# This file is the result of combining several RDB files, specifically # T0390.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0390.t2k.stride-ebghtl.rdb (weight 1.24869) # T0390.t2k.str.rdb (weight 1.53983) # 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 T0390.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0390 # 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 T0390.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 117 # # ============================================ # Comments from T0390.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0390 # 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 T0390.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 117 # # ============================================ # Comments from T0390.t2k.str.rdb # ============================================ # TARGET T0390 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0390.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 117 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0570 0.1062 0.8368 2 A 0.0711 0.1897 0.7392 3 P 0.0650 0.3666 0.5684 4 E 0.0390 0.6751 0.2859 5 H 0.0426 0.6833 0.2741 6 H 0.0461 0.6716 0.2823 7 H 0.0434 0.6989 0.2577 8 H 0.0216 0.7583 0.2201 9 H 0.0069 0.9083 0.0848 10 H 0.0055 0.9427 0.0518 11 D 0.0047 0.9603 0.0351 12 Y 0.0043 0.9669 0.0287 13 D 0.0038 0.9718 0.0244 14 I 0.0037 0.9717 0.0245 15 P 0.0037 0.9695 0.0267 16 T 0.0037 0.9682 0.0280 17 T 0.0041 0.9666 0.0293 18 E 0.0041 0.9591 0.0368 19 N 0.0045 0.9389 0.0566 20 L 0.0049 0.8926 0.1024 21 Y 0.0083 0.8108 0.1808 22 F 0.0157 0.7196 0.2647 23 Q 0.0244 0.6192 0.3564 24 G 0.0327 0.5823 0.3850 25 A 0.0452 0.6038 0.3509 26 M 0.0598 0.6367 0.3035 27 D 0.0946 0.5595 0.3459 28 A 0.1574 0.4711 0.3715 29 A 0.2232 0.3577 0.4190 30 D 0.2724 0.2290 0.4986 31 R 0.2875 0.0975 0.6150 32 H 0.3628 0.0457 0.5915 33 T 0.6847 0.0265 0.2888 34 V 0.8391 0.0196 0.1413 35 F 0.8373 0.0223 0.1404 36 W 0.7249 0.0248 0.2502 37 N 0.3548 0.0295 0.6157 38 S 0.1529 0.0454 0.8017 39 S 0.0940 0.0535 0.8525 40 N 0.0876 0.0576 0.8548 41 P 0.1342 0.2162 0.6497 42 K 0.2488 0.2871 0.4641 43 F 0.3485 0.2855 0.3661 44 R 0.3199 0.2206 0.4595 45 N 0.1368 0.1604 0.7028 46 E 0.0426 0.0704 0.8871 47 D 0.0846 0.0228 0.8925 48 Y 0.5840 0.0055 0.4106 49 T 0.9114 0.0026 0.0860 50 I 0.9365 0.0027 0.0608 51 H 0.9311 0.0035 0.0654 52 V 0.8339 0.0029 0.1633 53 Q 0.6582 0.0060 0.3358 54 L 0.2935 0.0578 0.6487 55 N 0.1194 0.0912 0.7894 56 D 0.2120 0.1014 0.6866 57 Y 0.4237 0.0557 0.5207 58 V 0.6647 0.0292 0.3061 59 D 0.6932 0.0134 0.2934 60 I 0.8171 0.0088 0.1741 61 I 0.8247 0.0065 0.1689 62 C 0.6290 0.0094 0.3616 63 P 0.3925 0.0195 0.5879 64 H 0.2209 0.0325 0.7466 65 Y 0.1203 0.0398 0.8399 66 E 0.0687 0.0394 0.8919 67 D 0.0405 0.0596 0.9000 68 H 0.0396 0.0639 0.8966 69 S 0.0684 0.0499 0.8817 70 V 0.0788 0.0379 0.8833 71 A 0.0690 0.0405 0.8906 72 D 0.0583 0.0899 0.8518 73 A 0.0702 0.0709 0.8589 74 A 0.2002 0.0758 0.7240 75 M 0.4642 0.0416 0.4942 76 E 0.7316 0.0191 0.2493 77 Q 0.9084 0.0079 0.0837 78 Y 0.9452 0.0039 0.0509 79 I 0.9651 0.0035 0.0314 80 L 0.9696 0.0028 0.0276 81 Y 0.9606 0.0032 0.0362 82 L 0.9196 0.0030 0.0774 83 V 0.6870 0.0037 0.3093 84 E 0.2782 0.0125 0.7093 85 H 0.0196 0.7252 0.2551 86 E 0.0091 0.7776 0.2133 87 E 0.0112 0.8229 0.1659 88 Y 0.0262 0.7939 0.1798 89 Q 0.0664 0.6188 0.3148 90 L 0.1130 0.4511 0.4359 91 C 0.1754 0.2121 0.6125 92 Q 0.2119 0.1220 0.6661 93 P 0.2195 0.1519 0.6286 94 Q 0.1352 0.1272 0.7375 95 S 0.1149 0.1099 0.7753 96 K 0.0691 0.1067 0.8242 97 D 0.0686 0.0841 0.8473 98 Q 0.2668 0.0430 0.6902 99 V 0.5626 0.0153 0.4220 100 R 0.8195 0.0077 0.1728 101 W 0.8684 0.0085 0.1231 102 Q 0.8081 0.0102 0.1817 103 C 0.4759 0.0150 0.5091 104 N 0.1762 0.0173 0.8065 105 R 0.0784 0.0179 0.9036 106 P 0.0896 0.0392 0.8713 107 S 0.0815 0.0580 0.8605 108 A 0.0268 0.0607 0.9125 109 K 0.0214 0.0787 0.8999 110 H 0.0567 0.0793 0.8639 111 G 0.0747 0.0536 0.8717 112 P 0.1341 0.1555 0.7104 113 E 0.2091 0.2367 0.5542 114 K 0.4173 0.1642 0.4185 115 L 0.4588 0.2207 0.3205 116 S 0.5240 0.2037 0.2724 117 E 0.5556 0.2390 0.2054 118 K 0.5138 0.2765 0.2096 119 F 0.5313 0.2500 0.2186 120 Q 0.5600 0.2254 0.2146 121 R 0.5849 0.1695 0.2456 122 F 0.4897 0.1189 0.3914 123 T 0.2423 0.0447 0.7129 124 P 0.1326 0.0848 0.7826 125 F 0.0681 0.0761 0.8558 126 T 0.0549 0.1252 0.8198 127 L 0.0517 0.1078 0.8405 128 G 0.1233 0.1298 0.7469 129 K 0.3317 0.0889 0.5793 130 E 0.5738 0.0644 0.3618 131 F 0.6317 0.0370 0.3313 132 K 0.3376 0.0262 0.6363 133 E 0.0387 0.0284 0.9329 134 G 0.0204 0.0200 0.9596 135 H 0.2233 0.0143 0.7624 136 S 0.6069 0.0045 0.3886 137 Y 0.9526 0.0024 0.0449 138 Y 0.9766 0.0024 0.0211 139 Y 0.9782 0.0024 0.0194 140 I 0.9589 0.0025 0.0386 141 S 0.8137 0.0030 0.1833 142 K 0.3761 0.0069 0.6170 143 P 0.1300 0.0157 0.8542 144 I 0.0505 0.0329 0.9166 145 H 0.0266 0.0692 0.9042 146 Q 0.0297 0.0872 0.8831 147 H 0.0295 0.2372 0.7333 148 E 0.0272 0.2870 0.6858 149 D 0.0501 0.3199 0.6301 150 R 0.1108 0.3581 0.5311 151 C 0.1406 0.4043 0.4550 152 L 0.1435 0.3824 0.4741 153 R 0.1507 0.2654 0.5839 154 L 0.1154 0.1352 0.7494 155 K 0.1871 0.0318 0.7811 156 V 0.4866 0.0122 0.5012 157 T 0.8520 0.0051 0.1429 158 V 0.9032 0.0035 0.0933 159 S 0.8653 0.0037 0.1310 160 G 0.5293 0.0125 0.4583 161 K 0.1092 0.0430 0.8478 162 I 0.0566 0.0534 0.8900 163 T 0.1667 0.0569 0.7764 164 H 0.3223 0.0271 0.6505 165 S 0.6927 0.0166 0.2907 166 P 0.8074 0.0135 0.1791 167 Q 0.8255 0.0158 0.1587 168 A 0.7884 0.0204 0.1911 169 H 0.6298 0.0215 0.3487 170 V 0.3610 0.0178 0.6213 171 N 0.1822 0.0177 0.8001 172 P 0.0661 0.0248 0.9091 173 Q 0.0248 0.1018 0.8734 174 E 0.0207 0.1236 0.8558 175 K 0.0404 0.0953 0.8643 176 R 0.0753 0.0630 0.8617 177 L 0.0902 0.0530 0.8568 178 A 0.0425 0.1277 0.8298 179 A 0.0237 0.1260 0.8503 180 D 0.0316 0.0990 0.8694 181 D 0.0297 0.0541 0.9162 182 P 0.0102 0.0188 0.9710