# This file is the result of combining several RDB files, specifically # T0389.t2k.str2.rdb (weight 1.54425) # T0389.t2k.str4.rdb (weight 0.924988) # T0389.t2k.pb.rdb (weight 0.789901) # T0389.t2k.bys.rdb (weight 0.748322) # T0389.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 T0389.t2k.str2.rdb # ============================================ # TARGET T0389 # 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 T0389.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 384 # # ============================================ # Comments from T0389.t2k.str4.rdb # ============================================ # TARGET T0389 # 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 T0389.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 384 # # ============================================ # Comments from T0389.t2k.pb.rdb # ============================================ # TARGET T0389 # 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 T0389.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 384 # # ============================================ # Comments from T0389.t2k.bys.rdb # ============================================ # TARGET T0389 # 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 T0389.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 384 # # ============================================ # Comments from T0389.t2k.alpha.rdb # ============================================ # TARGET T0389 # 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 T0389.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 384 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.4043 0.1011 0.4946 2 I 0.3358 0.1112 0.5530 3 G 0.2760 0.1435 0.5805 4 T 0.3008 0.2294 0.4698 5 Q 0.3390 0.2739 0.3871 6 I 0.3164 0.3307 0.3529 7 V 0.1555 0.4837 0.3609 8 T 0.0296 0.8208 0.1496 9 E 0.0108 0.8858 0.1034 10 R 0.0089 0.9160 0.0751 11 L 0.0086 0.9192 0.0722 12 V 0.0084 0.9190 0.0726 13 A 0.0084 0.9135 0.0780 14 L 0.0100 0.8866 0.1034 15 L 0.0145 0.8208 0.1647 16 E 0.0338 0.6452 0.3211 17 S 0.0666 0.2709 0.6625 18 G 0.0571 0.1066 0.8363 19 T 0.1640 0.0898 0.7462 20 E 0.2153 0.1005 0.6842 21 K 0.4541 0.0384 0.5075 22 V 0.7275 0.0073 0.2652 23 L 0.8036 0.0053 0.1911 24 L 0.7918 0.0048 0.2034 25 I 0.7809 0.0093 0.2098 26 D 0.6154 0.0128 0.3717 27 S 0.3643 0.0857 0.5500 28 R 0.3100 0.0382 0.6518 29 P 0.2134 0.1146 0.6720 30 F 0.1157 0.4753 0.4090 31 V 0.0966 0.6282 0.2752 32 E 0.1266 0.5819 0.2915 33 Y 0.1466 0.5371 0.3163 34 N 0.1320 0.4345 0.4336 35 T 0.0856 0.4833 0.4312 36 S 0.1083 0.3966 0.4951 37 H 0.1768 0.2940 0.5292 38 I 0.2035 0.2851 0.5114 39 L 0.1632 0.3358 0.5010 40 E 0.1560 0.2659 0.5781 41 A 0.2995 0.2399 0.4606 42 I 0.4219 0.1509 0.4272 43 N 0.4334 0.0843 0.4823 44 I 0.3567 0.0790 0.5643 45 N 0.2190 0.0585 0.7225 46 C 0.0868 0.3963 0.5169 47 S 0.0259 0.7205 0.2537 48 K 0.0195 0.8229 0.1576 49 L 0.0143 0.8797 0.1060 50 M 0.0143 0.8814 0.1043 51 K 0.0145 0.8746 0.1109 52 R 0.0237 0.8327 0.1435 53 R 0.0325 0.7647 0.2028 54 L 0.0387 0.6872 0.2741 55 Q 0.0540 0.5362 0.4098 56 Q 0.0816 0.4163 0.5021 57 D 0.0871 0.3665 0.5465 58 K 0.0775 0.4918 0.4307 59 V 0.1380 0.5094 0.3526 60 L 0.1659 0.5373 0.2968 61 I 0.1455 0.6152 0.2393 62 T 0.1364 0.6418 0.2218 63 E 0.1493 0.6078 0.2429 64 L 0.1977 0.4850 0.3172 65 I 0.2175 0.3796 0.4029 66 Q 0.1582 0.3806 0.4611 67 H 0.1076 0.4105 0.4819 68 S 0.0823 0.4414 0.4763 69 A 0.0614 0.5568 0.3818 70 K 0.0883 0.5287 0.3830 71 H 0.1428 0.4391 0.4181 72 K 0.2098 0.3120 0.4783 73 V 0.2715 0.2380 0.4905 74 D 0.2606 0.1692 0.5702 75 I 0.2261 0.2387 0.5353 76 D 0.1829 0.1644 0.6527 77 C 0.1598 0.2344 0.6058 78 S 0.2040 0.1148 0.6812 79 Q 0.3462 0.0435 0.6103 80 K 0.5914 0.0151 0.3935 81 V 0.7907 0.0054 0.2039 82 V 0.8099 0.0048 0.1853 83 V 0.8045 0.0055 0.1900 84 Y 0.7560 0.0120 0.2319 85 D 0.5259 0.0228 0.4513 86 Q 0.2166 0.2081 0.5753 87 S 0.1478 0.2016 0.6506 88 S 0.1414 0.2150 0.6436 89 Q 0.1137 0.3646 0.5217 90 D 0.1438 0.3470 0.5092 91 V 0.0936 0.5346 0.3718 92 A 0.0783 0.5771 0.3446 93 S 0.0783 0.5552 0.3665 94 L 0.1052 0.4333 0.4615 95 S 0.0992 0.3633 0.5374 96 S 0.0311 0.6527 0.3162 97 D 0.0222 0.7511 0.2267 98 C 0.0172 0.8543 0.1285 99 F 0.0119 0.8947 0.0935 100 L 0.0100 0.9132 0.0768 101 T 0.0091 0.9203 0.0706 102 V 0.0089 0.9198 0.0712 103 L 0.0091 0.9084 0.0825 104 L 0.0102 0.8817 0.1081 105 G 0.0137 0.8145 0.1718 106 K 0.0243 0.7570 0.2187 107 L 0.0359 0.6875 0.2766 108 E 0.0450 0.5900 0.3650 109 K 0.0672 0.4010 0.5318 110 S 0.1013 0.2235 0.6752 111 F 0.1606 0.1519 0.6875 112 N 0.2060 0.1280 0.6660 113 S 0.3874 0.0727 0.5399 114 V 0.6537 0.0270 0.3194 115 H 0.7548 0.0178 0.2274 116 L 0.7494 0.0221 0.2285 117 L 0.6305 0.0585 0.3110 118 A 0.3519 0.1579 0.4902 119 G 0.1403 0.2014 0.6583 120 G 0.1056 0.2995 0.5949 121 F 0.0420 0.6700 0.2881 122 A 0.0171 0.8549 0.1281 123 E 0.0130 0.8927 0.0944 124 F 0.0127 0.8942 0.0931 125 S 0.0127 0.8750 0.1123 126 R 0.0138 0.7818 0.2044 127 C 0.0368 0.5710 0.3922 128 F 0.1302 0.2166 0.6531 129 P 0.0633 0.4328 0.5040 130 G 0.0584 0.3732 0.5684 131 L 0.1296 0.3744 0.4961 132 C 0.2081 0.2183 0.5736 133 E 0.1621 0.1838 0.6541 134 G 0.1255 0.1110 0.7635 135 K 0.2333 0.0869 0.6798 136 S 0.3198 0.0861 0.5941 137 T 0.3498 0.0700 0.5802 138 L 0.3335 0.0669 0.5995 139 V 0.3152 0.0412 0.6436 140 P 0.2695 0.0846 0.6459 141 T 0.2644 0.1069 0.6287 142 C 0.2433 0.1190 0.6377 143 I 0.2277 0.1463 0.6260 144 S 0.2183 0.1139 0.6678 145 Q 0.2421 0.0537 0.7042 146 P 0.1797 0.0984 0.7219 147 A 0.1519 0.2199 0.6281 148 H 0.1533 0.1896 0.6571 149 H 0.1661 0.1695 0.6643 150 H 0.1684 0.1903 0.6413 151 H 0.1748 0.1719 0.6532 152 H 0.1657 0.1848 0.6495 153 H 0.1705 0.1409 0.6886