# This file is the result of combining several RDB files, specifically # T0375.t04.dssp-ebghstl.rdb (weight 1.53986) # T0375.t04.stride-ebghtl.rdb (weight 1.24869) # T0375.t04.str2.rdb (weight 1.54758) # T0375.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 T0375.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0375 # 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 T0375.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 2089 # # ============================================ # Comments from T0375.t04.stride-ebghtl.rdb # ============================================ # TARGET T0375 # 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 T0375.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 2089 # # ============================================ # Comments from T0375.t04.str2.rdb # ============================================ # TARGET T0375 # 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 T0375.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 2089 # # ============================================ # Comments from T0375.t04.alpha.rdb # ============================================ # TARGET T0375 # 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 T0375.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 2089 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.0559 0.0270 0.9171 2 S 0.1501 0.0116 0.8383 3 Q 0.4800 0.0116 0.5084 4 I 0.9045 0.0038 0.0917 5 L 0.9270 0.0036 0.0694 6 C 0.9235 0.0037 0.0728 7 V 0.8174 0.0165 0.1661 8 G 0.3651 0.0329 0.6020 9 L 0.2861 0.0873 0.6266 10 V 0.3779 0.1484 0.4736 11 V 0.5296 0.1912 0.2792 12 L 0.6315 0.1565 0.2120 13 D 0.6033 0.1828 0.2139 14 V 0.6804 0.1603 0.1593 15 I 0.6576 0.1905 0.1519 16 S 0.6385 0.1534 0.2081 17 L 0.5629 0.1160 0.3210 18 V 0.3832 0.1154 0.5014 19 D 0.1800 0.1360 0.6840 20 K 0.1200 0.1135 0.7665 21 Y 0.1294 0.0350 0.8356 22 P 0.1033 0.0464 0.8502 23 K 0.0778 0.0683 0.8539 24 E 0.0501 0.1371 0.8127 25 D 0.0541 0.1215 0.8244 26 S 0.1201 0.1252 0.7547 27 E 0.3209 0.1033 0.5759 28 I 0.4454 0.0737 0.4810 29 R 0.4088 0.0621 0.5291 30 C 0.3939 0.1082 0.4979 31 L 0.3588 0.1594 0.4818 32 S 0.3550 0.1977 0.4474 33 Q 0.4464 0.2118 0.3418 34 R 0.5663 0.1693 0.2644 35 W 0.5807 0.1646 0.2547 36 Q 0.3918 0.1575 0.4508 37 R 0.1613 0.1743 0.6644 38 G 0.0872 0.1063 0.8065 39 G 0.0946 0.1708 0.7346 40 N 0.0660 0.3883 0.5457 41 A 0.0198 0.8331 0.1471 42 S 0.0096 0.9184 0.0720 43 N 0.0066 0.9453 0.0481 44 S 0.0056 0.9581 0.0363 45 C 0.0046 0.9611 0.0343 46 T 0.0046 0.9616 0.0338 47 I 0.0046 0.9615 0.0339 48 L 0.0047 0.9595 0.0358 49 S 0.0048 0.9520 0.0431 50 L 0.0062 0.9054 0.0884 51 L 0.0432 0.5083 0.4485 52 G 0.0368 0.0326 0.9306 53 A 0.0556 0.0120 0.9324 54 P 0.1683 0.0185 0.8133 55 C 0.7499 0.0163 0.2338 56 A 0.8797 0.0154 0.1049 57 F 0.9191 0.0066 0.0742 58 M 0.8976 0.0131 0.0892 59 G 0.8077 0.0210 0.1713 60 S 0.6318 0.0276 0.3406 61 M 0.2856 0.0521 0.6623 62 A 0.1182 0.0368 0.8450 63 P 0.0524 0.1516 0.7960 64 G 0.0396 0.2393 0.7210 65 H 0.0324 0.5606 0.4070 66 V 0.0146 0.7922 0.1932 67 A 0.0054 0.9302 0.0644 68 D 0.0048 0.9487 0.0465 69 F 0.0053 0.9509 0.0438 70 V 0.0050 0.9539 0.0411 71 L 0.0047 0.9589 0.0364 72 D 0.0047 0.9591 0.0362 73 D 0.0048 0.9584 0.0368 74 L 0.0048 0.9540 0.0412 75 R 0.0052 0.9366 0.0582 76 R 0.0067 0.8556 0.1377 77 Y 0.0475 0.3647 0.5878 78 S 0.0497 0.0262 0.9241 79 V 0.1233 0.0116 0.8651 80 D 0.3946 0.0097 0.5957 81 L 0.5537 0.0376 0.4088 82 R 0.5447 0.0645 0.3908 83 Y 0.7321 0.0275 0.2404 84 T 0.8526 0.0081 0.1394 85 V 0.8918 0.0053 0.1029 86 F 0.8214 0.0107 0.1679 87 Q 0.4604 0.0179 0.5217 88 T 0.1189 0.0821 0.7990 89 T 0.0662 0.0436 0.8901 90 G 0.1216 0.0320 0.8464 91 S 0.2158 0.0265 0.7577 92 V 0.4137 0.0165 0.5698 93 P 0.5956 0.0164 0.3881 94 I 0.8191 0.0141 0.1668 95 A 0.9044 0.0065 0.0891 96 T 0.9256 0.0042 0.0703 97 V 0.9270 0.0041 0.0689 98 I 0.9197 0.0042 0.0761 99 I 0.8752 0.0087 0.1161 100 N 0.6559 0.0144 0.3297 101 E 0.2068 0.0863 0.7068 102 A 0.1053 0.1212 0.7735 103 S 0.0643 0.0586 0.8772 104 G 0.0708 0.0423 0.8869 105 S 0.3381 0.0275 0.6344 106 R 0.6497 0.0136 0.3367 107 T 0.8043 0.0134 0.1823 108 I 0.9008 0.0092 0.0900 109 L 0.8840 0.0135 0.1025 110 Y 0.7907 0.0180 0.1913 111 Y 0.4730 0.0441 0.4829 112 D 0.1731 0.1299 0.6970 113 R 0.0665 0.2173 0.7162 114 S 0.0722 0.1447 0.7831 115 L 0.0736 0.1054 0.8210 116 P 0.0291 0.2490 0.7219 117 D 0.0429 0.1936 0.7634 118 V 0.1532 0.0677 0.7791 119 S 0.0926 0.0303 0.8771 120 A 0.0064 0.8391 0.1545 121 T 0.0068 0.8261 0.1670 122 D 0.0104 0.8037 0.1859 123 F 0.0387 0.6089 0.3524 124 E 0.0333 0.4949 0.4718 125 K 0.0244 0.6844 0.2912 126 V 0.0331 0.6267 0.3402 127 D 0.0405 0.4920 0.4676 128 L 0.0576 0.4434 0.4990 129 T 0.0284 0.3990 0.5726 130 Q 0.0534 0.2375 0.7091 131 F 0.1856 0.0260 0.7884 132 K 0.2118 0.0423 0.7459 133 W 0.9140 0.0038 0.0822 134 I 0.9306 0.0033 0.0661 135 H 0.9318 0.0032 0.0651 136 I 0.8974 0.0064 0.0962 137 E 0.5899 0.0266 0.3834 138 G 0.1843 0.0332 0.7825 139 R 0.1183 0.0586 0.8231 140 N 0.1085 0.0516 0.8399 141 A 0.0388 0.3667 0.5945 142 S 0.0083 0.8456 0.1461 143 E 0.0072 0.8929 0.0999 144 Q 0.0052 0.9370 0.0578 145 V 0.0048 0.9522 0.0430 146 K 0.0050 0.9525 0.0425 147 M 0.0050 0.9527 0.0423 148 L 0.0047 0.9560 0.0393 149 Q 0.0047 0.9577 0.0376 150 R 0.0048 0.9560 0.0392 151 I 0.0051 0.9524 0.0425 152 D 0.0050 0.9382 0.0568 153 A 0.0057 0.8692 0.1251 154 H 0.0446 0.3180 0.6373 155 N 0.0354 0.0202 0.9445 156 T 0.0746 0.0107 0.9147 157 R 0.3197 0.0095 0.6708 158 Q 0.4576 0.0112 0.5312 159 P 0.3457 0.0117 0.6427 160 P 0.2632 0.0201 0.7167 161 E 0.1602 0.0192 0.8206 162 Q 0.0406 0.2726 0.6868 163 K 0.0450 0.2428 0.7122 164 I 0.1061 0.2513 0.6425 165 R 0.1360 0.1638 0.7002 166 V 0.1415 0.2195 0.6391 167 S 0.1452 0.2654 0.5894 168 V 0.1279 0.3259 0.5462 169 E 0.1108 0.2732 0.6159 170 V 0.0800 0.2681 0.6519 171 E 0.0464 0.2112 0.7423 172 K 0.0530 0.2362 0.7108 173 P 0.0409 0.4227 0.5364 174 R 0.0147 0.8153 0.1699 175 E 0.0067 0.9196 0.0737 176 E 0.0069 0.9256 0.0675 177 L 0.0066 0.9248 0.0686 178 F 0.0074 0.9163 0.0763 179 Q 0.0082 0.8644 0.1273 180 L 0.0136 0.7454 0.2409 181 F 0.0556 0.4121 0.5323 182 G 0.0276 0.2797 0.6926 183 Y 0.0620 0.1646 0.7733 184 G 0.1481 0.0242 0.8277 185 D 0.1793 0.0527 0.7680 186 V 0.8579 0.0099 0.1322 187 V 0.8932 0.0091 0.0977 188 F 0.8525 0.0073 0.1402 189 V 0.5257 0.0211 0.4531 190 S 0.0973 0.0118 0.8909 191 K 0.0051 0.9170 0.0779 192 D 0.0051 0.9431 0.0518 193 V 0.0050 0.9488 0.0462 194 A 0.0051 0.9485 0.0464 195 K 0.0051 0.9058 0.0891 196 H 0.0075 0.7616 0.2309 197 L 0.0511 0.2709 0.6780 198 G 0.0361 0.0281 0.9359 199 F 0.0728 0.0300 0.8972 200 Q 0.0481 0.0824 0.8695 201 S 0.0836 0.0556 0.8608 202 A 0.0049 0.9455 0.0496 203 E 0.0047 0.9593 0.0360 204 E 0.0047 0.9598 0.0356 205 A 0.0047 0.9600 0.0354 206 L 0.0047 0.9597 0.0356 207 R 0.0047 0.9583 0.0370 208 G 0.0049 0.9525 0.0426 209 L 0.0053 0.9328 0.0619 210 Y 0.0079 0.8805 0.1116 211 G 0.0117 0.6440 0.3443 212 R 0.0274 0.4796 0.4930 213 V 0.0559 0.1632 0.7808 214 R 0.0303 0.2100 0.7597 215 K 0.0619 0.0939 0.8442 216 G 0.1734 0.0191 0.8074 217 A 0.3978 0.0234 0.5788 218 V 0.9179 0.0033 0.0788 219 L 0.9298 0.0034 0.0668 220 V 0.9326 0.0032 0.0642 221 C 0.9189 0.0038 0.0773 222 A 0.7627 0.0056 0.2317 223 W 0.3796 0.0258 0.5946 224 A 0.1342 0.0651 0.8007 225 E 0.0819 0.2026 0.7155 226 E 0.0783 0.1327 0.7889 227 G 0.1454 0.0936 0.7610 228 A 0.4408 0.0530 0.5062 229 D 0.7759 0.0359 0.1882 230 A 0.8655 0.0179 0.1166 231 L 0.8372 0.0160 0.1468 232 G 0.2938 0.0151 0.6911 233 P 0.0283 0.0936 0.8781 234 D 0.0454 0.0232 0.9314 235 G 0.0699 0.0345 0.8956 236 K 0.3710 0.0117 0.6173 237 L 0.8746 0.0044 0.1210 238 L 0.8471 0.0118 0.1410 239 H 0.8560 0.0082 0.1358 240 S 0.6974 0.0134 0.2892 241 D 0.3848 0.0270 0.5882 242 A 0.2042 0.0475 0.7483 243 F 0.1531 0.0185 0.8284 244 P 0.0875 0.0128 0.8997 245 P 0.0740 0.0107 0.9153 246 P 0.1997 0.0171 0.7832 247 R 0.5076 0.0198 0.4726 248 V 0.7079 0.0167 0.2754 249 V 0.6762 0.0357 0.2882 250 D 0.5308 0.0300 0.4392 251 T 0.2380 0.0800 0.6820 252 L 0.1385 0.1014 0.7601 253 G 0.0875 0.1148 0.7976 254 A 0.0362 0.4214 0.5423 255 G 0.0190 0.7272 0.2538 256 D 0.0074 0.9254 0.0672 257 T 0.0048 0.9571 0.0381 258 F 0.0047 0.9588 0.0364 259 N 0.0047 0.9600 0.0354 260 A 0.0047 0.9607 0.0346 261 S 0.0046 0.9615 0.0339 262 V 0.0046 0.9615 0.0339 263 I 0.0047 0.9610 0.0344 264 F 0.0047 0.9601 0.0352 265 S 0.0047 0.9548 0.0405 266 L 0.0052 0.9408 0.0540 267 S 0.0074 0.8542 0.1384 268 Q 0.0442 0.3217 0.6341 269 G 0.0406 0.0350 0.9244 270 R 0.0613 0.0147 0.9239 271 S 0.0814 0.0138 0.9048 272 V 0.0048 0.9505 0.0447 273 Q 0.0046 0.9615 0.0338 274 E 0.0046 0.9615 0.0338 275 A 0.0046 0.9614 0.0339 276 L 0.0047 0.9604 0.0349 277 R 0.0046 0.9608 0.0346 278 F 0.0046 0.9603 0.0350 279 G 0.0047 0.9607 0.0346 280 C 0.0047 0.9604 0.0349 281 Q 0.0047 0.9606 0.0348 282 V 0.0048 0.9579 0.0374 283 A 0.0048 0.9551 0.0401 284 G 0.0050 0.9522 0.0428 285 K 0.0059 0.9424 0.0516 286 K 0.0077 0.9134 0.0789 287 C 0.0192 0.8241 0.1567 288 G 0.0518 0.5590 0.3893 289 L 0.0969 0.3831 0.5200 290 Q 0.0869 0.2702 0.6430 291 G 0.0837 0.1218 0.7946 292 F 0.1189 0.1253 0.7558 293 D 0.1095 0.1575 0.7330 294 G 0.0844 0.1287 0.7870 295 I 0.0908 0.0779 0.8313 296 V 0.0768 0.0318 0.8914