# 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) # T0466.t04.str2.rdb (weight 1.54425) # T0466.t04.str4.rdb (weight 0.924988) # T0466.t04.pb.rdb (weight 0.789901) # T0466.t04.bys.rdb (weight 0.748322) # T0466.t04.alpha.rdb (weight 0.678173) # T0466.t2k.str2.rdb (weight 1.54425) # T0466.t2k.str4.rdb (weight 0.924988) # T0466.t2k.pb.rdb (weight 0.789901) # T0466.t2k.bys.rdb (weight 0.748322) # T0466.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 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 # # ============================================ # Comments from T0466.t04.str2.rdb # ============================================ # TARGET T0466 # 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 T0466.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 16.3137 # # ============================================ # Comments from T0466.t04.str4.rdb # ============================================ # TARGET T0466 # 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 T0466.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 16.3137 # # ============================================ # Comments from T0466.t04.pb.rdb # ============================================ # TARGET T0466 # 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 T0466.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 16.3137 # # ============================================ # Comments from T0466.t04.bys.rdb # ============================================ # TARGET T0466 # 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 T0466.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 16.3137 # # ============================================ # Comments from T0466.t04.alpha.rdb # ============================================ # TARGET T0466 # 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 T0466.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 16.3137 # # ============================================ # Comments from T0466.t2k.str2.rdb # ============================================ # TARGET T0466 # 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 T0466.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 11.5051 # # ============================================ # Comments from T0466.t2k.str4.rdb # ============================================ # TARGET T0466 # 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 T0466.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 11.5051 # # ============================================ # Comments from T0466.t2k.pb.rdb # ============================================ # TARGET T0466 # 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 T0466.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 11.5051 # # ============================================ # Comments from T0466.t2k.bys.rdb # ============================================ # TARGET T0466 # 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 T0466.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 11.5051 # # ============================================ # Comments from T0466.t2k.alpha.rdb # ============================================ # TARGET T0466 # 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 T0466.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 11.5051 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1745 0.6055 0.2201 2 M 0.2014 0.5731 0.2254 3 R 0.2056 0.5312 0.2632 4 L 0.1532 0.5359 0.3108 5 A 0.1356 0.4312 0.4332 6 N 0.0964 0.1671 0.7364 7 G 0.1529 0.0875 0.7596 8 I 0.4157 0.0368 0.5475 9 V 0.6009 0.0336 0.3655 10 L 0.5371 0.0518 0.4110 11 D 0.2987 0.0421 0.6592 12 K 0.1110 0.4583 0.4307 13 D 0.0812 0.5024 0.4164 14 T 0.1411 0.4212 0.4376 15 T 0.1618 0.3401 0.4981 16 F 0.1729 0.3225 0.5046 17 G 0.1899 0.3417 0.4684 18 E 0.3528 0.3222 0.3250 19 L 0.4817 0.2624 0.2560 20 K 0.4772 0.2744 0.2484 21 F 0.4773 0.2801 0.2426 22 S 0.3551 0.3650 0.2799 23 A 0.3202 0.3519 0.3280 24 L 0.2760 0.3068 0.4173 25 R 0.2575 0.2239 0.5186 26 R 0.2771 0.2437 0.4792 27 E 0.4595 0.1470 0.3935 28 V 0.6457 0.0521 0.3022 29 R 0.6427 0.0527 0.3046 30 I 0.6478 0.0744 0.2779 31 Q 0.5347 0.0982 0.3671 32 N 0.3456 0.1002 0.5541 33 E 0.1430 0.2884 0.5685 34 D 0.1029 0.1696 0.7275 35 G 0.1075 0.0863 0.8062 36 S 0.1996 0.0582 0.7423 37 V 0.1982 0.1941 0.6077 38 S 0.1818 0.3236 0.4946 39 D 0.1512 0.5242 0.3246 40 E 0.2657 0.4648 0.2695 41 I 0.3945 0.3868 0.2186 42 K 0.3694 0.3971 0.2334 43 E 0.4319 0.2761 0.2920 44 R 0.4953 0.1758 0.3289 45 T 0.5565 0.1016 0.3420 46 Y 0.6015 0.0854 0.3131 47 D 0.5574 0.0745 0.3682 48 L 0.4761 0.1448 0.3791 49 K 0.4193 0.1385 0.4422 50 S 0.3736 0.1058 0.5206 51 K 0.1815 0.2337 0.5848 52 G 0.1866 0.1910 0.6224 53 Q 0.2403 0.1197 0.6399 54 G 0.2207 0.0796 0.6998 55 R 0.3332 0.0777 0.5892 56 M 0.6146 0.0290 0.3564 57 I 0.7339 0.0093 0.2568 58 Q 0.7813 0.0058 0.2129 59 V 0.8005 0.0060 0.1935 60 S 0.7592 0.0082 0.2326 61 I 0.6415 0.0145 0.3439 62 P 0.4290 0.0285 0.5424 63 A 0.2982 0.1689 0.5330 64 S 0.2578 0.1240 0.6182 65 V 0.3136 0.0547 0.6318 66 P 0.2140 0.0666 0.7194 67 L 0.2001 0.2986 0.5013 68 K 0.2472 0.3023 0.4505 69 E 0.3276 0.1691 0.5033 70 F 0.3266 0.0623 0.6111 71 D 0.2273 0.0773 0.6955 72 Y 0.1595 0.2901 0.5504 73 N 0.1760 0.2033 0.6207 74 A 0.3124 0.1431 0.5446 75 R 0.5225 0.0601 0.4174 76 V 0.6659 0.0279 0.3062 77 E 0.6915 0.0478 0.2607 78 L 0.6790 0.0568 0.2642 79 I 0.6497 0.0557 0.2947 80 N 0.5434 0.0539 0.4027 81 P 0.3298 0.2319 0.4383 82 I 0.3740 0.2101 0.4159 83 A 0.4343 0.2170 0.3487 84 D 0.4274 0.2576 0.3150 85 T 0.3747 0.3753 0.2500 86 V 0.3635 0.3887 0.2478 87 A 0.3693 0.3789 0.2518 88 T 0.3275 0.3740 0.2985 89 A 0.3142 0.3525 0.3333 90 T 0.2447 0.3086 0.4467 91 Y 0.2359 0.2331 0.5310 92 Q 0.1475 0.1379 0.7146 93 G 0.1058 0.0834 0.8108 94 A 0.2790 0.0548 0.6662 95 D 0.4668 0.0469 0.4863 96 V 0.5608 0.0659 0.3734 97 D 0.5743 0.0526 0.3732 98 W 0.7248 0.0419 0.2333 99 Y 0.7392 0.0253 0.2355 100 I 0.7600 0.0185 0.2215 101 K 0.6395 0.0277 0.3327 102 A 0.4741 0.0959 0.4300 103 D 0.3469 0.1605 0.4927 104 D 0.4257 0.1285 0.4459 105 I 0.6049 0.0670 0.3281 106 V 0.6745 0.0444 0.2811 107 L 0.6131 0.0448 0.3421 108 T 0.4415 0.0914 0.4671 109 K 0.2519 0.1434 0.6048 110 D 0.1554 0.1715 0.6730 111 S 0.1189 0.2356 0.6456 112 S 0.1529 0.2617 0.5854 113 S 0.1926 0.2604 0.5470 114 F 0.2051 0.2515 0.5435 115 K 0.1854 0.2645 0.5501 116 A 0.2023 0.1827 0.6150 117 Q 0.2101 0.1131 0.6768 118 P 0.1285 0.3500 0.5215 119 Q 0.1278 0.3408 0.5314 120 A 0.1446 0.2924 0.5630 121 K 0.1636 0.2166 0.6198 122 K 0.1904 0.1574 0.6522 123 E 0.2312 0.0814 0.6874 124 P 0.1967 0.1471 0.6563 125 T 0.2275 0.1198 0.6527 126 Q 0.1803 0.1968 0.6230 127 D 0.1664 0.1665 0.6672 128 K 0.1606 0.1889 0.6505