# This file is the result of combining several RDB files, specifically # T0345.t06.dssp-ebghstl.rdb (weight 1.53986) # T0345.t06.stride-ebghtl.rdb (weight 1.24869) # T0345.t06.str2.rdb (weight 1.54758) # T0345.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 T0345.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0345 # 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 T0345.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 42.6718 # # ============================================ # Comments from T0345.t06.stride-ebghtl.rdb # ============================================ # TARGET T0345 # 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 T0345.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 42.6718 # # ============================================ # Comments from T0345.t06.str2.rdb # ============================================ # TARGET T0345 # 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 T0345.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 42.6718 # # ============================================ # Comments from T0345.t06.alpha.rdb # ============================================ # TARGET T0345 # 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 T0345.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 42.6718 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0684 0.1471 0.7845 2 I 0.1079 0.1791 0.7129 3 A 0.1316 0.1475 0.7209 4 K 0.1217 0.1555 0.7228 5 S 0.1981 0.1239 0.6780 6 F 0.2565 0.1979 0.5456 7 Y 0.3854 0.1177 0.4969 8 D 0.4517 0.0516 0.4967 9 L 0.4918 0.0287 0.4795 10 S 0.6471 0.0221 0.3308 11 A 0.7684 0.0267 0.2049 12 I 0.7683 0.0213 0.2103 13 N 0.5403 0.0176 0.4421 14 L 0.1591 0.0928 0.7481 15 D 0.0641 0.0261 0.9098 16 G 0.0362 0.0348 0.9290 17 E 0.2468 0.0236 0.7295 18 K 0.7309 0.0088 0.2603 19 V 0.7048 0.0080 0.2872 20 D 0.5697 0.0076 0.4227 21 F 0.0558 0.7231 0.2211 22 N 0.0285 0.7957 0.1757 23 T 0.0397 0.7742 0.1861 24 F 0.1193 0.4191 0.4616 25 R 0.0684 0.1390 0.7926 26 G 0.0344 0.0480 0.9176 27 R 0.3201 0.0164 0.6635 28 A 0.7896 0.0043 0.2061 29 V 0.9167 0.0046 0.0786 30 L 0.9283 0.0038 0.0679 31 I 0.9264 0.0055 0.0681 32 E 0.8728 0.0262 0.1010 33 N 0.6827 0.0341 0.2832 34 V 0.3915 0.1108 0.4977 35 A 0.2781 0.1997 0.5222 36 S 0.1822 0.2660 0.5518 37 L 0.1313 0.2609 0.6078 38 C 0.1236 0.1566 0.7198 39 G 0.0753 0.1234 0.8013 40 T 0.0938 0.1293 0.7769 41 T 0.1009 0.1209 0.7782 42 T 0.0443 0.2926 0.6631 43 R 0.0336 0.3555 0.6109 44 D 0.0407 0.3256 0.6337 45 F 0.0086 0.8706 0.1208 46 T 0.0051 0.9187 0.0762 47 Q 0.0051 0.9281 0.0668 48 L 0.0048 0.9469 0.0483 49 N 0.0048 0.9538 0.0415 50 E 0.0048 0.9445 0.0506 51 L 0.0051 0.9291 0.0658 52 Q 0.0072 0.9002 0.0926 53 C 0.0106 0.8243 0.1651 54 R 0.0210 0.6576 0.3214 55 F 0.0758 0.0775 0.8467 56 P 0.0277 0.1515 0.8208 57 R 0.0392 0.1809 0.7799 58 R 0.1928 0.0814 0.7258 59 L 0.7806 0.0060 0.2134 60 V 0.9098 0.0041 0.0861 61 V 0.9301 0.0030 0.0669 62 L 0.8772 0.0282 0.0946 63 G 0.8507 0.0063 0.1431 64 F 0.4483 0.0124 0.5393 65 P 0.2140 0.0207 0.7653 66 C 0.0896 0.2124 0.6979 67 N 0.0518 0.3284 0.6198 68 Q 0.0594 0.3803 0.5603 69 F 0.0835 0.3059 0.6106 70 G 0.0620 0.2193 0.7187 71 H 0.0815 0.1771 0.7415 72 Q 0.1465 0.1459 0.7076 73 E 0.1272 0.0950 0.7778 74 N 0.0833 0.0896 0.8271 75 C 0.0639 0.0717 0.8644 76 Q 0.0667 0.0909 0.8423 77 N 0.0157 0.8153 0.1690 78 E 0.0051 0.9425 0.0524 79 E 0.0056 0.9456 0.0488 80 I 0.0082 0.9384 0.0535 81 L 0.0152 0.9167 0.0682 82 N 0.0333 0.8481 0.1186 83 S 0.0564 0.7638 0.1798 84 L 0.1715 0.6341 0.1944 85 K 0.2524 0.5626 0.1850 86 Y 0.3544 0.4063 0.2393 87 V 0.3539 0.2181 0.4279 88 R 0.1880 0.0471 0.7650 89 P 0.0690 0.1049 0.8261 90 G 0.0614 0.0722 0.8664 91 G 0.0690 0.0634 0.8677 92 G 0.0923 0.0549 0.8528 93 Y 0.3141 0.0340 0.6519 94 Q 0.2943 0.0281 0.6776 95 P 0.3649 0.0302 0.6049 96 T 0.4556 0.0353 0.5091 97 F 0.4946 0.0380 0.4674 98 T 0.4637 0.0418 0.4945 99 L 0.5609 0.0819 0.3572 100 V 0.5923 0.0771 0.3307 101 Q 0.6719 0.0477 0.2805 102 K 0.7690 0.0354 0.1955 103 C 0.7608 0.0213 0.2179 104 E 0.7729 0.0183 0.2088 105 V 0.6051 0.0330 0.3619 106 N 0.2774 0.0579 0.6646 107 G 0.1038 0.0377 0.8584 108 Q 0.0399 0.1710 0.7891 109 N 0.0467 0.1749 0.7783 110 E 0.0529 0.2438 0.7033 111 H 0.0527 0.3340 0.6133 112 P 0.0229 0.8229 0.1542 113 V 0.0126 0.9231 0.0643 114 F 0.0095 0.9416 0.0489 115 A 0.0073 0.9480 0.0446 116 Y 0.0054 0.9460 0.0485 117 L 0.0067 0.9264 0.0668 118 K 0.0098 0.8988 0.0914 119 D 0.0117 0.7839 0.2044 120 K 0.0261 0.5137 0.4601 121 L 0.0770 0.0454 0.8776 122 P 0.0576 0.0612 0.8812 123 Y 0.0925 0.0404 0.8671 124 P 0.1032 0.0757 0.8211 125 Y 0.1004 0.0846 0.8150 126 D 0.0771 0.0735 0.8494 127 D 0.0834 0.0594 0.8573 128 P 0.0794 0.1891 0.7315 129 F 0.1325 0.2385 0.6290 130 S 0.1880 0.2441 0.5679 131 L 0.2579 0.2530 0.4891 132 M 0.2792 0.1730 0.5478 133 T 0.2180 0.1201 0.6618 134 D 0.1501 0.0581 0.7918 135 P 0.0571 0.3724 0.5704 136 K 0.0921 0.4221 0.4858 137 L 0.2237 0.4105 0.3659 138 I 0.3922 0.2629 0.3449 139 I 0.4642 0.1796 0.3562 140 W 0.3608 0.1525 0.4867 141 S 0.2134 0.0909 0.6957 142 P 0.1312 0.1729 0.6959 143 V 0.2130 0.1700 0.6171 144 R 0.2537 0.1417 0.6045 145 R 0.1411 0.2323 0.6267 146 S 0.1051 0.1864 0.7086 147 D 0.2022 0.1573 0.6405 148 V 0.4044 0.1449 0.4507 149 A 0.4781 0.1322 0.3897 150 W 0.6227 0.1211 0.2562 151 N 0.6336 0.0662 0.3002 152 F 0.6592 0.0668 0.2741 153 E 0.6834 0.0820 0.2346 154 K 0.7585 0.0778 0.1636 155 F 0.8136 0.0519 0.1344 156 L 0.8533 0.0275 0.1191 157 I 0.8088 0.0199 0.1714 158 G 0.1510 0.0154 0.8336 159 P 0.0130 0.1074 0.8796 160 E 0.0417 0.0298 0.9285 161 G 0.0652 0.0328 0.9020 162 E 0.2985 0.0153 0.6862 163 P 0.8302 0.0073 0.1626 164 F 0.7952 0.0281 0.1767 165 R 0.7872 0.0325 0.1803 166 R 0.7385 0.0474 0.2142 167 Y 0.5616 0.0503 0.3880 168 S 0.2825 0.0558 0.6618 169 R 0.0959 0.1044 0.7997 170 T 0.1011 0.0822 0.8167 171 F 0.1210 0.0256 0.8534 172 P 0.1096 0.0240 0.8664 173 T 0.0644 0.4465 0.4891 174 I 0.0267 0.6415 0.3318 175 N 0.0548 0.6155 0.3297 176 I 0.0353 0.6817 0.2830 177 E 0.0101 0.8207 0.1693 178 P 0.0064 0.9288 0.0648 179 D 0.0074 0.9323 0.0603 180 I 0.0052 0.9453 0.0495 181 K 0.0048 0.9482 0.0470 182 R 0.0051 0.9299 0.0650 183 L 0.0063 0.8435 0.1501 184 L 0.0170 0.6520 0.3310 185 K 0.0155 0.1302 0.8543