# This file is the result of combining several RDB files, specifically # T0500.t2k.str2.rdb (weight 1.54425) # T0500.t2k.str4.rdb (weight 0.924988) # T0500.t2k.pb.rdb (weight 0.789901) # T0500.t2k.bys.rdb (weight 0.748322) # T0500.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 T0500.t2k.str2.rdb # ============================================ # TARGET T0500 # 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 T0500.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 8.05968 # # ============================================ # Comments from T0500.t2k.str4.rdb # ============================================ # TARGET T0500 # 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 T0500.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 8.05968 # # ============================================ # Comments from T0500.t2k.pb.rdb # ============================================ # TARGET T0500 # 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 T0500.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 8.05968 # # ============================================ # Comments from T0500.t2k.bys.rdb # ============================================ # TARGET T0500 # 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 T0500.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 8.05968 # # ============================================ # Comments from T0500.t2k.alpha.rdb # ============================================ # TARGET T0500 # 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 T0500.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 8.05968 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.2276 0.2037 0.5686 2 A 0.2286 0.1201 0.6513 3 G 0.2181 0.0808 0.7011 4 P 0.2068 0.1621 0.6311 5 Y 0.3154 0.1195 0.5650 6 A 0.4455 0.0574 0.4971 7 T 0.5565 0.0440 0.3996 8 V 0.6155 0.0595 0.3250 9 Q 0.6323 0.0452 0.3226 10 R 0.5613 0.0446 0.3941 11 R 0.4129 0.0389 0.5482 12 V 0.2897 0.1114 0.5989 13 G 0.2048 0.0970 0.6982 14 R 0.2133 0.1694 0.6173 15 S 0.2381 0.1782 0.5836 16 H 0.2593 0.2101 0.5306 17 S 0.3057 0.2074 0.4869 18 V 0.3025 0.2371 0.4603 19 R 0.3083 0.1903 0.5014 20 A 0.2786 0.1089 0.6125 21 P 0.1599 0.2664 0.5737 22 A 0.1491 0.2469 0.6041 23 G 0.1094 0.1859 0.7047 24 A 0.1188 0.2823 0.5989 25 D 0.1280 0.2717 0.6002 26 K 0.1415 0.2826 0.5758 27 N 0.1960 0.1669 0.6371 28 V 0.2469 0.2028 0.5503 29 N 0.2313 0.1513 0.6174 30 R 0.2436 0.2485 0.5079 31 S 0.2644 0.1945 0.5411 32 Q 0.2951 0.2086 0.4963 33 S 0.2616 0.2318 0.5066 34 F 0.3131 0.2690 0.4178 35 A 0.3715 0.2480 0.3806 36 V 0.4711 0.1422 0.3867 37 R 0.4391 0.0667 0.4942 38 P 0.3033 0.2626 0.4341 39 R 0.2429 0.2834 0.4737 40 K 0.1972 0.3171 0.4856 41 K 0.2006 0.1778 0.6216 42 G 0.2117 0.0646 0.7237 43 P 0.2151 0.0484 0.7365 44 P 0.2556 0.0661 0.6784 45 P 0.2513 0.0922 0.6564 46 P 0.2400 0.0692 0.6908 47 P 0.2373 0.0635 0.6991 48 P 0.1908 0.1659 0.6433 49 K 0.2101 0.1951 0.5948 50 R 0.2203 0.1897 0.5900 51 S 0.2247 0.1983 0.5770 52 S 0.2541 0.1864 0.5595 53 S 0.2836 0.2061 0.5103 54 A 0.2865 0.3117 0.4018 55 L 0.3366 0.2810 0.3825 56 A 0.3570 0.2194 0.4236 57 S 0.2831 0.2084 0.5085 58 A 0.2118 0.2985 0.4897 59 N 0.1829 0.2247 0.5924 60 L 0.1754 0.2429 0.5817 61 A 0.1485 0.2398 0.6118 62 D 0.1535 0.2000 0.6464 63 E 0.2401 0.1030 0.6569 64 P 0.2448 0.0967 0.6585 65 V 0.2602 0.0405 0.6993 66 P 0.1624 0.1487 0.6888 67 D 0.1677 0.1807 0.6516 68 A 0.1933 0.1338 0.6728 69 E 0.2093 0.0644 0.7264 70 P 0.1440 0.1388 0.7171 71 E 0.0871 0.2957 0.6172 72 D 0.1004 0.2083 0.6913 73 G 0.1176 0.2303 0.6521 74 L 0.2191 0.2335 0.5475 75 L 0.2430 0.1819 0.5751 76 G 0.2351 0.1535 0.6114 77 V 0.2721 0.1975 0.5305 78 R 0.3109 0.2750 0.4141 79 A 0.2611 0.4375 0.3014 80 Q 0.2064 0.5378 0.2558 81 C 0.1780 0.5658 0.2562 82 R 0.1521 0.5577 0.2903 83 R 0.1534 0.4603 0.3863 84 A 0.1320 0.4196 0.4484 85 S 0.1060 0.3359 0.5581 86 D 0.1088 0.2960 0.5952 87 L 0.1492 0.2672 0.5836 88 A 0.2525 0.1781 0.5695 89 G 0.3209 0.0988 0.5803 90 S 0.3489 0.0908 0.5603 91 V 0.2392 0.2309 0.5298 92 D 0.2106 0.2131 0.5763 93 T 0.1560 0.1668 0.6772 94 G 0.1114 0.1355 0.7531 95 S 0.1680 0.1706 0.6614 96 A 0.1369 0.2544 0.6087 97 G 0.1383 0.2728 0.5889 98 S 0.1896 0.3534 0.4571 99 V 0.1183 0.5962 0.2855 100 K 0.0942 0.7092 0.1966 101 S 0.0792 0.7936 0.1272 102 I 0.0642 0.8234 0.1124 103 A 0.0977 0.7879 0.1143 104 A 0.1219 0.7569 0.1212 105 M 0.1431 0.6936 0.1634 106 L 0.2140 0.5487 0.2373 107 E 0.2549 0.4277 0.3174 108 L 0.2563 0.3006 0.4430 109 S 0.2022 0.2155 0.5823 110 S 0.1522 0.2702 0.5776 111 I 0.1121 0.2254 0.6625 112 G 0.1075 0.1355 0.7570 113 G 0.1270 0.1289 0.7441 114 G 0.1308 0.1524 0.7168 115 G 0.1839 0.2562 0.5599 116 R 0.1914 0.3180 0.4906 117 A 0.1864 0.3786 0.4350 118 A 0.1661 0.3398 0.4941 119 R 0.1935 0.1859 0.6206 120 R 0.2567 0.0459 0.6974 121 P 0.1891 0.0425 0.7684 122 P 0.1348 0.2377 0.6276 123 E 0.1092 0.2241 0.6667 124 G 0.1134 0.1373 0.7493 125 H 0.2042 0.0386 0.7572 126 P 0.2205 0.0972 0.6823 127 T 0.2765 0.0563 0.6672 128 P 0.2152 0.0882 0.6965 129 R 0.2383 0.0488 0.7130 130 P 0.1493 0.1588 0.6919 131 A 0.1653 0.1527 0.6820 132 S 0.2072 0.0543 0.7385 133 P 0.1372 0.1840 0.6788 134 E 0.2099 0.1043 0.6858 135 P 0.1647 0.2285 0.6068 136 G 0.1893 0.2454 0.5653 137 R 0.2504 0.2848 0.4648 138 V 0.2772 0.3566 0.3662 139 A 0.2839 0.3951 0.3210 140 T 0.2820 0.3869 0.3311 141 V 0.2108 0.4839 0.3054 142 L 0.1983 0.4628 0.3389 143 A 0.2082 0.4146 0.3771 144 S 0.2144 0.3138 0.4718 145 V 0.2643 0.2394 0.4964 146 K 0.2294 0.2657 0.5049 147 H 0.2025 0.2886 0.5089 148 K 0.1583 0.4849 0.3569 149 E 0.1963 0.4069 0.3967 150 A 0.3334 0.2286 0.4380 151 I 0.3795 0.1328 0.4877 152 G 0.2341 0.0497 0.7162 153 P 0.1541 0.1921 0.6539 154 G 0.0947 0.1233 0.7821 155 G 0.1586 0.0865 0.7549 156 E 0.3975 0.0352 0.5674 157 V 0.6064 0.0374 0.3562 158 V 0.5734 0.0481 0.3785 159 N 0.5367 0.0565 0.4068 160 R 0.5189 0.0927 0.3883 161 R 0.5790 0.0650 0.3560 162 R 0.5921 0.0373 0.3707 163 T 0.5051 0.0409 0.4540 164 L 0.4059 0.1064 0.4877 165 S 0.3353 0.1222 0.5425 166 G 0.2492 0.1612 0.5896 167 P 0.1750 0.2605 0.5645 168 V 0.1254 0.4243 0.4502 169 T 0.0716 0.6120 0.3164 170 G 0.0389 0.7181 0.2430 171 L 0.0292 0.8209 0.1499 172 L 0.0203 0.8872 0.0925 173 A 0.0185 0.8905 0.0910 174 T 0.0274 0.8514 0.1212 175 A 0.0489 0.7557 0.1954 176 R 0.0817 0.5620 0.3564 177 R 0.0994 0.2781 0.6225 178 G 0.1359 0.0915 0.7726 179 P 0.1145 0.1938 0.6918 180 G 0.1066 0.2470 0.6463 181 E 0.1463 0.2838 0.5700 182 S 0.1820 0.1990 0.6190 183 A 0.2146 0.1289 0.6565 184 D 0.2047 0.0511 0.7441 185 P 0.1475 0.1829 0.6695 186 G 0.1837 0.1029 0.7134 187 P 0.2175 0.1448 0.6377 188 F 0.3375 0.1346 0.5279 189 V 0.3359 0.1548 0.5092 190 E 0.2466 0.1982 0.5552 191 D 0.1552 0.1496 0.6952 192 G 0.1205 0.1599 0.7196 193 T 0.1547 0.1481 0.6971 194 G 0.1959 0.1383 0.6658 195 R 0.3392 0.1139 0.5469 196 Q 0.4106 0.0833 0.5061 197 R 0.3407 0.0308 0.6285 198 P 0.2396 0.1020 0.6583 199 R 0.1851 0.1497 0.6653 200 G 0.1395 0.0949 0.7656