# This file is the result of combining several RDB files, specifically # T0399.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0399.t2k.stride-ebghtl.rdb (weight 1.24869) # T0399.t2k.str2.rdb (weight 1.54758) # T0399.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 T0399.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0399 # 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 T0399.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 29 # # ============================================ # Comments from T0399.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0399 # 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 T0399.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 29 # # ============================================ # Comments from T0399.t2k.str2.rdb # ============================================ # TARGET T0399 # 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 T0399.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 29 # # ============================================ # Comments from T0399.t2k.alpha.rdb # ============================================ # TARGET T0399 # 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 T0399.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 29 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0500 0.0778 0.8722 2 S 0.0666 0.1904 0.7430 3 M 0.0681 0.3324 0.5996 4 K 0.0482 0.4999 0.4519 5 K 0.0765 0.5210 0.4025 6 T 0.0869 0.5893 0.3238 7 K 0.0580 0.7011 0.2409 8 N 0.0293 0.8356 0.1351 9 W 0.0102 0.9232 0.0665 10 L 0.0063 0.9486 0.0452 11 L 0.0050 0.9559 0.0392 12 V 0.0047 0.9598 0.0355 13 F 0.0047 0.9605 0.0349 14 L 0.0047 0.9598 0.0355 15 T 0.0047 0.9582 0.0371 16 V 0.0048 0.9585 0.0368 17 T 0.0053 0.9561 0.0386 18 F 0.0070 0.9537 0.0392 19 C 0.0121 0.9466 0.0413 20 F 0.0183 0.9360 0.0457 21 L 0.0336 0.9126 0.0538 22 M 0.0480 0.8722 0.0798 23 L 0.0949 0.7294 0.1757 24 G 0.1382 0.4756 0.3862 25 C 0.1420 0.2000 0.6579 26 Q 0.0970 0.1245 0.7785 27 S 0.0669 0.1458 0.7873 28 K 0.0684 0.1632 0.7684 29 E 0.0686 0.1718 0.7596 30 D 0.0961 0.1613 0.7426 31 K 0.1084 0.1821 0.7095 32 K 0.1151 0.1946 0.6903 33 G 0.0952 0.2221 0.6827 34 G 0.1031 0.2107 0.6862 35 T 0.1070 0.2917 0.6013 36 K 0.1046 0.3077 0.5877 37 P 0.1155 0.3023 0.5821 38 S 0.1424 0.3404 0.5172 39 N 0.1398 0.3426 0.5176 40 E 0.0978 0.4789 0.4233 41 A 0.0545 0.5726 0.3729 42 A 0.0500 0.5414 0.4086 43 L 0.0689 0.4702 0.4609 44 T 0.0813 0.4218 0.4969 45 K 0.0814 0.4426 0.4760 46 T 0.0571 0.5413 0.4015 47 E 0.0469 0.5480 0.4051 48 N 0.0652 0.5118 0.4229 49 L 0.0416 0.7016 0.2568 50 D 0.0579 0.6734 0.2687 51 F 0.0544 0.6586 0.2869 52 R 0.0650 0.5114 0.4235 53 L 0.0567 0.4140 0.5293 54 S 0.0701 0.3201 0.6098 55 F 0.0918 0.3263 0.5819 56 N 0.1150 0.2707 0.6142 57 K 0.2932 0.2499 0.4569 58 I 0.4639 0.1801 0.3560 59 K 0.5377 0.1548 0.3076 60 V 0.4633 0.2173 0.3194 61 T 0.3934 0.2521 0.3544 62 T 0.4251 0.2479 0.3270 63 D 0.4614 0.2602 0.2784 64 Q 0.4000 0.2699 0.3302 65 N 0.3445 0.2351 0.4204 66 H 0.3725 0.1573 0.4703 67 F 0.4113 0.0804 0.5084 68 S 0.3449 0.0628 0.5922 69 G 0.1720 0.0692 0.7588 70 G 0.1153 0.0365 0.8482 71 T 0.2026 0.0167 0.7807 72 S 0.1767 0.0198 0.8035 73 I 0.0049 0.9374 0.0577 74 E 0.0047 0.9491 0.0461 75 Q 0.0047 0.9514 0.0439 76 L 0.0047 0.9530 0.0422 77 K 0.0052 0.9425 0.0523 78 Q 0.0065 0.9162 0.0773 79 W 0.0121 0.8394 0.1486 80 F 0.0551 0.5205 0.4244 81 G 0.0497 0.1135 0.8368 82 D 0.0758 0.0469 0.8772 83 P 0.0855 0.1524 0.7621 84 N 0.0919 0.1660 0.7421 85 K 0.1313 0.1776 0.6911 86 S 0.1396 0.1549 0.7055 87 E 0.1716 0.1187 0.7097 88 Q 0.2398 0.1015 0.6587 89 R 0.4442 0.0845 0.4713 90 N 0.4505 0.0836 0.4659 91 A 0.3367 0.1276 0.5357 92 G 0.1505 0.0887 0.7608 93 N 0.2436 0.0525 0.7039 94 I 0.7107 0.0102 0.2791 95 T 0.8571 0.0063 0.1366 96 L 0.8912 0.0044 0.1043 97 D 0.8841 0.0066 0.1093 98 S 0.8892 0.0067 0.1042 99 Y 0.9079 0.0053 0.0868 100 T 0.9024 0.0062 0.0914 101 W 0.8769 0.0116 0.1115 102 V 0.7211 0.0184 0.2605 103 K 0.3109 0.0563 0.6328 104 D 0.1115 0.0409 0.8475 105 G 0.1544 0.0666 0.7790 106 A 0.6549 0.0120 0.3331 107 V 0.8895 0.0040 0.1065 108 I 0.9194 0.0035 0.0771 109 N 0.9295 0.0032 0.0673 110 A 0.9253 0.0033 0.0715 111 Q 0.9198 0.0036 0.0766 112 L 0.8758 0.0047 0.1196 113 Y 0.6134 0.0207 0.3659 114 K 0.0781 0.0453 0.8766 115 N 0.0511 0.0499 0.8990 116 S 0.5222 0.0337 0.4440 117 T 0.8256 0.0220 0.1524 118 V 0.8399 0.0404 0.1197 119 A 0.7861 0.0622 0.1516 120 R 0.5995 0.2246 0.1759 121 S 0.4643 0.2998 0.2359 122 I 0.3028 0.3992 0.2980 123 S 0.1676 0.2646 0.5677 124 N 0.1148 0.1180 0.7672 125 F 0.1947 0.0887 0.7167 126 S 0.2816 0.0955 0.6229 127 F 0.1925 0.1657 0.6418 128 S 0.1170 0.1903 0.6927 129 R 0.0908 0.2458 0.6634 130 E 0.0993 0.2136 0.6872 131 A 0.1175 0.1360 0.7465 132 K 0.1932 0.0631 0.7437 133 I 0.2608 0.0204 0.7188 134 G 0.1214 0.0237 0.8549 135 K 0.0089 0.8809 0.1102 136 E 0.0069 0.8974 0.0957 137 D 0.0073 0.9134 0.0794 138 Y 0.0084 0.9273 0.0643 139 D 0.0100 0.9066 0.0834 140 E 0.0105 0.8648 0.1247 141 L 0.0257 0.8122 0.1622 142 K 0.0464 0.6673 0.2863 143 I 0.0336 0.3373 0.6291 144 G 0.0331 0.0708 0.8961 145 E 0.1091 0.0367 0.8542 146 S 0.1407 0.0391 0.8202 147 Y 0.0054 0.9264 0.0683 148 K 0.0048 0.9467 0.0486 149 K 0.0048 0.9502 0.0450 150 V 0.0051 0.9536 0.0413 151 V 0.0052 0.9465 0.0483 152 E 0.0070 0.9279 0.0652 153 K 0.0121 0.8611 0.1268 154 L 0.0533 0.5954 0.3513 155 G 0.0501 0.1479 0.8020 156 E 0.0682 0.0586 0.8731 157 P 0.0734 0.1625 0.7640 158 D 0.0775 0.2041 0.7183 159 V 0.1505 0.2146 0.6349 160 L 0.2643 0.1979 0.5378 161 S 0.3428 0.2108 0.4464 162 Q 0.3840 0.2741 0.3419 163 S 0.3543 0.2537 0.3920 164 M 0.3634 0.1871 0.4494 165 S 0.2926 0.1434 0.5640 166 S 0.1367 0.1011 0.7622 167 D 0.1055 0.0657 0.8287 168 K 0.2566 0.0672 0.6762 169 E 0.4699 0.0553 0.4749 170 E 0.7108 0.0348 0.2544 171 M 0.8308 0.0230 0.1462 172 Q 0.8794 0.0187 0.1019 173 T 0.9065 0.0137 0.0798 174 V 0.9032 0.0155 0.0813 175 W 0.8860 0.0215 0.0925 176 S 0.8215 0.0446 0.1339 177 S 0.6258 0.0815 0.2928 178 G 0.4929 0.0580 0.4491 179 I 0.5322 0.0326 0.4352 180 K 0.4938 0.0416 0.4646 181 T 0.2798 0.0868 0.6333 182 K 0.1222 0.0815 0.7962 183 S 0.0851 0.1044 0.8105 184 S 0.1196 0.0974 0.7830 185 S 0.1713 0.0860 0.7427 186 A 0.3762 0.0366 0.5872 187 T 0.6907 0.0113 0.2981 188 I 0.8622 0.0043 0.1335 189 E 0.9161 0.0033 0.0806 190 L 0.9227 0.0034 0.0739 191 Y 0.9230 0.0037 0.0733 192 F 0.8981 0.0040 0.0978 193 E 0.7282 0.0437 0.2281 194 N 0.0862 0.0229 0.8909 195 G 0.0630 0.0524 0.8846 196 L 0.6545 0.0224 0.3231 197 L 0.8764 0.0089 0.1147 198 K 0.8166 0.0315 0.1519 199 N 0.7850 0.0471 0.1678 200 K 0.5250 0.1655 0.3095 201 T 0.3907 0.1670 0.4422 202 Q 0.2291 0.2832 0.4877 203 K 0.1482 0.1847 0.6671 204 D 0.1209 0.1186 0.7605 205 L 0.0961 0.0414 0.8625 206 E 0.0478 0.0326 0.9196