# This file is the result of combining several RDB files, specifically # T0389.t04.dssp-ebghstl.rdb (weight 1.53986) # T0389.t04.stride-ebghtl.rdb (weight 1.24869) # T0389.t04.str2.rdb (weight 1.54758) # T0389.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 T0389.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0389 # 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 T0389.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 2363 # # ============================================ # Comments from T0389.t04.stride-ebghtl.rdb # ============================================ # TARGET T0389 # 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 T0389.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 2363 # # ============================================ # Comments from T0389.t04.str2.rdb # ============================================ # TARGET T0389 # 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 T0389.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 2363 # # ============================================ # Comments from T0389.t04.alpha.rdb # ============================================ # TARGET T0389 # 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 T0389.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 2363 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0720 0.0281 0.8999 2 I 0.1084 0.0607 0.8309 3 G 0.1345 0.0502 0.8153 4 T 0.2514 0.0485 0.7001 5 Q 0.5991 0.0183 0.3826 6 I 0.5730 0.0085 0.4185 7 V 0.2067 0.0102 0.7831 8 T 0.0059 0.9427 0.0514 9 E 0.0047 0.9598 0.0356 10 R 0.0047 0.9597 0.0356 11 L 0.0047 0.9599 0.0354 12 V 0.0047 0.9597 0.0356 13 A 0.0047 0.9573 0.0380 14 L 0.0048 0.9485 0.0467 15 L 0.0056 0.9043 0.0901 16 E 0.0078 0.7160 0.2762 17 S 0.0416 0.3320 0.6264 18 G 0.0401 0.0791 0.8808 19 T 0.0611 0.0779 0.8610 20 E 0.0686 0.0866 0.8448 21 K 0.4129 0.0235 0.5636 22 V 0.8558 0.0040 0.1402 23 L 0.9301 0.0033 0.0666 24 L 0.9329 0.0031 0.0640 25 I 0.9162 0.0041 0.0797 26 D 0.8222 0.0044 0.1735 27 S 0.3384 0.0235 0.6380 28 R 0.1242 0.0224 0.8534 29 P 0.0788 0.0410 0.8803 30 F 0.0150 0.7231 0.2619 31 V 0.0185 0.8192 0.1623 32 E 0.0273 0.8140 0.1587 33 Y 0.0515 0.7370 0.2115 34 N 0.0473 0.6046 0.3481 35 T 0.0395 0.4321 0.5284 36 S 0.0827 0.2470 0.6703 37 H 0.1649 0.1658 0.6693 38 I 0.1822 0.1324 0.6854 39 L 0.0999 0.2320 0.6681 40 E 0.1657 0.1909 0.6434 41 A 0.3945 0.1853 0.4202 42 I 0.5205 0.1513 0.3282 43 N 0.4853 0.0951 0.4196 44 I 0.3517 0.0469 0.6015 45 N 0.1825 0.0365 0.7810 46 C 0.0109 0.8220 0.1671 47 S 0.0055 0.9297 0.0648 48 K 0.0051 0.9399 0.0550 49 L 0.0062 0.9313 0.0626 50 M 0.0089 0.9104 0.0807 51 K 0.0110 0.8744 0.1146 52 R 0.0214 0.7726 0.2060 53 R 0.0301 0.6981 0.2717 54 L 0.0504 0.5653 0.3843 55 Q 0.0530 0.4788 0.4682 56 Q 0.0530 0.3869 0.5600 57 D 0.0603 0.3033 0.6364 58 K 0.0852 0.2735 0.6413 59 V 0.1633 0.2206 0.6161 60 L 0.1852 0.1776 0.6372 61 I 0.1362 0.1449 0.7189 62 T 0.0738 0.1639 0.7622 63 E 0.0081 0.8886 0.1033 64 L 0.0072 0.9117 0.0811 65 I 0.0096 0.8894 0.1010 66 Q 0.0117 0.8714 0.1169 67 H 0.0098 0.8796 0.1105 68 S 0.0100 0.8603 0.1297 69 A 0.0093 0.8531 0.1377 70 K 0.0169 0.8207 0.1623 71 H 0.0174 0.7150 0.2676 72 K 0.0244 0.5868 0.3888 73 V 0.0751 0.2560 0.6689 74 D 0.0828 0.0571 0.8601 75 I 0.1336 0.0321 0.8342 76 D 0.0962 0.0355 0.8683 77 C 0.0383 0.1678 0.7939 78 S 0.0462 0.0955 0.8583 79 Q 0.2014 0.0248 0.7739 80 K 0.6267 0.0040 0.3693 81 V 0.9123 0.0036 0.0841 82 V 0.9313 0.0033 0.0654 83 V 0.9282 0.0033 0.0685 84 Y 0.8781 0.0060 0.1159 85 D 0.5277 0.0083 0.4640 86 Q 0.1309 0.0901 0.7790 87 S 0.0826 0.0633 0.8540 88 S 0.0851 0.0995 0.8154 89 Q 0.0612 0.1871 0.7518 90 D 0.1224 0.2205 0.6570 91 V 0.0691 0.4694 0.4615 92 A 0.0484 0.4721 0.4794 93 S 0.0530 0.4865 0.4605 94 L 0.0465 0.4572 0.4963 95 S 0.0396 0.4000 0.5605 96 S 0.0258 0.6026 0.3716 97 D 0.0099 0.8532 0.1369 98 C 0.0048 0.9499 0.0453 99 F 0.0047 0.9595 0.0358 100 L 0.0048 0.9587 0.0365 101 T 0.0047 0.9610 0.0344 102 V 0.0047 0.9606 0.0348 103 L 0.0047 0.9589 0.0364 104 L 0.0048 0.9551 0.0401 105 G 0.0051 0.9431 0.0519 106 K 0.0063 0.8965 0.0972 107 L 0.0367 0.5677 0.3956 108 E 0.0360 0.0908 0.8732 109 K 0.0492 0.0842 0.8665 110 S 0.0697 0.0890 0.8412 111 F 0.0985 0.0948 0.8067 112 N 0.0868 0.0947 0.8185 113 S 0.2651 0.0842 0.6507 114 V 0.7160 0.0343 0.2497 115 H 0.8474 0.0246 0.1280 116 L 0.8642 0.0323 0.1034 117 L 0.7122 0.0707 0.2171 118 A 0.3449 0.1358 0.5192 119 G 0.1352 0.1186 0.7461 120 G 0.1097 0.2608 0.6294 121 F 0.0292 0.8339 0.1369 122 A 0.0073 0.9313 0.0614 123 E 0.0070 0.9347 0.0583 124 F 0.0071 0.9291 0.0639 125 S 0.0087 0.8990 0.0923 126 R 0.0116 0.8138 0.1745 127 C 0.0277 0.6665 0.3058 128 F 0.0696 0.0979 0.8324 129 P 0.0370 0.1655 0.7975 130 G 0.0645 0.1804 0.7551 131 L 0.1689 0.1885 0.6426 132 C 0.2408 0.1189 0.6403 133 E 0.1651 0.1041 0.7308 134 G 0.0958 0.0549 0.8493 135 K 0.1452 0.0410 0.8138 136 S 0.2093 0.0435 0.7471 137 T 0.2396 0.0358 0.7246 138 L 0.2265 0.0237 0.7498 139 V 0.1644 0.0168 0.8189 140 P 0.1702 0.0545 0.7753 141 T 0.1759 0.0860 0.7381 142 C 0.2064 0.0868 0.7068 143 I 0.1924 0.0734 0.7342 144 S 0.1787 0.0593 0.7620 145 Q 0.1371 0.0412 0.8217 146 P 0.1447 0.0523 0.8030 147 A 0.1741 0.0944 0.7315 148 H 0.2706 0.1076 0.6218 149 H 0.2966 0.1396 0.5639 150 H 0.2518 0.1187 0.6295 151 H 0.1885 0.0897 0.7218 152 H 0.1466 0.0616 0.7918 153 H 0.0746 0.0446 0.8808