# 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 135.12 # # ============================================ # 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 135.12 # # ============================================ # 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 135.12 # # ============================================ # 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 135.12 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.1776 0.0295 0.7929 2 Y 0.3000 0.0355 0.6644 3 T 0.2824 0.0492 0.6684 4 G 0.1505 0.0315 0.8180 5 R 0.1370 0.0165 0.8464 6 P 0.0912 0.0177 0.8911 7 P 0.0609 0.0725 0.8667 8 D 0.0574 0.0998 0.8428 9 E 0.0585 0.2447 0.6967 10 P 0.0716 0.4526 0.4758 11 A 0.1482 0.5884 0.2634 12 V 0.1883 0.6106 0.2011 13 L 0.1311 0.5982 0.2707 14 G 0.0837 0.5584 0.3579 15 V 0.0663 0.6924 0.2413 16 A 0.0622 0.7607 0.1771 17 L 0.0307 0.7979 0.1714 18 N 0.0361 0.7855 0.1784 19 E 0.0162 0.8324 0.1513 20 V 0.0171 0.8287 0.1542 21 F 0.0153 0.8600 0.1247 22 V 0.0074 0.9205 0.0721 23 P 0.0052 0.9430 0.0518 24 I 0.0055 0.9476 0.0469 25 L 0.0059 0.9384 0.0558 26 Q 0.0072 0.8900 0.1028 27 K 0.0074 0.7746 0.2180 28 Q 0.0145 0.5704 0.4151 29 F 0.0575 0.1180 0.8245 30 P 0.0467 0.1545 0.7988 31 E 0.2048 0.1496 0.6456 32 I 0.6223 0.0587 0.3189 33 V 0.7151 0.0605 0.2244 34 D 0.8174 0.0233 0.1593 35 F 0.8014 0.0202 0.1785 36 Y 0.7713 0.0145 0.2142 37 L 0.4546 0.0142 0.5312 38 P 0.1365 0.0165 0.8471 39 P 0.0352 0.4570 0.5078 40 E 0.0253 0.4628 0.5119 41 G 0.0496 0.4613 0.4891 42 C 0.1765 0.2170 0.6064 43 S 0.3036 0.1308 0.5656 44 Y 0.3759 0.0946 0.5294 45 R 0.5381 0.0477 0.4142 46 L 0.8286 0.0148 0.1566 47 A 0.9062 0.0097 0.0841 48 V 0.9227 0.0110 0.0663 49 V 0.9054 0.0204 0.0743 50 T 0.8818 0.0273 0.0909 51 I 0.7825 0.0478 0.1697 52 K 0.5904 0.0836 0.3260 53 K 0.3755 0.1816 0.4429 54 Q 0.1719 0.2224 0.6058 55 Y 0.0870 0.1791 0.7339 56 A 0.0200 0.4972 0.4828 57 G 0.0126 0.6526 0.3348 58 H 0.0088 0.8576 0.1336 59 A 0.0051 0.9431 0.0519 60 K 0.0047 0.9557 0.0396 61 R 0.0047 0.9594 0.0359 62 V 0.0047 0.9599 0.0355 63 M 0.0047 0.9588 0.0365 64 M 0.0047 0.9571 0.0382 65 G 0.0048 0.9488 0.0464 66 V 0.0051 0.9367 0.0583 67 W 0.0064 0.9096 0.0841 68 S 0.0094 0.8154 0.1752 69 F 0.0157 0.7500 0.2343 70 L 0.0295 0.6578 0.3127 71 R 0.0274 0.5645 0.4081 72 Q 0.0410 0.4986 0.4604 73 F 0.1108 0.3273 0.5619 74 M 0.1594 0.1747 0.6659 75 Y 0.2353 0.1215 0.6432 76 T 0.3390 0.0258 0.6352 77 K 0.4711 0.0250 0.5039 78 F 0.9030 0.0042 0.0928 79 V 0.9263 0.0038 0.0699 80 I 0.9317 0.0035 0.0648 81 V 0.9247 0.0035 0.0718 82 C 0.8585 0.0093 0.1323 83 D 0.4739 0.0155 0.5107 84 D 0.0637 0.1070 0.8293 85 D 0.0731 0.0604 0.8665 86 V 0.1825 0.0323 0.7853 87 N 0.2104 0.0164 0.7732 88 A 0.0780 0.1905 0.7316 89 R 0.0753 0.1187 0.8060 90 D 0.1018 0.0388 0.8594 91 W 0.0051 0.9308 0.0642 92 N 0.0049 0.9477 0.0474 93 D 0.0050 0.9523 0.0427 94 V 0.0047 0.9597 0.0356 95 I 0.0052 0.9590 0.0358 96 W 0.0054 0.9582 0.0364 97 A 0.0061 0.9526 0.0412 98 I 0.0072 0.9378 0.0551 99 T 0.0093 0.8803 0.1104 100 T 0.0311 0.7114 0.2575 101 R 0.0592 0.3491 0.5916 102 M 0.1216 0.0871 0.7913 103 D 0.1039 0.0153 0.8808 104 P 0.0147 0.3122 0.6730 105 A 0.0211 0.2872 0.6917 106 R 0.0677 0.2360 0.6963 107 D 0.1983 0.0689 0.7328 108 T 0.6614 0.0394 0.2992 109 V 0.8739 0.0175 0.1087 110 L 0.8834 0.0149 0.1017 111 V 0.7070 0.0144 0.2786 112 E 0.2481 0.0644 0.6875 113 N 0.0894 0.0379 0.8726 114 T 0.1977 0.0188 0.7835 115 P 0.2330 0.0295 0.7375 116 I 0.2465 0.0652 0.6883 117 D 0.2330 0.0652 0.7018 118 Y 0.1766 0.1813 0.6420 119 L 0.2312 0.1164 0.6525 120 D 0.1977 0.0743 0.7280 121 F 0.0626 0.1783 0.7591 122 A 0.0729 0.1311 0.7960 123 S 0.0894 0.0499 0.8606 124 P 0.0658 0.0893 0.8449 125 V 0.1131 0.1188 0.7681 126 S 0.0769 0.1431 0.7800 127 G 0.0692 0.0924 0.8384 128 L 0.1464 0.0989 0.7546 129 G 0.1590 0.0571 0.7839 130 S 0.2496 0.0590 0.6914 131 K 0.5511 0.0641 0.3848 132 M 0.8000 0.0316 0.1684 133 G 0.8706 0.0214 0.1080 134 L 0.8615 0.0238 0.1147 135 D 0.7817 0.0352 0.1831 136 A 0.4514 0.0789 0.4697 137 T 0.2335 0.1014 0.6652 138 N 0.1491 0.0708 0.7801 139 K 0.1142 0.0743 0.8115 140 W 0.0863 0.0421 0.8715 141 P 0.0621 0.1313 0.8066 142 G 0.0472 0.2022 0.7506 143 E 0.1059 0.2792 0.6149 144 T 0.1548 0.2543 0.5909 145 Q 0.2017 0.2408 0.5575 146 R 0.2427 0.2167 0.5406 147 E 0.2704 0.2001 0.5296 148 W 0.2015 0.1507 0.6478 149 G 0.1327 0.0815 0.7859 150 R 0.1747 0.0468 0.7786 151 P 0.2400 0.0645 0.6954 152 I 0.2636 0.1047 0.6317 153 K 0.2398 0.0676 0.6926 154 K 0.1339 0.0454 0.8208 155 D 0.0853 0.0161 0.8986 156 P 0.0053 0.8848 0.1100 157 D 0.0058 0.9049 0.0893 158 V 0.0050 0.9440 0.0510 159 V 0.0051 0.9551 0.0398 160 A 0.0050 0.9500 0.0450 161 H 0.0047 0.9472 0.0481 162 I 0.0048 0.9508 0.0444 163 D 0.0047 0.9545 0.0408 164 A 0.0048 0.9531 0.0422 165 I 0.0049 0.9515 0.0436 166 W 0.0052 0.9477 0.0471 167 D 0.0052 0.9312 0.0637 168 E 0.0062 0.8933 0.1005 169 L 0.0424 0.6352 0.3224 170 A 0.0327 0.1697 0.7976 171 I 0.0619 0.1759 0.7622 172 F 0.0838 0.2413 0.6749 173 N 0.0721 0.2669 0.6611 174 N 0.0637 0.1966 0.7397 175 G 0.0533 0.0793 0.8673 176 K 0.0516 0.0598 0.8886 177 S 0.0533 0.0257 0.9210