# This file is the result of combining several RDB files, specifically # T0586.t2k.str2.rdb (weight 1.54425) # T0586.t2k.str4.rdb (weight 0.924988) # T0586.t2k.pb.rdb (weight 0.789901) # T0586.t2k.bys.rdb (weight 0.748322) # T0586.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 T0586.t2k.str2.rdb # ============================================ # TARGET T0586 # 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 T0586.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 5246 # # ============================================ # Comments from T0586.t2k.str4.rdb # ============================================ # TARGET T0586 # 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 T0586.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 5246 # # ============================================ # Comments from T0586.t2k.pb.rdb # ============================================ # TARGET T0586 # 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 T0586.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 5246 # # ============================================ # Comments from T0586.t2k.bys.rdb # ============================================ # TARGET T0586 # 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 T0586.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 5246 # # ============================================ # Comments from T0586.t2k.alpha.rdb # ============================================ # TARGET T0586 # 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 T0586.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 5246 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2405 0.1747 0.5849 2 N 0.2614 0.1462 0.5923 3 A 0.4108 0.1022 0.4870 4 M 0.5420 0.0497 0.4083 5 N 0.4778 0.0302 0.4921 6 P 0.3407 0.1592 0.5001 7 T 0.2645 0.1361 0.5994 8 F 0.1404 0.3031 0.5565 9 H 0.1260 0.2111 0.6630 10 A 0.0983 0.2497 0.6519 11 D 0.0896 0.2077 0.7027 12 K 0.1842 0.1573 0.6585 13 P 0.1553 0.3593 0.4854 14 I 0.0377 0.7428 0.2195 15 Y 0.0114 0.8865 0.1021 16 S 0.0084 0.9190 0.0726 17 Q 0.0083 0.9234 0.0683 18 I 0.0083 0.9214 0.0703 19 S 0.0083 0.9230 0.0687 20 D 0.0083 0.9247 0.0670 21 W 0.0083 0.9247 0.0671 22 M 0.0083 0.9217 0.0700 23 K 0.0084 0.9178 0.0739 24 K 0.0084 0.9144 0.0772 25 Q 0.0089 0.9033 0.0878 26 M 0.0103 0.8890 0.1007 27 I 0.0242 0.7672 0.2086 28 T 0.0575 0.3332 0.6094 29 G 0.0557 0.1305 0.8138 30 E 0.2206 0.0893 0.6902 31 W 0.3098 0.0506 0.6397 32 K 0.2355 0.0546 0.7100 33 G 0.1299 0.1956 0.6746 34 E 0.0904 0.1693 0.7403 35 D 0.1426 0.1666 0.6908 36 K 0.2242 0.1295 0.6463 37 L 0.2165 0.0513 0.7322 38 P 0.1690 0.1687 0.6622 39 S 0.1321 0.3686 0.4993 40 V 0.0121 0.7933 0.1946 41 R 0.0108 0.8690 0.1202 42 E 0.0105 0.9148 0.0746 43 M 0.0103 0.9143 0.0754 44 G 0.0097 0.9094 0.0809 45 V 0.0100 0.9040 0.0860 46 K 0.0211 0.7946 0.1844 47 L 0.0560 0.4773 0.4667 48 A 0.0843 0.1587 0.7570 49 V 0.1678 0.1042 0.7280 50 N 0.1719 0.0359 0.7923 51 P 0.0131 0.7013 0.2855 52 N 0.0101 0.8211 0.1689 53 T 0.0109 0.8942 0.0948 54 V 0.0087 0.9103 0.0810 55 S 0.0083 0.9212 0.0705 56 R 0.0083 0.9246 0.0671 57 A 0.0083 0.9240 0.0677 58 Y 0.0083 0.9225 0.0692 59 Q 0.0083 0.9230 0.0687 60 E 0.0083 0.9207 0.0710 61 L 0.0084 0.9160 0.0755 62 E 0.0087 0.8971 0.0942 63 R 0.0185 0.7863 0.1952 64 A 0.0591 0.2786 0.6623 65 G 0.0831 0.0851 0.8318 66 Y 0.3838 0.0374 0.5788 67 I 0.6732 0.0286 0.2982 68 Y 0.7394 0.0219 0.2386 69 A 0.7138 0.0249 0.2613 70 K 0.5855 0.0374 0.3772 71 R 0.4494 0.0694 0.4812 72 G 0.2856 0.0671 0.6473 73 M 0.3950 0.0580 0.5469 74 G 0.5106 0.0387 0.4507 75 S 0.7032 0.0248 0.2720 76 F 0.7453 0.0162 0.2385 77 V 0.7205 0.0235 0.2560 78 T 0.5631 0.0424 0.3945 79 S 0.3098 0.1639 0.5263 80 D 0.1641 0.2106 0.6253 81 K 0.1077 0.4195 0.4728 82 A 0.0966 0.5276 0.3757 83 L 0.0994 0.5357 0.3649 84 F 0.0965 0.5883 0.3153 85 D 0.0657 0.6602 0.2741 86 Q 0.0544 0.6999 0.2457 87 L 0.0606 0.6951 0.2443 88 K 0.0514 0.7070 0.2416 89 K 0.0441 0.7384 0.2175 90 E 0.0411 0.7548 0.2041 91 L 0.0410 0.7477 0.2113 92 A 0.0281 0.8220 0.1499 93 D 0.0136 0.8754 0.1110 94 A 0.0107 0.8937 0.0956 95 I 0.0119 0.8964 0.0917 96 T 0.0117 0.9000 0.0883 97 E 0.0087 0.9075 0.0837 98 R 0.0084 0.9176 0.0739 99 F 0.0093 0.9153 0.0754 100 L 0.0084 0.9165 0.0751 101 E 0.0083 0.9226 0.0691 102 E 0.0085 0.9190 0.0726 103 A 0.0093 0.9072 0.0835 104 K 0.0092 0.8935 0.0973 105 S 0.0149 0.8097 0.1754 106 I 0.0571 0.3675 0.5754 107 G 0.0505 0.0859 0.8636 108 L 0.1547 0.0629 0.7823 109 D 0.1566 0.0422 0.8012 110 D 0.0173 0.7216 0.2611 111 Q 0.0094 0.8637 0.1268 112 T 0.0092 0.9105 0.0803 113 A 0.0084 0.9164 0.0752 114 I 0.0083 0.9220 0.0697 115 E 0.0083 0.9247 0.0670 116 L 0.0083 0.9243 0.0675 117 L 0.0084 0.9190 0.0726 118 I 0.0085 0.9104 0.0811 119 K 0.0099 0.8580 0.1321 120 R 0.0270 0.7287 0.2443 121 S 0.0535 0.5203 0.4262 122 R 0.0488 0.4402 0.5110 123 N 0.0579 0.2621 0.6799 124 H 0.1093 0.2172 0.6735 125 E 0.1864 0.2206 0.5930