# This file is the result of combining several RDB files, specifically # T0449.t04.str2.rdb (weight 1.54425) # T0449.t04.str4.rdb (weight 0.924988) # T0449.t04.pb.rdb (weight 0.789901) # T0449.t04.bys.rdb (weight 0.748322) # T0449.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 T0449.t04.str2.rdb # ============================================ # TARGET T0449 # 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 T0449.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 1139 # # ============================================ # Comments from T0449.t04.str4.rdb # ============================================ # TARGET T0449 # 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 T0449.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 1139 # # ============================================ # Comments from T0449.t04.pb.rdb # ============================================ # TARGET T0449 # 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 T0449.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 1139 # # ============================================ # Comments from T0449.t04.bys.rdb # ============================================ # TARGET T0449 # 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 T0449.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 1139 # # ============================================ # Comments from T0449.t04.alpha.rdb # ============================================ # TARGET T0449 # 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 T0449.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 1139 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.5577 0.0143 0.4281 2 D 0.7353 0.0088 0.2558 3 Y 0.8099 0.0051 0.1850 4 T 0.8053 0.0063 0.1884 5 I 0.7789 0.0079 0.2132 6 E 0.6290 0.0353 0.3357 7 N 0.3494 0.0402 0.6103 8 N 0.2324 0.0759 0.6917 9 M 0.4007 0.0378 0.5615 10 I 0.6538 0.0145 0.3317 11 K 0.7763 0.0077 0.2160 12 V 0.8227 0.0045 0.1728 13 V 0.8170 0.0046 0.1783 14 I 0.7665 0.0065 0.2270 15 S 0.5111 0.0353 0.4536 16 D 0.3158 0.1220 0.5622 17 H 0.1855 0.1304 0.6842 18 G 0.2573 0.0698 0.6730 19 A 0.5859 0.0239 0.3902 20 E 0.7261 0.0166 0.2573 21 I 0.7290 0.0110 0.2600 22 Q 0.7005 0.0269 0.2726 23 S 0.7748 0.0085 0.2167 24 V 0.7343 0.0153 0.2504 25 K 0.7063 0.0169 0.2768 26 S 0.4928 0.0349 0.4724 27 A 0.1522 0.1714 0.6764 28 H 0.0807 0.1346 0.7846 29 T 0.2234 0.0747 0.7019 30 D 0.3172 0.0780 0.6048 31 E 0.5020 0.1030 0.3950 32 E 0.6040 0.0989 0.2971 33 F 0.6266 0.1085 0.2649 34 M 0.5544 0.1224 0.3232 35 W 0.4525 0.1399 0.4076 36 Q 0.2829 0.1562 0.5609 37 A 0.2066 0.1497 0.6437 38 N 0.1959 0.0940 0.7102 39 P 0.0337 0.5684 0.3978 40 E 0.0383 0.6343 0.3274 41 I 0.1077 0.4981 0.3942 42 W 0.1344 0.3574 0.5082 43 G 0.1108 0.2243 0.6649 44 R 0.1247 0.2012 0.6742 45 H 0.1582 0.1156 0.7262 46 A 0.2710 0.0492 0.6798 47 P 0.3612 0.0636 0.5752 48 V 0.5871 0.0612 0.3517 49 L 0.6229 0.0549 0.3222 50 F 0.5366 0.0398 0.4236 51 P 0.4178 0.1286 0.4537 52 I 0.3043 0.2346 0.4611 53 V 0.2226 0.2075 0.5699 54 G 0.1714 0.1695 0.6591 55 R 0.2618 0.1791 0.5591 56 L 0.3128 0.1738 0.5133 57 K 0.1844 0.2020 0.6136 58 N 0.1268 0.1346 0.7386 59 D 0.1859 0.0985 0.7156 60 E 0.4042 0.0547 0.5411 61 Y 0.5691 0.0334 0.3975 62 T 0.6252 0.0248 0.3500 63 Y 0.5120 0.0644 0.4236 64 K 0.1990 0.0798 0.7212 65 G 0.1100 0.0820 0.8080 66 K 0.5433 0.0257 0.4310 67 T 0.6700 0.0193 0.3107 68 Y 0.7138 0.0206 0.2657 69 H 0.6748 0.0260 0.2991 70 L 0.5436 0.0623 0.3941 71 G 0.3339 0.1042 0.5618 72 Q 0.2350 0.2363 0.5287 73 H 0.2106 0.1650 0.6244 74 G 0.2246 0.1619 0.6135 75 F 0.2719 0.2039 0.5242 76 A 0.3085 0.2053 0.4863 77 R 0.2353 0.1976 0.5671 78 N 0.1894 0.1176 0.6930 79 A 0.2507 0.1066 0.6426 80 D 0.3057 0.0767 0.6176 81 F 0.4788 0.0499 0.4713 82 E 0.5951 0.0408 0.3640 83 V 0.6262 0.0480 0.3258 84 E 0.5472 0.0884 0.3645 85 N 0.4836 0.0695 0.4469 86 H 0.3805 0.0642 0.5553 87 T 0.2812 0.0378 0.6811 88 K 0.1657 0.2239 0.6104 89 E 0.2155 0.1250 0.6595 90 S 0.6217 0.0302 0.3480 91 I 0.7541 0.0070 0.2388 92 T 0.8133 0.0048 0.1819 93 F 0.8242 0.0044 0.1714 94 L 0.8148 0.0056 0.1796 95 L 0.7738 0.0083 0.2179 96 K 0.6732 0.0192 0.3076 97 D 0.4188 0.0293 0.5519 98 N 0.1926 0.1703 0.6371 99 E 0.0467 0.4126 0.5407 100 E 0.0605 0.4755 0.4640 101 T 0.1491 0.4167 0.4342 102 R 0.1681 0.4368 0.3950 103 K 0.2223 0.3462 0.4316 104 V 0.2928 0.1697 0.5376 105 Y 0.3606 0.0614 0.5780 106 P 0.3469 0.0982 0.5549 107 F 0.4909 0.0573 0.4518 108 K 0.6487 0.0270 0.3243 109 F 0.7657 0.0082 0.2261 110 E 0.8025 0.0058 0.1917 111 F 0.8241 0.0042 0.1716 112 R 0.8288 0.0043 0.1670 113 V 0.8269 0.0042 0.1689 114 N 0.8260 0.0043 0.1697 115 Y 0.8204 0.0047 0.1749 116 N 0.7964 0.0057 0.1979 117 L 0.7074 0.0185 0.2741 118 M 0.4800 0.0601 0.4599 119 N 0.2089 0.0841 0.7070 120 N 0.2053 0.1004 0.6943 121 L 0.5228 0.0456 0.4316 122 L 0.7036 0.0230 0.2735 123 E 0.7850 0.0113 0.2037 124 E 0.8012 0.0095 0.1892 125 N 0.7703 0.0135 0.2161 126 F 0.8038 0.0083 0.1879 127 S 0.7949 0.0093 0.1958 128 V 0.7884 0.0113 0.2003 129 V 0.7019 0.0227 0.2754 130 N 0.4574 0.0240 0.5186 131 K 0.1933 0.1802 0.6265 132 S 0.1655 0.1775 0.6570 133 D 0.1566 0.1605 0.6829 134 E 0.2135 0.1799 0.6066 135 T 0.3154 0.1671 0.5175 136 M 0.5051 0.0992 0.3957 137 I 0.5499 0.1153 0.3348 138 F 0.5592 0.1160 0.3248 139 G 0.4241 0.1398 0.4361 140 V 0.3156 0.2254 0.4590 141 G 0.2571 0.1776 0.5653 142 G 0.2332 0.1340 0.6329 143 H 0.2374 0.1004 0.6622 144 P 0.1317 0.3008 0.5675 145 G 0.1521 0.2702 0.5778 146 F 0.2711 0.1460 0.5829 147 N 0.3066 0.0856 0.6078 148 L 0.3119 0.0546 0.6335 149 P 0.2198 0.0968 0.6834 150 T 0.1802 0.1878 0.6320 151 D 0.1457 0.1974 0.6568 152 H 0.1193 0.1739 0.7068 153 G 0.1147 0.1353 0.7501 154 E 0.1804 0.1429 0.6767 155 N 0.2376 0.0757 0.6867 156 K 0.2013 0.2596 0.5392 157 E 0.2061 0.2888 0.5051 158 D 0.2970 0.1691 0.5339 159 F 0.5861 0.0300 0.3839 160 Y 0.7365 0.0132 0.2503 161 F 0.7902 0.0076 0.2023 162 D 0.7375 0.0092 0.2533 163 M 0.6436 0.0195 0.3369 164 H 0.3025 0.0219 0.6756 165 P 0.1145 0.3238 0.5617 166 S 0.1065 0.2659 0.6276 167 V 0.2199 0.1706 0.6095 168 T 0.3384 0.0693 0.5923 169 R 0.4425 0.0937 0.4638 170 V 0.4789 0.0761 0.4450 171 R 0.4354 0.0492 0.5154 172 I 0.3746 0.0313 0.5941 173 P 0.2655 0.0584 0.6761 174 L 0.1923 0.1680 0.6397 175 K 0.1275 0.2488 0.6237 176 D 0.1640 0.2665 0.5695 177 A 0.2318 0.2675 0.5007 178 S 0.3216 0.2121 0.4663 179 L 0.3999 0.1538 0.4462 180 D 0.3141 0.1333 0.5527 181 W 0.1594 0.3734 0.4672 182 N 0.1007 0.2502 0.6492 183 N 0.0884 0.1538 0.7579 184 R 0.2231 0.0745 0.7024 185 S 0.2717 0.1257 0.6027 186 L 0.2629 0.1384 0.5987 187 A 0.2487 0.0834 0.6679 188 P 0.1895 0.1680 0.6425 189 T 0.1597 0.2440 0.5963 190 D 0.1365 0.2266 0.6369 191 S 0.2057 0.1770 0.6173 192 L 0.2976 0.1435 0.5589 193 I 0.4745 0.0873 0.4382 194 A 0.4521 0.0975 0.4504 195 L 0.3445 0.1529 0.5026 196 S 0.2077 0.1531 0.6393 197 D 0.0885 0.3983 0.5132 198 D 0.1052 0.3728 0.5219 199 L 0.1919 0.2843 0.5238 200 F 0.2522 0.1974 0.5504 201 K 0.2262 0.1801 0.5936 202 D 0.1821 0.1992 0.6187 203 D 0.2164 0.1953 0.5883 204 A 0.4769 0.1143 0.4088 205 L 0.6476 0.0707 0.2817 206 I 0.6401 0.0789 0.2809 207 Y 0.5346 0.1083 0.3571 208 E 0.3779 0.1486 0.4735 209 L 0.2167 0.2346 0.5487 210 R 0.1540 0.1787 0.6673 211 G 0.1349 0.1177 0.7474 212 N 0.1881 0.0937 0.7183 213 D 0.2615 0.0999 0.6387 214 N 0.3687 0.0741 0.5572 215 K 0.6626 0.0273 0.3102 216 V 0.7724 0.0080 0.2196 217 S 0.7973 0.0062 0.1965 218 L 0.7950 0.0089 0.1961 219 R 0.7436 0.0187 0.2376 220 T 0.5357 0.0153 0.4490 221 D 0.1943 0.2764 0.5293 222 K 0.1080 0.2620 0.6300 223 N 0.1256 0.1316 0.7428 224 K 0.2733 0.0570 0.6697 225 F 0.6041 0.0149 0.3810 226 H 0.7595 0.0076 0.2329 227 V 0.8192 0.0046 0.1762 228 N 0.8138 0.0048 0.1813 229 V 0.8098 0.0049 0.1852 230 W 0.7480 0.0143 0.2377 231 T 0.5695 0.0336 0.3968 232 R 0.2866 0.0932 0.6201 233 D 0.1730 0.0823 0.7447 234 A 0.2968 0.0352 0.6680 235 P 0.3669 0.0616 0.5715 236 F 0.6453 0.0370 0.3177 237 V 0.7787 0.0109 0.2104 238 G 0.7833 0.0079 0.2087 239 I 0.7956 0.0092 0.1952 240 W 0.7208 0.0263 0.2529 241 S 0.4888 0.0290 0.4822 242 Q 0.2535 0.1463 0.6002 243 Y 0.2194 0.0919 0.6887 244 P 0.1352 0.2668 0.5980 245 K 0.1068 0.2706 0.6225 246 T 0.1292 0.2051 0.6657 247 D 0.1735 0.1585 0.6680 248 N 0.2550 0.1319 0.6131 249 Y 0.4581 0.0694 0.4724 250 V 0.6102 0.0425 0.3473 251 C 0.6471 0.0338 0.3192 252 I 0.5982 0.0430 0.3589 253 E 0.5033 0.0382 0.4585 254 P 0.3072 0.1280 0.5648 255 W 0.2008 0.2246 0.5746 256 W 0.1710 0.2053 0.6237 257 G 0.1554 0.1473 0.6973 258 I 0.2142 0.1619 0.6239 259 A 0.1731 0.2506 0.5762 260 D 0.1663 0.1810 0.6526 261 R 0.1456 0.2955 0.5588 262 D 0.1268 0.2898 0.5834 263 D 0.1437 0.1969 0.6594 264 A 0.1087 0.3369 0.5544 265 D 0.1121 0.3495 0.5384 266 G 0.0759 0.4793 0.4448 267 D 0.0831 0.5341 0.3828 268 L 0.1179 0.5243 0.3577 269 E 0.1591 0.4352 0.4058 270 H 0.1444 0.3529 0.5027 271 K 0.1436 0.2630 0.5934 272 Y 0.1574 0.1444 0.6982 273 G 0.1307 0.0866 0.7827 274 M 0.3228 0.0578 0.6193 275 N 0.5346 0.0391 0.4263 276 H 0.6620 0.0259 0.3121 277 L 0.5668 0.0255 0.4077 278 K 0.3231 0.0198 0.6572 279 P 0.1668 0.0997 0.7335 280 G 0.0615 0.1070 0.8315 281 K 0.3677 0.0441 0.5882 282 E 0.6222 0.0399 0.3380 283 F 0.6967 0.0344 0.2689 284 Q 0.7041 0.0360 0.2599 285 A 0.7282 0.0266 0.2451 286 G 0.7584 0.0147 0.2269 287 F 0.8010 0.0062 0.1928 288 S 0.8127 0.0055 0.1818 289 M 0.8246 0.0048 0.1706 290 T 0.8121 0.0058 0.1821 291 Y 0.7816 0.0088 0.2095 292 H 0.6727 0.0204 0.3069 293 S 0.4467 0.0623 0.4910 294 T 0.2306 0.1122 0.6572 295 T 0.0855 0.4143 0.5002 296 D 0.0557 0.5606 0.3837 297 E 0.0851 0.6459 0.2690 298 V 0.1309 0.6417 0.2275 299 K 0.1052 0.6695 0.2253 300 L 0.0840 0.7148 0.2012 301 E 0.0751 0.6892 0.2358 302 H 0.0885 0.6007 0.3108 303 H 0.1096 0.4555 0.4349 304 H 0.1491 0.3305 0.5204 305 H 0.1930 0.2310 0.5760 306 H 0.1767 0.1972 0.6261 307 H 0.1747 0.1864 0.6389