# This file is the result of combining several RDB files, specifically # T0232.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0232.t2k.stride-ebghtl.rdb (weight 1.24869) # T0232.t2k.str2.rdb (weight 1.54758) # T0232.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 T0232.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0232 # 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 T0232.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 1 # # ============================================ # Comments from T0232.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0232 # 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 T0232.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 1 # # ============================================ # Comments from T0232.t2k.str2.rdb # ============================================ # TARGET T0232 # 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 T0232.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 1 # # ============================================ # Comments from T0232.t2k.alpha.rdb # ============================================ # TARGET T0232 # 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 T0232.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0675 0.0879 0.8446 2 E 0.0944 0.1494 0.7562 3 D 0.0714 0.1957 0.7329 4 G 0.0827 0.1785 0.7388 5 M 0.1684 0.1710 0.6606 6 N 0.2330 0.1477 0.6193 7 T 0.3002 0.2027 0.4970 8 F 0.4026 0.1755 0.4219 9 D 0.4401 0.1704 0.3896 10 L 0.5185 0.1585 0.3230 11 Y 0.5442 0.1337 0.3221 12 Y 0.5952 0.0966 0.3082 13 W 0.4886 0.0679 0.4435 14 P 0.3661 0.0639 0.5700 15 V 0.2710 0.0822 0.6468 16 P 0.1945 0.1183 0.6873 17 F 0.1508 0.2104 0.6388 18 R 0.1119 0.3178 0.5703 19 G 0.0834 0.4559 0.4606 20 Q 0.1266 0.5843 0.2891 21 L 0.2054 0.6003 0.1944 22 I 0.1833 0.6645 0.1522 23 R 0.1561 0.6936 0.1503 24 G 0.1271 0.7030 0.1699 25 I 0.1358 0.7311 0.1331 26 L 0.1507 0.6923 0.1570 27 A 0.1207 0.6381 0.2411 28 H 0.1127 0.5165 0.3708 29 C 0.1091 0.2964 0.5945 30 G 0.0989 0.1195 0.7816 31 C 0.1398 0.1033 0.7570 32 S 0.1535 0.1230 0.7235 33 W 0.1089 0.2446 0.6465 34 D 0.0911 0.2310 0.6779 35 E 0.0488 0.5029 0.4483 36 H 0.0511 0.4827 0.4663 37 D 0.0725 0.5157 0.4118 38 V 0.0486 0.6887 0.2627 39 D 0.0478 0.7385 0.2137 40 A 0.0360 0.7902 0.1738 41 I 0.0378 0.8106 0.1515 42 E 0.0447 0.7508 0.2046 43 G 0.0522 0.6637 0.2842 44 L 0.0704 0.6470 0.2826 45 M 0.1031 0.6079 0.2890 46 D 0.0831 0.5036 0.4133 47 C 0.0700 0.3615 0.5685 48 G 0.0575 0.2219 0.7207 49 A 0.0707 0.2778 0.6515 50 E 0.0924 0.2750 0.6326 51 K 0.1136 0.2393 0.6471 52 Q 0.1545 0.1319 0.7135 53 P 0.2064 0.1493 0.6443 54 V 0.3337 0.2098 0.4565 55 A 0.3826 0.2129 0.4045 56 F 0.3670 0.1891 0.4439 57 M 0.2656 0.1135 0.6209 58 G 0.1517 0.0406 0.8077 59 P 0.1499 0.0485 0.8016 60 P 0.2739 0.0588 0.6674 61 V 0.5672 0.0711 0.3616 62 L 0.6678 0.0630 0.2691 63 I 0.5833 0.0768 0.3399 64 D 0.3956 0.1042 0.5002 65 R 0.1488 0.3111 0.5402 66 E 0.1179 0.3607 0.5214 67 R 0.1148 0.3455 0.5397 68 N 0.1274 0.2797 0.5929 69 F 0.2618 0.2611 0.4771 70 A 0.2860 0.2917 0.4223 71 I 0.2102 0.4293 0.3605 72 S 0.1705 0.4142 0.4153 73 Q 0.1449 0.3970 0.4581 74 M 0.1736 0.2642 0.5622 75 P 0.1596 0.3849 0.4555 76 A 0.2351 0.5242 0.2408 77 I 0.2958 0.5519 0.1523 78 A 0.3405 0.5236 0.1359 79 I 0.3277 0.5164 0.1558 80 Y 0.3094 0.4670 0.2236 81 L 0.1549 0.4661 0.3790 82 G 0.1000 0.3238 0.5762 83 E 0.1258 0.3305 0.5437 84 R 0.1863 0.3532 0.4605 85 L 0.1973 0.3500 0.4527 86 D 0.2022 0.2709 0.5270 87 I 0.2410 0.2512 0.5078 88 L 0.2568 0.1559 0.5873 89 P 0.2090 0.2450 0.5461 90 A 0.2300 0.3103 0.4597 91 T 0.2401 0.2869 0.4730 92 V 0.2515 0.2617 0.4867 93 E 0.1592 0.2352 0.6056 94 G 0.1243 0.1839 0.6918 95 R 0.2407 0.1890 0.5703 96 T 0.4102 0.1874 0.4024 97 L 0.3813 0.2700 0.3487 98 S 0.3506 0.3172 0.3321 99 A 0.2582 0.4809 0.2610 100 K 0.3056 0.4429 0.2516 101 I 0.3383 0.4142 0.2475 102 V 0.2863 0.3591 0.3545 103 N 0.1633 0.3128 0.5239 104 D 0.1000 0.2912 0.6088 105 A 0.0446 0.5339 0.4214 106 N 0.0444 0.5126 0.4429 107 D 0.0582 0.5446 0.3972 108 V 0.0881 0.5924 0.3195 109 L 0.1095 0.5923 0.2982 110 D 0.1207 0.5477 0.3316 111 E 0.1687 0.5118 0.3195 112 L 0.3040 0.3613 0.3347 113 T 0.3612 0.2500 0.3888 114 L 0.2522 0.2169 0.5309 115 N 0.1309 0.1605 0.7086 116 G 0.0759 0.1109 0.8132 117 G 0.1022 0.1072 0.7906 118 R 0.2313 0.1404 0.6282 119 E 0.3223 0.1647 0.5130 120 M 0.2969 0.1579 0.5452 121 W 0.2425 0.1116 0.6460 122 T 0.1316 0.0692 0.7992 123 P 0.0519 0.5131 0.4349 124 E 0.0258 0.6725 0.3016 125 K 0.0293 0.7182 0.2525 126 W 0.0224 0.7853 0.1924 127 Q 0.0188 0.8029 0.1783 128 E 0.0205 0.7718 0.2077 129 F 0.0263 0.7241 0.2496 130 V 0.0396 0.6812 0.2792 131 P 0.0178 0.7670 0.2152 132 R 0.0208 0.7784 0.2008 133 L 0.0199 0.8531 0.1270 134 Q 0.0183 0.8761 0.1056 135 K 0.0229 0.8833 0.0938 136 W 0.0287 0.8859 0.0855 137 I 0.0460 0.8767 0.0773 138 R 0.0628 0.8575 0.0797 139 I 0.0729 0.8239 0.1032 140 F 0.0986 0.7496 0.1518 141 A 0.0727 0.6873 0.2400 142 D 0.0584 0.5594 0.3822 143 T 0.0621 0.3927 0.5451 144 G 0.0698 0.2516 0.6786 145 A 0.1009 0.2666 0.6324 146 R 0.1239 0.3004 0.5757 147 N 0.0908 0.2700 0.6392 148 G 0.1047 0.1879 0.7074 149 L 0.2017 0.2117 0.5866 150 S 0.2609 0.2368 0.5023 151 A 0.1752 0.3790 0.4458 152 A 0.1657 0.3823 0.4521 153 S 0.1514 0.3224 0.5263 154 G 0.2109 0.2305 0.5586 155 F 0.3867 0.1984 0.4149 156 M 0.5092 0.1556 0.3352 157 L 0.3810 0.1850 0.4340 158 G 0.2597 0.1533 0.5870 159 T 0.2260 0.2326 0.5414 160 E 0.2427 0.2641 0.4932 161 K 0.2516 0.2791 0.4693 162 I 0.2129 0.2554 0.5317 163 G 0.1994 0.2274 0.5731 164 V 0.1375 0.5776 0.2849 165 A 0.0832 0.7359 0.1809 166 D 0.0863 0.7698 0.1440 167 I 0.0837 0.8126 0.1037 168 V 0.1023 0.8049 0.0928 169 T 0.1079 0.8090 0.0831 170 A 0.0997 0.8211 0.0792 171 I 0.1008 0.8154 0.0839 172 L 0.0897 0.8117 0.0986 173 W 0.0888 0.7711 0.1400 174 T 0.0820 0.7305 0.1874 175 T 0.0787 0.6886 0.2327 176 V 0.0436 0.7360 0.2203 177 A 0.0285 0.7148 0.2567 178 D 0.0264 0.6055 0.3681 179 R 0.0301 0.5658 0.4042 180 F 0.0681 0.4274 0.5045 181 P 0.0465 0.5342 0.4193 182 A 0.0690 0.5915 0.3395 183 I 0.0998 0.6136 0.2866 184 K 0.1050 0.5513 0.3437 185 G 0.1391 0.4555 0.4055 186 I 0.2311 0.4200 0.3490 187 I 0.2583 0.3608 0.3809 188 E 0.1795 0.2862 0.5343 189 D 0.1240 0.1859 0.6901 190 T 0.1066 0.1541 0.7393 191 S 0.1176 0.1171 0.7653 192 P 0.1985 0.1902 0.6114 193 I 0.4052 0.2320 0.3627 194 I 0.5057 0.2040 0.2903 195 W 0.4045 0.2331 0.3624 196 G 0.3133 0.2291 0.4576 197 L 0.2720 0.2897 0.4383 198 S 0.2635 0.2846 0.4519 199 R 0.2413 0.3655 0.3932 200 R 0.3180 0.3467 0.3353 201 V 0.3299 0.4192 0.2508 202 V 0.3273 0.4113 0.2614 203 A 0.2610 0.4255 0.3135 204 T 0.2038 0.4029 0.3933 205 A 0.1660 0.2988 0.5352 206 P 0.1287 0.4011 0.4702 207 L 0.0732 0.6226 0.3042 208 A 0.0682 0.6470 0.2849 209 A 0.0754 0.6161 0.3085 210 L 0.0897 0.4916 0.4187 211 N 0.1039 0.3366 0.5595 212 S 0.0793 0.4173 0.5034 213 K 0.0765 0.5027 0.4208 214 S 0.1065 0.4703 0.4233 215 F 0.0885 0.6109 0.3006 216 E 0.0784 0.6574 0.2642 217 E 0.0782 0.6435 0.2783 218 Y 0.0796 0.5302 0.3902 219 G 0.0845 0.3052 0.6103 220 N 0.1101 0.2761 0.6139 221 A 0.1570 0.3328 0.5101 222 Y 0.1744 0.2983 0.5273 223 C 0.1466 0.2530 0.6004 224 G 0.0824 0.2741 0.6435 225 G 0.0795 0.4324 0.4881 226 E 0.1109 0.5681 0.3211 227 I 0.0979 0.6583 0.2438 228 E 0.0827 0.6864 0.2309 229 K 0.0555 0.7457 0.1989 230 S 0.0519 0.7446 0.2035 231 L 0.0613 0.7356 0.2032 232 R 0.0734 0.7012 0.2254 233 K 0.0792 0.6319 0.2889 234 V 0.0859 0.4695 0.4446 235 A 0.0640 0.2532 0.6829 236 S 0.0376 0.0500 0.9125