# This file is the result of combining several RDB files, specifically # T0495.t04.str2.rdb (weight 1.54425) # T0495.t04.str4.rdb (weight 0.924988) # T0495.t04.pb.rdb (weight 0.789901) # T0495.t04.bys.rdb (weight 0.748322) # T0495.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 T0495.t04.str2.rdb # ============================================ # TARGET T0495 # 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 T0495.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 129 # # ============================================ # Comments from T0495.t04.str4.rdb # ============================================ # TARGET T0495 # 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 T0495.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 129 # # ============================================ # Comments from T0495.t04.pb.rdb # ============================================ # TARGET T0495 # 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 T0495.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 129 # # ============================================ # Comments from T0495.t04.bys.rdb # ============================================ # TARGET T0495 # 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 T0495.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 129 # # ============================================ # Comments from T0495.t04.alpha.rdb # ============================================ # TARGET T0495 # 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 T0495.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 129 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2051 0.0748 0.7201 2 P 0.1448 0.2311 0.6241 3 M 0.1284 0.3158 0.5558 4 T 0.1417 0.3407 0.5176 5 L 0.1731 0.2958 0.5311 6 D 0.1896 0.2409 0.5695 7 L 0.1568 0.3049 0.5383 8 Q 0.1439 0.2659 0.5902 9 P 0.0390 0.6752 0.2858 10 G 0.0123 0.8536 0.1341 11 Q 0.0090 0.9104 0.0806 12 R 0.0086 0.9188 0.0726 13 L 0.0084 0.9194 0.0722 14 A 0.0085 0.9132 0.0783 15 R 0.0085 0.9192 0.0724 16 G 0.0086 0.9149 0.0765 17 V 0.0084 0.9184 0.0732 18 A 0.0084 0.9213 0.0703 19 R 0.0083 0.9197 0.0720 20 H 0.0091 0.9088 0.0821 21 L 0.0091 0.8976 0.0933 22 R 0.0100 0.8692 0.1207 23 A 0.0191 0.7153 0.2655 24 H 0.0603 0.2229 0.7168 25 G 0.0572 0.0735 0.8693 26 F 0.2472 0.0367 0.7161 27 V 0.5088 0.0279 0.4634 28 S 0.5911 0.0216 0.3874 29 V 0.5019 0.0732 0.4249 30 E 0.4335 0.1340 0.4325 31 E 0.4783 0.1253 0.3964 32 F 0.4000 0.0669 0.5331 33 V 0.3428 0.0310 0.6262 34 P 0.2234 0.0868 0.6898 35 A 0.1178 0.2794 0.6027 36 R 0.0775 0.1742 0.7483 37 G 0.0820 0.1029 0.8151 38 L 0.2732 0.0545 0.6723 39 R 0.5274 0.0396 0.4329 40 V 0.6000 0.0385 0.3614 41 D 0.5896 0.0602 0.3502 42 V 0.7405 0.0501 0.2094 43 M 0.7035 0.0519 0.2446 44 G 0.7428 0.0216 0.2356 45 L 0.6456 0.0356 0.3189 46 G 0.2925 0.0213 0.6861 47 P 0.1693 0.1775 0.6532 48 K 0.1227 0.1367 0.7405 49 G 0.1526 0.0693 0.7782 50 E 0.4637 0.0267 0.5096 51 I 0.7324 0.0078 0.2598 52 W 0.7807 0.0079 0.2115 53 V 0.8202 0.0049 0.1749 54 I 0.8172 0.0054 0.1774 55 E 0.8031 0.0063 0.1906 56 C 0.7874 0.0077 0.2049 57 K 0.6927 0.0245 0.2828 58 S 0.5962 0.0315 0.3723 59 S 0.2703 0.0652 0.6645 60 R 0.0760 0.5616 0.3624 61 A 0.0617 0.6486 0.2897 62 D 0.0778 0.6317 0.2905 63 F 0.0710 0.6529 0.2762 64 Q 0.0634 0.6743 0.2624 65 A 0.0762 0.6344 0.2894 66 D 0.0997 0.4731 0.4272 67 A 0.0688 0.5643 0.3669 68 K 0.0792 0.5937 0.3270 69 W 0.0719 0.6333 0.2948 70 Q 0.0419 0.7150 0.2431 71 G 0.0328 0.7271 0.2401 72 Y 0.0431 0.7371 0.2198 73 L 0.0421 0.7715 0.1864 74 E 0.0393 0.7575 0.2032 75 W 0.0641 0.6319 0.3040 76 C 0.1482 0.4587 0.3931 77 D 0.1640 0.3476 0.4884 78 R 0.3318 0.2032 0.4650 79 Y 0.5528 0.0795 0.3677 80 F 0.6704 0.0482 0.2813 81 W 0.7109 0.0372 0.2520 82 A 0.6376 0.0398 0.3225 83 V 0.4743 0.0476 0.4781 84 D 0.2667 0.0807 0.6526 85 M 0.0797 0.3909 0.5294 86 E 0.1178 0.2324 0.6498 87 F 0.2495 0.0293 0.7212 88 P 0.1766 0.0231 0.8003 89 A 0.0269 0.6504 0.3227 90 E 0.0312 0.6710 0.2977 91 L 0.0706 0.4592 0.4703 92 L 0.2286 0.0668 0.7045 93 P 0.1768 0.0707 0.7525 94 A 0.0908 0.3451 0.5642 95 E 0.1271 0.2291 0.6438 96 S 0.3419 0.0766 0.5814 97 G 0.5884 0.0288 0.3829 98 L 0.7784 0.0069 0.2147 99 L 0.7943 0.0067 0.1990 100 I 0.7975 0.0060 0.1965 101 A 0.7027 0.0240 0.2734 102 D 0.4259 0.0338 0.5403 103 A 0.1684 0.2388 0.5928 104 Y 0.1399 0.1831 0.6770 105 D 0.1967 0.1121 0.6912 106 A 0.4297 0.0996 0.4707 107 E 0.5756 0.1207 0.3037 108 I 0.6783 0.0776 0.2441 109 V 0.6732 0.0802 0.2466 110 R 0.6079 0.0963 0.2958 111 M 0.4579 0.1111 0.4309 112 A 0.2792 0.0574 0.6634 113 P 0.1316 0.2373 0.6310 114 E 0.1002 0.3965 0.5033 115 Q 0.1456 0.3048 0.5496 116 K 0.1395 0.2895 0.5710 117 L 0.1574 0.2375 0.6051 118 A 0.1372 0.1938 0.6690 119 P 0.0737 0.4886 0.4377 120 A 0.0483 0.6572 0.2944 121 R 0.0351 0.7387 0.2261 122 R 0.0123 0.8652 0.1225 123 K 0.0089 0.9070 0.0841 124 V 0.0083 0.9223 0.0693 125 L 0.0083 0.9230 0.0687 126 I 0.0083 0.9209 0.0708 127 Q 0.0083 0.9217 0.0700 128 K 0.0084 0.9160 0.0757 129 F 0.0085 0.9072 0.0843 130 A 0.0084 0.9092 0.0824 131 T 0.0084 0.9049 0.0867 132 H 0.0085 0.9063 0.0852 133 A 0.0085 0.9065 0.0850 134 A 0.0085 0.9051 0.0864 135 R 0.0085 0.9098 0.0818 136 R 0.0098 0.8928 0.0975 137 L 0.0120 0.8759 0.1121 138 Q 0.0135 0.8401 0.1464 139 A 0.0247 0.7615 0.2137 140 L 0.0511 0.6013 0.3476 141 R 0.1252 0.3418 0.5330 142 D 0.1716 0.1207 0.7077 143 P 0.0261 0.5086 0.4653 144 E 0.0420 0.3566 0.6014 145 G 0.0843 0.2788 0.6368 146 H 0.1733 0.2218 0.6049 147 G 0.2137 0.2678 0.5185 148 I 0.2438 0.2472 0.5090 149 F 0.2511 0.1739 0.5749 150 E 0.1896 0.1791 0.6313