# This file is the result of combining several RDB files, specifically # T0316.t04.dssp-ebghstl.rdb (weight 1.53986) # T0316.t04.stride-ebghtl.rdb (weight 1.24869) # T0316.t04.str2.rdb (weight 1.54758) # T0316.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 T0316.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1909 # # ============================================ # Comments from T0316.t04.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1909 # # ============================================ # Comments from T0316.t04.str2.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1909 # # ============================================ # Comments from T0316.t04.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1909 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0813 0.0410 0.8777 2 S 0.1242 0.0675 0.8083 3 D 0.1061 0.1146 0.7793 4 N 0.0888 0.1319 0.7793 5 S 0.0574 0.1385 0.8041 6 K 0.0537 0.0839 0.8624 7 T 0.1527 0.0246 0.8227 8 R 0.7184 0.0044 0.2773 9 V 0.9222 0.0034 0.0744 10 V 0.9331 0.0032 0.0637 11 V 0.9319 0.0033 0.0648 12 G 0.9190 0.0054 0.0756 13 M 0.8626 0.0079 0.1295 14 S 0.5614 0.0150 0.4236 15 G 0.1603 0.0316 0.8081 16 G 0.0836 0.0652 0.8512 17 V 0.0523 0.3895 0.5581 18 D 0.0268 0.6596 0.3135 19 S 0.0052 0.9341 0.0607 20 S 0.0048 0.9568 0.0385 21 V 0.0047 0.9600 0.0353 22 T 0.0047 0.9606 0.0347 23 A 0.0046 0.9614 0.0340 24 L 0.0046 0.9616 0.0338 25 L 0.0047 0.9610 0.0344 26 L 0.0047 0.9603 0.0351 27 K 0.0048 0.9558 0.0394 28 E 0.0057 0.9123 0.0820 29 Q 0.0410 0.3616 0.5975 30 G 0.0391 0.0163 0.9446 31 Y 0.0679 0.0089 0.9233 32 D 0.4357 0.0138 0.5505 33 V 0.8663 0.0036 0.1301 34 I 0.9059 0.0049 0.0892 35 G 0.9275 0.0034 0.0691 36 I 0.9226 0.0037 0.0737 37 F 0.8980 0.0052 0.0968 38 M 0.8002 0.0111 0.1887 39 K 0.6673 0.0302 0.3024 40 N 0.4928 0.0314 0.4758 41 W 0.2783 0.0601 0.6616 42 D 0.2122 0.0712 0.7166 43 D 0.1729 0.1217 0.7054 44 T 0.1354 0.0966 0.7680 45 D 0.0672 0.1721 0.7607 46 E 0.0489 0.1997 0.7514 47 N 0.0872 0.1227 0.7900 48 G 0.0818 0.0651 0.8531 49 V 0.2111 0.0593 0.7296 50 C 0.2064 0.0496 0.7440 51 T 0.0991 0.0551 0.8458 52 A 0.0606 0.1282 0.8113 53 T 0.0312 0.5927 0.3760 54 E 0.0290 0.6872 0.2839 55 D 0.0312 0.6790 0.2898 56 Y 0.0059 0.9345 0.0596 57 K 0.0048 0.9557 0.0395 58 D 0.0047 0.9579 0.0374 59 V 0.0047 0.9594 0.0359 60 V 0.0046 0.9614 0.0340 61 A 0.0046 0.9613 0.0341 62 V 0.0046 0.9615 0.0339 63 A 0.0047 0.9605 0.0348 64 D 0.0048 0.9533 0.0419 65 Q 0.0055 0.9252 0.0693 66 I 0.0447 0.4652 0.4901 67 G 0.0448 0.0138 0.9413 68 I 0.0646 0.0079 0.9275 69 P 0.2279 0.0106 0.7615 70 Y 0.8476 0.0062 0.1462 71 Y 0.9083 0.0046 0.0871 72 S 0.9234 0.0037 0.0729 73 V 0.8504 0.0105 0.1391 74 N 0.4855 0.0067 0.5079 75 F 0.0892 0.3039 0.6069 76 E 0.0349 0.5384 0.4267 77 K 0.0136 0.8085 0.1780 78 E 0.0165 0.8590 0.1245 79 Y 0.0154 0.8790 0.1056 80 W 0.0106 0.9136 0.0758 81 D 0.0085 0.9170 0.0745 82 R 0.0087 0.9199 0.0715 83 V 0.0102 0.9165 0.0733 84 F 0.0156 0.9083 0.0761 85 E 0.0176 0.9082 0.0742 86 Y 0.0260 0.8845 0.0895 87 F 0.0244 0.8657 0.1098 88 L 0.0172 0.9007 0.0821 89 A 0.0086 0.9264 0.0650 90 E 0.0084 0.9257 0.0659 91 Y 0.0183 0.8983 0.0834 92 R 0.0229 0.8352 0.1419 93 A 0.0379 0.4705 0.4916 94 G 0.0271 0.0850 0.8878 95 R 0.0818 0.0337 0.8844 96 T 0.1276 0.0147 0.8577 97 P 0.1134 0.0348 0.8517 98 N 0.1102 0.0409 0.8489 99 P 0.0562 0.2192 0.7246 100 D 0.0734 0.3368 0.5898 101 V 0.0932 0.4972 0.4096 102 M 0.0971 0.4330 0.4699 103 C 0.0694 0.4578 0.4728 104 N 0.0349 0.4962 0.4689 105 K 0.0131 0.8268 0.1601 106 E 0.0167 0.8793 0.1040 107 I 0.0270 0.8840 0.0889 108 K 0.0213 0.8799 0.0988 109 F 0.0087 0.9329 0.0584 110 K 0.0069 0.9422 0.0509 111 A 0.0051 0.9548 0.0401 112 F 0.0048 0.9569 0.0383 113 L 0.0047 0.9605 0.0348 114 D 0.0047 0.9607 0.0347 115 Y 0.0047 0.9612 0.0341 116 A 0.0047 0.9609 0.0345 117 I 0.0048 0.9545 0.0407 118 T 0.0051 0.9365 0.0584 119 L 0.0403 0.4572 0.5025 120 G 0.0618 0.0126 0.9256 121 A 0.0845 0.0203 0.8952 122 D 0.0681 0.0587 0.8731 123 Y 0.8658 0.0162 0.1180 124 V 0.9172 0.0093 0.0735 125 A 0.9065 0.0129 0.0806 126 T 0.7760 0.0435 0.1805 127 G 0.4022 0.0541 0.5437 128 H 0.2397 0.0931 0.6672 129 Y 0.2217 0.1167 0.6616 130 A 0.2073 0.2050 0.5878 131 R 0.1483 0.3001 0.5516 132 V 0.1598 0.3017 0.5385 133 A 0.1945 0.2922 0.5133 134 R 0.2100 0.2327 0.5572 135 D 0.1649 0.1775 0.6576 136 E 0.1307 0.2115 0.6577 137 D 0.0972 0.1784 0.7245 138 G 0.1160 0.1944 0.6896 139 T 0.3314 0.3051 0.3635 140 V 0.4826 0.3071 0.2103 141 H 0.4814 0.3169 0.2017 142 M 0.4479 0.3600 0.1922 143 L 0.3473 0.4203 0.2324 144 R 0.2102 0.4251 0.3647 145 G 0.1433 0.3746 0.4821 146 V 0.1357 0.4055 0.4588 147 D 0.0905 0.3665 0.5429 148 N 0.0556 0.3331 0.6113 149 G 0.0508 0.2073 0.7419 150 K 0.0476 0.2577 0.6947 151 D 0.0578 0.2672 0.6750 152 Q 0.0779 0.3553 0.5668 153 T 0.0872 0.4119 0.5009 154 Y 0.0880 0.4967 0.4153 155 F 0.1194 0.4847 0.3959 156 L 0.1036 0.5328 0.3637 157 S 0.0720 0.4600 0.4680 158 Q 0.0873 0.3810 0.5316 159 L 0.1206 0.1504 0.7290 160 S 0.0766 0.1439 0.7795 161 Q 0.0067 0.8180 0.1753 162 E 0.0093 0.8126 0.1781 163 Q 0.0158 0.7619 0.2224 164 L 0.0500 0.6181 0.3319 165 Q 0.1509 0.4528 0.3962 166 K 0.3279 0.3632 0.3089 167 T 0.5035 0.2788 0.2176 168 M 0.5531 0.1713 0.2756 169 F 0.4364 0.1372 0.4264 170 P 0.2516 0.1632 0.5852 171 L 0.0878 0.4114 0.5008 172 G 0.0646 0.3630 0.5724 173 H 0.0761 0.2948 0.6291 174 L 0.1176 0.0434 0.8390 175 E 0.0636 0.0258 0.9106 176 K 0.0116 0.9306 0.0578 177 P 0.0047 0.9595 0.0358 178 E 0.0047 0.9609 0.0345 179 V 0.0047 0.9607 0.0346 180 R 0.0046 0.9611 0.0343 181 R 0.0046 0.9615 0.0338 182 L 0.0046 0.9618 0.0336 183 A 0.0046 0.9613 0.0341 184 E 0.0048 0.9560 0.0392 185 E 0.0054 0.9391 0.0554 186 A 0.0426 0.4707 0.4867 187 G 0.0446 0.0178 0.9376 188 L 0.0618 0.0085 0.9297 189 S 0.1154 0.0327 0.8519 190 T 0.2562 0.1918 0.5520 191 A 0.2413 0.2471 0.5115 192 K 0.2350 0.2056 0.5593 193 K 0.1663 0.0558 0.7779 194 K 0.0962 0.0910 0.8128 195 D 0.1085 0.0515 0.8400 196 S 0.1052 0.0894 0.8053 197 T 0.1103 0.1200 0.7697 198 G 0.1593 0.1245 0.7162 199 I 0.2760 0.1318 0.5921 200 C 0.3901 0.1047 0.5052 201 F 0.3411 0.0929 0.5660 202 I 0.2002 0.1023 0.6975 203 G 0.1008 0.0993 0.7999 204 E 0.0527 0.3314 0.6159 205 K 0.0417 0.5143 0.4440 206 N 0.0503 0.5739 0.3758 207 F 0.0322 0.7626 0.2052 208 K 0.0248 0.7955 0.1798 209 N 0.0290 0.7332 0.2377 210 F 0.0318 0.7596 0.2086 211 L 0.0430 0.7154 0.2416 212 S 0.0168 0.7567 0.2265 213 N 0.0176 0.6764 0.3060 214 Y 0.0436 0.5691 0.3873 215 L 0.0730 0.2618 0.6652 216 P 0.0607 0.2610 0.6783 217 A 0.0769 0.1747 0.7485 218 Q 0.0720 0.0360 0.8920 219 P 0.0414 0.1562 0.8024 220 G 0.0569 0.1287 0.8145 221 R 0.2709 0.1294 0.5997 222 M 0.5663 0.0974 0.3363 223 M 0.6470 0.0831 0.2699 224 T 0.6395 0.0679 0.2926 225 V 0.4455 0.1139 0.4406 226 D 0.2417 0.0891 0.6693 227 G 0.1549 0.1059 0.7393 228 R 0.2338 0.1145 0.6517 229 D 0.3482 0.1727 0.4791 230 M 0.2108 0.3220 0.4672 231 G 0.1572 0.2533 0.5895 232 E 0.1620 0.2682 0.5698 233 H 0.1812 0.2236 0.5952 234 A 0.1034 0.2055 0.6912 235 G 0.1348 0.0998 0.7654 236 L 0.3058 0.0532 0.6410 237 M 0.5293 0.0445 0.4261 238 Y 0.8076 0.0269 0.1654 239 Y 0.8303 0.0251 0.1445 240 T 0.8319 0.0367 0.1314 241 I 0.7158 0.0948 0.1895 242 G 0.6243 0.0861 0.2896 243 Q 0.4594 0.1386 0.4020 244 R 0.3085 0.1720 0.5195 245 G 0.1497 0.1050 0.7454 246 G 0.1694 0.0707 0.7599 247 L 0.2958 0.0534 0.6508 248 G 0.3405 0.0512 0.6083 249 I 0.4008 0.0775 0.5217 250 G 0.3936 0.0688 0.5376 251 G 0.3700 0.0659 0.5641 252 Q 0.2833 0.0625 0.6542 253 H 0.1860 0.0655 0.7485 254 G 0.1606 0.0733 0.7661 255 G 0.1131 0.0808 0.8060 256 D 0.0877 0.0725 0.8398 257 N 0.0629 0.1644 0.7727 258 A 0.1112 0.1286 0.7602 259 P 0.1828 0.1686 0.6486 260 W 0.4114 0.1919 0.3967 261 F 0.5528 0.1461 0.3011 262 R 0.5560 0.1228 0.3212 263 Y 0.4959 0.0745 0.4297 264 R 0.3840 0.0477 0.5683 265 Q 0.1996 0.0231 0.7773 266 P 0.1134 0.0458 0.8408 267 D 0.1489 0.0588 0.7923 268 S 0.3483 0.0299 0.6217 269 K 0.5086 0.0211 0.4703 270 V 0.7610 0.0072 0.2318 271 T 0.8916 0.0045 0.1038 272 V 0.9070 0.0045 0.0885 273 H 0.8440 0.0070 0.1490 274 V 0.6691 0.0159 0.3150 275 K 0.2485 0.0588 0.6926 276 G 0.0810 0.0951 0.8239 277 E 0.0861 0.1126 0.8013 278 K 0.2552 0.0920 0.6527 279 T 0.6261 0.0406 0.3332 280 E 0.8016 0.0404 0.1580 281 V 0.8554 0.0464 0.0982 282 I 0.8125 0.0690 0.1184 283 F 0.7479 0.0565 0.1956 284 A 0.4456 0.0869 0.4675 285 E 0.1887 0.1911 0.6202 286 P 0.1195 0.3132 0.5672 287 Q 0.1973 0.3896 0.4131 288 R 0.3343 0.3384 0.3273 289 A 0.4854 0.2222 0.2924 290 I 0.4263 0.1851 0.3886 291 T 0.2799 0.0292 0.6909 292 P 0.0670 0.0601 0.8728 293 G 0.0788 0.0298 0.8914 294 Q 0.6356 0.0097 0.3547 295 A 0.8747 0.0037 0.1216 296 V 0.9229 0.0034 0.0737 297 V 0.9295 0.0031 0.0674 298 F 0.9094 0.0043 0.0862 299 Y 0.7984 0.0082 0.1934 300 D 0.2184 0.0236 0.7580 301 G 0.0839 0.0231 0.8930 302 E 0.3141 0.0622 0.6237 303 E 0.7900 0.0141 0.1959 304 C 0.8739 0.0090 0.1171 305 L 0.7922 0.0330 0.1748 306 G 0.5600 0.0366 0.4034 307 G 0.3883 0.0402 0.5714 308 G 0.5120 0.0478 0.4402 309 L 0.6716 0.0440 0.2845 310 I 0.6014 0.0752 0.3235 311 D 0.3602 0.2161 0.4237 312 N 0.2014 0.2588 0.5398 313 A 0.2423 0.2371 0.5206 314 Y 0.2178 0.1736 0.6086 315 R 0.1887 0.1383 0.6730 316 D 0.1310 0.0890 0.7799 317 G 0.0950 0.1638 0.7411 318 Q 0.2567 0.1449 0.5984 319 V 0.5672 0.1163 0.3166 320 C 0.5925 0.0607 0.3468 321 Q 0.6239 0.0565 0.3196 322 Y 0.4876 0.0513 0.4610 323 I 0.2388 0.0440 0.7172