# This file is the result of combining several RDB files, specifically # T0518.t06.str2.rdb (weight 1.54425) # T0518.t06.str4.rdb (weight 0.924988) # T0518.t06.pb.rdb (weight 0.789901) # T0518.t06.bys.rdb (weight 0.748322) # T0518.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 T0518.t06.str2.rdb # ============================================ # TARGET T0518 # 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 T0518.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 997 # # ============================================ # Comments from T0518.t06.str4.rdb # ============================================ # TARGET T0518 # 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 T0518.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 997 # # ============================================ # Comments from T0518.t06.pb.rdb # ============================================ # TARGET T0518 # 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 T0518.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 997 # # ============================================ # Comments from T0518.t06.bys.rdb # ============================================ # TARGET T0518 # 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 T0518.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 997 # # ============================================ # Comments from T0518.t06.alpha.rdb # ============================================ # TARGET T0518 # 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 T0518.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 997 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2539 0.2300 0.5161 2 K 0.2688 0.2190 0.5122 3 K 0.2652 0.2771 0.4576 4 V 0.2261 0.3066 0.4673 5 F 0.2299 0.2702 0.4999 6 Y 0.2196 0.2091 0.5713 7 P 0.1058 0.4629 0.4314 8 L 0.0474 0.7154 0.2371 9 A 0.0234 0.8599 0.1167 10 C 0.0108 0.9114 0.0778 11 C 0.0084 0.9205 0.0712 12 C 0.0083 0.9234 0.0683 13 L 0.0083 0.9239 0.0678 14 A 0.0083 0.9243 0.0674 15 A 0.0083 0.9242 0.0675 16 G 0.0083 0.9242 0.0675 17 V 0.0083 0.9223 0.0694 18 F 0.0084 0.9176 0.0740 19 A 0.0091 0.8997 0.0912 20 S 0.0132 0.8512 0.1356 21 C 0.0242 0.7337 0.2421 22 G 0.0370 0.5846 0.3784 23 G 0.0567 0.5366 0.4067 24 Q 0.0660 0.5695 0.3645 25 K 0.0668 0.5654 0.3678 26 K 0.0772 0.5262 0.3966 27 A 0.0850 0.4948 0.4202 28 N 0.0889 0.4278 0.4833 29 A 0.0738 0.4713 0.4548 30 Q 0.1117 0.3544 0.5339 31 E 0.1171 0.2944 0.5885 32 E 0.1728 0.1323 0.6949 33 P 0.1350 0.2678 0.5972 34 S 0.1272 0.3473 0.5255 35 K 0.1404 0.4132 0.4465 36 V 0.1715 0.4447 0.3838 37 A 0.1803 0.4628 0.3569 38 L 0.1614 0.4968 0.3419 39 S 0.1529 0.4636 0.3835 40 Y 0.1643 0.4102 0.4254 41 S 0.1425 0.4104 0.4471 42 K 0.1302 0.4045 0.4653 43 S 0.1539 0.3075 0.5386 44 L 0.1285 0.2816 0.5899 45 K 0.1456 0.1915 0.6628 46 A 0.2072 0.0778 0.7150 47 P 0.1725 0.1338 0.6937 48 E 0.1642 0.1897 0.6461 49 T 0.1890 0.1727 0.6383 50 D 0.1835 0.1756 0.6409 51 S 0.1567 0.2633 0.5800 52 L 0.1771 0.2175 0.6054 53 N 0.1951 0.1238 0.6810 54 L 0.2548 0.0557 0.6895 55 P 0.2418 0.0716 0.6866 56 V 0.2716 0.1112 0.6172 57 D 0.1975 0.0895 0.7131 58 E 0.0824 0.3550 0.5625 59 N 0.0963 0.2476 0.6562 60 G 0.1664 0.1597 0.6739 61 Y 0.4389 0.1021 0.4590 62 I 0.6016 0.0731 0.3253 63 T 0.5814 0.0965 0.3222 64 I 0.4318 0.1623 0.4058 65 F 0.3617 0.1363 0.5020 66 D 0.2466 0.0990 0.6543 67 G 0.1235 0.0957 0.7808 68 E 0.2084 0.1443 0.6473 69 T 0.2418 0.1259 0.6324 70 F 0.1484 0.2572 0.5944 71 N 0.1403 0.1831 0.6766 72 G 0.1825 0.1322 0.6853 73 W 0.3985 0.0825 0.5189 74 R 0.5224 0.0742 0.4035 75 G 0.4772 0.0871 0.4357 76 Y 0.3614 0.1055 0.5331 77 G 0.2285 0.0893 0.6823 78 K 0.1907 0.1574 0.6519 79 D 0.1960 0.1581 0.6459 80 R 0.2395 0.1168 0.6437 81 V 0.3132 0.0469 0.6398 82 P 0.2767 0.0644 0.6588 83 T 0.3562 0.0773 0.5665 84 K 0.5573 0.0421 0.4006 85 W 0.7230 0.0115 0.2655 86 T 0.7553 0.0090 0.2357 87 I 0.7008 0.0149 0.2843 88 E 0.5862 0.0705 0.3433 89 D 0.3247 0.0605 0.6148 90 G 0.3387 0.0428 0.6185 91 C 0.6817 0.0096 0.3087 92 I 0.7713 0.0063 0.2224 93 K 0.8097 0.0057 0.1847 94 F 0.7903 0.0064 0.2033 95 N 0.7007 0.0155 0.2838 96 G 0.5119 0.0347 0.4535 97 S 0.3330 0.0659 0.6011 98 G 0.1700 0.1090 0.7211 99 G 0.1413 0.1180 0.7407 100 G 0.1695 0.1077 0.7228 101 E 0.2111 0.1416 0.6473 102 A 0.2208 0.1374 0.6418 103 Q 0.2271 0.1383 0.6346 104 D 0.1946 0.1281 0.6773 105 G 0.1752 0.1184 0.7064 106 D 0.2090 0.1274 0.6637 107 G 0.2815 0.0914 0.6271 108 G 0.4607 0.0797 0.4596 109 D 0.6439 0.0543 0.3018 110 L 0.7352 0.0353 0.2295 111 I 0.7218 0.0440 0.2342 112 F 0.6671 0.0387 0.2942 113 A 0.4502 0.1835 0.3663 114 H 0.3744 0.1714 0.4542 115 K 0.3698 0.1701 0.4601 116 F 0.3418 0.1114 0.5468 117 K 0.3406 0.1314 0.5280 118 N 0.4291 0.0594 0.5116 119 F 0.6965 0.0166 0.2869 120 E 0.7893 0.0061 0.2047 121 L 0.8120 0.0048 0.1832 122 E 0.8329 0.0041 0.1630 123 L 0.8320 0.0042 0.1639 124 E 0.8286 0.0044 0.1670 125 W 0.8195 0.0047 0.1758 126 K 0.7765 0.0083 0.2152 127 V 0.6964 0.0198 0.2839 128 A 0.4389 0.0566 0.5045 129 K 0.2004 0.1349 0.6647 130 G 0.1388 0.1208 0.7404 131 S 0.1963 0.1270 0.6767 132 N 0.2431 0.1023 0.6546 133 S 0.3382 0.1277 0.5342 134 G 0.6363 0.0653 0.2984 135 I 0.7695 0.0239 0.2066 136 L 0.7871 0.0186 0.1943 137 Y 0.7646 0.0204 0.2150 138 L 0.6674 0.0297 0.3029 139 A 0.4618 0.0549 0.4834 140 Q 0.3105 0.1235 0.5660 141 E 0.2452 0.1536 0.6011 142 V 0.2008 0.1986 0.6006 143 T 0.1699 0.2141 0.6160 144 S 0.1861 0.1654 0.6485 145 K 0.1999 0.1769 0.6232 146 D 0.1762 0.1663 0.6575 147 K 0.1294 0.2599 0.6107 148 D 0.1114 0.1859 0.7027 149 G 0.0877 0.1544 0.7579 150 N 0.1627 0.1441 0.6932 151 D 0.1957 0.2181 0.5861 152 V 0.2711 0.2249 0.5040 153 L 0.3429 0.1604 0.4967 154 E 0.4130 0.0997 0.4873 155 P 0.4076 0.1255 0.4669 156 I 0.4347 0.1078 0.4575 157 Y 0.3909 0.0687 0.5404 158 I 0.2848 0.1571 0.5580 159 S 0.1978 0.1399 0.6623 160 A 0.3033 0.0482 0.6485 161 P 0.2916 0.1340 0.5743 162 E 0.5665 0.1057 0.3278 163 Y 0.6894 0.0490 0.2617 164 Q 0.6951 0.0522 0.2527 165 I 0.6895 0.0559 0.2546 166 L 0.4906 0.1207 0.3887 167 D 0.3073 0.1908 0.5019 168 N 0.1778 0.1709 0.6512 169 A 0.1288 0.2235 0.6476 170 N 0.1214 0.1425 0.7361 171 H 0.2142 0.0560 0.7299 172 P 0.1540 0.2393 0.6067 173 D 0.1873 0.2197 0.5930 174 A 0.2239 0.2842 0.4919 175 K 0.3218 0.2419 0.4363 176 L 0.3324 0.1619 0.5056 177 G 0.2392 0.0949 0.6659 178 K 0.2806 0.0999 0.6195 179 D 0.2089 0.1515 0.6396 180 N 0.1498 0.1706 0.6796 181 N 0.1762 0.1892 0.6346 182 R 0.1952 0.2111 0.5937 183 Q 0.2147 0.2219 0.5635 184 S 0.2316 0.2156 0.5527 185 A 0.2318 0.2322 0.5360 186 S 0.3029 0.2547 0.4425 187 L 0.3092 0.3045 0.3863 188 Y 0.2809 0.2821 0.4370 189 D 0.2356 0.2242 0.5402 190 M 0.2584 0.1655 0.5761 191 I 0.2549 0.0580 0.6870 192 P 0.2142 0.1138 0.6720 193 A 0.1993 0.1489 0.6518 194 V 0.2306 0.0756 0.6938 195 P 0.1508 0.2260 0.6232 196 Q 0.1360 0.2375 0.6265 197 N 0.1675 0.1878 0.6447 198 S 0.2036 0.1407 0.6556 199 K 0.2528 0.0492 0.6980 200 P 0.2070 0.0704 0.7226 201 F 0.1110 0.1986 0.6904 202 G 0.0966 0.1167 0.7868 203 E 0.3716 0.0896 0.5387 204 W 0.5985 0.0439 0.3576 205 N 0.6362 0.0359 0.3279 206 K 0.7931 0.0080 0.1988 207 A 0.8086 0.0055 0.1859 208 K 0.8277 0.0043 0.1680 209 I 0.8333 0.0042 0.1625 210 M 0.8242 0.0046 0.1712 211 V 0.7922 0.0052 0.2027 212 Y 0.6914 0.0191 0.2896 213 K 0.3076 0.0485 0.6440 214 G 0.2295 0.0645 0.7059 215 T 0.6558 0.0131 0.3312 216 V 0.7486 0.0065 0.2449 217 V 0.8054 0.0058 0.1887 218 H 0.8114 0.0051 0.1836 219 G 0.7559 0.0096 0.2344 220 Q 0.7022 0.0278 0.2700 221 N 0.3625 0.0393 0.5982 222 D 0.1880 0.0668 0.7452 223 E 0.5324 0.0362 0.4313 224 N 0.6590 0.0288 0.3122 225 V 0.7124 0.0359 0.2517 226 L 0.7209 0.0415 0.2376 227 E 0.7254 0.0370 0.2375 228 Y 0.6788 0.0482 0.2730 229 H 0.5547 0.0622 0.3831 230 L 0.3376 0.1625 0.4999 231 W 0.2151 0.2268 0.5580 232 T 0.2048 0.1964 0.5988 233 K 0.1328 0.3367 0.5305 234 Q 0.1310 0.3464 0.5226 235 W 0.1293 0.4116 0.4591 236 T 0.0658 0.5986 0.3356 237 D 0.0629 0.6151 0.3219 238 M 0.0740 0.6591 0.2668 239 L 0.0972 0.6162 0.2866 240 Q 0.1187 0.5055 0.3758 241 A 0.1310 0.4268 0.4423 242 S 0.1622 0.2837 0.5541 243 K 0.0776 0.4001 0.5224 244 F 0.1297 0.2631 0.6072 245 S 0.1508 0.1755 0.6737 246 E 0.0392 0.4537 0.5072 247 D 0.0748 0.3464 0.5788 248 K 0.1069 0.3215 0.5716 249 W 0.1763 0.2962 0.5275 250 P 0.1405 0.4536 0.4060 251 L 0.1017 0.5491 0.3493 252 A 0.1155 0.5740 0.3105 253 F 0.1200 0.6026 0.2774 254 E 0.1714 0.5353 0.2933 255 L 0.1918 0.3988 0.4094 256 L 0.1499 0.2692 0.5809 257 N 0.1312 0.2725 0.5963 258 N 0.1491 0.1973 0.6536 259 C 0.1616 0.1574 0.6810 260 G 0.1409 0.1228 0.7363 261 G 0.1577 0.0915 0.7508 262 E 0.2156 0.1203 0.6640 263 N 0.1957 0.1386 0.6658 264 H 0.1737 0.1872 0.6391 265 E 0.1864 0.1444 0.6692 266 G 0.2861 0.0843 0.6296 267 F 0.5280 0.0446 0.4274 268 I 0.6884 0.0313 0.2803 269 G 0.7043 0.0356 0.2601 270 L 0.6831 0.0453 0.2715 271 Q 0.5658 0.0606 0.3736 272 D 0.3885 0.1052 0.5063 273 H 0.2182 0.1092 0.6726 274 G 0.1532 0.0719 0.7750 275 D 0.2483 0.0627 0.6890 276 D 0.4210 0.0611 0.5179 277 V 0.6682 0.0310 0.3008 278 W 0.7252 0.0185 0.2564 279 F 0.7024 0.0166 0.2810 280 R 0.6193 0.0470 0.3337 281 N 0.6259 0.0244 0.3496 282 I 0.7157 0.0087 0.2757 283 R 0.7553 0.0110 0.2336 284 V 0.7366 0.0086 0.2548 285 K 0.7152 0.0216 0.2632 286 V 0.6579 0.0195 0.3225 287 L 0.4462 0.0452 0.5086 288 D 0.2405 0.0586 0.7010