# This file is the result of combining several RDB files, specifically # T0376.t04.dssp-ebghstl.rdb (weight 1.53986) # T0376.t04.stride-ebghtl.rdb (weight 1.24869) # T0376.t04.str2.rdb (weight 1.54758) # T0376.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 T0376.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0376 # 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 T0376.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 938 # # ============================================ # Comments from T0376.t04.stride-ebghtl.rdb # ============================================ # TARGET T0376 # 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 T0376.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 938 # # ============================================ # Comments from T0376.t04.str2.rdb # ============================================ # TARGET T0376 # 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 T0376.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 938 # # ============================================ # Comments from T0376.t04.alpha.rdb # ============================================ # TARGET T0376 # 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 T0376.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 938 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0682 0.0195 0.9123 2 T 0.0824 0.0378 0.8798 3 A 0.0836 0.1757 0.7407 4 S 0.1024 0.2117 0.6859 5 I 0.1712 0.1845 0.6443 6 F 0.2877 0.0716 0.6407 7 S 0.3277 0.0862 0.5862 8 G 0.4800 0.0340 0.4860 9 V 0.6113 0.0166 0.3721 10 I 0.6782 0.0174 0.3043 11 P 0.5765 0.0176 0.4059 12 A 0.5061 0.0249 0.4690 13 L 0.4912 0.0198 0.4890 14 M 0.3864 0.0250 0.5886 15 T 0.2491 0.0193 0.7316 16 P 0.2317 0.0302 0.7381 17 C 0.2630 0.0425 0.6945 18 R 0.1013 0.0365 0.8622 19 Q 0.0212 0.1267 0.8522 20 D 0.0535 0.0425 0.9040 21 R 0.0451 0.0499 0.9050 22 T 0.1154 0.0306 0.8541 23 P 0.2517 0.0365 0.7117 24 D 0.1079 0.0535 0.8386 25 F 0.0048 0.9506 0.0446 26 D 0.0047 0.9600 0.0353 27 A 0.0047 0.9605 0.0349 28 L 0.0047 0.9605 0.0348 29 V 0.0047 0.9584 0.0369 30 R 0.0047 0.9526 0.0427 31 K 0.0048 0.9425 0.0526 32 G 0.0047 0.9530 0.0422 33 K 0.0047 0.9569 0.0384 34 E 0.0047 0.9589 0.0364 35 L 0.0047 0.9573 0.0380 36 I 0.0049 0.9484 0.0468 37 A 0.0053 0.9091 0.0856 38 D 0.0389 0.4378 0.5233 39 G 0.0383 0.0351 0.9266 40 M 0.1126 0.0093 0.8780 41 S 0.1874 0.0347 0.7779 42 A 0.9017 0.0041 0.0942 43 V 0.9287 0.0033 0.0680 44 V 0.9286 0.0033 0.0681 45 Y 0.8715 0.0071 0.1215 46 C 0.4431 0.0233 0.5335 47 G 0.1528 0.0381 0.8092 48 S 0.1399 0.0726 0.7875 49 M 0.1426 0.1294 0.7280 50 G 0.1051 0.1303 0.7646 51 D 0.1200 0.1946 0.6854 52 W 0.1089 0.2673 0.6238 53 P 0.0696 0.2896 0.6408 54 L 0.1078 0.1963 0.6959 55 L 0.1182 0.0313 0.8506 56 T 0.0593 0.0174 0.9233 57 D 0.0048 0.9433 0.0519 58 E 0.0047 0.9596 0.0357 59 Q 0.0047 0.9603 0.0350 60 R 0.0047 0.9597 0.0356 61 M 0.0047 0.9596 0.0357 62 E 0.0047 0.9526 0.0427 63 G 0.0047 0.9449 0.0504 64 V 0.0047 0.9501 0.0452 65 E 0.0047 0.9553 0.0400 66 R 0.0049 0.9518 0.0432 67 L 0.0069 0.9372 0.0558 68 V 0.0128 0.9052 0.0819 69 K 0.0200 0.7645 0.2155 70 A 0.0415 0.1973 0.7612 71 G 0.0346 0.0255 0.9398 72 I 0.1827 0.0085 0.8088 73 P 0.5596 0.0055 0.4349 74 V 0.9033 0.0043 0.0925 75 I 0.9165 0.0048 0.0787 76 V 0.8902 0.0159 0.0939 77 G 0.7600 0.0175 0.2225 78 T 0.3971 0.0305 0.5724 79 G 0.1648 0.0515 0.7837 80 A 0.1035 0.1282 0.7682 81 V 0.0669 0.2111 0.7220 82 N 0.0902 0.2290 0.6808 83 T 0.0068 0.9092 0.0840 84 A 0.0047 0.9593 0.0360 85 S 0.0047 0.9609 0.0345 86 A 0.0047 0.9608 0.0345 87 V 0.0047 0.9610 0.0343 88 A 0.0046 0.9614 0.0340 89 H 0.0047 0.9593 0.0360 90 A 0.0047 0.9600 0.0353 91 V 0.0047 0.9604 0.0350 92 H 0.0046 0.9606 0.0347 93 A 0.0047 0.9588 0.0365 94 Q 0.0048 0.9486 0.0466 95 K 0.0051 0.9134 0.0816 96 V 0.0390 0.4425 0.5185 97 G 0.0470 0.0201 0.9329 98 A 0.0973 0.0086 0.8941 99 K 0.1597 0.0423 0.7980 100 G 0.8967 0.0070 0.0963 101 L 0.9303 0.0037 0.0661 102 M 0.9301 0.0035 0.0664 103 V 0.8911 0.0055 0.1035 104 I 0.5084 0.0124 0.4792 105 P 0.2068 0.0519 0.7413 106 R 0.1145 0.2632 0.6224 107 V 0.1221 0.3839 0.4940 108 L 0.1401 0.3102 0.5498 109 S 0.1193 0.1774 0.7033 110 R 0.0811 0.1108 0.8081 111 G 0.0575 0.1413 0.8012 112 S 0.0735 0.1728 0.7537 113 V 0.0468 0.4844 0.4688 114 I 0.0052 0.9261 0.0686 115 A 0.0050 0.9514 0.0436 116 A 0.0053 0.9521 0.0426 117 Q 0.0047 0.9567 0.0387 118 K 0.0047 0.9597 0.0356 119 A 0.0048 0.9566 0.0386 120 H 0.0047 0.9547 0.0406 121 F 0.0047 0.9595 0.0358 122 K 0.0047 0.9610 0.0344 123 A 0.0047 0.9611 0.0342 124 I 0.0048 0.9559 0.0393 125 L 0.0050 0.9389 0.0562 126 S 0.0057 0.8576 0.1367 127 A 0.0109 0.6650 0.3241 128 A 0.0663 0.0943 0.8393 129 P 0.0143 0.1570 0.8287 130 E 0.0204 0.0900 0.8896 131 I 0.0821 0.0188 0.8991 132 P 0.2127 0.0126 0.7747 133 A 0.8878 0.0051 0.1071 134 V 0.9246 0.0043 0.0710 135 I 0.9245 0.0054 0.0701 136 Y 0.8876 0.0105 0.1019 137 N 0.5714 0.0185 0.4101 138 S 0.2212 0.0250 0.7538 139 P 0.0926 0.1270 0.7804 140 Y 0.0839 0.1875 0.7285 141 Y 0.0879 0.1281 0.7839 142 G 0.1048 0.0917 0.8035 143 F 0.2096 0.0582 0.7322 144 A 0.2845 0.0567 0.6588 145 T 0.2201 0.0613 0.7186 146 R 0.1092 0.0942 0.7966 147 A 0.0062 0.9259 0.0679 148 D 0.0050 0.9504 0.0446 149 L 0.0050 0.9565 0.0384 150 F 0.0047 0.9592 0.0362 151 F 0.0047 0.9598 0.0355 152 A 0.0049 0.9573 0.0377 153 L 0.0054 0.9425 0.0521 154 R 0.0069 0.9136 0.0796 155 A 0.0089 0.8142 0.1768 156 E 0.0154 0.6142 0.3704 157 H 0.0764 0.1308 0.7928 158 K 0.0183 0.1687 0.8129 159 N 0.0396 0.0929 0.8675 160 L 0.5315 0.0564 0.4121 161 V 0.7601 0.0367 0.2032 162 G 0.8646 0.0226 0.1128 163 F 0.8436 0.0279 0.1285 164 K 0.7263 0.0760 0.1978 165 E 0.5172 0.1107 0.3720 166 F 0.1677 0.1260 0.7064 167 G 0.0824 0.0607 0.8569 168 G 0.0488 0.0365 0.9146 169 P 0.0540 0.3048 0.6411 170 A 0.0416 0.3455 0.6129 171 D 0.0696 0.4226 0.5078 172 M 0.0056 0.9356 0.0588 173 R 0.0048 0.9538 0.0413 174 Y 0.0048 0.9547 0.0405 175 A 0.0052 0.9558 0.0390 176 A 0.0050 0.9567 0.0383 177 E 0.0053 0.9516 0.0431 178 N 0.0056 0.9398 0.0546 179 I 0.0091 0.9082 0.0827 180 T 0.0141 0.7944 0.1916 181 S 0.0261 0.5695 0.4043 182 R 0.0635 0.1899 0.7466 183 D 0.0490 0.0744 0.8766 184 D 0.0261 0.1241 0.8497 185 E 0.1068 0.0623 0.8309 186 V 0.6196 0.0159 0.3645 187 T 0.8496 0.0057 0.1447 188 L 0.9132 0.0050 0.0818 189 M 0.8620 0.0098 0.1282 190 I 0.6702 0.0257 0.3041 191 G 0.2503 0.0360 0.7137 192 V 0.1238 0.1181 0.7581 193 D 0.0748 0.2907 0.6345 194 T 0.0438 0.5701 0.3861 195 A 0.0528 0.6971 0.2501 196 V 0.0679 0.7058 0.2263 197 V 0.0481 0.7831 0.1688 198 H 0.0244 0.8386 0.1370 199 G 0.0265 0.8530 0.1205 200 F 0.0300 0.8687 0.1013 201 V 0.0514 0.8334 0.1152 202 N 0.0472 0.7911 0.1617 203 C 0.0595 0.5019 0.4385 204 G 0.0577 0.0816 0.8607 205 A 0.1045 0.0530 0.8426 206 T 0.1967 0.1005 0.7029 207 G 0.6639 0.0506 0.2855 208 A 0.8379 0.0407 0.1213 209 I 0.8681 0.0417 0.0902 210 T 0.7802 0.0782 0.1415 211 G 0.5166 0.1824 0.3010 212 I 0.2588 0.4027 0.3385 213 G 0.1489 0.4560 0.3950 214 N 0.0871 0.4001 0.5128 215 V 0.0762 0.3310 0.5928 216 L 0.0629 0.1734 0.7638 217 P 0.0123 0.6926 0.2951 218 K 0.0049 0.9513 0.0438 219 E 0.0048 0.9563 0.0388 220 V 0.0047 0.9593 0.0360 221 I 0.0047 0.9609 0.0345 222 H 0.0046 0.9611 0.0342 223 L 0.0047 0.9603 0.0351 224 C 0.0047 0.9603 0.0351 225 K 0.0047 0.9594 0.0359 226 L 0.0047 0.9543 0.0410 227 S 0.0047 0.9489 0.0463 228 Q 0.0047 0.9399 0.0554 229 A 0.0049 0.9194 0.0757 230 A 0.0058 0.9048 0.0895 231 A 0.0091 0.7860 0.2049 232 K 0.0443 0.3904 0.5652 233 G 0.0331 0.1424 0.8244 234 D 0.0759 0.1123 0.8117 235 A 0.0065 0.8563 0.1372 236 D 0.0073 0.9046 0.0880 237 A 0.0051 0.9427 0.0522 238 R 0.0049 0.9525 0.0425 239 A 0.0050 0.9465 0.0485 240 R 0.0048 0.9317 0.0635 241 A 0.0048 0.9360 0.0593 242 L 0.0048 0.9334 0.0619 243 E 0.0050 0.9245 0.0706 244 L 0.0051 0.9350 0.0599 245 E 0.0048 0.9444 0.0507 246 Q 0.0047 0.9511 0.0442 247 A 0.0048 0.9518 0.0434 248 L 0.0048 0.9525 0.0427 249 A 0.0052 0.9420 0.0528 250 V 0.0055 0.9199 0.0746 251 L 0.0095 0.8723 0.1182 252 S 0.0154 0.7591 0.2255 253 S 0.0258 0.5981 0.3761 254 F 0.0632 0.3180 0.6188 255 D 0.0550 0.1944 0.7505 256 E 0.0419 0.2079 0.7503 257 G 0.0464 0.0908 0.8628 258 P 0.0369 0.4328 0.5303 259 D 0.0503 0.6311 0.3186 260 L 0.0234 0.8595 0.1172 261 V 0.0107 0.9322 0.0571 262 L 0.0067 0.9524 0.0409 263 Y 0.0053 0.9572 0.0375 264 F 0.0047 0.9600 0.0353 265 K 0.0047 0.9613 0.0341 266 Y 0.0047 0.9606 0.0348 267 M 0.0047 0.9604 0.0349 268 M 0.0047 0.9592 0.0361 269 V 0.0053 0.9517 0.0431 270 L 0.0092 0.9050 0.0858 271 K 0.0426 0.5144 0.4430 272 G 0.0322 0.0668 0.9010 273 D 0.0689 0.0661 0.8650 274 K 0.0883 0.1455 0.7662 275 E 0.0897 0.1551 0.7553 276 Y 0.1290 0.0971 0.7740 277 T 0.2492 0.0650 0.6858 278 L 0.3479 0.0592 0.5929 279 H 0.3307 0.0545 0.6148 280 F 0.1846 0.0938 0.7216 281 N 0.1092 0.1045 0.7863 282 E 0.0806 0.1248 0.7946 283 T 0.0707 0.1198 0.8095 284 D 0.0425 0.1645 0.7930 285 A 0.0658 0.1322 0.8020 286 L 0.0947 0.0328 0.8725 287 T 0.0517 0.0241 0.9242 288 D 0.0049 0.9378 0.0573 289 S 0.0048 0.9471 0.0481 290 Q 0.0051 0.9475 0.0473 291 R 0.0047 0.9581 0.0372 292 G 0.0047 0.9592 0.0361 293 Y 0.0047 0.9584 0.0369 294 V 0.0047 0.9596 0.0357 295 E 0.0047 0.9605 0.0348 296 A 0.0047 0.9593 0.0360 297 Q 0.0047 0.9566 0.0387 298 F 0.0047 0.9550 0.0403 299 K 0.0049 0.9378 0.0573 300 L 0.0054 0.8857 0.1089 301 F 0.0090 0.8066 0.1843 302 N 0.0098 0.6987 0.2915 303 S 0.0145 0.7030 0.2825 304 W 0.0303 0.7399 0.2298 305 Y 0.0591 0.6609 0.2800 306 A 0.0469 0.6415 0.3116 307 D 0.0558 0.5877 0.3566 308 W 0.0444 0.6213 0.3343 309 S 0.0591 0.4860 0.4549 310 K 0.0737 0.4196 0.5067 311 L 0.0909 0.1843 0.7248 312 P 0.0494 0.3146 0.6360 313 G 0.0676 0.2752 0.6572 314 A 0.1187 0.4361 0.4452 315 V 0.1302 0.5240 0.3458 316 Q 0.1148 0.5131 0.3720 317 T 0.0955 0.4746 0.4299 318 C 0.0975 0.3622 0.5403 319 K 0.0653 0.3395 0.5953 320 A 0.0714 0.2648 0.6638 321 A 0.0536 0.1155 0.8309