# This file is the result of combining several RDB files, specifically # T0373.t06.dssp-ebghstl.rdb (weight 1.53986) # T0373.t06.stride-ebghtl.rdb (weight 1.24869) # T0373.t06.str2.rdb (weight 1.54758) # T0373.t06.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 T0373.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0373 # 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 T0373.t06-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 191.992 # # ============================================ # Comments from T0373.t06.stride-ebghtl.rdb # ============================================ # TARGET T0373 # Using neural net t06-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 T0373.t06-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 191.992 # # ============================================ # Comments from T0373.t06.str2.rdb # ============================================ # TARGET T0373 # Using neural net t06-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 T0373.t06-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 191.992 # # ============================================ # Comments from T0373.t06.alpha.rdb # ============================================ # TARGET T0373 # Using neural net t06-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 T0373.t06-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 191.992 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0565 0.0095 0.9340 2 P 0.0601 0.0276 0.9123 3 T 0.0477 0.1188 0.8335 4 N 0.0336 0.3179 0.6484 5 Q 0.0245 0.5502 0.4253 6 D 0.0308 0.6836 0.2856 7 L 0.0166 0.8329 0.1505 8 Q 0.0139 0.8699 0.1161 9 L 0.0097 0.9108 0.0795 10 A 0.0085 0.9251 0.0664 11 A 0.0065 0.9419 0.0516 12 H 0.0062 0.9439 0.0500 13 L 0.0054 0.9450 0.0496 14 R 0.0052 0.9480 0.0469 15 S 0.0051 0.9489 0.0460 16 Q 0.0051 0.9497 0.0452 17 V 0.0049 0.9528 0.0423 18 T 0.0048 0.9534 0.0418 19 T 0.0050 0.9535 0.0415 20 L 0.0051 0.9512 0.0438 21 T 0.0051 0.9518 0.0431 22 R 0.0050 0.9527 0.0423 23 R 0.0051 0.9498 0.0451 24 L 0.0052 0.9428 0.0520 25 R 0.0056 0.9328 0.0616 26 R 0.0051 0.9284 0.0665 27 E 0.0058 0.8904 0.1038 28 A 0.0135 0.8225 0.1639 29 Q 0.0186 0.6587 0.3228 30 A 0.0218 0.4460 0.5322 31 D 0.0591 0.0892 0.8516 32 P 0.0355 0.0862 0.8782 33 V 0.1007 0.0314 0.8679 34 Q 0.0772 0.0282 0.8947 35 F 0.0050 0.9360 0.0590 36 S 0.0048 0.9503 0.0450 37 Q 0.0048 0.9572 0.0380 38 L 0.0047 0.9605 0.0348 39 V 0.0047 0.9606 0.0347 40 V 0.0047 0.9607 0.0346 41 L 0.0047 0.9605 0.0348 42 G 0.0047 0.9594 0.0359 43 A 0.0048 0.9580 0.0372 44 I 0.0051 0.9540 0.0409 45 D 0.0058 0.9422 0.0519 46 R 0.0079 0.8765 0.1156 47 L 0.0455 0.4043 0.5502 48 G 0.0359 0.0283 0.9358 49 G 0.0440 0.0241 0.9319 50 D 0.1443 0.0223 0.8335 51 V 0.1745 0.0105 0.8151 52 T 0.0789 0.0107 0.9103 53 P 0.0048 0.9491 0.0461 54 S 0.0047 0.9595 0.0359 55 E 0.0047 0.9598 0.0355 56 L 0.0047 0.9594 0.0359 57 A 0.0047 0.9557 0.0396 58 A 0.0050 0.9331 0.0619 59 A 0.0059 0.8790 0.1151 60 E 0.0452 0.5594 0.3954 61 R 0.0328 0.1353 0.8319 62 M 0.0714 0.0358 0.8928 63 R 0.0546 0.0386 0.9068 64 S 0.0191 0.7185 0.2625 65 S 0.0083 0.8223 0.1695 66 N 0.0094 0.8765 0.1142 67 L 0.0048 0.9515 0.0438 68 A 0.0047 0.9595 0.0358 69 A 0.0047 0.9602 0.0351 70 L 0.0047 0.9589 0.0365 71 L 0.0047 0.9596 0.0357 72 R 0.0047 0.9592 0.0361 73 E 0.0047 0.9580 0.0373 74 L 0.0049 0.9526 0.0425 75 E 0.0051 0.9259 0.0690 76 R 0.0104 0.7532 0.2365 77 G 0.0434 0.2225 0.7341 78 G 0.0377 0.0269 0.9354 79 L 0.2418 0.0308 0.7274 80 I 0.8011 0.0093 0.1896 81 V 0.8413 0.0116 0.1470 82 R 0.8309 0.0120 0.1571 83 H 0.7193 0.0093 0.2713 84 A 0.5706 0.0128 0.4166 85 D 0.2191 0.0107 0.7702 86 P 0.0146 0.1560 0.8294 87 Q 0.0208 0.1093 0.8699 88 D 0.0698 0.1202 0.8100 89 G 0.0655 0.0646 0.8699 90 R 0.2937 0.0329 0.6734 91 R 0.5636 0.0170 0.4193 92 T 0.7736 0.0081 0.2183 93 R 0.8944 0.0041 0.1015 94 V 0.9162 0.0045 0.0793 95 S 0.9014 0.0066 0.0920 96 L 0.7244 0.0101 0.2655 97 S 0.1721 0.0123 0.8156 98 S 0.0065 0.8029 0.1906 99 E 0.0065 0.8235 0.1700 100 G 0.0064 0.8914 0.1022 101 R 0.0090 0.9282 0.0628 102 R 0.0105 0.9248 0.0647 103 N 0.0105 0.9091 0.0804 104 L 0.0107 0.8901 0.0993 105 Y 0.0100 0.8511 0.1389 106 G 0.0107 0.7955 0.1938 107 N 0.0115 0.7772 0.2113 108 R 0.0084 0.8541 0.1375 109 A 0.0055 0.9144 0.0801 110 K 0.0053 0.9309 0.0638 111 R 0.0053 0.9394 0.0553 112 E 0.0048 0.9505 0.0447 113 E 0.0048 0.9566 0.0387 114 W 0.0047 0.9566 0.0387 115 L 0.0047 0.9579 0.0374 116 V 0.0047 0.9591 0.0362 117 R 0.0048 0.9560 0.0392 118 A 0.0049 0.9464 0.0487 119 M 0.0054 0.9289 0.0657 120 H 0.0058 0.8669 0.1273 121 A 0.0109 0.6625 0.3266 122 C 0.0177 0.3840 0.5983 123 L 0.0711 0.0604 0.8685 124 D 0.0509 0.0305 0.9186 125 E 0.0048 0.9433 0.0519 126 S 0.0047 0.9526 0.0427 127 E 0.0048 0.9573 0.0379 128 R 0.0047 0.9604 0.0349 129 A 0.0047 0.9588 0.0365 130 L 0.0047 0.9549 0.0405 131 L 0.0047 0.9521 0.0432 132 A 0.0052 0.9449 0.0500 133 A 0.0055 0.8851 0.1095 134 A 0.0076 0.8308 0.1616 135 G 0.0052 0.8897 0.1052 136 P 0.0047 0.9370 0.0583 137 L 0.0047 0.9489 0.0464 138 L 0.0047 0.9535 0.0418 139 T 0.0048 0.9510 0.0442 140 R 0.0053 0.9339 0.0608 141 L 0.0062 0.9018 0.0920 142 A 0.0223 0.7630 0.2147 143 Q 0.0201 0.5414 0.4385 144 F 0.0475 0.2658 0.6867 145 E 0.0639 0.1494 0.7867 146 E 0.0621 0.0605 0.8773 147 P 0.0744 0.0601 0.8655 148 M 0.0745 0.0251 0.9004 149 P 0.0664 0.0507 0.8829 150 T 0.0486 0.1585 0.7929 151 N 0.0570 0.2646 0.6784 152 Q 0.0622 0.3493 0.5885 153 D 0.0963 0.4389 0.4648 154 L 0.1151 0.5465 0.3384 155 Q 0.1263 0.5304 0.3434 156 L 0.0954 0.5965 0.3081 157 A 0.0621 0.6480 0.2899 158 A 0.0195 0.8151 0.1653 159 H 0.0154 0.7886 0.1960 160 L 0.0212 0.7792 0.1996 161 R 0.0221 0.7825 0.1954 162 S 0.0207 0.7542 0.2251 163 Q 0.0221 0.7793 0.1986 164 V 0.0309 0.8513 0.1178 165 T 0.0361 0.8749 0.0890 166 T 0.0330 0.8895 0.0775 167 L 0.0227 0.9031 0.0741 168 T 0.0193 0.8977 0.0830 169 R 0.0145 0.9040 0.0815 170 R 0.0162 0.8936 0.0902 171 L 0.0259 0.8573 0.1168 172 R 0.0332 0.8090 0.1578 173 R 0.0200 0.8518 0.1282 174 E 0.0204 0.8256 0.1540 175 A 0.0374 0.7366 0.2260 176 Q 0.0651 0.4724 0.4625 177 A 0.0836 0.2359 0.6805 178 D 0.0856 0.0641 0.8503 179 P 0.0584 0.1648 0.7769 180 V 0.1850 0.1402 0.6748 181 Q 0.2852 0.1645 0.5503 182 F 0.1696 0.4298 0.4006 183 S 0.1417 0.4638 0.3945 184 Q 0.1788 0.4605 0.3607 185 L 0.2944 0.4250 0.2806 186 V 0.3809 0.4229 0.1962 187 V 0.3732 0.4693 0.1575 188 L 0.2522 0.4955 0.2522 189 G 0.1949 0.4175 0.3877 190 A 0.2594 0.4987 0.2420 191 I 0.3276 0.5175 0.1549 192 D 0.2784 0.5737 0.1479 193 R 0.2087 0.5793 0.2120 194 L 0.1377 0.3805 0.4819 195 G 0.0680 0.0597 0.8723 196 G 0.0443 0.0675 0.8882 197 D 0.1078 0.0541 0.8381 198 V 0.1838 0.0376 0.7786 199 T 0.0994 0.0272 0.8734 200 P 0.0106 0.9080 0.0814 201 S 0.0066 0.9435 0.0500 202 E 0.0058 0.9488 0.0454 203 L 0.0068 0.9466 0.0466 204 A 0.0083 0.9333 0.0584 205 A 0.0120 0.8904 0.0976 206 A 0.0147 0.8223 0.1631 207 E 0.0263 0.6793 0.2945 208 R 0.0280 0.4808 0.4912 209 M 0.0650 0.2856 0.6494 210 R 0.0778 0.2742 0.6479 211 S 0.0621 0.4279 0.5100 212 S 0.0572 0.4525 0.4903 213 N 0.0815 0.6188 0.2997 214 L 0.0713 0.8413 0.0874 215 A 0.0563 0.8896 0.0541 216 A 0.0778 0.8708 0.0514 217 L 0.1070 0.8257 0.0673 218 L 0.1079 0.7950 0.0971 219 R 0.0775 0.7959 0.1266 220 E 0.0514 0.7856 0.1629 221 L 0.0354 0.7468 0.2178 222 E 0.0369 0.6294 0.3337 223 R 0.0581 0.4293 0.5126 224 G 0.0744 0.1204 0.8052 225 G 0.2159 0.0560 0.7282 226 L 0.7547 0.0293 0.2161 227 I 0.8810 0.0237 0.0953 228 V 0.8779 0.0243 0.0978 229 R 0.8112 0.0436 0.1452 230 H 0.7284 0.0200 0.2516 231 A 0.4739 0.0207 0.5054 232 D 0.2016 0.0137 0.7847 233 P 0.0131 0.3712 0.6158 234 Q 0.0145 0.2700 0.7155 235 D 0.0503 0.2931 0.6566 236 G 0.0582 0.0968 0.8449 237 R 0.1831 0.0594 0.7576 238 R 0.5288 0.0332 0.4380 239 T 0.7075 0.0153 0.2772 240 R 0.8668 0.0093 0.1239 241 V 0.8952 0.0096 0.0952 242 S 0.8861 0.0113 0.1026 243 L 0.7384 0.0337 0.2278 244 S 0.4119 0.0379 0.5502 245 S 0.1561 0.4013 0.4426 246 E 0.0709 0.5035 0.4256 247 G 0.0686 0.5264 0.4050 248 R 0.0782 0.6715 0.2503 249 R 0.0810 0.7164 0.2026 250 N 0.0527 0.6522 0.2951 251 L 0.0519 0.5083 0.4399 252 Y 0.0620 0.3970 0.5410 253 G 0.0601 0.2952 0.6446 254 N 0.0559 0.2660 0.6781 255 R 0.0507 0.3245 0.6248 256 A 0.0479 0.5590 0.3931 257 K 0.0169 0.7623 0.2208 258 R 0.0066 0.9315 0.0618 259 E 0.0066 0.9112 0.0822 260 E 0.0103 0.9111 0.0787 261 W 0.0053 0.9376 0.0571 262 L 0.0047 0.9426 0.0528 263 V 0.0058 0.9393 0.0548 264 R 0.0151 0.8978 0.0871 265 A 0.0172 0.8210 0.1618 266 M 0.0183 0.7281 0.2535 267 H 0.0302 0.5981 0.3716 268 A 0.0229 0.5151 0.4621 269 C 0.0513 0.4060 0.5428 270 L 0.0487 0.3005 0.6508 271 D 0.0358 0.3197 0.6445 272 E 0.0134 0.7003 0.2863 273 S 0.0124 0.7508 0.2369 274 E 0.0057 0.9277 0.0666 275 R 0.0047 0.9487 0.0466 276 A 0.0047 0.9470 0.0483 277 L 0.0047 0.9429 0.0524 278 L 0.0049 0.9304 0.0647 279 A 0.0057 0.8504 0.1439 280 A 0.0060 0.7183 0.2758 281 A 0.0098 0.6980 0.2922 282 G 0.0095 0.6981 0.2925 283 P 0.0076 0.8432 0.1492 284 L 0.0107 0.8860 0.1034 285 L 0.0300 0.8798 0.0903 286 T 0.0296 0.8663 0.1041 287 R 0.0120 0.8767 0.1112 288 L 0.0112 0.8408 0.1480 289 A 0.0179 0.7308 0.2513 290 Q 0.0256 0.6075 0.3669 291 F 0.0456 0.3613 0.5931 292 E 0.0710 0.2051 0.7239 293 E 0.0744 0.0567 0.8689 294 P 0.0481 0.0491 0.9028