# This file is the result of combining several RDB files, specifically # T0356.t04.dssp-ebghstl.rdb (weight 1.53986) # T0356.t04.stride-ebghtl.rdb (weight 1.24869) # T0356.t04.str2.rdb (weight 1.54758) # T0356.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 T0356.t04.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.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 214.113 # # ============================================ # Comments from T0356.t04.stride-ebghtl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 214.113 # # ============================================ # Comments from T0356.t04.str2.rdb # ============================================ # TARGET T0356 # 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 T0356.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 214.113 # # ============================================ # Comments from T0356.t04.alpha.rdb # ============================================ # TARGET T0356 # 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 T0356.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 214.113 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.2333 0.0287 0.7380 2 Y 0.3521 0.0400 0.6079 3 T 0.3592 0.0424 0.5985 4 G 0.1864 0.0342 0.7795 5 R 0.1415 0.0172 0.8414 6 P 0.0840 0.0173 0.8987 7 P 0.0457 0.0865 0.8678 8 D 0.0479 0.1045 0.8476 9 E 0.0504 0.3177 0.6319 10 P 0.0436 0.4842 0.4722 11 A 0.1003 0.6472 0.2525 12 V 0.1338 0.6726 0.1936 13 L 0.0877 0.6784 0.2339 14 G 0.0609 0.6479 0.2912 15 V 0.0464 0.7847 0.1689 16 A 0.0362 0.8432 0.1206 17 L 0.0236 0.8539 0.1225 18 N 0.0240 0.8422 0.1337 19 E 0.0145 0.8651 0.1203 20 V 0.0126 0.8658 0.1216 21 F 0.0109 0.8794 0.1098 22 V 0.0061 0.9284 0.0655 23 P 0.0049 0.9423 0.0529 24 I 0.0050 0.9475 0.0475 25 L 0.0051 0.9405 0.0545 26 Q 0.0066 0.9065 0.0869 27 K 0.0074 0.8154 0.1772 28 Q 0.0175 0.6237 0.3587 29 F 0.0516 0.1394 0.8090 30 P 0.0353 0.1825 0.7822 31 E 0.1442 0.1647 0.6911 32 I 0.6279 0.0634 0.3087 33 V 0.7144 0.0716 0.2141 34 D 0.8075 0.0311 0.1614 35 F 0.7803 0.0293 0.1905 36 Y 0.7352 0.0214 0.2434 37 L 0.3862 0.0167 0.5971 38 P 0.1295 0.0186 0.8519 39 P 0.0342 0.4140 0.5518 40 E 0.0302 0.4071 0.5627 41 G 0.0530 0.4222 0.5249 42 C 0.1651 0.2147 0.6202 43 S 0.2372 0.1413 0.6215 44 Y 0.3476 0.1030 0.5494 45 R 0.4549 0.0600 0.4850 46 L 0.8095 0.0175 0.1730 47 A 0.9042 0.0062 0.0896 48 V 0.9277 0.0050 0.0672 49 V 0.9132 0.0089 0.0779 50 T 0.8989 0.0097 0.0913 51 I 0.8164 0.0313 0.1522 52 K 0.6748 0.0573 0.2679 53 K 0.4884 0.1235 0.3881 54 Q 0.2386 0.1553 0.6060 55 Y 0.1035 0.1296 0.7669 56 A 0.0275 0.4487 0.5238 57 G 0.0156 0.6903 0.2942 58 H 0.0093 0.8720 0.1188 59 A 0.0051 0.9443 0.0507 60 K 0.0047 0.9580 0.0373 61 R 0.0047 0.9607 0.0346 62 V 0.0047 0.9595 0.0358 63 M 0.0047 0.9586 0.0367 64 M 0.0047 0.9574 0.0379 65 G 0.0047 0.9507 0.0445 66 V 0.0049 0.9424 0.0527 67 W 0.0054 0.9286 0.0660 68 S 0.0074 0.8533 0.1393 69 F 0.0118 0.7864 0.2018 70 L 0.0251 0.6577 0.3171 71 R 0.0236 0.5853 0.3911 72 Q 0.0311 0.5640 0.4049 73 F 0.0782 0.3749 0.5469 74 M 0.1196 0.2103 0.6701 75 Y 0.1965 0.1403 0.6631 76 T 0.2891 0.0280 0.6829 77 K 0.4901 0.0176 0.4923 78 F 0.9010 0.0039 0.0951 79 V 0.9283 0.0032 0.0684 80 I 0.9322 0.0033 0.0645 81 V 0.9275 0.0034 0.0691 82 C 0.8624 0.0088 0.1288 83 D 0.4294 0.0154 0.5553 84 D 0.0584 0.1100 0.8315 85 D 0.0669 0.0658 0.8673 86 V 0.1309 0.0352 0.8339 87 N 0.1389 0.0223 0.8387 88 A 0.0724 0.2347 0.6929 89 R 0.0989 0.1403 0.7608 90 D 0.1001 0.0788 0.8211 91 W 0.0050 0.9402 0.0548 92 N 0.0049 0.9532 0.0419 93 D 0.0049 0.9546 0.0405 94 V 0.0047 0.9585 0.0368 95 I 0.0047 0.9591 0.0362 96 W 0.0047 0.9603 0.0351 97 A 0.0052 0.9574 0.0374 98 I 0.0062 0.9449 0.0489 99 T 0.0093 0.8898 0.1009 100 T 0.0252 0.7462 0.2285 101 R 0.0496 0.3868 0.5636 102 M 0.1037 0.1175 0.7788 103 D 0.1098 0.0186 0.8716 104 P 0.0176 0.3857 0.5968 105 A 0.0204 0.3503 0.6292 106 R 0.0666 0.2654 0.6680 107 D 0.2475 0.0597 0.6928 108 T 0.6824 0.0381 0.2794 109 V 0.8859 0.0157 0.0984 110 L 0.8857 0.0178 0.0966 111 V 0.7517 0.0190 0.2293 112 E 0.3032 0.0703 0.6265 113 N 0.0933 0.0366 0.8701 114 T 0.1949 0.0198 0.7853 115 P 0.2662 0.0332 0.7006 116 I 0.2415 0.0800 0.6785 117 D 0.1914 0.0734 0.7352 118 Y 0.1641 0.1643 0.6717 119 L 0.1875 0.1267 0.6859 120 D 0.1892 0.0972 0.7136 121 F 0.0718 0.1855 0.7427 122 A 0.0880 0.1404 0.7716 123 S 0.0879 0.0595 0.8526 124 P 0.0715 0.1112 0.8173 125 V 0.1029 0.1246 0.7725 126 S 0.0659 0.1338 0.8003 127 G 0.0603 0.1087 0.8310 128 L 0.1320 0.1011 0.7669 129 G 0.1275 0.0669 0.8056 130 S 0.1986 0.0629 0.7384 131 K 0.4413 0.0665 0.4922 132 M 0.7142 0.0390 0.2468 133 G 0.8633 0.0234 0.1133 134 L 0.8600 0.0274 0.1126 135 D 0.7828 0.0317 0.1855 136 A 0.4467 0.0603 0.4931 137 T 0.2223 0.0881 0.6896 138 N 0.1245 0.0515 0.8240 139 K 0.0976 0.0551 0.8473 140 W 0.0916 0.0367 0.8717 141 P 0.0518 0.1168 0.8313 142 G 0.0418 0.1434 0.8148 143 E 0.1011 0.1994 0.6995 144 T 0.1438 0.1514 0.7049 145 Q 0.1813 0.1576 0.6611 146 R 0.2462 0.1407 0.6130 147 E 0.3016 0.1422 0.5562 148 W 0.2217 0.1145 0.6638 149 G 0.1366 0.0696 0.7937 150 R 0.1718 0.0358 0.7925 151 P 0.2506 0.0596 0.6897 152 I 0.2652 0.1472 0.5875 153 K 0.2355 0.1119 0.6527 154 K 0.1243 0.0581 0.8176 155 D 0.0862 0.0227 0.8911 156 P 0.0056 0.8481 0.1463 157 D 0.0070 0.8851 0.1080 158 V 0.0059 0.9327 0.0614 159 V 0.0068 0.9392 0.0540 160 A 0.0098 0.9254 0.0648 161 H 0.0068 0.9332 0.0600 162 I 0.0058 0.9496 0.0446 163 D 0.0052 0.9504 0.0444 164 A 0.0050 0.9504 0.0445 165 I 0.0051 0.9492 0.0457 166 W 0.0048 0.9487 0.0464 167 D 0.0050 0.9351 0.0599 168 E 0.0057 0.9032 0.0911 169 L 0.0199 0.7399 0.2402 170 A 0.0299 0.3564 0.6137 171 I 0.0715 0.3176 0.6109 172 F 0.0981 0.2695 0.6323 173 N 0.0636 0.2404 0.6960 174 N 0.0569 0.1747 0.7684 175 G 0.0515 0.1095 0.8390 176 K 0.0668 0.0565 0.8767 177 S 0.0609 0.0264 0.9127