# This file is the result of combining several RDB files, specifically # T0429.t06.str2.rdb (weight 1.54425) # T0429.t06.str4.rdb (weight 0.924988) # T0429.t06.pb.rdb (weight 0.789901) # T0429.t06.bys.rdb (weight 0.748322) # T0429.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 T0429.t06.str2.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.68398 # # ============================================ # Comments from T0429.t06.str4.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.68398 # # ============================================ # Comments from T0429.t06.pb.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.68398 # # ============================================ # Comments from T0429.t06.bys.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.68398 # # ============================================ # Comments from T0429.t06.alpha.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.68398 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2188 0.1229 0.6583 2 H 0.2105 0.1130 0.6765 3 H 0.2281 0.1254 0.6465 4 H 0.2270 0.1412 0.6318 5 H 0.2363 0.1256 0.6381 6 H 0.2243 0.1241 0.6516 7 H 0.1748 0.1426 0.6826 8 S 0.1321 0.2130 0.6550 9 S 0.1195 0.2044 0.6760 10 G 0.1165 0.1434 0.7401 11 R 0.2111 0.1139 0.6750 12 E 0.1914 0.2319 0.5768 13 N 0.2129 0.2168 0.5703 14 L 0.2531 0.2519 0.4950 15 Y 0.2684 0.2497 0.4819 16 F 0.2264 0.2843 0.4893 17 Q 0.1755 0.2431 0.5813 18 G 0.1622 0.2084 0.6294 19 M 0.2570 0.1885 0.5546 20 W 0.2926 0.2079 0.4995 21 D 0.2325 0.2093 0.5582 22 E 0.2007 0.2055 0.5938 23 T 0.1280 0.3137 0.5583 24 E 0.1433 0.2817 0.5749 25 L 0.2493 0.1640 0.5867 26 G 0.3102 0.1204 0.5694 27 L 0.5077 0.1010 0.3913 28 Y 0.5783 0.0811 0.3405 29 K 0.5506 0.0912 0.3582 30 V 0.3976 0.1630 0.4395 31 N 0.3276 0.1798 0.4926 32 E 0.3496 0.2118 0.4386 33 Y 0.4762 0.1280 0.3957 34 V 0.5428 0.0561 0.4012 35 D 0.3608 0.0688 0.5704 36 A 0.1764 0.3857 0.4380 37 R 0.1452 0.3905 0.4642 38 D 0.1890 0.2924 0.5186 39 T 0.1183 0.3264 0.5553 40 N 0.1283 0.2423 0.6294 41 M 0.1358 0.2045 0.6597 42 G 0.1476 0.1417 0.7107 43 A 0.4131 0.1185 0.4684 44 W 0.5990 0.0854 0.3157 45 F 0.6144 0.1037 0.2819 46 E 0.5836 0.1327 0.2837 47 A 0.6766 0.0762 0.2472 48 Q 0.6701 0.0768 0.2531 49 V 0.6798 0.0626 0.2577 50 V 0.6104 0.0721 0.3175 51 R 0.6449 0.0666 0.2885 52 V 0.5819 0.0690 0.3491 53 T 0.5463 0.0687 0.3850 54 R 0.4009 0.1157 0.4834 55 K 0.2783 0.1099 0.6117 56 A 0.2342 0.0507 0.7151 57 P 0.1399 0.2231 0.6370 58 S 0.1394 0.2034 0.6572 59 R 0.1291 0.2113 0.6596 60 D 0.1516 0.1304 0.7179 61 E 0.2287 0.0709 0.7003 62 P 0.2130 0.1101 0.6769 63 C 0.2128 0.1301 0.6572 64 S 0.1714 0.1520 0.6766 65 S 0.1335 0.2100 0.6565 66 T 0.1421 0.2087 0.6492 67 S 0.1668 0.1459 0.6872 68 R 0.2325 0.0779 0.6896 69 P 0.1813 0.1968 0.6219 70 A 0.2087 0.2199 0.5715 71 L 0.2128 0.2320 0.5552 72 E 0.1875 0.2521 0.5604 73 E 0.2876 0.1815 0.5308 74 D 0.4507 0.0632 0.4862 75 V 0.7287 0.0145 0.2567 76 I 0.7685 0.0084 0.2230 77 Y 0.8205 0.0054 0.1741 78 H 0.8080 0.0057 0.1863 79 V 0.8015 0.0059 0.1926 80 K 0.7426 0.0095 0.2479 81 Y 0.5774 0.0374 0.3853 82 D 0.2959 0.1326 0.5716 83 D 0.2163 0.1211 0.6626 84 Y 0.2732 0.0519 0.6749 85 P 0.1451 0.2300 0.6249 86 E 0.0789 0.3177 0.6034 87 N 0.0999 0.1674 0.7326 88 G 0.2045 0.0795 0.7160 89 V 0.5407 0.0228 0.4365 90 V 0.6976 0.0189 0.2835 91 Q 0.7164 0.0155 0.2681 92 M 0.6505 0.0195 0.3300 93 N 0.4024 0.0301 0.5675 94 S 0.2199 0.2299 0.5502 95 R 0.1335 0.3883 0.4782 96 D 0.1838 0.2948 0.5214 97 V 0.2841 0.1929 0.5230 98 R 0.2556 0.1912 0.5533 99 A 0.1222 0.5202 0.3576 100 R 0.0848 0.6250 0.2903 101 A 0.1272 0.6312 0.2416 102 R 0.1561 0.5990 0.2449 103 T 0.2073 0.5528 0.2399 104 I 0.2746 0.3978 0.3275 105 I 0.3759 0.2433 0.3808 106 K 0.3026 0.1782 0.5192 107 W 0.1578 0.3692 0.4730 108 Q 0.1148 0.3617 0.5235 109 D 0.1480 0.2446 0.6074 110 L 0.3234 0.0806 0.5960 111 E 0.3292 0.0587 0.6121 112 V 0.2638 0.1170 0.6191 113 G 0.2127 0.0804 0.7070 114 Q 0.5114 0.0268 0.4619 115 V 0.7251 0.0085 0.2665 116 V 0.7842 0.0096 0.2063 117 M 0.7908 0.0068 0.2024 118 L 0.7556 0.0148 0.2296 119 N 0.6374 0.0234 0.3392 120 Y 0.4622 0.0380 0.4998 121 N 0.2592 0.0233 0.7174 122 P 0.0549 0.3880 0.5571 123 D 0.0566 0.3001 0.6433 124 N 0.1365 0.1902 0.6733 125 P 0.1021 0.3573 0.5406 126 K 0.1066 0.3871 0.5064 127 E 0.1647 0.3177 0.5176 128 R 0.2397 0.1577 0.6026 129 G 0.3228 0.0917 0.5856 130 F 0.5670 0.0530 0.3801 131 W 0.6812 0.0612 0.2576 132 Y 0.6525 0.0848 0.2627 133 D 0.6057 0.0952 0.2991 134 A 0.6010 0.1804 0.2186 135 E 0.6355 0.1535 0.2110 136 I 0.6228 0.1546 0.2225 137 S 0.4769 0.2354 0.2877 138 R 0.3873 0.2551 0.3575 139 K 0.3032 0.2590 0.4377 140 R 0.2510 0.2663 0.4826 141 E 0.2147 0.2567 0.5286 142 T 0.2336 0.2130 0.5534 143 R 0.2257 0.2008 0.5735 144 T 0.2584 0.1599 0.5816 145 A 0.1461 0.4658 0.3882 146 R 0.1643 0.5200 0.3157 147 E 0.3727 0.3470 0.2803 148 L 0.5539 0.1598 0.2864 149 Y 0.6688 0.0900 0.2413 150 A 0.7526 0.0442 0.2032 151 N 0.7473 0.0361 0.2166 152 V 0.7748 0.0218 0.2034 153 V 0.7058 0.0357 0.2585 154 L 0.5584 0.0461 0.3955 155 G 0.2445 0.0500 0.7056 156 D 0.1506 0.1791 0.6703 157 D 0.1243 0.2388 0.6368 158 S 0.1580 0.2654 0.5766 159 L 0.1692 0.2463 0.5846 160 N 0.1383 0.2228 0.6389 161 D 0.1695 0.1749 0.6557 162 C 0.3488 0.0891 0.5621 163 R 0.5450 0.0564 0.3986 164 I 0.7179 0.0276 0.2545 165 I 0.7059 0.0367 0.2574 166 F 0.6512 0.0474 0.3015 167 V 0.4519 0.2114 0.3367 168 D 0.3691 0.3059 0.3250 169 E 0.4382 0.2886 0.2732 170 V 0.5639 0.1771 0.2591 171 F 0.6155 0.1122 0.2722 172 K 0.6794 0.0713 0.2493 173 I 0.6397 0.0549 0.3054 174 E 0.5687 0.0555 0.3757 175 R 0.3850 0.0339 0.5811 176 P 0.1836 0.1040 0.7124 177 G 0.1248 0.0952 0.7801 178 E 0.1940 0.1200 0.6860