# This file is the result of combining several RDB files, specifically # T0234.t04.dssp-ebghstl.rdb (weight 1.53986) # T0234.t04.stride-ebghtl.rdb (weight 1.24869) # T0234.t04.str2.rdb (weight 1.54758) # T0234.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 T0234.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0234 # 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 T0234.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 364 # # ============================================ # Comments from T0234.t04.stride-ebghtl.rdb # ============================================ # TARGET T0234 # 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 T0234.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 364 # # ============================================ # Comments from T0234.t04.str2.rdb # ============================================ # TARGET T0234 # 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 T0234.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 364 # # ============================================ # Comments from T0234.t04.alpha.rdb # ============================================ # TARGET T0234 # 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 T0234.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 364 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0432 0.0907 0.8661 2 S 0.0428 0.2326 0.7246 3 Q 0.0364 0.4535 0.5101 4 L 0.0263 0.6211 0.3526 5 E 0.0255 0.6835 0.2910 6 K 0.0349 0.5726 0.3925 7 A 0.0272 0.5729 0.3999 8 Q 0.0067 0.9231 0.0702 9 A 0.0048 0.9537 0.0415 10 E 0.0048 0.9542 0.0410 11 Y 0.0051 0.9523 0.0426 12 A 0.0048 0.9531 0.0421 13 G 0.0049 0.9358 0.0594 14 F 0.0054 0.9199 0.0747 15 I 0.0059 0.8985 0.0957 16 Q 0.0067 0.8264 0.1669 17 E 0.0146 0.4749 0.5105 18 F 0.0716 0.1489 0.7795 19 Q 0.0926 0.1019 0.8056 20 S 0.7598 0.0394 0.2008 21 A 0.9067 0.0084 0.0849 22 I 0.9247 0.0061 0.0692 23 I 0.9085 0.0080 0.0835 24 S 0.8382 0.0100 0.1517 25 T 0.7514 0.0084 0.2402 26 I 0.6677 0.0163 0.3160 27 S 0.2241 0.0190 0.7569 28 E 0.0237 0.1307 0.8456 29 Q 0.0433 0.0397 0.9170 30 G 0.0471 0.0384 0.9145 31 I 0.1515 0.0118 0.8367 32 P 0.5015 0.0221 0.4764 33 N 0.5035 0.0394 0.4571 34 G 0.5814 0.0350 0.3836 35 S 0.6159 0.0188 0.3653 36 Y 0.6542 0.0169 0.3289 37 A 0.6126 0.0138 0.3736 38 P 0.6691 0.0187 0.3122 39 F 0.7328 0.0181 0.2492 40 V 0.8684 0.0069 0.1247 41 I 0.8464 0.0093 0.1443 42 D 0.5304 0.0236 0.4459 43 D 0.1352 0.0789 0.7859 44 A 0.0514 0.0714 0.8772 45 K 0.0747 0.0476 0.8777 46 N 0.4331 0.0120 0.5549 47 I 0.8711 0.0035 0.1254 48 Y 0.9268 0.0035 0.0697 49 I 0.9282 0.0035 0.0683 50 Y 0.9110 0.0056 0.0834 51 V 0.7754 0.0135 0.2111 52 S 0.2955 0.0468 0.6578 53 G 0.0801 0.1437 0.7762 54 L 0.0747 0.2828 0.6424 55 A 0.0862 0.4416 0.4722 56 V 0.0965 0.6272 0.2764 57 H 0.1067 0.7234 0.1699 58 T 0.0718 0.8040 0.1242 59 K 0.0270 0.8680 0.1050 60 N 0.0504 0.8186 0.1310 61 I 0.0356 0.8306 0.1338 62 E 0.0308 0.7319 0.2373 63 A 0.0462 0.4843 0.4696 64 N 0.1051 0.0227 0.8722 65 P 0.0389 0.1183 0.8428 66 L 0.1246 0.0870 0.7884 67 V 0.6249 0.0175 0.3576 68 N 0.8591 0.0047 0.1362 69 V 0.9220 0.0033 0.0747 70 L 0.9224 0.0036 0.0739 71 F 0.9082 0.0051 0.0867 72 V 0.7453 0.0088 0.2459 73 D 0.3757 0.0200 0.6044 74 D 0.0976 0.1236 0.7788 75 E 0.0511 0.2438 0.7051 76 A 0.0726 0.2571 0.6703 77 K 0.0805 0.2558 0.6637 78 T 0.0977 0.2878 0.6145 79 N 0.1225 0.2844 0.5931 80 Q 0.1709 0.3288 0.5003 81 I 0.2434 0.3812 0.3754 82 F 0.3046 0.2982 0.3971 83 A 0.3794 0.2213 0.3993 84 R 0.4127 0.1241 0.4632 85 R 0.4801 0.0441 0.4758 86 R 0.8036 0.0099 0.1864 87 L 0.9016 0.0036 0.0947 88 S 0.9204 0.0040 0.0756 89 F 0.9128 0.0042 0.0829 90 D 0.8680 0.0207 0.1114 91 C 0.8853 0.0052 0.1094 92 T 0.9038 0.0036 0.0925 93 A 0.8971 0.0037 0.0992 94 T 0.8866 0.0051 0.1083 95 L 0.8779 0.0038 0.1183 96 I 0.5859 0.0163 0.3979 97 E 0.2714 0.0209 0.7076 98 R 0.0542 0.2404 0.7054 99 E 0.0223 0.6106 0.3670 100 S 0.0119 0.7945 0.1936 101 Q 0.0109 0.8668 0.1223 102 K 0.0102 0.8782 0.1116 103 W 0.0059 0.9298 0.0643 104 N 0.0055 0.9357 0.0588 105 Q 0.0053 0.9368 0.0579 106 V 0.0052 0.9395 0.0553 107 V 0.0051 0.9514 0.0435 108 D 0.0047 0.9568 0.0384 109 Q 0.0048 0.9579 0.0373 110 F 0.0049 0.9504 0.0447 111 Q 0.0050 0.9433 0.0517 112 E 0.0060 0.9173 0.0766 113 R 0.0101 0.8520 0.1380 114 F 0.0415 0.6654 0.2930 115 G 0.0143 0.7178 0.2679 116 Q 0.0192 0.7927 0.1881 117 I 0.0176 0.8694 0.1130 118 I 0.0202 0.8808 0.0990 119 E 0.0249 0.8566 0.1185 120 V 0.0338 0.8084 0.1578 121 L 0.0604 0.6670 0.2726 122 R 0.0554 0.4626 0.4820 123 G 0.0508 0.2757 0.6735 124 L 0.0863 0.1367 0.7770 125 A 0.0690 0.1615 0.7696 126 D 0.1096 0.0990 0.7914 127 F 0.4128 0.0281 0.5592 128 R 0.7194 0.0065 0.2741 129 I 0.9146 0.0032 0.0821 130 F 0.9155 0.0042 0.0803 131 Q 0.9227 0.0036 0.0737 132 L 0.8905 0.0045 0.1050 133 T 0.7263 0.0066 0.2671 134 P 0.5487 0.0530 0.3983 135 K 0.4191 0.1184 0.4625 136 E 0.6827 0.0817 0.2357 137 G 0.8330 0.0156 0.1514 138 R 0.8736 0.0131 0.1133 139 F 0.8808 0.0095 0.1097 140 V 0.7851 0.0154 0.1995 141 I 0.5577 0.0437 0.3986 142 G 0.2909 0.0394 0.6697 143 F 0.2652 0.0586 0.6762 144 G 0.2401 0.0533 0.7066 145 A 0.3172 0.0603 0.6225 146 A 0.4085 0.0783 0.5132 147 Y 0.4810 0.0689 0.4501 148 H 0.4965 0.0358 0.4677 149 I 0.3938 0.0226 0.5836 150 S 0.2062 0.0255 0.7683 151 G 0.0302 0.5791 0.3906 152 D 0.0293 0.6148 0.3559 153 R 0.0438 0.6674 0.2888 154 L 0.1139 0.5192 0.3670 155 D 0.1534 0.4299 0.4167 156 T 0.2758 0.3110 0.4132 157 L 0.3679 0.1420 0.4901 158 V 0.3960 0.0634 0.5406 159 P 0.3529 0.0834 0.5637 160 I 0.3146 0.1288 0.5566 161 T 0.2920 0.1459 0.5621 162 G 0.1641 0.1086 0.7274 163 D 0.1243 0.0906 0.7851 164 K 0.1036 0.0835 0.8129 165 G 0.0560 0.0396 0.9045