# This file is the result of combining several RDB files, specifically # T0449.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0449.t2k.stride-ebghtl.rdb (weight 1.24869) # T0449.t2k.str2.rdb (weight 1.54758) # T0449.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 T0449.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0449 # 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 T0449.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 399 # # ============================================ # Comments from T0449.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0449 # 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 T0449.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 399 # # ============================================ # Comments from T0449.t2k.str2.rdb # ============================================ # TARGET T0449 # 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 T0449.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 399 # # ============================================ # Comments from T0449.t2k.alpha.rdb # ============================================ # TARGET T0449 # 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 T0449.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 399 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1152 0.0114 0.8734 2 D 0.4775 0.0109 0.5116 3 Y 0.7927 0.0083 0.1991 4 T 0.8525 0.0078 0.1398 5 I 0.8065 0.0116 0.1820 6 E 0.5304 0.0448 0.4248 7 N 0.1287 0.0596 0.8117 8 N 0.0495 0.0909 0.8596 9 M 0.2466 0.0420 0.7114 10 I 0.7738 0.0065 0.2198 11 K 0.9110 0.0038 0.0852 12 V 0.9245 0.0033 0.0721 13 V 0.9191 0.0039 0.0770 14 I 0.8730 0.0066 0.1205 15 S 0.6474 0.0220 0.3306 16 D 0.2782 0.1242 0.5976 17 H 0.2076 0.0771 0.7153 18 G 0.4156 0.0394 0.5450 19 A 0.7216 0.0087 0.2697 20 E 0.8800 0.0061 0.1139 21 I 0.9264 0.0029 0.0707 22 Q 0.8813 0.0139 0.1049 23 S 0.9163 0.0036 0.0800 24 V 0.9054 0.0056 0.0890 25 K 0.8642 0.0065 0.1293 26 S 0.7024 0.0160 0.2816 27 A 0.1337 0.0706 0.7957 28 H 0.0653 0.0575 0.8772 29 T 0.1640 0.0608 0.7752 30 D 0.4119 0.0525 0.5356 31 E 0.6953 0.0356 0.2691 32 E 0.7777 0.0363 0.1860 33 F 0.7754 0.0445 0.1800 34 M 0.6893 0.0651 0.2456 35 W 0.5211 0.0986 0.3803 36 Q 0.2991 0.1112 0.5898 37 A 0.1443 0.1015 0.7541 38 N 0.1013 0.0799 0.8188 39 P 0.0884 0.1926 0.7190 40 E 0.1133 0.2243 0.6624 41 I 0.1476 0.2408 0.6117 42 W 0.1554 0.2037 0.6409 43 G 0.1170 0.1766 0.7064 44 R 0.0954 0.1216 0.7830 45 H 0.1306 0.0709 0.7985 46 A 0.2287 0.0322 0.7391 47 P 0.3317 0.0393 0.6290 48 V 0.6285 0.0504 0.3211 49 L 0.6718 0.0521 0.2761 50 F 0.6112 0.0285 0.3603 51 P 0.4745 0.0513 0.4743 52 I 0.3803 0.0635 0.5562 53 V 0.2638 0.0983 0.6379 54 G 0.2027 0.0765 0.7208 55 R 0.2505 0.0690 0.6805 56 L 0.2365 0.0918 0.6717 57 K 0.1013 0.1010 0.7977 58 N 0.0665 0.0466 0.8869 59 D 0.1144 0.0435 0.8421 60 E 0.5120 0.0236 0.4644 61 Y 0.8325 0.0072 0.1603 62 T 0.7883 0.0127 0.1990 63 Y 0.6452 0.0318 0.3229 64 K 0.0888 0.0356 0.8755 65 G 0.0676 0.0469 0.8855 66 K 0.5912 0.0175 0.3913 67 T 0.8087 0.0095 0.1818 68 Y 0.7773 0.0100 0.2127 69 H 0.6312 0.0186 0.3502 70 L 0.3324 0.0447 0.6230 71 G 0.1768 0.1067 0.7165 72 Q 0.1480 0.1582 0.6938 73 H 0.2106 0.1407 0.6488 74 G 0.2543 0.1365 0.6092 75 F 0.3179 0.1616 0.5205 76 A 0.3444 0.1387 0.5169 77 R 0.2617 0.1372 0.6011 78 N 0.1925 0.0622 0.7453 79 A 0.2205 0.0333 0.7463 80 D 0.3122 0.0402 0.6475 81 F 0.7189 0.0135 0.2676 82 E 0.8343 0.0070 0.1587 83 V 0.8769 0.0049 0.1182 84 E 0.8379 0.0195 0.1426 85 N 0.8108 0.0109 0.1783 86 H 0.6305 0.0236 0.3459 87 T 0.3893 0.0259 0.5848 88 K 0.0951 0.0725 0.8324 89 E 0.0901 0.0694 0.8405 90 S 0.6274 0.0188 0.3538 91 I 0.8667 0.0043 0.1290 92 T 0.9144 0.0044 0.0812 93 F 0.9097 0.0042 0.0861 94 L 0.8942 0.0042 0.1016 95 L 0.8245 0.0097 0.1658 96 K 0.5748 0.0135 0.4117 97 D 0.2774 0.0187 0.7039 98 N 0.0841 0.0217 0.8942 99 E 0.0086 0.7113 0.2801 100 E 0.0078 0.7618 0.2305 101 T 0.0136 0.7770 0.2094 102 R 0.0242 0.6872 0.2886 103 K 0.0507 0.4923 0.4571 104 V 0.1021 0.2976 0.6003 105 Y 0.1649 0.0565 0.7786 106 P 0.1205 0.0671 0.8124 107 F 0.2397 0.0328 0.7276 108 K 0.4456 0.0230 0.5314 109 F 0.8298 0.0043 0.1658 110 E 0.8999 0.0034 0.0967 111 F 0.9208 0.0033 0.0759 112 R 0.9280 0.0031 0.0689 113 V 0.9285 0.0032 0.0683 114 N 0.9280 0.0031 0.0689 115 Y 0.9240 0.0036 0.0724 116 N 0.9204 0.0039 0.0757 117 L 0.8940 0.0053 0.1007 118 M 0.6091 0.0143 0.3767 119 N 0.0637 0.0493 0.8870 120 N 0.0383 0.0639 0.8978 121 L 0.5842 0.0135 0.4023 122 L 0.8980 0.0034 0.0986 123 E 0.9256 0.0033 0.0711 124 E 0.9283 0.0033 0.0684 125 N 0.9289 0.0031 0.0680 126 F 0.9261 0.0034 0.0705 127 S 0.9244 0.0033 0.0723 128 V 0.9143 0.0033 0.0824 129 V 0.8527 0.0125 0.1348 130 N 0.5474 0.0102 0.4424 131 K 0.1005 0.0855 0.8140 132 S 0.0677 0.0382 0.8941 133 D 0.0855 0.0454 0.8692 134 E 0.1477 0.0235 0.8287 135 T 0.2805 0.0327 0.6868 136 M 0.2752 0.0195 0.7053 137 I 0.4026 0.0271 0.5703 138 F 0.5929 0.0383 0.3687 139 G 0.6405 0.0495 0.3100 140 V 0.6012 0.0656 0.3332 141 G 0.4679 0.0666 0.4655 142 G 0.3860 0.0690 0.5451 143 H 0.2322 0.0627 0.7051 144 P 0.1934 0.1677 0.6389 145 G 0.3053 0.1848 0.5099 146 F 0.4691 0.1357 0.3952 147 N 0.5566 0.0503 0.3931 148 L 0.3687 0.0327 0.5987 149 P 0.2485 0.0710 0.6805 150 T 0.1153 0.1391 0.7455 151 D 0.0976 0.2117 0.6907 152 H 0.0918 0.2421 0.6661 153 G 0.1554 0.1801 0.6645 154 E 0.3712 0.1318 0.4969 155 N 0.5457 0.1050 0.3493 156 K 0.4812 0.1889 0.3299 157 E 0.3209 0.2726 0.4065 158 D 0.2249 0.2725 0.5026 159 F 0.2484 0.2823 0.4692 160 Y 0.3369 0.2649 0.3982 161 F 0.3514 0.2731 0.3755 162 D 0.3099 0.2639 0.4262 163 M 0.2326 0.2688 0.4987 164 H 0.1584 0.3005 0.5410 165 P 0.0879 0.4378 0.4743 166 S 0.0868 0.4223 0.4909 167 V 0.1171 0.3572 0.5257 168 T 0.1554 0.2782 0.5663 169 R 0.1669 0.2466 0.5865 170 V 0.1777 0.2610 0.5613 171 R 0.1762 0.2800 0.5437 172 I 0.1667 0.2700 0.5633 173 P 0.1535 0.2685 0.5779 174 L 0.1402 0.2258 0.6341 175 K 0.1219 0.1924 0.6857 176 D 0.0974 0.2183 0.6843 177 A 0.0924 0.2281 0.6795 178 S 0.1106 0.2107 0.6787 179 L 0.1380 0.2007 0.6613 180 D 0.1654 0.2041 0.6305 181 W 0.1386 0.2186 0.6428 182 N 0.1440 0.1972 0.6588 183 N 0.1549 0.2301 0.6151 184 R 0.1342 0.2459 0.6199 185 S 0.1296 0.2256 0.6449 186 L 0.1246 0.2410 0.6344 187 A 0.1127 0.2711 0.6162 188 P 0.0954 0.2893 0.6153 189 T 0.0796 0.2984 0.6220 190 D 0.0736 0.3001 0.6264 191 S 0.1082 0.2887 0.6031 192 L 0.1560 0.2782 0.5658 193 I 0.1788 0.2912 0.5300 194 A 0.1794 0.2846 0.5360 195 L 0.1268 0.3069 0.5662 196 S 0.0928 0.3151 0.5921 197 D 0.0749 0.3395 0.5857 198 D 0.1139 0.3534 0.5326 199 L 0.1542 0.3202 0.5257 200 F 0.1519 0.2467 0.6014 201 K 0.1125 0.2930 0.5945 202 D 0.0651 0.4228 0.5121 203 D 0.0700 0.4956 0.4343 204 A 0.1224 0.5944 0.2832 205 L 0.2137 0.5673 0.2189 206 I 0.2564 0.5457 0.1980 207 Y 0.2652 0.5278 0.2070 208 E 0.2654 0.4864 0.2482 209 L 0.2808 0.3489 0.3703 210 R 0.2101 0.1966 0.5933 211 G 0.1352 0.1044 0.7605 212 N 0.1087 0.1014 0.7899 213 D 0.0930 0.0878 0.8192 214 N 0.1881 0.0677 0.7441 215 K 0.4720 0.0374 0.4905 216 V 0.7713 0.0170 0.2117 217 S 0.8769 0.0088 0.1143 218 L 0.8853 0.0082 0.1066 219 R 0.8620 0.0110 0.1271 220 T 0.7106 0.0123 0.2770 221 D 0.2268 0.0602 0.7130 222 K 0.0356 0.1181 0.8462 223 N 0.0538 0.0772 0.8689 224 K 0.1195 0.0414 0.8390 225 F 0.4478 0.0152 0.5370 226 H 0.8408 0.0049 0.1543 227 V 0.9135 0.0037 0.0828 228 N 0.9229 0.0033 0.0738 229 V 0.9103 0.0040 0.0857 230 W 0.8360 0.0076 0.1565 231 T 0.5185 0.0356 0.4459 232 R 0.0843 0.1026 0.8132 233 D 0.0648 0.0611 0.8741 234 A 0.1666 0.0402 0.7932 235 P 0.1747 0.0688 0.7565 236 F 0.5107 0.0356 0.4537 237 V 0.8470 0.0085 0.1445 238 G 0.9094 0.0046 0.0860 239 I 0.9175 0.0044 0.0781 240 W 0.8702 0.0086 0.1212 241 S 0.6184 0.0103 0.3713 242 Q 0.2963 0.0411 0.6626 243 Y 0.1369 0.0613 0.8017 244 P 0.0734 0.1060 0.8206 245 K 0.0389 0.1517 0.8094 246 T 0.0461 0.1017 0.8522 247 D 0.0914 0.0478 0.8608 248 N 0.1321 0.0732 0.7947 249 Y 0.5652 0.0453 0.3896 250 V 0.7571 0.0174 0.2254 251 C 0.7777 0.0127 0.2095 252 I 0.7015 0.0230 0.2755 253 E 0.4620 0.0218 0.5162 254 P 0.2344 0.0560 0.7096 255 W 0.1346 0.0928 0.7726 256 W 0.0955 0.0980 0.8065 257 G 0.0851 0.0954 0.8195 258 I 0.0851 0.1247 0.7902 259 A 0.0763 0.2375 0.6862 260 D 0.0829 0.2387 0.6784 261 R 0.1256 0.2622 0.6123 262 D 0.2022 0.2420 0.5558 263 D 0.1995 0.1887 0.6118 264 A 0.1124 0.2804 0.6072 265 D 0.0762 0.3489 0.5749 266 G 0.0591 0.4754 0.4655 267 D 0.0649 0.5798 0.3553 268 L 0.0909 0.5794 0.3297 269 E 0.0969 0.5034 0.3998 270 H 0.1081 0.3832 0.5088 271 K 0.0985 0.2113 0.6902 272 Y 0.1187 0.1504 0.7309 273 G 0.1881 0.0816 0.7303 274 M 0.4396 0.0379 0.5225 275 N 0.7596 0.0201 0.2202 276 H 0.7982 0.0102 0.1916 277 L 0.5870 0.0106 0.4024 278 K 0.1708 0.0149 0.8143 279 P 0.0319 0.0630 0.9051 280 G 0.0470 0.0330 0.9200 281 K 0.2993 0.0153 0.6854 282 E 0.7732 0.0047 0.2221 283 F 0.8613 0.0056 0.1331 284 Q 0.8829 0.0041 0.1130 285 A 0.8923 0.0048 0.1029 286 G 0.9087 0.0032 0.0881 287 F 0.9173 0.0036 0.0792 288 S 0.9278 0.0031 0.0691 289 M 0.9236 0.0034 0.0730 290 T 0.9136 0.0036 0.0829 291 Y 0.8651 0.0042 0.1307 292 H 0.5777 0.0093 0.4130 293 S 0.3278 0.0252 0.6471 294 T 0.1485 0.0451 0.8064 295 T 0.1121 0.1348 0.7531 296 D 0.1075 0.1691 0.7235 297 E 0.1379 0.1832 0.6789 298 V 0.1150 0.2448 0.6403 299 K 0.0919 0.2505 0.6576 300 L 0.1570 0.2275 0.6156 301 E 0.1760 0.1608 0.6632 302 H 0.1129 0.0805 0.8066 303 H 0.0217 0.3220 0.6563 304 H 0.0271 0.3205 0.6524 305 H 0.0777 0.2526 0.6697 306 H 0.1002 0.1242 0.7757 307 H 0.0491 0.0429 0.9081