# 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 177.873 # # ============================================ # 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 177.873 # # ============================================ # 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 177.873 # # ============================================ # 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 177.873 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.1703 0.0286 0.8011 2 Y 0.2890 0.0367 0.6743 3 T 0.2767 0.0502 0.6730 4 G 0.1495 0.0323 0.8182 5 R 0.1391 0.0173 0.8436 6 P 0.0914 0.0183 0.8903 7 P 0.0590 0.0764 0.8646 8 D 0.0557 0.1026 0.8417 9 E 0.0577 0.2386 0.7037 10 P 0.0689 0.4513 0.4799 11 A 0.1328 0.6013 0.2659 12 V 0.1695 0.6269 0.2036 13 L 0.1205 0.6164 0.2631 14 G 0.0818 0.5827 0.3355 15 V 0.0630 0.7181 0.2189 16 A 0.0564 0.7820 0.1615 17 L 0.0300 0.8114 0.1587 18 N 0.0316 0.8069 0.1615 19 E 0.0163 0.8421 0.1416 20 V 0.0171 0.8337 0.1493 21 F 0.0151 0.8604 0.1245 22 V 0.0075 0.9157 0.0768 23 P 0.0059 0.9389 0.0552 24 I 0.0057 0.9457 0.0486 25 L 0.0066 0.9381 0.0553 26 Q 0.0075 0.8939 0.0986 27 K 0.0079 0.7858 0.2063 28 Q 0.0147 0.5773 0.4080 29 F 0.0538 0.1344 0.8118 30 P 0.0465 0.1614 0.7921 31 E 0.2277 0.1536 0.6187 32 I 0.6505 0.0592 0.2902 33 V 0.7290 0.0612 0.2098 34 D 0.8110 0.0294 0.1596 35 F 0.7928 0.0281 0.1790 36 Y 0.7791 0.0179 0.2029 37 L 0.4788 0.0162 0.5050 38 P 0.1443 0.0169 0.8387 39 P 0.0446 0.4177 0.5378 40 E 0.0297 0.4473 0.5230 41 G 0.0555 0.4462 0.4983 42 C 0.1779 0.2370 0.5851 43 S 0.3204 0.1414 0.5382 44 Y 0.3931 0.1120 0.4949 45 R 0.5618 0.0585 0.3797 46 L 0.8202 0.0225 0.1573 47 A 0.8972 0.0166 0.0863 48 V 0.9127 0.0189 0.0683 49 V 0.8902 0.0329 0.0769 50 T 0.8582 0.0449 0.0969 51 I 0.7272 0.0705 0.2023 52 K 0.5210 0.1043 0.3747 53 K 0.3071 0.2303 0.4626 54 Q 0.1449 0.2542 0.6010 55 Y 0.0825 0.1785 0.7390 56 A 0.0220 0.4713 0.5067 57 G 0.0139 0.6358 0.3503 58 H 0.0080 0.8550 0.1370 59 A 0.0048 0.9424 0.0529 60 K 0.0047 0.9555 0.0398 61 R 0.0047 0.9597 0.0356 62 V 0.0047 0.9602 0.0351 63 M 0.0047 0.9585 0.0368 64 M 0.0047 0.9559 0.0394 65 G 0.0048 0.9461 0.0491 66 V 0.0050 0.9348 0.0602 67 W 0.0057 0.9120 0.0823 68 S 0.0085 0.8342 0.1573 69 F 0.0135 0.7722 0.2143 70 L 0.0313 0.6558 0.3129 71 R 0.0256 0.5437 0.4307 72 Q 0.0386 0.4986 0.4627 73 F 0.1046 0.3496 0.5458 74 M 0.1549 0.1923 0.6528 75 Y 0.2347 0.1265 0.6388 76 T 0.3236 0.0228 0.6537 77 K 0.4098 0.0285 0.5617 78 F 0.9015 0.0042 0.0943 79 V 0.9262 0.0038 0.0700 80 I 0.9317 0.0035 0.0648 81 V 0.9244 0.0034 0.0722 82 C 0.8535 0.0090 0.1375 83 D 0.4566 0.0152 0.5282 84 D 0.0630 0.1060 0.8310 85 D 0.0732 0.0578 0.8689 86 V 0.1910 0.0291 0.7799 87 N 0.2117 0.0148 0.7735 88 A 0.0816 0.1844 0.7340 89 R 0.0777 0.1170 0.8053 90 D 0.1027 0.0383 0.8590 91 W 0.0051 0.9262 0.0687 92 N 0.0049 0.9443 0.0508 93 D 0.0051 0.9502 0.0448 94 V 0.0049 0.9583 0.0367 95 I 0.0056 0.9579 0.0365 96 W 0.0059 0.9572 0.0370 97 A 0.0074 0.9505 0.0421 98 I 0.0088 0.9354 0.0558 99 T 0.0121 0.8772 0.1106 100 T 0.0356 0.7032 0.2612 101 R 0.0686 0.3287 0.6027 102 M 0.1249 0.0885 0.7865 103 D 0.1056 0.0142 0.8801 104 P 0.0132 0.3378 0.6490 105 A 0.0203 0.3103 0.6694 106 R 0.0638 0.2649 0.6713 107 D 0.2020 0.0799 0.7181 108 T 0.6541 0.0450 0.3008 109 V 0.8682 0.0199 0.1119 110 L 0.8804 0.0159 0.1038 111 V 0.7139 0.0163 0.2697 112 E 0.2782 0.0684 0.6534 113 N 0.1023 0.0408 0.8569 114 T 0.1949 0.0195 0.7856 115 P 0.2264 0.0325 0.7412 116 I 0.2389 0.0669 0.6942 117 D 0.2277 0.0665 0.7059 118 Y 0.1615 0.1865 0.6521 119 L 0.2108 0.1237 0.6654 120 D 0.1857 0.0815 0.7328 121 F 0.0586 0.1863 0.7551 122 A 0.0708 0.1357 0.7936 123 S 0.0892 0.0492 0.8616 124 P 0.0620 0.0971 0.8408 125 V 0.1088 0.1325 0.7587 126 S 0.0743 0.1544 0.7712 127 G 0.0698 0.0975 0.8327 128 L 0.1499 0.0949 0.7552 129 G 0.1526 0.0555 0.7919 130 S 0.2348 0.0519 0.7133 131 K 0.4893 0.0564 0.4542 132 M 0.7908 0.0272 0.1819 133 G 0.8724 0.0182 0.1094 134 L 0.8655 0.0195 0.1150 135 D 0.7899 0.0272 0.1829 136 A 0.4568 0.0667 0.4766 137 T 0.2421 0.0903 0.6676 138 N 0.1553 0.0613 0.7834 139 K 0.1184 0.0647 0.8169 140 W 0.0912 0.0392 0.8696 141 P 0.0645 0.1117 0.8238 142 G 0.0504 0.1710 0.7787 143 E 0.1044 0.2522 0.6434 144 T 0.1560 0.2256 0.6184 145 Q 0.2158 0.2120 0.5723 146 R 0.2833 0.1853 0.5315 147 E 0.3122 0.1842 0.5036 148 W 0.2340 0.1488 0.6172 149 G 0.1461 0.0841 0.7698 150 R 0.1549 0.0567 0.7884 151 P 0.2033 0.0831 0.7136 152 I 0.2204 0.1236 0.6560 153 K 0.2081 0.0803 0.7116 154 K 0.1266 0.0521 0.8213 155 D 0.0856 0.0175 0.8969 156 P 0.0053 0.8861 0.1087 157 D 0.0062 0.9046 0.0893 158 V 0.0049 0.9446 0.0505 159 V 0.0052 0.9555 0.0393 160 A 0.0052 0.9510 0.0438 161 H 0.0047 0.9489 0.0464 162 I 0.0048 0.9529 0.0423 163 D 0.0047 0.9531 0.0422 164 A 0.0048 0.9489 0.0463 165 I 0.0049 0.9454 0.0497 166 W 0.0058 0.9381 0.0561 167 D 0.0056 0.9207 0.0737 168 E 0.0068 0.8806 0.1126 169 L 0.0382 0.6260 0.3358 170 A 0.0327 0.1839 0.7834 171 I 0.0659 0.2064 0.7277 172 F 0.0733 0.2494 0.6774 173 N 0.0531 0.2632 0.6838 174 N 0.0621 0.2121 0.7259 175 G 0.0567 0.1107 0.8327 176 K 0.0679 0.2896 0.6425 177 S 0.1067 0.4452 0.4481 178 A 0.1457 0.5676 0.2868 179 L 0.2159 0.5294 0.2547 180 E 0.2441 0.4800 0.2759 181 H 0.1937 0.3970 0.4093 182 H 0.1461 0.3080 0.5458 183 H 0.1581 0.2329 0.6089 184 H 0.1851 0.1972 0.6177 185 H 0.1344 0.1267 0.7390 186 H 0.0619 0.0312 0.9069