 0.5357 0.0952 0.3691 237 Y 0.6730 0.0620 0.2650 238 V 0.7327 0.0648 0.2025 239 S 0.7004 0.0887 0.2109 240 V 0.6832 0.1107 0.2060 241 A 0.5825 0.1667 0.2508 242 G 0.5116 0.2014 0.2870 243 Q 0.4455 0.2561 0.2983 244 Y 0.3726 0.3119 0.3155 245 E 0.2714 0.4099 0.3187 246 A 0.2159 0.3980 0.3861 247 A 0.1814 0.3500 0.4686 248 K 0.1639 0.2656 0.5705 249 N 0.1579 0.2012 0.6409 250 N 0.1186 0.2795 0.6019 251 E 0.1270 0.3007 0.5723 252 V 0.1572 0.2351 0.6078 253 G 0.1564 0.1946 0.6490 254 S 0.2026 0.2125 0.5849 255 I 0.2014 0.2633 0.5353 256 K 0.1814 0.1958 0.6227 257 G 0.1542 0.1466 0.6992 258 K 0.2055 0.1662 0.6283 259 K 0.2507 0.1685 0.5808 260 H 0.2697 0.1994 0.5309 261 E 0.2857 0.2138 0.5005 262 Q 0.3079 0.2102 0.4820 263 T 0.3497 0.1824 0.4680 264 Q 0.5363 0.1164 0.3473 265 V 0.6687 0.0763 0.2550 266 A 0.6972 0.0519 0.2510 267 A 0.7115 0.0472 0.2413 268 T 0.6881 0.0355 0.2764 269 A 0.7058 0.0342 0.2601 270 A 0.7032 0.0366 0.2602 271 Y 0.6759 0.0374 0.2866 272 R 0.5562 0.0548 0.3890 273 F 0.3674 0.1029 0.5297 274 G 0.1949 0.1181 0.6871 275 N 0.1444 0.2527 0.6029 276 V 0.1587 0.2824 0.5589 277 T 0.2286 0.2359 0.5355 278 P 0.1509 0.4810 0.3682 279 R 0.1696 0.5563 0.2741 280 V 0.2905 0.5074 0.2021 281 S 0.3947 0.4283 0.1769 282 Y 0.4494 0.3670 0.1836 283 A 0.4597 0.3017 0.2386 284 H 0.4500 0.2252 0.3247 285 G 0.3908 0.1752 0.4340 286 F 0.3922 0.1677 0.4401 287 K 0.3858 0.1839 0.4303 288 A 0.3635 0.2047 0.4318 289 K 0.3174 0.1869 0.4957 290 V 0.2564 0.2340 0.5096 291 N 0.1686 0.1458 0.6856 292 G 0.1449 0.1153 0.7397 293 V 0.2316 0.1375 0.6310 294 K 0.2390 0.1498 0.6112 295 D 0.2033 0.1662 0.6305 296 A 0.1446 0.2600 0.5954 297 N 0.1791 0.1850 0.6359 298 Y 0.2093 0.1727 0.6180 299 Q 0.2645 0.1177 0.6178 300 Y 0.3216 0.1392 0.5392 301 D 0.4054 0.1105 0.4841 302 Q 0.7002 0.0416 0.2582 303 V 0.7365 0.0212 0.2424 304 I 0.7670 0.0142 0.2187 305 V 0.7268 0.0306 0.2426 306 G 0.6729 0.0328 0.2943 307 A 0.6639 0.0460 0.2901 308 D 0.5729 0.0667 0.3603 309 Y 0.5060 0.1392 0.3548 310 D 0.3339 0.1851 0.4810 311 F 0.2758 0.2118 0.5125 312 S 0.2119 0.1512 0.6369 313 K 0.0861 0.4021 0.5119 314 R 0.1127 0.3876 0.4997 315 T 0.2054 0.3823 0.4123 316 S 0.2310 0.4924 0.2766 317 A 0.3196 0.4859 0.1945 318 L 0.3223 0.5037 0.1740 319 V 0.3376 0.5051 0.1573 320 S 0.2793 0.5374 0.1834 321 A 0.1845 0.6435 0.1720 322 G 0.1557 0.6804 0.1639 323 W 0.1573 0.6953 0.1474 324 L 0.1836 0.6482 0.1682 325 K 0.1799 0.5434 0.2767 326 Q 0.1087 0.3003 0.5910 327 G 0.0908 0.1583 0.7509 328 K 0.1036 0.1327 0.7637 329 G 0.1149 0.1142 0.7709 330 A 0.1769 0.1646 0.6585 331 G 0.1504 0.1443 0.7053 332 K 0.3504 0.0971 0.5524 333 V 0.5524 0.0535 0.3941 334 E 0.6188 0.0558 0.3254 335 Q 0.6360 0.0513 0.3127 336 T 0.5837 0.0557 0.3606 337 A 0.4944 0.1006 0.4049 338 S 0.3967 0.1160 0.4873 339 M 0.2577 0.1283 0.6141