# This file is the result of combining several RDB files, specifically # T0448.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0448.t2k.stride-ebghtl.rdb (weight 1.24869) # T0448.t2k.str2.rdb (weight 1.54758) # T0448.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 T0448.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0448 # 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 T0448.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 124 # # ============================================ # Comments from T0448.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0448 # 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 T0448.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 124 # # ============================================ # Comments from T0448.t2k.str2.rdb # ============================================ # TARGET T0448 # 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 T0448.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 124 # # ============================================ # Comments from T0448.t2k.alpha.rdb # ============================================ # TARGET T0448 # 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 T0448.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 124 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0907 0.0562 0.8530 2 I 0.2685 0.1425 0.5890 3 A 0.2698 0.2195 0.5107 4 M 0.2769 0.2858 0.4373 5 I 0.3075 0.3357 0.3568 6 V 0.3419 0.3677 0.2904 7 K 0.2973 0.4137 0.2890 8 G 0.2792 0.4229 0.2979 9 G 0.1885 0.5434 0.2680 10 L 0.1221 0.6211 0.2568 11 A 0.1085 0.6489 0.2426 12 M 0.0911 0.6908 0.2182 13 A 0.1053 0.6591 0.2356 14 I 0.1083 0.6140 0.2777 15 S 0.0904 0.5359 0.3737 16 N 0.0936 0.3785 0.5279 17 G 0.0776 0.2780 0.6444 18 H 0.0645 0.2642 0.6713 19 V 0.0591 0.1863 0.7547 20 S 0.0723 0.1237 0.8040 21 F 0.1299 0.0582 0.8119 22 K 0.3724 0.0273 0.6003 23 R 0.7896 0.0077 0.2027 24 P 0.9104 0.0041 0.0855 25 A 0.9202 0.0042 0.0756 26 W 0.9093 0.0045 0.0861 27 L 0.7824 0.0230 0.1945 28 G 0.4481 0.0271 0.5248 29 D 0.2135 0.0606 0.7259 30 S 0.2325 0.1206 0.6469 31 I 0.2460 0.2320 0.5220 32 T 0.2306 0.2273 0.5422 33 A 0.1491 0.2315 0.6195 34 N 0.0958 0.1808 0.7235 35 N 0.1122 0.1400 0.7478 36 G 0.1073 0.1138 0.7789 37 L 0.1125 0.1266 0.7610 38 A 0.0838 0.1476 0.7686 39 T 0.0633 0.1759 0.7608 40 V 0.0531 0.1851 0.7618 41 H 0.0678 0.2337 0.6985 42 Y 0.0990 0.2471 0.6539 43 H 0.0543 0.6615 0.2842 44 D 0.0173 0.8835 0.0992 45 I 0.0093 0.9132 0.0775 46 L 0.0081 0.9245 0.0674 47 A 0.0078 0.9120 0.0803 48 A 0.0100 0.8907 0.0993 49 D 0.0107 0.8203 0.1690 50 W 0.0232 0.6771 0.2997 51 D 0.0721 0.2989 0.6290 52 V 0.0780 0.0606 0.8614 53 E 0.3550 0.0286 0.6163 54 R 0.6978 0.0236 0.2786 55 S 0.8664 0.0125 0.1210 56 D 0.8593 0.0203 0.1204 57 N 0.8077 0.0218 0.1705 58 L 0.6010 0.0537 0.3453 59 G 0.4703 0.0634 0.4663 60 I 0.2918 0.0809 0.6274 61 S 0.1787 0.0998 0.7215 62 G 0.1257 0.2195 0.6548 63 S 0.1150 0.3897 0.4953 64 T 0.1337 0.4915 0.3748 65 I 0.0874 0.6797 0.2329 66 G 0.0748 0.6797 0.2455 67 S 0.0657 0.6762 0.2582 68 R 0.0556 0.6890 0.2554 69 Y 0.0520 0.7096 0.2384 70 D 0.0504 0.7042 0.2455 71 A 0.0413 0.6932 0.2655 72 M 0.0410 0.6581 0.3009 73 A 0.0483 0.6365 0.3152 74 V 0.0527 0.5639 0.3834 75 R 0.0605 0.5955 0.3440 76 Y 0.0454 0.6389 0.3157 77 Q 0.0389 0.6481 0.3129 78 A 0.0358 0.6337 0.3304 79 I 0.0422 0.5833 0.3744 80 P 0.0453 0.4054 0.5492 81 E 0.0617 0.2139 0.7244 82 D 0.1061 0.0570 0.8368 83 A 0.1042 0.0177 0.8780 84 D 0.1386 0.0441 0.8173 85 F 0.9187 0.0036 0.0776 86 I 0.9338 0.0032 0.0630 87 A 0.9332 0.0032 0.0636 88 V 0.9253 0.0036 0.0712 89 F 0.8467 0.0096 0.1437 90 G 0.4959 0.0275 0.4766 91 G 0.3016 0.0456 0.6527 92 V 0.2519 0.1296 0.6185 93 N 0.2047 0.2007 0.5946 94 D 0.1483 0.3120 0.5397 95 Y 0.0665 0.3769 0.5566 96 G 0.0743 0.3234 0.6022 97 R 0.1088 0.2274 0.6638 98 D 0.1332 0.1461 0.7208 99 Q 0.1549 0.1151 0.7300 100 P 0.1463 0.1569 0.6969 101 L 0.0935 0.2448 0.6617 102 G 0.0740 0.1971 0.7289 103 Q 0.0930 0.1806 0.7264 104 Y 0.1446 0.1282 0.7273 105 G 0.0852 0.1122 0.8027 106 D 0.0975 0.0861 0.8164 107 C 0.1928 0.0467 0.7605 108 D 0.1219 0.0416 0.8365 109 M 0.0099 0.8774 0.1127 110 T 0.0063 0.8903 0.1035 111 T 0.0065 0.9150 0.0785 112 F 0.0070 0.9228 0.0702 113 Y 0.0050 0.9465 0.0485 114 G 0.0048 0.9496 0.0456 115 A 0.0048 0.9532 0.0419 116 L 0.0047 0.9590 0.0363 117 M 0.0047 0.9602 0.0351 118 M 0.0047 0.9600 0.0353 119 L 0.0047 0.9597 0.0356 120 L 0.0047 0.9582 0.0371 121 T 0.0047 0.9554 0.0399 122 G 0.0048 0.9423 0.0529 123 L 0.0053 0.9222 0.0725 124 Q 0.0070 0.8702 0.1228 125 T 0.0114 0.7243 0.2643 126 N 0.0398 0.3908 0.5694 127 W 0.0682 0.0672 0.8646 128 P 0.0709 0.0452 0.8839 129 T 0.1920 0.0374 0.7706 130 V 0.5344 0.0172 0.4483 131 P 0.8441 0.0072 0.1487 132 K 0.9150 0.0046 0.0804 133 L 0.9108 0.0051 0.0841 134 F 0.8902 0.0064 0.1035 135 I 0.7696 0.0104 0.2200 136 S 0.4611 0.0217 0.5171 137 A 0.2511 0.0610 0.6878 138 I 0.1698 0.1109 0.7192 139 H 0.1340 0.1353 0.7306 140 I 0.1066 0.1416 0.7517 141 G 0.0975 0.1928 0.7097 142 S 0.0716 0.3676 0.5608 143 D 0.0821 0.3812 0.5367 144 F 0.1108 0.3163 0.5728 145 G 0.1144 0.2156 0.6700 146 G 0.1137 0.1769 0.7094 147 S 0.1028 0.2312 0.6659 148 F 0.0801 0.2815 0.6384 149 S 0.0669 0.3357 0.5974 150 A 0.0623 0.3999 0.5378 151 V 0.0716 0.4800 0.4484 152 T 0.0671 0.5303 0.4025 153 N 0.0554 0.5454 0.3992 154 G 0.0388 0.5817 0.3795 155 L 0.0381 0.6281 0.3338 156 G 0.0269 0.6923 0.2808 157 Y 0.0210 0.7840 0.1950 158 R 0.0155 0.8244 0.1601 159 Q 0.0085 0.8947 0.0967 160 S 0.0073 0.9100 0.0827 161 D 0.0070 0.9162 0.0768 162 Y 0.0052 0.9386 0.0563 163 E 0.0048 0.9509 0.0444 164 A 0.0047 0.9542 0.0411 165 A 0.0047 0.9570 0.0383 166 I 0.0047 0.9572 0.0380 167 A 0.0047 0.9558 0.0395 168 Q 0.0048 0.9558 0.0394 169 M 0.0048 0.9531 0.0421 170 T 0.0051 0.9425 0.0524 171 A 0.0060 0.9049 0.0891 172 D 0.0106 0.8033 0.1861 173 Y 0.0507 0.3522 0.5972 174 G 0.0403 0.0341 0.9256 175 V 0.0867 0.0133 0.9000 176 P 0.2804 0.0228 0.6969 177 H 0.7005 0.0337 0.2658 178 L 0.7388 0.0359 0.2253 179 S 0.5917 0.0397 0.3686 180 L 0.1701 0.3720 0.4579 181 Y 0.0890 0.4447 0.4664 182 R 0.0628 0.5547 0.3825 183 D 0.0568 0.5908 0.3523 184 A 0.0630 0.5123 0.4248 185 G 0.0689 0.4524 0.4787 186 M 0.0705 0.4467 0.4828 187 T 0.0779 0.3648 0.5573 188 F 0.0514 0.4406 0.5080 189 A 0.0518 0.3980 0.5502 190 I 0.0581 0.3837 0.5581 191 P 0.0263 0.5070 0.4667 192 A 0.0343 0.4851 0.4806 193 Q 0.0449 0.5099 0.4452 194 A 0.0386 0.6161 0.3454 195 A 0.0435 0.6123 0.3442 196 I 0.0703 0.5417 0.3880 197 Y 0.1297 0.3094 0.5609 198 S 0.1023 0.1645 0.7332 199 V 0.0683 0.1622 0.7695 200 D 0.0656 0.1137 0.8207 201 T 0.0799 0.1038 0.8162 202 L 0.1946 0.0634 0.7420 203 H 0.1768 0.0349 0.7883 204 P 0.0739 0.0856 0.8406 205 N 0.0445 0.0982 0.8573 206 N 0.0107 0.8745 0.1149 207 A 0.0110 0.9235 0.0654 208 G 0.0063 0.9312 0.0625 209 H 0.0049 0.9544 0.0407 210 R 0.0047 0.9582 0.0371 211 V 0.0048 0.9572 0.0380 212 I 0.0048 0.9540 0.0413 213 A 0.0047 0.9567 0.0385 214 R 0.0050 0.9549 0.0401 215 K 0.0048 0.9507 0.0445 216 L 0.0049 0.9492 0.0459 217 Q 0.0047 0.9543 0.0409 218 S 0.0048 0.9487 0.0465 219 F 0.0049 0.9416 0.0534 220 L 0.0064 0.9263 0.0673 221 D 0.0062 0.8924 0.1013 222 S 0.0119 0.7858 0.2024 223 H 0.0258 0.6463 0.3278 224 F 0.0565 0.4808 0.4627 225 L 0.0412 0.4369 0.5219 226 E 0.0547 0.3588 0.5865 227 H 0.0635 0.2896 0.6469 228 H 0.0641 0.2463 0.6896 229 H 0.0729 0.2096 0.7176 230 H 0.0761 0.1853 0.7386 231 H 0.0650 0.1202 0.8148 232 H 0.0500 0.0407 0.9093