# This file is the result of combining several RDB files, specifically # T0503.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0503.t2k.stride-ebghtl.rdb (weight 1.24869) # T0503.t2k.str2.rdb (weight 1.54758) # T0503.t2k.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 T0503.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0503 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0503.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 458 # # ============================================ # Comments from T0503.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0503 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0503.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 458 # # ============================================ # Comments from T0503.t2k.str2.rdb # ============================================ # TARGET T0503 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0503.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 458 # # ============================================ # Comments from T0503.t2k.alpha.rdb # ============================================ # TARGET T0503 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0503.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 458 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0585 0.2220 0.7195 2 H 0.0431 0.6454 0.3115 3 T 0.0209 0.8150 0.1641 4 A 0.0227 0.8491 0.1282 5 L 0.0250 0.8601 0.1149 6 I 0.0206 0.8725 0.1069 7 N 0.0201 0.8212 0.1588 8 H 0.0265 0.6868 0.2868 9 I 0.1008 0.3671 0.5321 10 R 0.0633 0.3428 0.5939 11 K 0.0753 0.3706 0.5542 12 F 0.0848 0.3729 0.5422 13 I 0.0858 0.2265 0.6877 14 F 0.0903 0.0983 0.8114 15 L 0.0855 0.0187 0.8958 16 T 0.0528 0.0171 0.9302 17 D 0.0056 0.9163 0.0781 18 E 0.0048 0.9370 0.0582 19 D 0.0052 0.9448 0.0501 20 A 0.0047 0.9559 0.0393 21 G 0.0051 0.9490 0.0459 22 T 0.0049 0.9414 0.0537 23 L 0.0059 0.9322 0.0619 24 S 0.0066 0.9082 0.0852 25 A 0.0095 0.7938 0.1968 26 F 0.0298 0.4787 0.4915 27 F 0.1884 0.1561 0.6555 28 Q 0.3783 0.0799 0.5418 29 L 0.7186 0.0330 0.2484 30 K 0.7827 0.0259 0.1913 31 K 0.8283 0.0091 0.1626 32 V 0.5476 0.0116 0.4408 33 R 0.1781 0.0186 0.8033 34 K 0.0330 0.0594 0.9076 35 K 0.0446 0.0368 0.9186 36 E 0.4803 0.0136 0.5061 37 T 0.8327 0.0049 0.1624 38 L 0.8840 0.0060 0.1100 39 L 0.8320 0.0103 0.1578 40 K 0.6077 0.0129 0.3794 41 T 0.1515 0.0845 0.7639 42 G 0.0737 0.0473 0.8791 43 E 0.2518 0.0370 0.7112 44 I 0.3980 0.0546 0.5474 45 C 0.3462 0.0622 0.5916 46 R 0.3335 0.0645 0.6021 47 I 0.6769 0.0243 0.2988 48 N 0.8704 0.0069 0.1227 49 Y 0.9141 0.0050 0.0808 50 F 0.9259 0.0037 0.0704 51 V 0.9011 0.0075 0.0914 52 V 0.8404 0.0151 0.1444 53 K 0.5921 0.0270 0.3809 54 G 0.4574 0.0214 0.5212 55 C 0.7976 0.0100 0.1924 56 L 0.9022 0.0034 0.0944 57 R 0.9113 0.0047 0.0840 58 L 0.9226 0.0031 0.0743 59 F 0.9131 0.0037 0.0832 60 F 0.8941 0.0042 0.1017 61 I 0.8632 0.0060 0.1309 62 D 0.3682 0.0121 0.6197 63 E 0.0181 0.1101 0.8718 64 K 0.0466 0.0179 0.9354 65 G 0.0631 0.0264 0.9105 66 I 0.3223 0.0122 0.6655 67 E 0.8780 0.0032 0.1189 68 Q 0.8786 0.0107 0.1108 69 T 0.9142 0.0049 0.0809 70 T 0.8840 0.0119 0.1041 71 Q 0.8839 0.0110 0.1052 72 F 0.8709 0.0160 0.1131 73 A 0.7787 0.0151 0.2062 74 I 0.3903 0.0187 0.5910 75 E 0.0588 0.0948 0.8464 76 N 0.0387 0.0723 0.8891 77 W 0.2014 0.1511 0.6475 78 W 0.5366 0.1720 0.2914 79 L 0.5720 0.2331 0.1950 80 S 0.4176 0.3369 0.2455 81 D 0.2719 0.4879 0.2403 82 Y 0.1369 0.6622 0.2008 83 M 0.1044 0.7273 0.1683 84 A 0.0975 0.7078 0.1947 85 F 0.0861 0.6796 0.2343 86 Q 0.0909 0.5687 0.3404 87 K 0.0603 0.2988 0.6409 88 Q 0.0537 0.1049 0.8414 89 Q 0.1177 0.0426 0.8397 90 P 0.1794 0.0466 0.7740 91 A 0.2283 0.0671 0.7046 92 D 0.3624 0.1834 0.4542 93 F 0.5033 0.1850 0.3117 94 Y 0.6729 0.1258 0.2013 95 I 0.7779 0.0871 0.1350 96 Q 0.8180 0.0506 0.1315 97 S 0.7786 0.0657 0.1557 98 V 0.6826 0.0658 0.2516 99 E 0.5712 0.0423 0.3865 100 N 0.4843 0.0428 0.4729 101 C 0.6894 0.0141 0.2964 102 E 0.8704 0.0069 0.1227 103 L 0.9116 0.0039 0.0845 104 L 0.9034 0.0048 0.0918 105 S 0.8906 0.0045 0.1049 106 I 0.7046 0.0072 0.2883 107 T 0.3568 0.0099 0.6333 108 Y 0.0077 0.8085 0.1838 109 T 0.0050 0.9073 0.0876 110 E 0.0054 0.9304 0.0642 111 Q 0.0048 0.9504 0.0448 112 E 0.0047 0.9515 0.0437 113 N 0.0048 0.9471 0.0481 114 L 0.0051 0.9396 0.0554 115 F 0.0058 0.9165 0.0778 116 E 0.0063 0.7815 0.2122 117 R 0.0140 0.6196 0.3664 118 I 0.0673 0.1799 0.7528 119 P 0.0078 0.8131 0.1790 120 A 0.0059 0.8825 0.1116 121 L 0.0050 0.9308 0.0642 122 E 0.0048 0.9520 0.0432 123 R 0.0048 0.9539 0.0413 124 Y 0.0048 0.9553 0.0399 125 F 0.0047 0.9561 0.0392 126 R 0.0047 0.9582 0.0370 127 L 0.0048 0.9563 0.0389 128 V 0.0048 0.9556 0.0396 129 Y 0.0049 0.9537 0.0414 130 Q 0.0050 0.9524 0.0426 131 K 0.0052 0.9461 0.0487 132 S 0.0050 0.9439 0.0511 133 F 0.0049 0.9474 0.0477 134 A 0.0050 0.9433 0.0517 135 A 0.0049 0.9414 0.0537 136 A 0.0052 0.9421 0.0527 137 Q 0.0053 0.9462 0.0485 138 L 0.0055 0.9427 0.0518 139 R 0.0054 0.9415 0.0531 140 S 0.0053 0.9445 0.0502 141 K 0.0056 0.9398 0.0546 142 F 0.0065 0.9017 0.0919 143 Q 0.0091 0.7966 0.1944 144 H 0.0183 0.6217 0.3600 145 M 0.0314 0.3439 0.6247 146 Y 0.0470 0.1224 0.8306 147 S 0.0564 0.0652 0.8784 148 K 0.0058 0.9269 0.0673 149 E 0.0050 0.9513 0.0437 150 E 0.0049 0.9550 0.0400 151 Q 0.0047 0.9583 0.0370 152 Y 0.0047 0.9578 0.0374 153 H 0.0048 0.9578 0.0375 154 N 0.0048 0.9562 0.0390 155 F 0.0049 0.9509 0.0443 156 S 0.0052 0.9371 0.0577 157 S 0.0060 0.8635 0.1304 158 R 0.0126 0.7177 0.2697 159 F 0.0703 0.1682 0.7614 160 P 0.0178 0.3029 0.6793 161 E 0.0281 0.3800 0.5919 162 F 0.1138 0.4620 0.4242 163 I 0.1901 0.3424 0.4675 164 Q 0.3074 0.2225 0.4701 165 R 0.3226 0.1436 0.5338 166 V 0.2229 0.0441 0.7330 167 P 0.1683 0.0456 0.7861 168 Q 0.0062 0.9026 0.0912 169 Y 0.0079 0.9221 0.0699 170 L 0.0097 0.9237 0.0666 171 L 0.0105 0.9339 0.0556 172 A 0.0083 0.9307 0.0610 173 S 0.0083 0.9029 0.0887 174 Y 0.0112 0.8524 0.1364 175 L 0.0518 0.4577 0.4905 176 G 0.0530 0.0798 0.8672 177 F 0.0880 0.0220 0.8900 178 T 0.0631 0.0202 0.9167 179 P 0.0078 0.8952 0.0970 180 E 0.0049 0.9276 0.0675 181 Y 0.0054 0.9433 0.0513 182 L 0.0047 0.9572 0.0381 183 S 0.0047 0.9580 0.0373 184 E 0.0047 0.9580 0.0373 185 I 0.0047 0.9565 0.0388 186 R 0.0048 0.9451 0.0501 187 K 0.0052 0.9123 0.0825 188 K 0.0064 0.8547 0.1389 189 Y 0.0168 0.7157 0.2674 190 I 0.0193 0.5293 0.4514 191 S 0.0177 0.1046 0.8776