# This file is the result of combining several RDB files, specifically # T0356.t06.dssp-ebghstl.rdb (weight 1.53986) # T0356.t06.stride-ebghtl.rdb (weight 1.24869) # T0356.t06.str2.rdb (weight 1.54758) # T0356.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 T0356.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.1135 # # ============================================ # Comments from T0356.t06.stride-ebghtl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.1135 # # ============================================ # Comments from T0356.t06.str2.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.1135 # # ============================================ # Comments from T0356.t06.alpha.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.1135 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.1092 0.0339 0.8569 2 W 0.1915 0.0613 0.7472 3 G 0.3691 0.0411 0.5899 4 L 0.7736 0.0165 0.2099 5 T 0.8678 0.0109 0.1213 6 V 0.8801 0.0104 0.1094 7 T 0.8157 0.0129 0.1714 8 R 0.6311 0.0220 0.3469 9 G 0.2384 0.0130 0.7485 10 P 0.0470 0.1043 0.8487 11 H 0.0461 0.1025 0.8515 12 K 0.0640 0.1272 0.8088 13 E 0.0861 0.0929 0.8211 14 R 0.3540 0.0679 0.5781 15 Q 0.5370 0.0766 0.3864 16 N 0.5556 0.0825 0.3619 17 L 0.4767 0.1518 0.3716 18 G 0.6087 0.1406 0.2507 19 I 0.6764 0.1541 0.1694 20 Y 0.6817 0.1561 0.1622 21 R 0.6392 0.1838 0.1770 22 Q 0.6549 0.1977 0.1473 23 Q 0.6606 0.2110 0.1285 24 L 0.6582 0.1816 0.1602 25 I 0.4569 0.1962 0.3468 26 G 0.2176 0.0414 0.7410 27 K 0.0344 0.0861 0.8795 28 N 0.0973 0.0548 0.8479 29 K 0.7708 0.0194 0.2098 30 L 0.9006 0.0051 0.0944 31 I 0.9234 0.0048 0.0717 32 M 0.9208 0.0044 0.0748 33 R 0.8998 0.0060 0.0941 34 W 0.8751 0.0086 0.1163 35 L 0.6902 0.0232 0.2866 36 S 0.3824 0.0677 0.5499 37 H 0.1454 0.1395 0.7150 38 R 0.0870 0.1643 0.7487 39 G 0.0613 0.1478 0.7910 40 G 0.1052 0.2862 0.6086 41 A 0.1328 0.5595 0.3077 42 L 0.0957 0.7063 0.1980 43 D 0.0880 0.7387 0.1733 44 Y 0.0160 0.9168 0.0672 45 Q 0.0095 0.9423 0.0482 46 E 0.0108 0.9416 0.0476 47 W 0.0091 0.9370 0.0539 48 C 0.0142 0.9092 0.0766 49 A 0.0180 0.8324 0.1496 50 A 0.0294 0.6768 0.2939 51 H 0.0574 0.0772 0.8654 52 P 0.0202 0.0963 0.8836 53 G 0.0168 0.0463 0.9369 54 E 0.1199 0.0380 0.8421 55 R 0.2302 0.0136 0.7562 56 F 0.3740 0.0079 0.6181 57 P 0.4419 0.0054 0.5527 58 V 0.8918 0.0048 0.1033 59 S 0.9236 0.0040 0.0725 60 V 0.9291 0.0046 0.0663 61 A 0.9045 0.0084 0.0871 62 L 0.6908 0.0313 0.2779 63 G 0.2209 0.0258 0.7533 64 A 0.0905 0.0227 0.8869 65 D 0.1084 0.0230 0.8685 66 P 0.0075 0.8817 0.1107 67 A 0.0097 0.9186 0.0718 68 T 0.0217 0.9122 0.0662 69 I 0.0538 0.8860 0.0602 70 L 0.0577 0.8625 0.0798 71 G 0.0665 0.7957 0.1378 72 A 0.0935 0.6806 0.2259 73 V 0.1205 0.4834 0.3961 74 T 0.1332 0.0849 0.7819 75 P 0.1339 0.0449 0.8212 76 V 0.1156 0.0222 0.8622 77 P 0.0692 0.0512 0.8796 78 D 0.0288 0.1391 0.8321 79 T 0.0524 0.1266 0.8210 80 L 0.0923 0.1110 0.7967 81 S 0.0878 0.1547 0.7575 82 E 0.0214 0.8971 0.0815 83 Y 0.0239 0.9128 0.0634 84 A 0.0267 0.9129 0.0603 85 F 0.0252 0.9156 0.0592 86 A 0.0179 0.9170 0.0651 87 G 0.0267 0.8915 0.0819 88 L 0.0292 0.8673 0.1035 89 L 0.0392 0.7869 0.1739 90 R 0.0590 0.3065 0.6344 91 G 0.0276 0.0564 0.9160 92 T 0.0984 0.0266 0.8750 93 K 0.2135 0.0205 0.7660 94 T 0.4948 0.0121 0.4932 95 E 0.7699 0.0081 0.2219 96 V 0.8727 0.0076 0.1197 97 V 0.8460 0.0141 0.1399 98 K 0.7906 0.0114 0.1980 99 C 0.5817 0.0182 0.4001 100 I 0.4351 0.0549 0.5100 101 S 0.3084 0.0737 0.6179 102 N 0.1839 0.0609 0.7552 103 D 0.1598 0.0505 0.7896 104 L 0.2633 0.0320 0.7047 105 E 0.3605 0.0307 0.6088 106 V 0.3083 0.0209 0.6709 107 P 0.1577 0.0258 0.8165 108 A 0.1095 0.2150 0.6755 109 S 0.1450 0.1478 0.7072 110 A 0.3381 0.1281 0.5339 111 E 0.6124 0.0526 0.3349 112 I 0.8936 0.0138 0.0926 113 V 0.9157 0.0075 0.0768 114 L 0.9087 0.0069 0.0845 115 E 0.8702 0.0182 0.1115 116 G 0.8580 0.0088 0.1332 117 Y 0.8897 0.0079 0.1024 118 I 0.7701 0.0081 0.2219 119 E 0.2860 0.0147 0.6993 120 Q 0.0299 0.1061 0.8639 121 G 0.0280 0.0826 0.8894 122 E 0.1937 0.0785 0.7279 123 T 0.4799 0.0263 0.4938 124 A 0.2422 0.0238 0.7340 125 P 0.1520 0.0401 0.8078 126 E 0.1730 0.0501 0.7769 127 G 0.1222 0.0217 0.8561 128 P 0.1281 0.0467 0.8252 129 Y 0.2026 0.0688 0.7286 130 G 0.2657 0.0630 0.6712 131 D 0.3072 0.0794 0.6134 132 H 0.4332 0.0777 0.4891 133 T 0.4482 0.0769 0.4749 134 G 0.5131 0.0556 0.4313 135 Y 0.6740 0.0388 0.2871 136 Y 0.6475 0.0427 0.3099 137 N 0.3938 0.0326 0.5736 138 E 0.2098 0.1075 0.6827 139 V 0.1689 0.1528 0.6783 140 D 0.1459 0.1017 0.7523 141 S 0.1366 0.0863 0.7771 142 F 0.2469 0.0180 0.7351 143 P 0.3358 0.0138 0.6504 144 V 0.8046 0.0111 0.1843 145 F 0.9100 0.0041 0.0859 146 T 0.9155 0.0038 0.0808 147 V 0.8801 0.0041 0.1158 148 T 0.7938 0.0301 0.1762 149 H 0.8399 0.0100 0.1501 150 I 0.8310 0.0111 0.1579 151 T 0.8153 0.0170 0.1677 152 Q 0.6642 0.0270 0.3089 153 R 0.3132 0.0601 0.6268 154 E 0.1442 0.0983 0.7574 155 D 0.1605 0.0631 0.7764 156 A 0.1742 0.1425 0.6833 157 I 0.3563 0.1363 0.5074 158 Y 0.4656 0.1081 0.4263 159 H 0.4339 0.1348 0.4313 160 S 0.4873 0.1278 0.3849 161 T 0.5292 0.0999 0.3708 162 Y 0.4279 0.0772 0.4950 163 T 0.2705 0.0623 0.6671 164 G 0.1134 0.0394 0.8472 165 R 0.1103 0.0186 0.8711 166 P 0.0842 0.0205 0.8953 167 P 0.0505 0.0954 0.8541 168 D 0.0453 0.1371 0.8177 169 E 0.0493 0.2910 0.6598 170 P 0.0488 0.5309 0.4203 171 A 0.1005 0.6908 0.2086 172 V 0.1275 0.7339 0.1385 173 L 0.0869 0.7850 0.1282 174 G 0.0856 0.7569 0.1575 175 V 0.1012 0.7523 0.1465 176 A 0.0827 0.7681 0.1492 177 L 0.0548 0.8017 0.1435 178 N 0.0673 0.7296 0.2032 179 E 0.0769 0.6393 0.2838 180 V 0.0879 0.4401 0.4720 181 F 0.0486 0.0945 0.8568