# This file is the result of combining several RDB files, specifically # T0312.t06.dssp-ebghstl.rdb (weight 1.53986) # T0312.t06.stride-ebghtl.rdb (weight 1.24869) # T0312.t06.str2.rdb (weight 1.54758) # T0312.t06.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 T0312.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0312 # Using neural net t06-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 T0312.t06-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 184 # # ============================================ # Comments from T0312.t06.stride-ebghtl.rdb # ============================================ # TARGET T0312 # Using neural net t06-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 T0312.t06-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 184 # # ============================================ # Comments from T0312.t06.str2.rdb # ============================================ # TARGET T0312 # Using neural net t06-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 T0312.t06-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 184 # # ============================================ # Comments from T0312.t06.alpha.rdb # ============================================ # TARGET T0312 # Using neural net t06-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 T0312.t06-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 184 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1017 0.0105 0.8877 2 K 0.4465 0.0185 0.5351 3 V 0.5861 0.0439 0.3699 4 F 0.6371 0.0459 0.3170 5 E 0.6069 0.0568 0.3363 6 F 0.3860 0.0704 0.5437 7 E 0.2428 0.0763 0.6810 8 V 0.1822 0.0855 0.7323 9 G 0.1593 0.0439 0.7968 10 K 0.3473 0.0215 0.6312 11 G 0.6426 0.0077 0.3497 12 F 0.8425 0.0054 0.1521 13 L 0.9179 0.0033 0.0787 14 L 0.9181 0.0040 0.0779 15 R 0.9056 0.0037 0.0907 16 L 0.6965 0.0092 0.2943 17 D 0.2050 0.0150 0.7800 18 Y 0.0302 0.0998 0.8700 19 G 0.0284 0.1089 0.8627 20 K 0.0334 0.4140 0.5526 21 D 0.0663 0.6746 0.2591 22 L 0.0064 0.9243 0.0693 23 V 0.0050 0.9545 0.0406 24 R 0.0047 0.9577 0.0377 25 Q 0.0047 0.9571 0.0382 26 I 0.0047 0.9596 0.0357 27 E 0.0047 0.9607 0.0347 28 E 0.0046 0.9615 0.0339 29 F 0.0047 0.9607 0.0346 30 L 0.0047 0.9590 0.0364 31 E 0.0049 0.9467 0.0484 32 E 0.0077 0.8809 0.1114 33 K 0.0437 0.3931 0.5632 34 G 0.0482 0.0175 0.9343 35 I 0.1045 0.0097 0.8858 36 H 0.2969 0.0471 0.6561 37 A 0.8443 0.0059 0.1498 38 A 0.9038 0.0034 0.0929 39 H 0.9296 0.0039 0.0665 40 I 0.9235 0.0040 0.0725 41 S 0.8862 0.0081 0.1058 42 A 0.8434 0.0084 0.1482 43 I 0.6963 0.0592 0.2445 44 G 0.6078 0.0785 0.3137 45 A 0.6119 0.0586 0.3294 46 V 0.6071 0.0594 0.3335 47 R 0.5930 0.0651 0.3418 48 S 0.6853 0.0305 0.2843 49 A 0.7988 0.0132 0.1880 50 V 0.8989 0.0074 0.0938 51 I 0.9058 0.0072 0.0871 52 G 0.8698 0.0141 0.1161 53 Y 0.7662 0.0123 0.2215 54 Y 0.3934 0.0256 0.5809 55 D 0.1905 0.0321 0.7775 56 Q 0.0439 0.3686 0.5875 57 E 0.0441 0.4036 0.5523 58 K 0.0579 0.4327 0.5094 59 K 0.0915 0.4504 0.4581 60 E 0.1674 0.4175 0.4151 61 Y 0.2787 0.3375 0.3839 62 V 0.4494 0.1918 0.3588 63 K 0.5492 0.1839 0.2670 64 K 0.5887 0.1680 0.2433 65 E 0.5545 0.1700 0.2755 66 L 0.4791 0.1290 0.3918 67 M 0.2644 0.1311 0.6045 68 E 0.1917 0.0720 0.7363 69 P 0.2613 0.1355 0.6032 70 L 0.6554 0.0762 0.2684 71 E 0.8153 0.0422 0.1425 72 I 0.8739 0.0357 0.0904 73 L 0.8634 0.0390 0.0976 74 S 0.8802 0.0226 0.0973 75 L 0.8469 0.0289 0.1241 76 S 0.7534 0.0357 0.2109 77 G 0.6421 0.0328 0.3250 78 N 0.6505 0.0431 0.3064 79 V 0.6933 0.0425 0.2641 80 S 0.5626 0.0306 0.4068 81 M 0.2662 0.0472 0.6865 82 K 0.0912 0.0742 0.8345 83 D 0.0505 0.0692 0.8803 84 S 0.0588 0.0459 0.8953 85 K 0.1048 0.0252 0.8700 86 P 0.2325 0.0232 0.7442 87 F 0.5592 0.0234 0.4174 88 C 0.8114 0.0089 0.1798 89 H 0.8930 0.0047 0.1024 90 I 0.9158 0.0034 0.0809 91 H 0.9278 0.0032 0.0690 92 V 0.9303 0.0032 0.0665 93 L 0.9266 0.0034 0.0700 94 L 0.8980 0.0068 0.0953 95 G 0.7141 0.0150 0.2709 96 K 0.3439 0.0346 0.6216 97 D 0.0646 0.0473 0.8881 98 G 0.0786 0.0426 0.8788 99 E 0.5343 0.0212 0.4445 100 V 0.8416 0.0063 0.1521 101 Y 0.8021 0.0216 0.1763 102 G 0.7317 0.0202 0.2481 103 G 0.6451 0.0319 0.3231 104 H 0.6843 0.0319 0.2838 105 L 0.6122 0.0616 0.3262 106 F 0.4053 0.0677 0.5270 107 S 0.2804 0.0795 0.6401 108 A 0.2959 0.0949 0.6091 109 E 0.5642 0.0554 0.3804 110 V 0.7239 0.0308 0.2453 111 F 0.7389 0.0161 0.2450 112 A 0.7679 0.0084 0.2237 113 C 0.8462 0.0072 0.1466 114 E 0.9045 0.0047 0.0907 115 V 0.9184 0.0058 0.0758 116 F 0.9194 0.0052 0.0754 117 V 0.8986 0.0079 0.0935 118 L 0.7887 0.0100 0.2013 119 P 0.6545 0.0134 0.3321 120 L 0.2784 0.0492 0.6724 121 S 0.0857 0.1017 0.8126 122 G 0.0390 0.0884 0.8725 123 E 0.0799 0.0978 0.8223 124 A 0.0982 0.0853 0.8165 125 P 0.1398 0.1872 0.6730 126 E 0.1730 0.2684 0.5587 127 R 0.2858 0.1873 0.5268 128 A 0.3258 0.1235 0.5507 129 F 0.3042 0.0767 0.6191 130 D 0.1406 0.0342 0.8251 131 E 0.0098 0.4099 0.5803 132 Q 0.0145 0.3328 0.6526 133 T 0.0612 0.3242 0.6146 134 G 0.0778 0.1536 0.7686 135 L 0.2772 0.1458 0.5770 136 F 0.4947 0.1754 0.3299 137 L 0.5505 0.2091 0.2404 138 W 0.5017 0.1756 0.3228 139 L 0.4564 0.1609 0.3826 140 E 0.3067 0.1860 0.5072 141 H 0.1798 0.1401 0.6801 142 H 0.1044 0.1353 0.7604 143 H 0.0740 0.0878 0.8383 144 H 0.0529 0.1101 0.8370 145 H 0.0559 0.0787 0.8654 146 H 0.0434 0.0372 0.9194