# This file is the result of combining several RDB files, specifically # T0557.t04.dssp-ebghstl.rdb (weight 1.53986) # T0557.t04.stride-ebghtl.rdb (weight 1.24869) # T0557.t04.str2.rdb (weight 1.54758) # T0557.t04.alpha.rdb (weight 0.659012) # 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.dssp-ebghstl.rdb # ============================================ # TARGET T0557 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # 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 876 # # ============================================ # Comments from T0557.t04.stride-ebghtl.rdb # ============================================ # TARGET T0557 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # 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 876 # # ============================================ # Comments from T0557.t04.str2.rdb # ============================================ # TARGET T0557 # Using neural net t04-2621-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 876 # # ============================================ # Comments from T0557.t04.alpha.rdb # ============================================ # TARGET T0557 # Using neural net t04-2621-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 876 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0594 0.0958 0.8447 2 R 0.0654 0.1341 0.8005 3 S 0.0627 0.1666 0.7706 4 A 0.0405 0.2822 0.6773 5 T 0.0088 0.8886 0.1026 6 D 0.0065 0.9042 0.0893 7 L 0.0054 0.9346 0.0600 8 L 0.0048 0.9511 0.0442 9 D 0.0048 0.9412 0.0539 10 E 0.0053 0.9114 0.0833 11 L 0.0087 0.8583 0.1329 12 N 0.0123 0.6703 0.3174 13 A 0.0200 0.3561 0.6238 14 V 0.0630 0.1376 0.7993 15 D 0.0666 0.0945 0.8389 16 E 0.0917 0.2503 0.6580 17 S 0.0974 0.2845 0.6181 18 A 0.0858 0.4420 0.4722 19 R 0.2044 0.4602 0.3354 20 I 0.3362 0.4867 0.1772 21 E 0.4320 0.4176 0.1504 22 A 0.5021 0.3225 0.1754 23 K 0.4628 0.3539 0.1833 24 R 0.3289 0.3584 0.3126 25 A 0.1501 0.3540 0.4959 26 S 0.0544 0.3101 0.6355 27 D 0.0350 0.2110 0.7540 28 M 0.0535 0.2143 0.7322 29 G 0.0380 0.2978 0.6643 30 K 0.0240 0.5671 0.4089 31 S 0.0375 0.7140 0.2486 32 V 0.0336 0.8261 0.1403 33 M 0.0332 0.8485 0.1182 34 E 0.0516 0.8396 0.1088 35 T 0.0955 0.8254 0.0791 36 V 0.1445 0.7950 0.0605 37 I 0.2009 0.7279 0.0711 38 A 0.2152 0.6841 0.1007 39 F 0.2469 0.5343 0.2188 40 A 0.2351 0.3261 0.4388 41 N 0.1667 0.1856 0.6477 42 E 0.1031 0.0763 0.8207 43 P 0.0472 0.1409 0.8119 44 G 0.0456 0.1654 0.7890 45 L 0.0911 0.1088 0.8001 46 D 0.0730 0.0841 0.8429 47 G 0.1915 0.0344 0.7741 48 G 0.5208 0.0105 0.4687 49 Y 0.8815 0.0040 0.1145 50 L 0.9304 0.0033 0.0664 51 L 0.9312 0.0031 0.0656 52 L 0.8948 0.0158 0.0895 53 G 0.8418 0.0089 0.1494 54 V 0.6627 0.0101 0.3272 55 D 0.4440 0.0151 0.5409 56 W 0.2566 0.0912 0.6522 57 A 0.2051 0.1257 0.6691 58 I 0.2148 0.1460 0.6393 59 N 0.1564 0.1214 0.7222 60 D 0.1285 0.1165 0.7550 61 K 0.1041 0.0814 0.8146 62 G 0.0997 0.0479 0.8524 63 D 0.2270 0.0315 0.7415 64 T 0.6123 0.0150 0.3727 65 V 0.7640 0.0096 0.2264 66 Y 0.8401 0.0057 0.1542 67 R 0.7714 0.0121 0.2164 68 P 0.6291 0.0208 0.3501 69 V 0.4162 0.0419 0.5420 70 G 0.2158 0.0393 0.7449 71 L 0.1153 0.0351 0.8495 72 P 0.0896 0.0397 0.8707 73 D 0.0941 0.0191 0.8868 74 P 0.0082 0.8182 0.1736 75 D 0.0064 0.9151 0.0785 76 K 0.0059 0.9397 0.0543 77 V 0.0050 0.9414 0.0537 78 Q 0.0047 0.9532 0.0421 79 R 0.0048 0.9560 0.0392 80 D 0.0048 0.9552 0.0400 81 L 0.0047 0.9573 0.0379 82 A 0.0047 0.9605 0.0349 83 S 0.0047 0.9591 0.0362 84 Q 0.0047 0.9566 0.0387 85 C 0.0049 0.9368 0.0583 86 A 0.0060 0.8927 0.1014 87 S 0.0083 0.7561 0.2356 88 M 0.0150 0.5277 0.4573 89 L 0.0743 0.2221 0.7036 90 N 0.0839 0.0700 0.8461 91 V 0.1128 0.0673 0.8199 92 A 0.1761 0.0590 0.7649 93 L 0.3282 0.0316 0.6402 94 R 0.3078 0.0162 0.6760 95 P 0.4345 0.0210 0.5445 96 E 0.7454 0.0139 0.2407 97 M 0.8546 0.0051 0.1403 98 Q 0.8864 0.0046 0.1090 99 L 0.9122 0.0036 0.0842 100 E 0.8888 0.0052 0.1061 101 Q 0.8746 0.0039 0.1215 102 V 0.6670 0.0198 0.3132 103 G 0.0925 0.0233 0.8841 104 G 0.0400 0.0328 0.9272 105 K 0.5708 0.0090 0.4201 106 T 0.8739 0.0033 0.1227 107 L 0.9183 0.0036 0.0781 108 L 0.9305 0.0033 0.0662 109 V 0.9323 0.0032 0.0645 110 V 0.9251 0.0036 0.0713 111 Y 0.9003 0.0035 0.0961 112 V 0.6781 0.0077 0.3142 113 P 0.3723 0.0130 0.6146 114 E 0.1536 0.0896 0.7568 115 A 0.0983 0.1112 0.7904 116 D 0.0825 0.1169 0.8006 117 V 0.0401 0.2600 0.7000 118 T 0.0704 0.1471 0.7825 119 H 0.1293 0.0649 0.8058 120 K 0.3153 0.0145 0.6702 121 P 0.6334 0.0141 0.3525 122 I 0.8383 0.0163 0.1454 123 Y 0.8612 0.0119 0.1269 124 K 0.7839 0.0202 0.1959 125 K 0.5752 0.0478 0.3770 126 A 0.2900 0.1200 0.5900 127 T 0.1347 0.0657 0.7996 128 G 0.0707 0.0399 0.8894 129 L 0.1689 0.0216 0.8095 130 P 0.1482 0.0626 0.7892 131 G 0.1032 0.0425 0.8543 132 G 0.4579 0.0255 0.5166 133 A 0.7664 0.0098 0.2238 134 Y 0.8881 0.0052 0.1067 135 R 0.9036 0.0056 0.0909 136 R 0.8956 0.0058 0.0986 137 I 0.7686 0.0195 0.2119 138 G 0.3636 0.0240 0.6124 139 S 0.1547 0.0498 0.7955 140 S 0.0955 0.1021 0.8024 141 D 0.1883 0.0784 0.7333 142 Q 0.3863 0.0522 0.5616 143 R 0.3852 0.0395 0.5753 144 C 0.2396 0.0300 0.7304 145 V 0.1111 0.0194 0.8696