# This file is the result of combining several RDB files, specifically # T0466.t06.str2.rdb (weight 1.54425) # T0466.t06.str4.rdb (weight 0.924988) # T0466.t06.pb.rdb (weight 0.789901) # T0466.t06.bys.rdb (weight 0.748322) # T0466.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 T0466.t06.str2.rdb # ============================================ # TARGET T0466 # 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 T0466.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 15.9667 # # ============================================ # Comments from T0466.t06.str4.rdb # ============================================ # TARGET T0466 # 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 T0466.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 15.9667 # # ============================================ # Comments from T0466.t06.pb.rdb # ============================================ # TARGET T0466 # 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 T0466.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 15.9667 # # ============================================ # Comments from T0466.t06.bys.rdb # ============================================ # TARGET T0466 # 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 T0466.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 15.9667 # # ============================================ # Comments from T0466.t06.alpha.rdb # ============================================ # TARGET T0466 # 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 T0466.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 15.9667 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2217 0.5114 0.2669 2 M 0.3100 0.4226 0.2674 3 R 0.3042 0.4056 0.2902 4 L 0.2615 0.3568 0.3817 5 A 0.1793 0.2963 0.5245 6 N 0.1226 0.1669 0.7105 7 G 0.2471 0.0794 0.6734 8 I 0.5565 0.0268 0.4167 9 V 0.6217 0.0231 0.3552 10 L 0.5330 0.0384 0.4286 11 D 0.2821 0.0361 0.6818 12 K 0.0599 0.4959 0.4442 13 D 0.0980 0.4676 0.4344 14 T 0.2043 0.4012 0.3946 15 T 0.2402 0.3203 0.4395 16 F 0.2263 0.3121 0.4616 17 G 0.2831 0.2729 0.4440 18 E 0.4754 0.2279 0.2968 19 L 0.5299 0.2089 0.2612 20 K 0.4379 0.3123 0.2498 21 F 0.3942 0.3696 0.2362 22 S 0.2825 0.4821 0.2354 23 A 0.3301 0.4152 0.2547 24 L 0.3057 0.3858 0.3086 25 R 0.3127 0.3427 0.3446 26 R 0.3174 0.3406 0.3420 27 E 0.4347 0.2599 0.3054 28 V 0.5521 0.1744 0.2735 29 R 0.5896 0.1408 0.2696 30 I 0.6435 0.0934 0.2631 31 Q 0.5670 0.1067 0.3263 32 N 0.3581 0.0970 0.5450 33 E 0.1225 0.3171 0.5603 34 D 0.0846 0.1537 0.7617 35 G 0.0894 0.0735 0.8371 36 S 0.2971 0.0407 0.6623 37 V 0.4471 0.0780 0.4749 38 S 0.3862 0.1618 0.4520 39 D 0.3440 0.3658 0.2902 40 E 0.4319 0.3462 0.2218 41 I 0.4873 0.3122 0.2005 42 K 0.4803 0.2678 0.2520 43 E 0.5775 0.1843 0.2382 44 R 0.5915 0.1293 0.2792 45 T 0.6805 0.0607 0.2589 46 Y 0.7073 0.0360 0.2567 47 D 0.6166 0.0471 0.3364 48 L 0.5499 0.1275 0.3226 49 K 0.4862 0.1518 0.3620 50 S 0.4285 0.1484 0.4231 51 K 0.2331 0.2650 0.5019 52 G 0.1975 0.2287 0.5739 53 Q 0.2013 0.1331 0.6657 54 G 0.1550 0.0710 0.7740 55 R 0.3313 0.0506 0.6181 56 M 0.6038 0.0155 0.3807 57 I 0.7629 0.0075 0.2296 58 Q 0.7668 0.0068 0.2264 59 V 0.7839 0.0072 0.2089 60 S 0.7475 0.0092 0.2434 61 I 0.5323 0.0158 0.4519 62 P 0.2969 0.0379 0.6652 63 A 0.1311 0.2900 0.5789 64 S 0.1606 0.1911 0.6483 65 V 0.2896 0.0347 0.6757 66 P 0.2259 0.0356 0.7384 67 L 0.1873 0.3087 0.5040 68 K 0.1805 0.3651 0.4544 69 E 0.2864 0.2412 0.4725 70 F 0.3790 0.0687 0.5523 71 D 0.2569 0.0595 0.6837 72 Y 0.1586 0.3801 0.4613 73 N 0.1500 0.2688 0.5812 74 A 0.2887 0.2158 0.4955 75 R 0.4903 0.1142 0.3955 76 V 0.6697 0.0396 0.2907 77 E 0.6412 0.0758 0.2830 78 L 0.6142 0.0719 0.3139 79 I 0.4702 0.1622 0.3677 80 N 0.3899 0.0699 0.5402 81 P 0.2155 0.2721 0.5124 82 I 0.2323 0.3458 0.4219 83 A 0.3397 0.2951 0.3652 84 D 0.3047 0.3356 0.3597 85 T 0.4293 0.3056 0.2651 86 V 0.4861 0.2605 0.2534 87 A 0.5469 0.2023 0.2507 88 T 0.5359 0.1691 0.2950 89 A 0.4327 0.1824 0.3849 90 T 0.3374 0.1685 0.4941 91 Y 0.2601 0.1609 0.5790 92 Q 0.1648 0.1318 0.7034 93 G 0.1349 0.0911 0.7740 94 A 0.3247 0.0467 0.6286 95 D 0.4662 0.0348 0.4990 96 V 0.5916 0.0323 0.3762 97 D 0.6181 0.0355 0.3464 98 W 0.7641 0.0146 0.2213 99 Y 0.7620 0.0139 0.2241 100 I 0.7601 0.0138 0.2260 101 K 0.6497 0.0292 0.3211 102 A 0.4340 0.1253 0.4408 103 D 0.2507 0.2125 0.5368 104 D 0.3065 0.1888 0.5047 105 I 0.4776 0.1341 0.3884 106 V 0.5705 0.1117 0.3178 107 L 0.5614 0.0911 0.3475 108 T 0.4451 0.1096 0.4452 109 K 0.2774 0.1476 0.5751 110 D 0.1733 0.1799 0.6468 111 S 0.1494 0.2028 0.6478 112 S 0.1397 0.2640 0.5963 113 S 0.1644 0.2827 0.5529 114 F 0.1837 0.2417 0.5747 115 K 0.1691 0.2471 0.5838 116 A 0.1842 0.1994 0.6164 117 Q 0.2174 0.0922 0.6904 118 P 0.1528 0.2127 0.6345 119 Q 0.1357 0.2675 0.5968 120 A 0.1207 0.2790 0.6003 121 K 0.1198 0.2349 0.6453 122 K 0.1815 0.1243 0.6942 123 E 0.2081 0.0670 0.7249 124 P 0.1773 0.1631 0.6596 125 T 0.2069 0.1696 0.6235 126 Q 0.2104 0.1438 0.6458 127 D 0.1758 0.1424 0.6818 128 K 0.1627 0.2016 0.6357