# This file is the result of combining several RDB files, specifically # T0415.t2k.str2.rdb (weight 1.54425) # T0415.t2k.str4.rdb (weight 0.924988) # T0415.t2k.pb.rdb (weight 0.789901) # T0415.t2k.bys.rdb (weight 0.748322) # T0415.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 T0415.t2k.str2.rdb # ============================================ # TARGET T0415 # 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 T0415.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 827 # # ============================================ # Comments from T0415.t2k.str4.rdb # ============================================ # TARGET T0415 # 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 T0415.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 827 # # ============================================ # Comments from T0415.t2k.pb.rdb # ============================================ # TARGET T0415 # 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 T0415.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 827 # # ============================================ # Comments from T0415.t2k.bys.rdb # ============================================ # TARGET T0415 # 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 T0415.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 827 # # ============================================ # Comments from T0415.t2k.alpha.rdb # ============================================ # TARGET T0415 # 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 T0415.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 827 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.1362 0.0627 0.8011 2 K 0.2150 0.1190 0.6660 3 S 0.2910 0.0900 0.6190 4 V 0.6313 0.0287 0.3401 5 V 0.7178 0.0098 0.2723 6 T 0.7675 0.0052 0.2273 7 L 0.7547 0.0091 0.2362 8 K 0.6558 0.0167 0.3275 9 T 0.4050 0.0564 0.5386 10 T 0.2087 0.1311 0.6602 11 D 0.1180 0.1414 0.7406 12 G 0.2609 0.0799 0.6592 13 W 0.5619 0.0332 0.4050 14 I 0.6546 0.0158 0.3297 15 P 0.6230 0.0097 0.3673 16 V 0.4762 0.0148 0.5090 17 P 0.2467 0.0182 0.7351 18 F 0.1218 0.4189 0.4593 19 S 0.1240 0.3928 0.4833 20 K 0.3708 0.1531 0.4761 21 V 0.6377 0.0559 0.3064 22 M 0.7218 0.0421 0.2361 23 Y 0.7938 0.0220 0.1843 24 L 0.7810 0.0179 0.2011 25 E 0.7572 0.0186 0.2241 26 A 0.6099 0.0441 0.3459 27 K 0.3646 0.1244 0.5110 28 D 0.2084 0.0898 0.7018 29 K 0.2710 0.0660 0.6631 30 K 0.6277 0.0157 0.3565 31 T 0.7625 0.0065 0.2310 32 Y 0.8152 0.0047 0.1801 33 V 0.8172 0.0049 0.1779 34 N 0.7559 0.0058 0.2383 35 A 0.6588 0.0208 0.3204 36 E 0.3682 0.1181 0.5137 37 E 0.2538 0.1253 0.6208 38 L 0.3178 0.1002 0.5820 39 T 0.4594 0.0782 0.4625 40 G 0.5311 0.0641 0.4048 41 T 0.6007 0.0597 0.3395 42 H 0.5700 0.0832 0.3468 43 K 0.4651 0.1544 0.3805 44 Y 0.4197 0.1793 0.4010 45 S 0.2418 0.1888 0.5694 46 L 0.0407 0.7183 0.2410 47 Q 0.0163 0.8382 0.1454 48 E 0.0152 0.8801 0.1046 49 F 0.0121 0.8816 0.1064 50 E 0.0132 0.8761 0.1106 51 Y 0.0179 0.7794 0.2027 52 L 0.0487 0.4693 0.4820 53 L 0.1732 0.1000 0.7268 54 P 0.1250 0.1284 0.7466 55 K 0.0312 0.4129 0.5560 56 D 0.0470 0.4170 0.5360 57 S 0.1239 0.3624 0.5137 58 F 0.3997 0.2137 0.3866 59 I 0.5481 0.1329 0.3191 60 R 0.5855 0.1082 0.3063 61 C 0.5229 0.1209 0.3562 62 H 0.4191 0.1055 0.4754 63 R 0.3203 0.2079 0.4718 64 S 0.3952 0.1950 0.4098 65 F 0.6081 0.1003 0.2916 66 I 0.6786 0.0654 0.2560 67 V 0.6559 0.0769 0.2671 68 N 0.4180 0.0685 0.5136 69 V 0.0962 0.5841 0.3197 70 N 0.0603 0.6496 0.2902 71 H 0.1144 0.5629 0.3227 72 I 0.1247 0.6677 0.2076 73 K 0.2084 0.5428 0.2488 74 A 0.3023 0.4336 0.2641 75 I 0.4200 0.2127 0.3673 76 Y 0.4403 0.0629 0.4968 77 P 0.2484 0.1951 0.5565 78 D 0.1618 0.1975 0.6406 79 T 0.1479 0.1869 0.6652 80 H 0.1500 0.1106 0.7394 81 S 0.2762 0.0638 0.6601 82 T 0.6042 0.0195 0.3763 83 F 0.7826 0.0062 0.2111 84 L 0.8180 0.0046 0.1774 85 L 0.8264 0.0045 0.1691 86 S 0.8088 0.0046 0.1866 87 M 0.7315 0.0072 0.2613 88 D 0.5038 0.0411 0.4552 89 N 0.1661 0.0774 0.7564 90 G 0.0819 0.0993 0.8188 91 E 0.4843 0.0286 0.4871 92 R 0.6483 0.0246 0.3271 93 V 0.6540 0.0180 0.3281 94 P 0.5262 0.0141 0.4597 95 V 0.4086 0.0500 0.5414 96 S 0.2309 0.0828 0.6863 97 Q 0.0367 0.6916 0.2717 98 S 0.0229 0.7779 0.1992 99 Y 0.0266 0.8219 0.1514 100 A 0.0096 0.9015 0.0889 101 S 0.0083 0.9203 0.0714 102 Y 0.0083 0.9227 0.0689 103 F 0.0084 0.9185 0.0730 104 R 0.0084 0.9169 0.0746 105 K 0.0086 0.9100 0.0813 106 L 0.0155 0.7995 0.1850 107 L 0.0562 0.4375 0.5063 108 G 0.0488 0.1086 0.8426 109 F 0.1523 0.0957 0.7520