# This file is the result of combining several RDB files, specifically # T0475.t04.str2.rdb (weight 1.54425) # T0475.t04.str4.rdb (weight 0.924988) # T0475.t04.pb.rdb (weight 0.789901) # T0475.t04.bys.rdb (weight 0.748322) # T0475.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 T0475.t04.str2.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1280 # # ============================================ # Comments from T0475.t04.str4.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1280 # # ============================================ # Comments from T0475.t04.pb.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1280 # # ============================================ # Comments from T0475.t04.bys.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1280 # # ============================================ # Comments from T0475.t04.alpha.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1280 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.2006 0.0952 0.7042 2 N 0.1631 0.0840 0.7529 3 S 0.0617 0.5150 0.4233 4 E 0.0527 0.5738 0.3735 5 I 0.0352 0.7019 0.2629 6 E 0.0230 0.8094 0.1676 7 L 0.0230 0.8697 0.1073 8 P 0.0165 0.8939 0.0896 9 V 0.0085 0.9176 0.0738 10 Q 0.0085 0.9218 0.0697 11 K 0.0085 0.9221 0.0694 12 Q 0.0085 0.9201 0.0714 13 L 0.0086 0.9158 0.0756 14 E 0.0087 0.9114 0.0798 15 A 0.0111 0.8867 0.1023 16 Y 0.0227 0.7756 0.2017 17 N 0.0516 0.5781 0.3703 18 A 0.0258 0.5216 0.4526 19 R 0.0402 0.3625 0.5973 20 D 0.0947 0.3496 0.5557 21 I 0.0122 0.7669 0.2210 22 D 0.0094 0.8728 0.1178 23 A 0.0084 0.9187 0.0728 24 F 0.0085 0.9151 0.0764 25 M 0.0090 0.9097 0.0813 26 A 0.0101 0.8905 0.0994 27 W 0.0162 0.8044 0.1794 28 W 0.0646 0.5107 0.4246 29 A 0.1007 0.3432 0.5561 30 D 0.0658 0.3357 0.5985 31 D 0.1167 0.1976 0.6857 32 C 0.3769 0.0765 0.5466 33 Q 0.6116 0.0607 0.3277 34 Y 0.7023 0.0375 0.2602 35 Y 0.6063 0.0521 0.3416 36 A 0.4696 0.0461 0.4842 37 F 0.2750 0.0566 0.6684 38 P 0.1834 0.1741 0.6425 39 A 0.1449 0.2303 0.6247 40 T 0.1526 0.2464 0.6010 41 L 0.2102 0.2553 0.5345 42 L 0.2461 0.2733 0.4806 43 A 0.1901 0.2797 0.5302 44 G 0.1499 0.2193 0.6308 45 N 0.1332 0.2403 0.6265 46 A 0.0169 0.7343 0.2488 47 A 0.0094 0.8656 0.1250 48 E 0.0085 0.9191 0.0724 49 I 0.0086 0.9202 0.0712 50 R 0.0083 0.9218 0.0699 51 V 0.0084 0.9218 0.0698 52 R 0.0086 0.9169 0.0745 53 H 0.0092 0.9018 0.0890 54 I 0.0092 0.8935 0.0973 55 E 0.0131 0.8294 0.1575 56 R 0.0353 0.6170 0.3477 57 F 0.0910 0.3159 0.5932 58 K 0.1096 0.1852 0.7052 59 E 0.1826 0.0784 0.7390 60 P 0.1329 0.2121 0.6550 61 D 0.1634 0.1908 0.6458 62 L 0.2793 0.1501 0.5707 63 Y 0.4326 0.0939 0.4734 64 G 0.5373 0.0502 0.4124 65 E 0.6142 0.0414 0.3444 66 L 0.6167 0.0460 0.3374 67 L 0.5709 0.0854 0.3438 68 T 0.6658 0.0599 0.2743 69 R 0.7009 0.0416 0.2576 70 V 0.7002 0.0393 0.2605 71 I 0.6298 0.0482 0.3220 72 V 0.3561 0.0734 0.5704 73 G 0.1779 0.0693 0.7528 74 N 0.2992 0.0682 0.6325 75 V 0.5919 0.0478 0.3603 76 V 0.7273 0.0263 0.2464 77 I 0.7805 0.0153 0.2041 78 D 0.7482 0.0212 0.2306 79 H 0.7612 0.0218 0.2170 80 E 0.7669 0.0184 0.2148 81 T 0.7662 0.0174 0.2163 82 V 0.7533 0.0217 0.2250 83 T 0.6928 0.0335 0.2738 84 R 0.6666 0.0385 0.2949 85 N 0.5123 0.0529 0.4348 86 F 0.3260 0.0508 0.6232 87 P 0.1573 0.1614 0.6814 88 E 0.0999 0.1434 0.7567 89 G 0.1673 0.0804 0.7523 90 K 0.3465 0.0843 0.5692 91 G 0.4966 0.0515 0.4519 92 E 0.6006 0.0405 0.3590 93 V 0.6832 0.0210 0.2958 94 D 0.7007 0.0277 0.2716 95 V 0.7929 0.0092 0.1979 96 A 0.7874 0.0087 0.2039 97 C 0.8076 0.0063 0.1860 98 I 0.8179 0.0051 0.1769 99 Y 0.8128 0.0057 0.1814 100 E 0.7970 0.0057 0.1974 101 V 0.7344 0.0170 0.2486 102 E 0.5025 0.0957 0.4018 103 N 0.1651 0.0811 0.7539 104 G 0.1240 0.0762 0.7998 105 R 0.5549 0.0231 0.4220 106 I 0.6677 0.0278 0.3045 107 A 0.6463 0.0751 0.2785 108 K 0.7483 0.0572 0.1945 109 A 0.7028 0.0747 0.2225 110 W 0.6865 0.0977 0.2158 111 F 0.6451 0.1152 0.2397 112 K 0.4985 0.1663 0.3352 113 I 0.3393 0.1553 0.5054 114 G 0.1838 0.0989 0.7173 115 E 0.1758 0.1501 0.6740 116 P 0.1341 0.3559 0.5100 117 R 0.1525 0.4410 0.4065 118 I 0.1322 0.5354 0.3324 119 V 0.1641 0.4932 0.3427 120 S 0.2043 0.3170 0.4788 121 Q 0.2252 0.1732 0.6016 122 K 0.1639 0.1514 0.6847