# This file is the result of combining several RDB files, specifically # T0629.t2k.str2.rdb (weight 1.54425) # T0629.t2k.str4.rdb (weight 0.924988) # T0629.t2k.pb.rdb (weight 0.789901) # T0629.t2k.bys.rdb (weight 0.748322) # T0629.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 T0629.t2k.str2.rdb # ============================================ # TARGET T0629 # 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 T0629.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 234.292 # # ============================================ # Comments from T0629.t2k.str4.rdb # ============================================ # TARGET T0629 # 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 T0629.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 234.292 # # ============================================ # Comments from T0629.t2k.pb.rdb # ============================================ # TARGET T0629 # 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 T0629.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 234.292 # # ============================================ # Comments from T0629.t2k.bys.rdb # ============================================ # TARGET T0629 # 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 T0629.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 234.292 # # ============================================ # Comments from T0629.t2k.alpha.rdb # ============================================ # TARGET T0629 # 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 T0629.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 234.292 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2294 0.1688 0.6018 2 S 0.2932 0.1430 0.5638 3 Y 0.3542 0.0657 0.5801 4 P 0.3176 0.0731 0.6093 5 I 0.2778 0.0935 0.6286 6 G 0.2677 0.0657 0.6666 7 A 0.3864 0.0357 0.5779 8 P 0.4681 0.0450 0.4869 9 I 0.4037 0.0304 0.5659 10 P 0.3140 0.0595 0.6265 11 W 0.2728 0.0415 0.6857 12 P 0.1688 0.1371 0.6941 13 S 0.1395 0.1789 0.6816 14 D 0.1248 0.2123 0.6629 15 S 0.2008 0.1200 0.6792 16 V 0.2247 0.0641 0.7113 17 P 0.1954 0.1193 0.6853 18 A 0.1573 0.2613 0.5813 19 G 0.1849 0.1981 0.6170 20 F 0.4570 0.1575 0.3855 21 A 0.6079 0.0968 0.2953 22 L 0.6100 0.0887 0.3013 23 M 0.5022 0.0995 0.3983 24 E 0.2218 0.1024 0.6758 25 G 0.1254 0.1052 0.7694 26 Q 0.2705 0.1233 0.6061 27 T 0.3837 0.1433 0.4730 28 F 0.3748 0.1062 0.5190 29 D 0.2085 0.0577 0.7337 30 K 0.0267 0.6655 0.3078 31 S 0.0222 0.7130 0.2648 32 A 0.0362 0.6349 0.3289 33 Y 0.0512 0.6714 0.2774 34 P 0.0172 0.8336 0.1492 35 K 0.0114 0.8861 0.1026 36 L 0.0147 0.8885 0.0968 37 A 0.0127 0.8948 0.0925 38 V 0.0255 0.8415 0.1330 39 A 0.0743 0.6221 0.3036 40 Y 0.1768 0.3213 0.5018 41 P 0.0778 0.3870 0.5353 42 S 0.0788 0.1918 0.7294 43 G 0.0830 0.1141 0.8029 44 V 0.2448 0.0749 0.6803 45 I 0.2596 0.0484 0.6920 46 P 0.2157 0.1494 0.6348 47 D 0.2056 0.1506 0.6437 48 M 0.2107 0.2219 0.5674 49 R 0.1910 0.1315 0.6774 50 G 0.2385 0.0919 0.6696 51 Q 0.4935 0.0607 0.4458 52 T 0.6703 0.0374 0.2923 53 I 0.6678 0.0330 0.2992 54 K 0.6001 0.0362 0.3637 55 G 0.3941 0.0431 0.5628 56 K 0.2948 0.0345 0.6707 57 P 0.1816 0.1891 0.6292 58 S 0.1305 0.1664 0.7032 59 G 0.1080 0.1418 0.7501 60 R 0.2676 0.1126 0.6198 61 A 0.4001 0.1039 0.4960 62 V 0.3873 0.1407 0.4720 63 L 0.3167 0.1434 0.5399 64 S 0.1906 0.3552 0.4542 65 A 0.1341 0.3859 0.4800 66 E 0.1501 0.4271 0.4228 67 A 0.1542 0.4407 0.4050 68 D 0.1497 0.2981 0.5522 69 G 0.1478 0.2084 0.6438 70 V 0.2439 0.2114 0.5448 71 K 0.2458 0.2483 0.5059 72 A 0.2298 0.2659 0.5043 73 H 0.1936 0.2929 0.5135 74 S 0.1804 0.3029 0.5166 75 H 0.2152 0.3074 0.4774 76 S 0.2551 0.2798 0.4651 77 A 0.2598 0.2850 0.4552 78 S 0.2541 0.1976 0.5483 79 A 0.2153 0.2652 0.5195 80 S 0.1995 0.2114 0.5892 81 S 0.1881 0.2192 0.5927 82 T 0.1752 0.2618 0.5630 83 D 0.1929 0.2434 0.5637 84 L 0.1836 0.2518 0.5646 85 G 0.1959 0.1914 0.6127 86 T 0.2336 0.1937 0.5727 87 K 0.2342 0.2161 0.5497 88 T 0.2608 0.1922 0.5470 89 T 0.2498 0.1823 0.5679 90 S 0.2404 0.1855 0.5740 91 S 0.2364 0.2256 0.5381 92 F 0.2325 0.2427 0.5249 93 D 0.2333 0.2293 0.5374 94 Y 0.2067 0.2068 0.5865 95 G 0.1899 0.1437 0.6664 96 T 0.2578 0.1502 0.5920 97 K 0.2651 0.1523 0.5826 98 G 0.2961 0.1296 0.5743 99 T 0.2765 0.1372 0.5863 100 N 0.2412 0.1283 0.6305 101 S 0.2215 0.1687 0.6098 102 T 0.1947 0.1306 0.6747 103 G 0.1774 0.0957 0.7269 104 G 0.2358 0.1077 0.6564 105 H 0.2979 0.1069 0.5952 106 T 0.3143 0.1068 0.5789 107 H 0.3148 0.1148 0.5704 108 S 0.2688 0.1026 0.6286 109 G 0.2305 0.0995 0.6700 110 S 0.2344 0.1025 0.6631 111 G 0.2232 0.1023 0.6745 112 S 0.2612 0.1043 0.6345 113 T 0.2543 0.1358 0.6100 114 S 0.2107 0.1485 0.6408 115 T 0.1702 0.1866 0.6432 116 N 0.1397 0.1335 0.7268 117 G 0.1292 0.1252 0.7456 118 E 0.2287 0.1333 0.6380 119 H 0.2939 0.1017 0.6043 120 S 0.3130 0.1208 0.5662 121 H 0.3526 0.1086 0.5388 122 Y 0.3566 0.1017 0.5417 123 I 0.3399 0.1354 0.5247 124 E 0.2838 0.1809 0.5353 125 A 0.2465 0.2351 0.5184 126 W 0.2355 0.2347 0.5298 127 N 0.1854 0.1488 0.6659 128 G 0.1627 0.1158 0.7215 129 T 0.1872 0.1160 0.6968 130 G 0.1944 0.0995 0.7061 131 V 0.2297 0.1386 0.6317 132 G 0.1901 0.1264 0.6834 133 G 0.1915 0.1509 0.6577 134 N 0.2211 0.1698 0.6091 135 K 0.2522 0.1635 0.5843 136 M 0.2742 0.1740 0.5518 137 S 0.2609 0.1693 0.5698 138 S 0.2665 0.1769 0.5566 139 Y 0.3275 0.1607 0.5118 140 A 0.4017 0.1506 0.4477 141 I 0.4448 0.1437 0.4115 142 S 0.4441 0.1224 0.4335 143 Y 0.3801 0.1233 0.4965 144 R 0.3114 0.1288 0.5598 145 A 0.2311 0.1203 0.6486 146 G 0.1804 0.1038 0.7158 147 G 0.2121 0.1061 0.6817 148 S 0.2799 0.1195 0.6006 149 N 0.3113 0.1073 0.5814 150 T 0.3178 0.1166 0.5656 151 N 0.2675 0.1199 0.6126 152 A 0.2302 0.1674 0.6024 153 A 0.1898 0.1491 0.6611 154 G 0.1654 0.1345 0.7001 155 N 0.2010 0.1400 0.6590 156 H 0.2146 0.1554 0.6300 157 S 0.2236 0.1668 0.6096 158 H 0.2283 0.1826 0.5892 159 T 0.2674 0.1652 0.5674 160 F 0.2919 0.1642 0.5438 161 S 0.3219 0.1444 0.5338 162 F 0.3210 0.1560 0.5230 163 G 0.3077 0.1236 0.5687 164 T 0.3457 0.1653 0.4889 165 S 0.2888 0.1787 0.5326 166 S 0.2729 0.1749 0.5522 167 A 0.1837 0.1705 0.6457 168 G 0.1416 0.1314 0.7270 169 D 0.1745 0.1800 0.6456 170 H 0.2114 0.1675 0.6211 171 S 0.2665 0.1757 0.5579 172 H 0.3234 0.1438 0.5328 173 S 0.3988 0.1269 0.4743 174 V 0.4217 0.1268 0.4515 175 G 0.3900 0.1003 0.5098 176 I 0.3160 0.1262 0.5577 177 G 0.2180 0.1167 0.6652 178 A 0.1790 0.2186 0.6024 179 H 0.1869 0.1975 0.6156 180 T 0.1960 0.2024 0.6016 181 H 0.2239 0.1722 0.6038 182 T 0.3289 0.1561 0.5150 183 V 0.3892 0.1548 0.4560 184 A 0.4070 0.1420 0.4510 185 I 0.3413 0.1529 0.5059 186 G 0.2471 0.1235 0.6294 187 S 0.2548 0.1727 0.5724 188 H 0.2427 0.1363 0.6209 189 G 0.2657 0.1122 0.6220 190 H 0.3577 0.0934 0.5489 191 T 0.4985 0.0674 0.4341 192 I 0.6142 0.0588 0.3270 193 T 0.6539 0.0399 0.3063 194 V 0.5965 0.0657 0.3378 195 N 0.4627 0.0620 0.4753 196 S 0.3170 0.1186 0.5644 197 T 0.2006 0.1507 0.6487 198 G 0.1706 0.1247 0.7047 199 N 0.2033 0.1685 0.6282 200 T 0.1921 0.2086 0.5993 201 E 0.1740 0.2995 0.5265 202 N 0.2011 0.2101 0.5887 203 T 0.2444 0.1818 0.5738 204 V 0.1785 0.3729 0.4485 205 K 0.0943 0.6108 0.2949 206 N 0.0517 0.8011 0.1473 207 I 0.0229 0.8591 0.1180 208 A 0.0165 0.8935 0.0901 209 F 0.0114 0.9131 0.0755 210 N 0.0106 0.9152 0.0742 211 Y 0.0105 0.9155 0.0740 212 I 0.0125 0.9124 0.0750 213 V 0.0121 0.9066 0.0813 214 R 0.0145 0.8742 0.1113 215 L 0.0270 0.7627 0.2103 216 A 0.0464 0.6192 0.3344