# This file is the result of combining several RDB files, specifically # T0249.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0249.t2k.stride-ebghtl.rdb (weight 1.24869) # T0249.t2k.str2.rdb (weight 1.54758) # T0249.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 T0249.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0249 # 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 T0249.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 129 # # ============================================ # Comments from T0249.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0249 # 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 T0249.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 129 # # ============================================ # Comments from T0249.t2k.str2.rdb # ============================================ # TARGET T0249 # 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 T0249.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 129 # # ============================================ # Comments from T0249.t2k.alpha.rdb # ============================================ # TARGET T0249 # 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 T0249.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 129 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0587 0.1527 0.7886 2 Q 0.0781 0.4597 0.4623 3 E 0.0606 0.4845 0.4550 4 Q 0.0490 0.4728 0.4782 5 R 0.0176 0.6716 0.3108 6 Q 0.0131 0.7236 0.2633 7 Q 0.0114 0.8200 0.1686 8 L 0.0056 0.9199 0.0746 9 L 0.0049 0.9403 0.0548 10 R 0.0049 0.9493 0.0458 11 S 0.0049 0.9494 0.0458 12 L 0.0058 0.9533 0.0410 13 E 0.0075 0.9523 0.0402 14 A 0.0090 0.9495 0.0415 15 L 0.0139 0.9410 0.0450 16 I 0.0157 0.9214 0.0629 17 F 0.0236 0.8616 0.1148 18 S 0.0451 0.7094 0.2455 19 S 0.0419 0.4896 0.4685 20 E 0.0287 0.0874 0.8839 21 E 0.0657 0.0358 0.8985 22 P 0.1453 0.0187 0.8360 23 V 0.3014 0.0111 0.6875 24 N 0.1441 0.0186 0.8373 25 L 0.0049 0.9235 0.0716 26 Q 0.0047 0.9326 0.0627 27 T 0.0048 0.9446 0.0505 28 L 0.0048 0.9458 0.0495 29 S 0.0052 0.9243 0.0705 30 Q 0.0062 0.8655 0.1283 31 I 0.0108 0.8059 0.1833 32 T 0.0427 0.5199 0.4373 33 A 0.0271 0.3572 0.6157 34 H 0.0244 0.2247 0.7509 35 K 0.0379 0.1338 0.8284 36 F 0.0741 0.0388 0.8871 37 T 0.0684 0.0292 0.9023 38 P 0.0075 0.8993 0.0931 39 S 0.0050 0.9337 0.0613 40 E 0.0052 0.9444 0.0504 41 L 0.0048 0.9542 0.0410 42 Q 0.0048 0.9579 0.0373 43 E 0.0048 0.9575 0.0377 44 A 0.0049 0.9555 0.0396 45 V 0.0048 0.9567 0.0386 46 D 0.0047 0.9560 0.0392 47 E 0.0048 0.9507 0.0446 48 L 0.0050 0.9423 0.0527 49 N 0.0061 0.9236 0.0703 50 R 0.0071 0.8847 0.1082 51 D 0.0146 0.8109 0.1745 52 Y 0.0348 0.6895 0.2757 53 E 0.0325 0.4950 0.4725 54 A 0.0534 0.2840 0.6626 55 T 0.0365 0.1731 0.7904 56 G 0.0508 0.0711 0.8781 57 R 0.1611 0.0273 0.8116 58 T 0.5853 0.0144 0.4003 59 F 0.8446 0.0061 0.1493 60 R 0.9040 0.0050 0.0911 61 I 0.9146 0.0039 0.0815 62 H 0.9044 0.0064 0.0892 63 A 0.9003 0.0056 0.0941 64 I 0.7991 0.0262 0.1747 65 A 0.2801 0.0437 0.6762 66 G 0.0662 0.0599 0.8739 67 G 0.5225 0.0349 0.4425 68 Y 0.8604 0.0073 0.1323 69 R 0.8887 0.0095 0.1017 70 F 0.8875 0.0091 0.1034 71 L 0.7706 0.0153 0.2141 72 T 0.4621 0.0150 0.5229 73 E 0.1544 0.0585 0.7871 74 P 0.0203 0.6394 0.3403 75 E 0.0129 0.7169 0.2702 76 F 0.0129 0.7710 0.2162 77 A 0.0081 0.8864 0.1055 78 D 0.0054 0.9187 0.0760 79 L 0.0050 0.9425 0.0525 80 V 0.0050 0.9450 0.0500 81 R 0.0052 0.9360 0.0588 82 Q 0.0063 0.9028 0.0909 83 L 0.0113 0.8168 0.1718 84 L 0.0357 0.6308 0.3335 85 A 0.0365 0.3324 0.6311 86 P 0.0490 0.2198 0.7312 87 V 0.0600 0.1855 0.7545 88 I 0.0683 0.1102 0.8214 89 Q 0.0749 0.0953 0.8298 90 R 0.0672 0.2368 0.6959 91 R 0.0800 0.2005 0.7195 92 L 0.0732 0.1854 0.7414 93 S 0.0571 0.1999 0.7430 94 R 0.0053 0.8926 0.1021 95 S 0.0048 0.9394 0.0558 96 M 0.0047 0.9494 0.0459 97 L 0.0050 0.9574 0.0376 98 E 0.0056 0.9558 0.0386 99 V 0.0075 0.9560 0.0365 100 L 0.0165 0.9469 0.0367 101 A 0.0267 0.9343 0.0390 102 V 0.0151 0.9426 0.0423 103 V 0.0187 0.9338 0.0475 104 A 0.0327 0.8960 0.0714 105 W 0.0357 0.8001 0.1642 106 H 0.0783 0.4898 0.4319 107 Q 0.0819 0.1430 0.7751 108 P 0.0784 0.1329 0.7887 109 V 0.1495 0.1346 0.7159 110 T 0.1245 0.1216 0.7538 111 K 0.0104 0.8970 0.0926 112 G 0.0118 0.9196 0.0686 113 E 0.0169 0.9205 0.0625 114 I 0.0209 0.9249 0.0542 115 Q 0.0335 0.8999 0.0665 116 Q 0.0279 0.8725 0.0997 117 I 0.0367 0.7788 0.1845 118 R 0.0704 0.4856 0.4441 119 G 0.0628 0.1972 0.7400 120 A 0.1033 0.0908 0.8059 121 S 0.1230 0.0742 0.8029 122 P 0.0294 0.4295 0.5411 123 D 0.0107 0.7658 0.2235 124 Y 0.0078 0.8998 0.0924 125 S 0.0056 0.9407 0.0537 126 I 0.0048 0.9538 0.0414 127 D 0.0048 0.9560 0.0392 128 R 0.0049 0.9566 0.0385 129 L 0.0048 0.9552 0.0400 130 L 0.0058 0.9457 0.0484 131 A 0.0052 0.8984 0.0964 132 R 0.0440 0.5505 0.4055 133 G 0.0348 0.2056 0.7595 134 L 0.0798 0.2266 0.6937 135 I 0.2794 0.2906 0.4301 136 E 0.2864 0.3829 0.3307 137 V 0.2711 0.4173 0.3116 138 R 0.2229 0.2411 0.5360 139 G 0.1782 0.0908 0.7310 140 R 0.2347 0.0627 0.7026 141 A 0.2714 0.0516 0.6769 142 D 0.1633 0.0597 0.7770 143 S 0.0996 0.0368 0.8636 144 P 0.0519 0.0603 0.8878 145 G 0.0600 0.0529 0.8872 146 R 0.1586 0.0363 0.8051 147 P 0.3359 0.0688 0.5953 148 L 0.4719 0.1321 0.3960 149 Q 0.5966 0.1533 0.2501 150 Y 0.5466 0.2007 0.2527 151 G 0.4930 0.1727 0.3343 152 T 0.4154 0.1850 0.3996 153 T 0.0785 0.3515 0.5701 154 E 0.0049 0.9320 0.0631 155 V 0.0048 0.9458 0.0494 156 F 0.0047 0.9525 0.0428 157 L 0.0048 0.9460 0.0491 158 D 0.0057 0.9083 0.0860 159 L 0.0081 0.8400 0.1519 160 F 0.0521 0.4123 0.5356 161 H 0.0640 0.0721 0.8639 162 L 0.1198 0.0596 0.8207 163 P 0.1160 0.1360 0.7480 164 S 0.1612 0.1433 0.6956 165 L 0.0179 0.7256 0.2565 166 K 0.0144 0.7110 0.2746 167 D 0.0238 0.6155 0.3607 168 L 0.1044 0.0969 0.7988 169 P 0.0560 0.1443 0.7997 170 K 0.0783 0.1926 0.7291 171 L 0.0283 0.6028 0.3689 172 R 0.0142 0.6943 0.2916 173 E 0.0163 0.6725 0.3112 174 I 0.0196 0.6675 0.3129 175 K 0.0140 0.7545 0.2315 176 E 0.0103 0.7942 0.1955 177 I 0.0113 0.8100 0.1788 178 L 0.0157 0.7905 0.1938 179 Q 0.0158 0.7974 0.1868 180 E 0.0115 0.8111 0.1774 181 H 0.0173 0.7864 0.1964 182 E 0.0157 0.8079 0.1764 183 E 0.0138 0.8198 0.1665 184 Q 0.0167 0.7898 0.1935 185 Q 0.0202 0.7647 0.2152 186 Y 0.0218 0.7653 0.2129 187 L 0.0190 0.7676 0.2134 188 A 0.0281 0.6607 0.3112 189 A 0.0309 0.5804 0.3888 190 D 0.0425 0.4389 0.5186 191 G 0.0370 0.2973 0.6657 192 D 0.0588 0.2525 0.6886 193 L 0.0714 0.1653 0.7633 194 P 0.0479 0.3283 0.6238 195 V 0.0622 0.3766 0.5612 196 A 0.0853 0.2820 0.6327 197 A 0.0810 0.2116 0.7074 198 D 0.0616 0.1504 0.7880 199 E 0.0181 0.3148 0.6671 200 D 0.0218 0.2915 0.6867 201 E 0.0404 0.2787 0.6809 202 K 0.0616 0.2838 0.6546 203 P 0.0488 0.3811 0.5701 204 R 0.0526 0.4298 0.5176 205 M 0.0660 0.5151 0.4189 206 E 0.1064 0.4488 0.4448 207 R 0.1057 0.3643 0.5300 208 I 0.0741 0.2053 0.7206 209 E 0.0286 0.0791 0.8923