# This file is the result of combining several RDB files, specifically # T0303.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0303.t2k.stride-ebghtl.rdb (weight 1.24869) # T0303.t2k.str2.rdb (weight 1.54758) # T0303.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 T0303.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0303 # 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 T0303.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 2283 # # ============================================ # Comments from T0303.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0303 # 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 T0303.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 2283 # # ============================================ # Comments from T0303.t2k.str2.rdb # ============================================ # TARGET T0303 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0303.t2k-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 2283 # # ============================================ # Comments from T0303.t2k.alpha.rdb # ============================================ # TARGET T0303 # 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 T0303.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 2283 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0565 0.0574 0.8861 2 T 0.0964 0.0516 0.8520 3 Q 0.1590 0.0443 0.7967 4 F 0.3853 0.0187 0.5959 5 K 0.6017 0.0349 0.3634 6 L 0.9098 0.0051 0.0851 7 I 0.9266 0.0036 0.0698 8 G 0.9203 0.0040 0.0757 9 F 0.8814 0.0053 0.1132 10 D 0.4773 0.0111 0.5116 11 L 0.0916 0.1095 0.7989 12 D 0.0648 0.0361 0.8991 13 G 0.0904 0.0586 0.8510 14 T 0.3984 0.0506 0.5510 15 L 0.6287 0.0547 0.3166 16 V 0.5157 0.0858 0.3985 17 N 0.2309 0.1015 0.6675 18 S 0.0640 0.1885 0.7474 19 L 0.0497 0.5035 0.4468 20 P 0.0116 0.8522 0.1362 21 D 0.0094 0.8917 0.0989 22 L 0.0061 0.9255 0.0684 23 A 0.0053 0.9354 0.0593 24 L 0.0050 0.9464 0.0487 25 S 0.0050 0.9489 0.0461 26 I 0.0048 0.9480 0.0471 27 N 0.0049 0.9466 0.0485 28 S 0.0049 0.9449 0.0502 29 A 0.0049 0.9435 0.0516 30 L 0.0058 0.9276 0.0666 31 K 0.0061 0.9032 0.0907 32 D 0.0090 0.8375 0.1534 33 V 0.0436 0.5381 0.4183 34 N 0.0382 0.0842 0.8775 35 L 0.0588 0.0733 0.8679 36 P 0.0758 0.0919 0.8324 37 Q 0.0747 0.1848 0.7405 38 A 0.0606 0.2462 0.6932 39 S 0.0346 0.5880 0.3774 40 E 0.0149 0.8556 0.1295 41 N 0.0162 0.8673 0.1165 42 L 0.0174 0.8828 0.0998 43 V 0.0207 0.8791 0.1001 44 M 0.0216 0.8730 0.1054 45 T 0.0222 0.8475 0.1303 46 W 0.0324 0.7733 0.1942 47 I 0.0398 0.6575 0.3028 48 G 0.0449 0.4627 0.4924 49 N 0.0418 0.3735 0.5847 50 G 0.0429 0.4117 0.5454 51 A 0.0324 0.6271 0.3405 52 D 0.0316 0.7566 0.2118 53 V 0.0348 0.8273 0.1379 54 L 0.0361 0.8467 0.1172 55 S 0.0401 0.8413 0.1186 56 Q 0.0412 0.8177 0.1410 57 R 0.0425 0.7585 0.1990 58 A 0.0479 0.6634 0.2887 59 V 0.0426 0.5565 0.4009 60 D 0.0258 0.6143 0.3599 61 W 0.0268 0.6917 0.2815 62 A 0.0314 0.7202 0.2484 63 C 0.0311 0.7385 0.2305 64 T 0.0259 0.7543 0.2198 65 Q 0.0208 0.7904 0.1888 66 A 0.0192 0.7686 0.2122 67 E 0.0196 0.7518 0.2286 68 K 0.0176 0.7498 0.2326 69 E 0.0207 0.7169 0.2624 70 L 0.0241 0.6313 0.3446 71 T 0.0266 0.5254 0.4480 72 E 0.0176 0.7407 0.2418 73 D 0.0140 0.7651 0.2209 74 E 0.0166 0.7623 0.2211 75 F 0.0133 0.8073 0.1794 76 K 0.0096 0.8483 0.1421 77 Y 0.0087 0.8512 0.1402 78 F 0.0090 0.8454 0.1456 79 K 0.0075 0.8691 0.1234 80 R 0.0068 0.8944 0.0988 81 Q 0.0070 0.8863 0.1067 82 F 0.0074 0.8626 0.1300 83 G 0.0068 0.8415 0.1517 84 F 0.0060 0.9076 0.0863 85 Y 0.0080 0.9131 0.0789 86 Y 0.0086 0.9126 0.0788 87 G 0.0075 0.9027 0.0897 88 E 0.0085 0.8925 0.0990 89 N 0.0116 0.8422 0.1462 90 L 0.0208 0.7294 0.2498 91 C 0.0303 0.6185 0.3512 92 N 0.0270 0.5641 0.4089 93 I 0.0344 0.4543 0.5113 94 S 0.0685 0.2404 0.6912 95 R 0.0910 0.1992 0.7098 96 L 0.1015 0.1846 0.7139 97 Y 0.0656 0.0684 0.8660 98 P 0.0145 0.3607 0.6248 99 N 0.0232 0.2768 0.7000 100 V 0.0111 0.8502 0.1387 101 K 0.0048 0.9492 0.0460 102 E 0.0047 0.9523 0.0429 103 T 0.0048 0.9563 0.0389 104 L 0.0048 0.9562 0.0390 105 E 0.0049 0.9576 0.0375 106 A 0.0050 0.9575 0.0375 107 L 0.0051 0.9548 0.0401 108 K 0.0051 0.9436 0.0514 109 A 0.0059 0.8999 0.0942 110 Q 0.0441 0.2870 0.6689 111 G 0.0408 0.0149 0.9443 112 Y 0.1077 0.0080 0.8843 113 I 0.5206 0.0076 0.4718 114 L 0.9260 0.0037 0.0704 115 A 0.9305 0.0034 0.0661 116 V 0.9307 0.0033 0.0661 117 V 0.8780 0.0067 0.1152 118 T 0.4222 0.0245 0.5533 119 N 0.0783 0.0314 0.8903 120 K 0.0622 0.0490 0.8888 121 P 0.0700 0.2002 0.7298 122 T 0.0143 0.7371 0.2486 123 K 0.0075 0.8266 0.1660 124 H 0.0073 0.8463 0.1464 125 V 0.0058 0.9269 0.0673 126 Q 0.0048 0.9488 0.0464 127 P 0.0047 0.9555 0.0398 128 I 0.0047 0.9570 0.0383 129 L 0.0048 0.9528 0.0424 130 T 0.0051 0.9354 0.0595 131 A 0.0061 0.8779 0.1161 132 F 0.0436 0.5066 0.4498 133 G 0.0489 0.0632 0.8879 134 I 0.0596 0.1224 0.8180 135 D 0.0591 0.3337 0.6072 136 H 0.0790 0.4850 0.4359 137 L 0.1875 0.4489 0.3636 138 F 0.2877 0.3447 0.3676 139 S 0.2571 0.3822 0.3607 140 E 0.4474 0.3221 0.2306 141 M 0.5715 0.2264 0.2022 142 L 0.5577 0.1495 0.2929 143 G 0.3084 0.1089 0.5828 144 G 0.0736 0.3106 0.6158 145 Q 0.0442 0.3766 0.5792 146 S 0.0583 0.3954 0.5463 147 L 0.0861 0.2752 0.6387 148 P 0.0674 0.2339 0.6987 149 E 0.0788 0.1807 0.7406 150 I 0.0953 0.0877 0.8169 151 K 0.1029 0.0486 0.8485 152 P 0.0876 0.0562 0.8562 153 H 0.0784 0.0525 0.8691 154 P 0.0198 0.5725 0.4077 155 A 0.0107 0.8455 0.1439 156 P 0.0051 0.9304 0.0645 157 F 0.0048 0.9566 0.0386 158 Y 0.0048 0.9578 0.0374 159 Y 0.0047 0.9595 0.0357 160 L 0.0047 0.9598 0.0356 161 C 0.0048 0.9582 0.0370 162 G 0.0053 0.9478 0.0469 163 K 0.0067 0.9077 0.0856 164 F 0.0463 0.4328 0.5210 165 G 0.0386 0.0223 0.9391 166 L 0.0771 0.0088 0.9140 167 Y 0.0842 0.0116 0.9042 168 P 0.0398 0.5422 0.4181 169 K 0.0393 0.5549 0.4058 170 Q 0.2929 0.3872 0.3198 171 I 0.8249 0.0170 0.1581 172 L 0.8813 0.0093 0.1094 173 F 0.8977 0.0065 0.0958 174 V 0.7686 0.0404 0.1910 175 G 0.3865 0.0300 0.5835 176 D 0.1210 0.0271 0.8518 177 S 0.0684 0.0441 0.8875 178 Q 0.0130 0.6421 0.3449 179 N 0.0100 0.7523 0.2377 180 D 0.0106 0.8468 0.1426 181 I 0.0065 0.9425 0.0510 182 F 0.0051 0.9510 0.0439 183 A 0.0052 0.9546 0.0403 184 A 0.0050 0.9535 0.0415 185 H 0.0052 0.9442 0.0507 186 S 0.0065 0.8740 0.1196 187 A 0.0422 0.3939 0.5639 188 G 0.0472 0.0249 0.9279 189 C 0.0968 0.0091 0.8941 190 A 0.4375 0.0267 0.5358 191 V 0.9198 0.0039 0.0763 192 V 0.9255 0.0043 0.0702 193 G 0.9246 0.0036 0.0718 194 L 0.8786 0.0070 0.1144 195 T 0.5804 0.0217 0.3980 196 Y 0.1560 0.0463 0.7977 197 G 0.0783 0.0661 0.8557 198 Y 0.0934 0.0949 0.8117 199 N 0.0850 0.1080 0.8070 200 Y 0.0612 0.1867 0.7521 201 N 0.0441 0.3797 0.5762 202 I 0.0315 0.4848 0.4837 203 P 0.0260 0.6554 0.3185 204 I 0.0204 0.7202 0.2594 205 A 0.0195 0.7434 0.2371 206 Q 0.0279 0.6372 0.3349 207 S 0.0573 0.3733 0.5694 208 K 0.0858 0.0985 0.8158 209 P 0.1249 0.0601 0.8150 210 D 0.3310 0.0926 0.5764 211 W 0.8116 0.0382 0.1503 212 I 0.8533 0.0262 0.1205 213 F 0.7436 0.0334 0.2231 214 D 0.1919 0.0994 0.7087 215 D 0.1081 0.0393 0.8526 216 F 0.0083 0.8324 0.1593 217 A 0.0061 0.8961 0.0978 218 D 0.0063 0.9087 0.0850 219 I 0.0061 0.9140 0.0799 220 L 0.0063 0.8846 0.1091 221 K 0.0076 0.8088 0.1837 222 I 0.0120 0.7169 0.2711 223 T 0.0710 0.4654 0.4636 224 Q 0.0191 0.2310 0.7499