# This file is the result of combining several RDB files, specifically # T0293.t06.dssp-ebghstl.rdb (weight 1.53986) # T0293.t06.stride-ebghtl.rdb (weight 1.24869) # T0293.t06.str2.rdb (weight 1.54758) # T0293.t06.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 T0293.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0293 # Using neural net t06-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 T0293.t06-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 6869 # # ============================================ # Comments from T0293.t06.stride-ebghtl.rdb # ============================================ # TARGET T0293 # Using neural net t06-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 T0293.t06-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 6869 # # ============================================ # Comments from T0293.t06.str2.rdb # ============================================ # TARGET T0293 # Using neural net t06-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 T0293.t06-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 6869 # # ============================================ # Comments from T0293.t06.alpha.rdb # ============================================ # TARGET T0293 # Using neural net t06-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 T0293.t06-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 6869 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.1981 0.0118 0.7902 2 S 0.3980 0.0151 0.5870 3 L 0.3806 0.0267 0.5927 4 N 0.3072 0.0243 0.6684 5 F 0.1605 0.0964 0.7431 6 K 0.1195 0.0839 0.7967 7 D 0.1032 0.0220 0.8748 8 P 0.0102 0.6230 0.3668 9 E 0.0164 0.6908 0.2929 10 A 0.0292 0.7756 0.1952 11 V 0.0866 0.6841 0.2294 12 R 0.1947 0.6011 0.2042 13 A 0.1872 0.6655 0.1473 14 L 0.1461 0.6813 0.1725 15 T 0.1800 0.6361 0.1839 16 C 0.2109 0.6213 0.1678 17 T 0.2281 0.5875 0.1844 18 L 0.2103 0.5238 0.2660 19 L 0.1892 0.4216 0.3892 20 R 0.1070 0.5214 0.3715 21 E 0.0520 0.5913 0.3568 22 D 0.0440 0.5689 0.3871 23 F 0.1038 0.3406 0.5555 24 G 0.1014 0.1275 0.7711 25 L 0.2077 0.1032 0.6891 26 S 0.2993 0.1019 0.5988 27 I 0.3352 0.0748 0.5900 28 D 0.3039 0.0483 0.6478 29 I 0.1967 0.0437 0.7596 30 P 0.1214 0.0562 0.8224 31 L 0.0354 0.4814 0.4833 32 E 0.0406 0.5550 0.4044 33 R 0.0947 0.4972 0.4082 34 L 0.2616 0.1580 0.5804 35 I 0.2078 0.0768 0.7154 36 P 0.1656 0.0926 0.7418 37 T 0.1600 0.1042 0.7358 38 V 0.1889 0.0660 0.7451 39 P 0.1579 0.0919 0.7502 40 L 0.1410 0.1568 0.7022 41 R 0.1110 0.1707 0.7184 42 L 0.0346 0.6272 0.3382 43 N 0.0346 0.6786 0.2868 44 Y 0.0341 0.7817 0.1842 45 I 0.0287 0.8582 0.1131 46 H 0.0160 0.9043 0.0798 47 W 0.0116 0.9251 0.0633 48 V 0.0059 0.9434 0.0507 49 E 0.0060 0.9461 0.0479 50 D 0.0061 0.9310 0.0629 51 L 0.0068 0.8907 0.1025 52 I 0.0166 0.7746 0.2088 53 G 0.0160 0.5653 0.4187 54 H 0.0216 0.4838 0.4946 55 Q 0.0355 0.3669 0.5976 56 D 0.0519 0.2350 0.7131 57 S 0.0371 0.2518 0.7111 58 D 0.0516 0.2053 0.7431 59 K 0.0432 0.2516 0.7052 60 S 0.0670 0.2477 0.6853 61 T 0.0783 0.2117 0.7101 62 L 0.1433 0.0785 0.7782 63 R 0.2517 0.0469 0.7014 64 R 0.7729 0.0125 0.2146 65 G 0.9102 0.0050 0.0848 66 I 0.9201 0.0039 0.0760 67 D 0.8833 0.0046 0.1120 68 I 0.5960 0.0489 0.3551 69 G 0.2256 0.0333 0.7411 70 T 0.1208 0.0729 0.8063 71 G 0.0823 0.1083 0.8094 72 A 0.0622 0.3634 0.5744 73 S 0.0386 0.5556 0.4058 74 C 0.0401 0.7252 0.2348 75 I 0.0238 0.8273 0.1490 76 Y 0.0108 0.9156 0.0736 77 P 0.0062 0.9480 0.0457 78 L 0.0059 0.9483 0.0458 79 L 0.0054 0.9363 0.0583 80 G 0.0064 0.9203 0.0733 81 A 0.0070 0.8639 0.1292 82 T 0.0113 0.7434 0.2452 83 L 0.0728 0.2726 0.6547 84 N 0.0475 0.0761 0.8764 85 G 0.0723 0.0575 0.8702 86 W 0.3541 0.0246 0.6213 87 Y 0.8661 0.0056 0.1283 88 F 0.9240 0.0033 0.0728 89 L 0.9203 0.0049 0.0748 90 A 0.9107 0.0045 0.0847 91 T 0.8595 0.0092 0.1313 92 E 0.6561 0.0091 0.3347 93 V 0.1422 0.0336 0.8242 94 D 0.0827 0.0180 0.8993 95 D 0.0053 0.8955 0.0992 96 M 0.0053 0.9172 0.0775 97 C 0.0048 0.9487 0.0465 98 F 0.0047 0.9583 0.0370 99 N 0.0047 0.9589 0.0364 100 Y 0.0047 0.9571 0.0382 101 A 0.0047 0.9565 0.0388 102 K 0.0047 0.9584 0.0369 103 K 0.0047 0.9558 0.0395 104 N 0.0048 0.9525 0.0427 105 V 0.0048 0.9481 0.0471 106 E 0.0051 0.9259 0.0691 107 Q 0.0068 0.8423 0.1509 108 N 0.0447 0.4001 0.5552 109 N 0.0448 0.0481 0.9071 110 L 0.0637 0.0995 0.8368 111 S 0.0517 0.3088 0.6395 112 D 0.0898 0.2804 0.6298 113 L 0.3965 0.1204 0.4831 114 I 0.6744 0.0167 0.3090 115 K 0.8778 0.0097 0.1124 116 V 0.9163 0.0051 0.0785 117 V 0.8876 0.0104 0.1021 118 K 0.8039 0.0123 0.1838 119 V 0.3680 0.0155 0.6165 120 P 0.1877 0.0318 0.7805 121 Q 0.0189 0.7149 0.2662 122 A 0.0136 0.7936 0.1928 123 T 0.0180 0.8165 0.1655 124 L 0.0343 0.8050 0.1607 125 L 0.0323 0.7757 0.1921 126 M 0.0145 0.8715 0.1140 127 D 0.0083 0.8901 0.1016 128 A 0.0074 0.8703 0.1223 129 L 0.0154 0.7985 0.1861 130 K 0.0208 0.6680 0.3112 131 E 0.0206 0.5380 0.4414 132 E 0.0408 0.3965 0.5626 133 S 0.0463 0.2370 0.7167 134 E 0.0672 0.1314 0.8014 135 I 0.1955 0.0547 0.7498 136 I 0.4006 0.0194 0.5800 137 Y 0.5650 0.0063 0.4287 138 D 0.5856 0.0164 0.3980 139 F 0.9196 0.0037 0.0767 140 C 0.9319 0.0033 0.0647 141 M 0.9249 0.0042 0.0709 142 C 0.8217 0.0106 0.1677 143 N 0.2509 0.0143 0.7348 144 P 0.0882 0.0898 0.8220 145 P 0.0491 0.2342 0.7168 146 F 0.0727 0.3097 0.6176 147 F 0.0905 0.2371 0.6724 148 A 0.0534 0.3644 0.5823 149 N 0.0584 0.3933 0.5483 150 Q 0.0381 0.6437 0.3182 151 L 0.0331 0.7387 0.2282 152 E 0.0397 0.7325 0.2278 153 A 0.0435 0.7200 0.2365 154 K 0.0709 0.5090 0.4201 155 G 0.0566 0.2487 0.6948 156 V 0.0904 0.2423 0.6673 157 N 0.1221 0.1914 0.6865 158 S 0.1012 0.1707 0.7281 159 R 0.0961 0.1465 0.7574 160 N 0.1037 0.0621 0.8342 161 P 0.0862 0.1050 0.8088 162 R 0.0926 0.0957 0.8117 163 R 0.0853 0.0427 0.8719 164 P 0.0623 0.0309 0.9068 165 P 0.0661 0.0413 0.8927 166 P 0.0684 0.1077 0.8239 167 S 0.0381 0.3997 0.5622 168 S 0.0273 0.6468 0.3259 169 V 0.0315 0.6872 0.2813 170 N 0.0414 0.6928 0.2658 171 T 0.0280 0.7691 0.2029 172 G 0.0131 0.8162 0.1708 173 G 0.0161 0.8473 0.1366 174 I 0.0145 0.8867 0.0988 175 T 0.0131 0.9033 0.0835 176 E 0.0174 0.8903 0.0923 177 I 0.0269 0.8473 0.1258 178 M 0.1415 0.6144 0.2441 179 A 0.1487 0.2280 0.6233 180 E 0.0408 0.1406 0.8186 181 G 0.0320 0.0352 0.9328 182 G 0.2408 0.0140 0.7452 183 E 0.8212 0.0045 0.1743 184 L 0.9238 0.0031 0.0731 185 E 0.9164 0.0045 0.0791 186 F 0.9157 0.0049 0.0794 187 V 0.8473 0.0120 0.1407 188 K 0.6725 0.0379 0.2896 189 R 0.3808 0.1087 0.5104 190 I 0.2580 0.2234 0.5187 191 I 0.1883 0.3164 0.4953 192 H 0.1003 0.4498 0.4499 193 D 0.0657 0.5606 0.3738 194 S 0.0408 0.7366 0.2226 195 L 0.0260 0.8158 0.1583 196 Q 0.0306 0.8099 0.1595 197 L 0.0266 0.7928 0.1807 198 G 0.0340 0.7215 0.2445 199 K 0.0419 0.7140 0.2440 200 R 0.0597 0.7248 0.2155 201 L 0.1048 0.6212 0.2740 202 R 0.1232 0.5748 0.3020 203 W 0.1743 0.5572 0.2685 204 Y 0.2267 0.4934 0.2800 205 S 0.2989 0.3852 0.3159 206 C 0.2965 0.3337 0.3697 207 M 0.2719 0.3396 0.3885 208 L 0.1632 0.3220 0.5148 209 G 0.1140 0.2077 0.6783 210 K 0.1715 0.2051 0.6234 211 A 0.1992 0.1808 0.6200 212 C 0.1228 0.0985 0.7787 213 S 0.1013 0.0559 0.8428 214 L 0.0170 0.8266 0.1564 215 A 0.0063 0.9414 0.0523 216 P 0.0057 0.9521 0.0423 217 L 0.0048 0.9569 0.0383 218 K 0.0047 0.9601 0.0352 219 E 0.0047 0.9597 0.0356 220 E 0.0047 0.9599 0.0354 221 L 0.0047 0.9590 0.0363 222 R 0.0048 0.9512 0.0440 223 I 0.0056 0.9130 0.0814 224 Q 0.0406 0.4410 0.5184 225 G 0.0413 0.0172 0.9415 226 V 0.0698 0.0080 0.9221 227 P 0.1721 0.0237 0.8042 228 K 0.6498 0.0524 0.2978 229 V 0.7716 0.0260 0.2024 230 T 0.8506 0.0186 0.1308 231 Y 0.8348 0.0256 0.1396 232 T 0.7677 0.0387 0.1935 233 E 0.6832 0.0725 0.2442 234 F 0.3992 0.1354 0.4654 235 C 0.2818 0.1616 0.5566 236 Q 0.0951 0.1324 0.7726 237 G 0.0658 0.0809 0.8533 238 R 0.2026 0.0826 0.7149 239 T 0.4683 0.0812 0.4505 240 M 0.6323 0.1007 0.2671 241 R 0.7146 0.1111 0.1743 242 W 0.7919 0.0976 0.1105 243 A 0.7872 0.1079 0.1049 244 L 0.7831 0.0978 0.1191 245 A 0.7415 0.1109 0.1477 246 W 0.6441 0.1081 0.2478 247 S 0.5817 0.0994 0.3190 248 F 0.4342 0.0972 0.4686 249 Y 0.2067 0.0651 0.7282 250 D 0.0800 0.0208 0.8992