# This file is the result of combining several RDB files, specifically # T0253.t04.dssp-ebghstl.rdb (weight 1.53986) # T0253.t04.stride-ebghtl.rdb (weight 1.24869) # T0253.t04.str2.rdb (weight 1.54758) # T0253.t04.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 T0253.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0253 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0253.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1378 # # ============================================ # Comments from T0253.t04.stride-ebghtl.rdb # ============================================ # TARGET T0253 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0253.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1378 # # ============================================ # Comments from T0253.t04.str2.rdb # ============================================ # TARGET T0253 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0253.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1378 # # ============================================ # Comments from T0253.t04.alpha.rdb # ============================================ # TARGET T0253 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0253.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1378 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0289 0.3395 0.6316 2 E 0.0249 0.7383 0.2368 3 A 0.0241 0.8522 0.1237 4 L 0.0250 0.8612 0.1139 5 K 0.0323 0.8665 0.1013 6 R 0.0293 0.8366 0.1341 7 K 0.0347 0.8026 0.1628 8 I 0.0971 0.7048 0.1981 9 E 0.1402 0.5950 0.2649 10 E 0.1524 0.5610 0.2865 11 E 0.1052 0.3399 0.5549 12 G 0.0833 0.1335 0.7833 13 V 0.1667 0.1114 0.7219 14 V 0.3164 0.0863 0.5973 15 L 0.1976 0.0861 0.7163 16 S 0.0989 0.2145 0.6866 17 D 0.0783 0.2348 0.6869 18 Q 0.2167 0.1587 0.6245 19 V 0.5374 0.0622 0.4005 20 L 0.6671 0.0455 0.2874 21 K 0.5810 0.0440 0.3749 22 V 0.3813 0.1181 0.5006 23 D 0.2201 0.1575 0.6224 24 S 0.1750 0.2752 0.5498 25 F 0.1593 0.3120 0.5287 26 L 0.1602 0.3548 0.4850 27 N 0.0973 0.3357 0.5670 28 H 0.0770 0.3290 0.5940 29 Q 0.1047 0.2975 0.5978 30 I 0.1060 0.2250 0.6690 31 D 0.0813 0.0783 0.8404 32 P 0.0055 0.9202 0.0744 33 L 0.0049 0.9468 0.0483 34 L 0.0048 0.9521 0.0431 35 M 0.0047 0.9565 0.0388 36 Q 0.0047 0.9565 0.0388 37 R 0.0048 0.9517 0.0435 38 I 0.0048 0.9482 0.0470 39 G 0.0047 0.9566 0.0387 40 D 0.0047 0.9611 0.0342 41 E 0.0047 0.9601 0.0352 42 F 0.0048 0.9550 0.0402 43 A 0.0048 0.9490 0.0461 44 S 0.0051 0.9306 0.0643 45 R 0.0066 0.8973 0.0962 46 F 0.0196 0.7674 0.2130 47 A 0.0127 0.5921 0.3952 48 K 0.0185 0.3990 0.5825 49 D 0.0487 0.1652 0.7861 50 G 0.0592 0.0422 0.8986 51 I 0.1451 0.0115 0.8433 52 T 0.3347 0.0381 0.6272 53 K 0.8980 0.0043 0.0977 54 I 0.9268 0.0032 0.0700 55 V 0.9122 0.0065 0.0814 56 T 0.7552 0.0076 0.2372 57 I 0.3152 0.0712 0.6135 58 E 0.1296 0.2587 0.6117 59 S 0.0604 0.3674 0.5722 60 S 0.0539 0.2415 0.7045 61 G 0.0526 0.1852 0.7622 62 I 0.0659 0.3296 0.6045 63 A 0.0274 0.7413 0.2314 64 P 0.0068 0.9274 0.0658 65 A 0.0058 0.9436 0.0506 66 V 0.0049 0.9563 0.0388 67 M 0.0052 0.9573 0.0375 68 T 0.0052 0.9576 0.0372 69 G 0.0047 0.9565 0.0388 70 L 0.0048 0.9547 0.0405 71 K 0.0055 0.9414 0.0531 72 L 0.0440 0.5789 0.3770 73 G 0.0347 0.0251 0.9403 74 V 0.0587 0.0089 0.9324 75 P 0.1844 0.0109 0.8047 76 V 0.7323 0.0290 0.2387 77 V 0.8128 0.0410 0.1461 78 F 0.8375 0.0431 0.1194 79 A 0.7569 0.0567 0.1864 80 R 0.6043 0.0653 0.3304 81 K 0.4543 0.0933 0.4524 82 H 0.3270 0.1180 0.5550 83 K 0.2889 0.0986 0.6125 84 S 0.2943 0.0772 0.6285 85 L 0.3097 0.0503 0.6400 86 T 0.2321 0.0466 0.7213 87 L 0.1808 0.0899 0.7293 88 T 0.1617 0.0910 0.7473 89 D 0.1154 0.1863 0.6983 90 N 0.2074 0.1537 0.6389 91 L 0.5420 0.1136 0.3444 92 L 0.6598 0.0630 0.2772 93 T 0.6084 0.0459 0.3458 94 A 0.4551 0.1298 0.4151 95 S 0.4372 0.1452 0.4175 96 V 0.4810 0.1952 0.3238 97 Y 0.5246 0.1549 0.3205 98 S 0.4114 0.1608 0.4279 99 F 0.2331 0.1475 0.6195 100 T 0.2239 0.1537 0.6225 101 K 0.2026 0.1527 0.6447 102 Q 0.2367 0.0936 0.6696 103 T 0.4490 0.0674 0.4837 104 E 0.4718 0.0851 0.4431 105 S 0.5454 0.0604 0.3942 106 Q 0.7888 0.0270 0.1842 107 I 0.8738 0.0124 0.1138 108 A 0.8632 0.0100 0.1268 109 V 0.8237 0.0134 0.1628 110 S 0.5924 0.0283 0.3793 111 G 0.3148 0.0603 0.6250 112 T 0.3244 0.0531 0.6225 113 H 0.4646 0.0526 0.4828 114 L 0.2675 0.0376 0.6948 115 S 0.1178 0.0522 0.8299 116 D 0.0321 0.1327 0.8353 117 Q 0.0518 0.0661 0.8821 118 D 0.1585 0.0249 0.8166 119 H 0.6469 0.0066 0.3465 120 V 0.9219 0.0036 0.0745 121 L 0.9325 0.0033 0.0642 122 I 0.9312 0.0033 0.0656 123 I 0.9043 0.0063 0.0894 124 D 0.6162 0.0262 0.3576 125 D 0.2803 0.0844 0.6354 126 F 0.2807 0.1736 0.5457 127 L 0.2523 0.2786 0.4692 128 A 0.1630 0.2558 0.5812 129 N 0.0686 0.1814 0.7500 130 G 0.0287 0.3091 0.6622 131 Q 0.0245 0.6760 0.2995 132 A 0.0125 0.8738 0.1136 133 A 0.0047 0.9586 0.0368 134 H 0.0047 0.9612 0.0342 135 G 0.0047 0.9609 0.0344 136 L 0.0047 0.9600 0.0353 137 V 0.0046 0.9616 0.0338 138 S 0.0046 0.9619 0.0335 139 I 0.0046 0.9618 0.0336 140 V 0.0046 0.9613 0.0340 141 K 0.0047 0.9586 0.0367 142 Q 0.0052 0.9362 0.0586 143 A 0.0381 0.4135 0.5484 144 G 0.0448 0.0183 0.9368 145 A 0.0730 0.0181 0.9089 146 S 0.2775 0.0581 0.6643 147 I 0.8527 0.0095 0.1378 148 A 0.8701 0.0144 0.1154 149 G 0.9023 0.0071 0.0906 150 I 0.9233 0.0034 0.0733 151 G 0.9242 0.0038 0.0720 152 I 0.9283 0.0035 0.0682 153 V 0.9020 0.0075 0.0905 154 I 0.8086 0.0100 0.1814 155 E 0.5805 0.0229 0.3966 156 K 0.2033 0.1067 0.6900 157 S 0.1027 0.1313 0.7659 158 F 0.0737 0.1497 0.7766 159 Q 0.0615 0.1366 0.8019 160 P 0.0396 0.2627 0.6977 161 G 0.0456 0.4201 0.5343 162 R 0.0370 0.6799 0.2830 163 D 0.0097 0.9171 0.0732 164 E 0.0086 0.9337 0.0577 165 L 0.0069 0.9424 0.0507 166 V 0.0091 0.9255 0.0654 167 K 0.0104 0.8559 0.1338 168 L 0.0436 0.3429 0.6136 169 G 0.0440 0.0231 0.9329 170 Y 0.0952 0.0101 0.8946 171 R 0.2674 0.0123 0.7203 172 V 0.6543 0.0475 0.2982 173 E 0.7498 0.0607 0.1895 174 S 0.8459 0.0434 0.1107 175 L 0.8662 0.0304 0.1034 176 A 0.8154 0.0302 0.1544 177 R 0.7229 0.0317 0.2454 178 I 0.3606 0.2061 0.4334 179 Q 0.1788 0.3421 0.4791 180 S 0.1354 0.4256 0.4390 181 L 0.0488 0.6931 0.2581 182 E 0.0470 0.6981 0.2549 183 E 0.0413 0.6245 0.3342 184 G 0.0728 0.4529 0.4743 185 K 0.1784 0.4013 0.4202 186 V 0.3087 0.3033 0.3880 187 S 0.3180 0.2559 0.4260 188 F 0.2570 0.2363 0.5067 189 V 0.1785 0.2473 0.5743 190 Q 0.1718 0.2555 0.5727 191 E 0.1886 0.1987 0.6127 192 V 0.2171 0.1618 0.6212 193 H 0.1331 0.0886 0.7783 194 S 0.0552 0.0487 0.8961