# This file is the result of combining several RDB files, specifically # T0557.t04.str2.rdb (weight 1.54425) # T0557.t04.str4.rdb (weight 0.924988) # T0557.t04.pb.rdb (weight 0.789901) # T0557.t04.bys.rdb (weight 0.748322) # T0557.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 T0557.t04.str2.rdb # ============================================ # TARGET T0557 # 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 T0557.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 874 # # ============================================ # Comments from T0557.t04.str4.rdb # ============================================ # TARGET T0557 # 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 T0557.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 874 # # ============================================ # Comments from T0557.t04.pb.rdb # ============================================ # TARGET T0557 # 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 T0557.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 874 # # ============================================ # Comments from T0557.t04.bys.rdb # ============================================ # TARGET T0557 # 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 T0557.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 874 # # ============================================ # Comments from T0557.t04.alpha.rdb # ============================================ # TARGET T0557 # 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 T0557.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 874 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2153 0.2004 0.5843 2 R 0.1865 0.2252 0.5883 3 S 0.1596 0.2859 0.5545 4 A 0.1122 0.3670 0.5207 5 T 0.0149 0.7538 0.2312 6 D 0.0109 0.8665 0.1226 7 L 0.0111 0.8978 0.0911 8 L 0.0096 0.9008 0.0896 9 D 0.0087 0.9044 0.0869 10 E 0.0096 0.8907 0.0997 11 L 0.0138 0.8431 0.1430 12 N 0.0294 0.7128 0.2579 13 A 0.0553 0.4932 0.4515 14 V 0.1289 0.2294 0.6417 15 D 0.1316 0.1626 0.7058 16 E 0.1365 0.2860 0.5776 17 S 0.2095 0.1864 0.6041 18 A 0.2974 0.2170 0.4856 19 R 0.4976 0.1532 0.3491 20 I 0.6834 0.0604 0.2562 21 E 0.7051 0.0534 0.2415 22 A 0.6917 0.0685 0.2398 23 K 0.5529 0.1848 0.2623 24 R 0.4836 0.2048 0.3115 25 A 0.2709 0.2752 0.4538 26 S 0.1378 0.3225 0.5397 27 D 0.0997 0.3250 0.5754 28 M 0.1229 0.2568 0.6203 29 G 0.0689 0.4893 0.4418 30 K 0.0351 0.7068 0.2581 31 S 0.0284 0.8063 0.1652 32 V 0.0184 0.8626 0.1190 33 M 0.0121 0.8986 0.0894 34 E 0.0111 0.9125 0.0764 35 T 0.0260 0.8894 0.0846 36 V 0.0519 0.8481 0.1000 37 I 0.0712 0.8218 0.1070 38 A 0.1040 0.7618 0.1342 39 F 0.1233 0.6539 0.2228 40 A 0.1563 0.4446 0.3991 41 N 0.1473 0.2344 0.6183 42 E 0.1826 0.1436 0.6738 43 P 0.1239 0.2229 0.6532 44 G 0.1130 0.1669 0.7201 45 L 0.1449 0.2081 0.6470 46 D 0.1451 0.1259 0.7290 47 G 0.1929 0.0686 0.7386 48 G 0.4654 0.0228 0.5117 49 Y 0.7608 0.0074 0.2319 50 L 0.8049 0.0058 0.1893 51 L 0.7872 0.0066 0.2062 52 L 0.7429 0.0160 0.2411 53 G 0.6477 0.0174 0.3349 54 V 0.5660 0.0406 0.3934 55 D 0.3592 0.0580 0.5828 56 W 0.2531 0.2931 0.4537 57 A 0.1904 0.3462 0.4635 58 I 0.2221 0.3363 0.4415 59 N 0.1801 0.2353 0.5847 60 D 0.1379 0.2611 0.6010 61 K 0.1105 0.1438 0.7457 62 G 0.0900 0.1071 0.8029 63 D 0.2478 0.0572 0.6951 64 T 0.4495 0.0235 0.5270 65 V 0.6331 0.0273 0.3396 66 Y 0.6986 0.0139 0.2875 67 R 0.6548 0.0165 0.3288 68 P 0.5385 0.0277 0.4338 69 V 0.3451 0.0694 0.5855 70 G 0.2076 0.0526 0.7399 71 L 0.2331 0.0506 0.7163 72 P 0.1886 0.0829 0.7285 73 D 0.1877 0.0385 0.7738 74 P 0.0169 0.6322 0.3509 75 D 0.0119 0.7809 0.2072 76 K 0.0116 0.8803 0.1081 77 V 0.0112 0.8993 0.0896 78 Q 0.0086 0.9137 0.0777 79 R 0.0083 0.9202 0.0715 80 D 0.0084 0.9200 0.0716 81 L 0.0084 0.9193 0.0724 82 A 0.0083 0.9200 0.0717 83 S 0.0083 0.9155 0.0762 84 Q 0.0084 0.9181 0.0736 85 C 0.0088 0.9048 0.0864 86 A 0.0095 0.8543 0.1363 87 S 0.0157 0.6745 0.3098 88 M 0.0538 0.4129 0.5333 89 L 0.1400 0.2125 0.6476 90 N 0.1935 0.1044 0.7021 91 V 0.2338 0.1661 0.6001 92 A 0.2954 0.0890 0.6156 93 L 0.3927 0.0526 0.5547 94 R 0.3761 0.0175 0.6065 95 P 0.4264 0.0553 0.5183 96 E 0.5640 0.0566 0.3794 97 M 0.6923 0.0126 0.2950 98 Q 0.7248 0.0132 0.2620 99 L 0.7458 0.0080 0.2462 100 E 0.7296 0.0166 0.2538 101 Q 0.6770 0.0123 0.3107 102 V 0.5254 0.0386 0.4361 103 G 0.1706 0.0623 0.7671 104 G 0.0808 0.0893 0.8299 105 K 0.3971 0.0153 0.5876 106 T 0.7108 0.0084 0.2808 107 L 0.8104 0.0048 0.1848 108 L 0.8208 0.0044 0.1748 109 V 0.8217 0.0041 0.1742 110 V 0.8203 0.0047 0.1749 111 Y 0.7860 0.0055 0.2085 112 V 0.5798 0.0123 0.4079 113 P 0.2803 0.0212 0.6986 114 E 0.1855 0.2092 0.6053 115 A 0.1958 0.1602 0.6441 116 D 0.1946 0.1092 0.6962 117 V 0.0901 0.3530 0.5569 118 T 0.1293 0.2355 0.6352 119 H 0.2204 0.1095 0.6701 120 K 0.3852 0.0295 0.5853 121 P 0.5459 0.0291 0.4250 122 I 0.6956 0.0344 0.2700 123 Y 0.7274 0.0268 0.2458 124 K 0.6871 0.0546 0.2583 125 K 0.5370 0.1081 0.3549 126 A 0.3191 0.2040 0.4769 127 T 0.1481 0.1276 0.7243 128 G 0.1176 0.0778 0.8046 129 L 0.2651 0.0343 0.7006 130 P 0.2366 0.0853 0.6781 131 G 0.2197 0.0630 0.7173 132 G 0.4515 0.0305 0.5181 133 A 0.7067 0.0201 0.2732 134 Y 0.7963 0.0084 0.1953 135 R 0.7895 0.0118 0.1987 136 R 0.7502 0.0118 0.2379 137 I 0.6065 0.0435 0.3500 138 G 0.3453 0.0526 0.6021 139 S 0.2426 0.1100 0.6474 140 S 0.1757 0.1745 0.6498 141 D 0.1980 0.1583 0.6437 142 Q 0.3143 0.1388 0.5469 143 R 0.4069 0.1303 0.4628 144 C 0.4382 0.1060 0.4558 145 V 0.3790 0.0805 0.5405