# This file is the result of combining several RDB files, specifically # T0397.t04.str2.rdb (weight 1.54425) # T0397.t04.str4.rdb (weight 0.924988) # T0397.t04.pb.rdb (weight 0.789901) # T0397.t04.bys.rdb (weight 0.748322) # T0397.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 T0397.t04.str2.rdb # ============================================ # TARGET T0397 # 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 T0397.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 9.32066 # # ============================================ # Comments from T0397.t04.str4.rdb # ============================================ # TARGET T0397 # 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 T0397.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 9.32066 # # ============================================ # Comments from T0397.t04.pb.rdb # ============================================ # TARGET T0397 # 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 T0397.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 9.32066 # # ============================================ # Comments from T0397.t04.bys.rdb # ============================================ # TARGET T0397 # 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 T0397.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 9.32066 # # ============================================ # Comments from T0397.t04.alpha.rdb # ============================================ # TARGET T0397 # 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 T0397.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 9.32066 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3285 0.0519 0.6196 2 K 0.3353 0.0367 0.6280 3 I 0.3603 0.0207 0.6191 4 P 0.4026 0.0477 0.5497 5 K 0.6573 0.0279 0.3148 6 I 0.7718 0.0072 0.2210 7 Y 0.7715 0.0079 0.2206 8 V 0.7388 0.0131 0.2481 9 E 0.6208 0.0405 0.3387 10 G 0.4784 0.0437 0.4779 11 E 0.5085 0.0484 0.4431 12 L 0.5038 0.0625 0.4337 13 N 0.3842 0.0820 0.5338 14 D 0.1870 0.1279 0.6851 15 G 0.1218 0.0850 0.7932 16 D 0.3377 0.0545 0.6078 17 R 0.6828 0.0114 0.3058 18 V 0.7764 0.0067 0.2168 19 A 0.8167 0.0048 0.1786 20 I 0.8176 0.0049 0.1774 21 E 0.7697 0.0095 0.2208 22 K 0.6592 0.0339 0.3069 23 D 0.3114 0.0568 0.6318 24 G 0.1696 0.0717 0.7587 25 N 0.4755 0.0436 0.4810 26 A 0.7162 0.0111 0.2727 27 I 0.7705 0.0073 0.2222 28 I 0.8163 0.0052 0.1784 29 F 0.7981 0.0058 0.1961 30 L 0.7653 0.0118 0.2228 31 E 0.6186 0.0224 0.3590 32 K 0.3443 0.1582 0.4975 33 D 0.2305 0.1824 0.5871 34 E 0.2804 0.2058 0.5139 35 E 0.3579 0.1680 0.4741 36 Y 0.3692 0.1243 0.5065 37 S 0.2242 0.1471 0.6287 38 G 0.1319 0.1830 0.6851 39 N 0.1347 0.1483 0.7170 40 G 0.1847 0.1143 0.7010 41 K 0.3706 0.1393 0.4901 42 L 0.5128 0.1565 0.3307 43 L 0.4950 0.2498 0.2552 44 Y 0.4095 0.3585 0.2319 45 Q 0.2922 0.5228 0.1850 46 V 0.2609 0.5584 0.1807 47 I 0.2156 0.5758 0.2085 48 Y 0.0243 0.8346 0.1411 49 D 0.0098 0.8945 0.0957 50 D 0.0100 0.8961 0.0939 51 L 0.0096 0.8883 0.1021 52 A 0.0099 0.8864 0.1036 53 K 0.0111 0.8332 0.1557 54 Y 0.0260 0.7446 0.2294 55 M 0.1102 0.5544 0.3354 56 S 0.1243 0.3392 0.5365 57 L 0.0630 0.5012 0.4357 58 D 0.0664 0.4413 0.4923 59 T 0.1399 0.4038 0.4562 60 L 0.2858 0.1866 0.5276 61 K 0.3562 0.1056 0.5382 62 K 0.4264 0.0850 0.4886 63 D 0.4901 0.0512 0.4587 64 V 0.7594 0.0077 0.2329 65 L 0.7783 0.0065 0.2152 66 I 0.7985 0.0051 0.1964 67 Q 0.7417 0.0120 0.2464 68 Y 0.4334 0.0129 0.5537 69 P 0.2331 0.0951 0.6718 70 D 0.1425 0.1188 0.7387 71 K 0.1620 0.1543 0.6837 72 H 0.2604 0.1120 0.6276 73 T 0.4970 0.0610 0.4420 74 L 0.6937 0.0314 0.2749 75 T 0.7683 0.0202 0.2115 76 Y 0.7808 0.0148 0.2043 77 L 0.7315 0.0321 0.2364 78 K 0.6017 0.0450 0.3534 79 A 0.2379 0.1279 0.6342 80 G 0.1111 0.0826 0.8063 81 T 0.3702 0.0456 0.5842 82 K 0.6097 0.0343 0.3561 83 L 0.7054 0.0178 0.2768 84 I 0.7325 0.0157 0.2518 85 S 0.7341 0.0093 0.2566 86 V 0.7163 0.0129 0.2708 87 P 0.6044 0.0153 0.3803 88 A 0.4814 0.0652 0.4534 89 E 0.2717 0.1054 0.6229 90 G 0.1914 0.0619 0.7467 91 Y 0.4477 0.0234 0.5289 92 K 0.6294 0.0162 0.3543 93 V 0.6660 0.0153 0.3187 94 Y 0.5754 0.0179 0.4068 95 P 0.5757 0.0362 0.3881 96 I 0.5559 0.0708 0.3733 97 M 0.4336 0.0982 0.4682 98 D 0.3141 0.1228 0.5631 99 F 0.1749 0.2455 0.5796 100 G 0.1390 0.1869 0.6741 101 F 0.3155 0.2193 0.4653 102 R 0.4872 0.1982 0.3146 103 V 0.4680 0.2214 0.3106 104 L 0.3973 0.2159 0.3868 105 K 0.1963 0.1920 0.6118 106 G 0.1238 0.1133 0.7629 107 Y 0.3268 0.0894 0.5838 108 R 0.5523 0.1050 0.3427 109 L 0.6435 0.0979 0.2586 110 A 0.7338 0.0507 0.2155 111 T 0.7689 0.0311 0.2000 112 L 0.7506 0.0388 0.2106 113 E 0.6887 0.0462 0.2651 114 S 0.4818 0.0520 0.4662 115 K 0.2357 0.1991 0.5653 116 K 0.1747 0.1240 0.7013 117 G 0.2214 0.0800 0.6986 118 D 0.5220 0.0357 0.4423 119 L 0.6818 0.0136 0.3046 120 R 0.7142 0.0195 0.2662 121 Y 0.7534 0.0107 0.2359 122 V 0.7063 0.0256 0.2681 123 N 0.6140 0.0345 0.3515 124 S 0.4643 0.0224 0.5133 125 P 0.3109 0.0738 0.6152 126 V 0.3411 0.0700 0.5889 127 S 0.2400 0.0829 0.6772 128 G 0.3690 0.0357 0.5953 129 T 0.6923 0.0116 0.2961 130 V 0.7833 0.0054 0.2113 131 I 0.8121 0.0057 0.1822 132 F 0.7964 0.0054 0.1982 133 M 0.7430 0.0155 0.2415 134 N 0.5844 0.0360 0.3796 135 E 0.4234 0.0596 0.5170 136 I 0.2891 0.0320 0.6788 137 P 0.1823 0.0995 0.7182 138 S 0.1217 0.2341 0.6442 139 E 0.1501 0.1645 0.6854 140 R 0.2324 0.0810 0.6866 141 A 0.2203 0.1861 0.5936 142 N 0.3321 0.1007 0.5672 143 Y 0.6904 0.0152 0.2945 144 V 0.7663 0.0073 0.2264 145 F 0.8202 0.0046 0.1752 146 Y 0.8234 0.0047 0.1719 147 M 0.7779 0.0077 0.2144 148 L 0.6054 0.0269 0.3677 149 E 0.3315 0.1099 0.5586 150 E 0.1996 0.2515 0.5489