# This file is the result of combining several RDB files, specifically # T0629.t06.str2.rdb (weight 1.54425) # T0629.t06.str4.rdb (weight 0.924988) # T0629.t06.pb.rdb (weight 0.789901) # T0629.t06.bys.rdb (weight 0.748322) # T0629.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 T0629.t06.str2.rdb # ============================================ # TARGET T0629 # 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 T0629.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 284.848 # # ============================================ # Comments from T0629.t06.str4.rdb # ============================================ # TARGET T0629 # 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 T0629.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 284.848 # # ============================================ # Comments from T0629.t06.pb.rdb # ============================================ # TARGET T0629 # 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 T0629.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 284.848 # # ============================================ # Comments from T0629.t06.bys.rdb # ============================================ # TARGET T0629 # 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 T0629.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 284.848 # # ============================================ # Comments from T0629.t06.alpha.rdb # ============================================ # TARGET T0629 # 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 T0629.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 284.848 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2164 0.1270 0.6567 2 S 0.2453 0.0955 0.6592 3 Y 0.3131 0.0293 0.6575 4 P 0.2893 0.0471 0.6636 5 I 0.3061 0.0845 0.6094 6 G 0.2969 0.0502 0.6529 7 A 0.4577 0.0257 0.5166 8 P 0.4844 0.0244 0.4912 9 I 0.5070 0.0214 0.4716 10 P 0.3865 0.0325 0.5810 11 W 0.3150 0.0399 0.6451 12 P 0.1789 0.1597 0.6613 13 S 0.1382 0.2242 0.6377 14 D 0.1384 0.2086 0.6530 15 S 0.2030 0.1355 0.6615 16 V 0.2465 0.0609 0.6926 17 P 0.2079 0.1174 0.6747 18 A 0.1414 0.2407 0.6179 19 G 0.1938 0.1747 0.6315 20 F 0.4925 0.1030 0.4046 21 A 0.6159 0.0870 0.2971 22 L 0.5451 0.1062 0.3487 23 M 0.4486 0.1036 0.4479 24 E 0.1939 0.1054 0.7008 25 G 0.1205 0.0828 0.7966 26 Q 0.2736 0.1159 0.6104 27 T 0.3536 0.1344 0.5119 28 F 0.3474 0.1222 0.5304 29 D 0.2124 0.0944 0.6932 30 K 0.0248 0.6790 0.2962 31 S 0.0248 0.6733 0.3019 32 A 0.0340 0.6861 0.2799 33 Y 0.0622 0.6903 0.2474 34 P 0.0111 0.8951 0.0938 35 K 0.0098 0.9051 0.0851 36 L 0.0105 0.9048 0.0847 37 A 0.0112 0.8832 0.1056 38 V 0.0164 0.8107 0.1729 39 A 0.0423 0.6079 0.3498 40 Y 0.1375 0.2273 0.6351 41 P 0.0810 0.3057 0.6133 42 S 0.0992 0.2456 0.6553 43 G 0.1611 0.2020 0.6369 44 V 0.3083 0.1426 0.5491 45 I 0.3211 0.0603 0.6186 46 P 0.2542 0.1545 0.5914 47 D 0.1999 0.1889 0.6112 48 M 0.1557 0.2948 0.5494 49 R 0.1516 0.1674 0.6810 50 G 0.1601 0.0991 0.7408 51 Q 0.3781 0.0530 0.5689 52 T 0.5678 0.0395 0.3928 53 I 0.5341 0.0559 0.4099 54 K 0.4282 0.0634 0.5085 55 G 0.2706 0.0544 0.6750 56 K 0.2637 0.0466 0.6897 57 P 0.1713 0.1626 0.6661 58 S 0.1350 0.1714 0.6936 59 G 0.1357 0.1171 0.7472 60 R 0.2413 0.1191 0.6396 61 A 0.3765 0.0923 0.5311 62 V 0.5150 0.0632 0.4217 63 L 0.5631 0.0496 0.3873 64 S 0.5541 0.0500 0.3959 65 A 0.4202 0.1740 0.4058 66 E 0.3252 0.2277 0.4471 67 A 0.1715 0.4146 0.4140 68 D 0.1067 0.3453 0.5480 69 G 0.0896 0.2209 0.6895 70 V 0.2124 0.1017 0.6859 71 K 0.1726 0.2251 0.6022 72 A 0.1708 0.3004 0.5287 73 H 0.2049 0.2528 0.5422 74 S 0.2605 0.1750 0.5645 75 H 0.3440 0.1073 0.5487 76 S 0.4166 0.0907 0.4927 77 A 0.4687 0.0809 0.4504 78 S 0.4405 0.0720 0.4876 79 A 0.3524 0.1172 0.5304 80 S 0.2969 0.1217 0.5813 81 S 0.2588 0.1349 0.6063 82 T 0.2243 0.1475 0.6282 83 D 0.1973 0.1386 0.6641 84 L 0.1494 0.1846 0.6660 85 G 0.1386 0.1423 0.7191 86 T 0.2417 0.1146 0.6437 87 K 0.2721 0.1273 0.6006 88 T 0.3022 0.1353 0.5625 89 T 0.2929 0.1557 0.5515 90 S 0.3044 0.1579 0.5377 91 S 0.2975 0.1596 0.5429 92 F 0.2614 0.1786 0.5600 93 D 0.2333 0.1821 0.5846 94 Y 0.2052 0.2108 0.5840 95 G 0.2037 0.1618 0.6345 96 T 0.2712 0.1491 0.5796 97 K 0.2859 0.1421 0.5720 98 G 0.3106 0.1119 0.5775 99 T 0.3157 0.1077 0.5765 100 N 0.2670 0.0950 0.6380 101 S 0.2260 0.1571 0.6170 102 T 0.1842 0.1380 0.6778 103 G 0.1441 0.0962 0.7597 104 G 0.1978 0.1027 0.6995 105 H 0.2890 0.1020 0.6090 106 T 0.3679 0.0907 0.5414 107 H 0.3895 0.0853 0.5252 108 S 0.3417 0.0813 0.5770 109 G 0.2579 0.0985 0.6435 110 S 0.2445 0.1021 0.6534 111 G 0.2356 0.1104 0.6540 112 S 0.2969 0.1167 0.5864 113 T 0.2975 0.1233 0.5792 114 S 0.2394 0.1261 0.6345 115 T 0.1642 0.2264 0.6093 116 N 0.1378 0.1641 0.6981 117 G 0.1369 0.1264 0.7367 118 E 0.2079 0.1589 0.6333 119 H 0.2716 0.1499 0.5785 120 S 0.2812 0.1790 0.5398 121 H 0.3320 0.1776 0.4904 122 Y 0.3661 0.1901 0.4438 123 I 0.3494 0.2072 0.4434 124 E 0.3334 0.1941 0.4725 125 A 0.2735 0.1930 0.5334 126 W 0.1967 0.2427 0.5606 127 N 0.1927 0.1666 0.6407 128 G 0.2008 0.1335 0.6657 129 T 0.2161 0.1227 0.6612 130 G 0.2004 0.1067 0.6929 131 V 0.1874 0.1686 0.6440 132 G 0.1333 0.1699 0.6968 133 G 0.1303 0.2227 0.6470 134 N 0.1758 0.1624 0.6618 135 K 0.2652 0.0815 0.6533 136 M 0.2676 0.1103 0.6221 137 S 0.2198 0.2360 0.5442 138 S 0.3591 0.1787 0.4622 139 Y 0.5543 0.1346 0.3111 140 A 0.6689 0.0868 0.2443 141 I 0.7069 0.0592 0.2339 142 S 0.6128 0.0758 0.3114 143 Y 0.5086 0.1010 0.3904 144 R 0.4179 0.1266 0.4555 145 A 0.3392 0.1681 0.4927 146 G 0.2243 0.1604 0.6153 147 G 0.1986 0.1402 0.6612 148 S 0.2273 0.1894 0.5832 149 N 0.2304 0.1628 0.6069 150 T 0.2734 0.1575 0.5691 151 N 0.2466 0.1390 0.6144 152 A 0.1799 0.2550 0.5651 153 A 0.1227 0.2083 0.6689 154 G 0.1013 0.1332 0.7655 155 N 0.1720 0.1246 0.7034 156 H 0.2418 0.1388 0.6194 157 S 0.2376 0.1887 0.5737 158 H 0.2890 0.1554 0.5557 159 T 0.4413 0.1012 0.4576 160 F 0.5328 0.0806 0.3866 161 S 0.5435 0.0878 0.3687 162 F 0.5443 0.1057 0.3501 163 G 0.4565 0.1286 0.4149 164 T 0.3973 0.1436 0.4592 165 S 0.2756 0.1767 0.5477 166 S 0.2068 0.2191 0.5741 167 A 0.1494 0.2289 0.6218 168 G 0.1395 0.1784 0.6821 169 D 0.1343 0.3161 0.5496 170 H 0.1524 0.3090 0.5385 171 S 0.1896 0.3194 0.4910 172 H 0.2937 0.2087 0.4976 173 S 0.4131 0.1529 0.4340 174 V 0.4243 0.1022 0.4735 175 G 0.3234 0.0860 0.5906 176 I 0.2823 0.1166 0.6011 177 G 0.2149 0.1082 0.6769 178 A 0.1948 0.2138 0.5913 179 H 0.2109 0.2024 0.5866 180 T 0.3035 0.1670 0.5295 181 H 0.4085 0.0891 0.5024 182 T 0.5315 0.0696 0.3989 183 V 0.6170 0.0627 0.3203 184 A 0.5876 0.0670 0.3454 185 I 0.4813 0.0849 0.4338 186 G 0.3118 0.0880 0.6002 187 S 0.2443 0.1438 0.6119 188 H 0.2049 0.1435 0.6517 189 G 0.2330 0.1102 0.6568 190 H 0.3677 0.0657 0.5666 191 T 0.6613 0.0272 0.3115 192 I 0.7646 0.0129 0.2225 193 T 0.7758 0.0115 0.2127 194 V 0.7097 0.0181 0.2722 195 N 0.4336 0.0337 0.5326 196 S 0.2589 0.1759 0.5651 197 T 0.1825 0.1646 0.6529 198 G 0.1401 0.1074 0.7525 199 N 0.1909 0.1034 0.7057 200 T 0.2098 0.2181 0.5721 201 E 0.1989 0.3078 0.4933 202 N 0.3019 0.2052 0.4930 203 T 0.3726 0.1114 0.5160 204 V 0.3413 0.1661 0.4926 205 K 0.2641 0.2133 0.5226 206 N 0.3138 0.1655 0.5207 207 I 0.4171 0.2023 0.3806 208 A 0.5642 0.1918 0.2441 209 F 0.5978 0.2023 0.1999 210 N 0.4949 0.2999 0.2052 211 Y 0.5886 0.2377 0.1737 212 I 0.4949 0.3457 0.1594 213 V 0.4632 0.3688 0.1680 214 R 0.2860 0.4926 0.2214 215 L 0.2082 0.4660 0.3257 216 A 0.1800 0.3386 0.4814