# This file is the result of combining several RDB files, specifically # T0386.t04.dssp-ebghstl.rdb (weight 1.53986) # T0386.t04.stride-ebghtl.rdb (weight 1.24869) # T0386.t04.str2.rdb (weight 1.54758) # T0386.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 T0386.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 538 # # ============================================ # Comments from T0386.t04.stride-ebghtl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 538 # # ============================================ # Comments from T0386.t04.str2.rdb # ============================================ # TARGET T0386 # 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 T0386.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 538 # # ============================================ # Comments from T0386.t04.alpha.rdb # ============================================ # TARGET T0386 # 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 T0386.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 538 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0496 0.1427 0.8077 2 P 0.0368 0.5138 0.4494 3 K 0.0336 0.7551 0.2113 4 A 0.0324 0.8108 0.1568 5 K 0.0375 0.8220 0.1405 6 A 0.0413 0.7700 0.1887 7 K 0.0473 0.6943 0.2584 8 T 0.1160 0.5524 0.3315 9 K 0.0968 0.4680 0.4352 10 N 0.1201 0.2698 0.6101 11 T 0.1017 0.3077 0.5906 12 E 0.0683 0.3909 0.5408 13 I 0.1609 0.3319 0.5072 14 I 0.3021 0.1878 0.5101 15 S 0.1873 0.1113 0.7014 16 P 0.0988 0.1237 0.7775 17 H 0.1574 0.1006 0.7420 18 H 0.2939 0.0879 0.6182 19 Y 0.3499 0.0442 0.6058 20 V 0.2734 0.0415 0.6851 21 Y 0.0819 0.2577 0.6605 22 P 0.0224 0.4932 0.4844 23 N 0.0389 0.5257 0.4354 24 T 0.0446 0.7167 0.2387 25 T 0.0298 0.8202 0.1500 26 T 0.0485 0.8487 0.1028 27 L 0.0361 0.8713 0.0927 28 K 0.0293 0.8599 0.1108 29 N 0.0212 0.7703 0.2085 30 K 0.0241 0.6180 0.3579 31 Y 0.0563 0.3388 0.6049 32 G 0.0591 0.1723 0.7686 33 I 0.1193 0.1652 0.7155 34 K 0.1098 0.2602 0.6300 35 N 0.1170 0.2632 0.6198 36 L 0.0390 0.5949 0.3661 37 N 0.0305 0.6809 0.2887 38 A 0.0244 0.7360 0.2396 39 F 0.0177 0.7883 0.1940 40 L 0.0174 0.8120 0.1706 41 E 0.0152 0.8517 0.1331 42 K 0.0179 0.8588 0.1233 43 C 0.0299 0.8140 0.1561 44 S 0.0309 0.7991 0.1699 45 H 0.0315 0.8252 0.1433 46 D 0.0172 0.8491 0.1336 47 T 0.0149 0.8586 0.1265 48 A 0.0047 0.9547 0.0406 49 K 0.0047 0.9607 0.0347 50 A 0.0046 0.9605 0.0348 51 M 0.0047 0.9598 0.0356 52 I 0.0047 0.9574 0.0379 53 N 0.0048 0.9506 0.0446 54 L 0.0050 0.9317 0.0632 55 R 0.0065 0.9027 0.0909 56 E 0.0085 0.8851 0.1063 57 E 0.0126 0.7904 0.1970 58 S 0.0216 0.5938 0.3845 59 L 0.0623 0.1409 0.7968 60 P 0.0335 0.1581 0.8084 61 E 0.0455 0.1505 0.8040 62 Y 0.0782 0.1163 0.8055 63 F 0.1296 0.0287 0.8416 64 D 0.0755 0.0189 0.9056 65 T 0.0049 0.9478 0.0473 66 A 0.0047 0.9603 0.0350 67 Y 0.0047 0.9608 0.0345 68 L 0.0047 0.9611 0.0342 69 C 0.0046 0.9611 0.0343 70 H 0.0047 0.9610 0.0344 71 I 0.0046 0.9608 0.0346 72 H 0.0047 0.9587 0.0366 73 Q 0.0047 0.9558 0.0395 74 Q 0.0049 0.9400 0.0550 75 L 0.0055 0.9131 0.0814 76 F 0.0090 0.8400 0.1510 77 K 0.0161 0.6970 0.2870 78 N 0.0253 0.4316 0.5431 79 T 0.0645 0.3451 0.5904 80 F 0.1055 0.2984 0.5961 81 E 0.1019 0.3279 0.5702 82 W 0.1313 0.2769 0.5918 83 A 0.1317 0.2009 0.6674 84 G 0.1850 0.0987 0.7163 85 Y 0.4942 0.0705 0.4353 86 L 0.7134 0.0316 0.2550 87 R 0.6917 0.0203 0.2880 88 H 0.5961 0.0201 0.3839 89 I 0.4884 0.0181 0.4936 90 P 0.4688 0.0295 0.5017 91 F 0.5136 0.0352 0.4513 92 T 0.6044 0.0324 0.3631 93 F 0.4890 0.0532 0.4578 94 A 0.3901 0.0528 0.5571 95 D 0.2054 0.0553 0.7393 96 G 0.2543 0.0522 0.6935 97 T 0.3565 0.0879 0.5557 98 T 0.5651 0.0758 0.3591 99 A 0.6974 0.0579 0.2447 100 A 0.7257 0.0568 0.2175 101 M 0.4473 0.0518 0.5009 102 P 0.2504 0.1627 0.5869 103 E 0.1338 0.1925 0.6736 104 M 0.1795 0.1975 0.6230 105 K 0.1733 0.1758 0.6509 106 R 0.1552 0.1750 0.6697 107 T 0.0998 0.1098 0.7904 108 G 0.1626 0.0555 0.7818 109 W 0.4442 0.0383 0.5175 110 K 0.6412 0.0515 0.3073 111 N 0.6985 0.0481 0.2534 112 A 0.6366 0.0574 0.3060 113 F 0.4050 0.0609 0.5341 114 A 0.2260 0.0647 0.7093 115 I 0.1019 0.0788 0.8193 116 G 0.0139 0.6185 0.3675 117 D 0.0067 0.7835 0.2098 118 E 0.0077 0.8351 0.1572 119 I 0.0067 0.8691 0.1242 120 Q 0.0051 0.9239 0.0710 121 E 0.0048 0.9285 0.0667 122 G 0.0049 0.9217 0.0734 123 L 0.0048 0.9440 0.0512 124 Q 0.0047 0.9506 0.0447 125 R 0.0048 0.9458 0.0493 126 L 0.0048 0.9463 0.0489 127 D 0.0047 0.9545 0.0408 128 Q 0.0047 0.9506 0.0447 129 T 0.0048 0.9444 0.0509 130 L 0.0052 0.9156 0.0792 131 A 0.0071 0.8072 0.1857 132 E 0.0094 0.6979 0.2927 133 K 0.0129 0.6352 0.3519 134 N 0.0260 0.4600 0.5139 135 N 0.0326 0.4567 0.5107 136 L 0.0564 0.4470 0.4966 137 Q 0.0358 0.3664 0.5978 138 G 0.0369 0.2434 0.7198 139 L 0.0794 0.1744 0.7462 140 T 0.0773 0.1498 0.7729 141 R 0.0393 0.5725 0.3882 142 E 0.0232 0.7099 0.2670 143 E 0.0083 0.8432 0.1485 144 F 0.0086 0.8582 0.1332 145 N 0.0073 0.8925 0.1002 146 S 0.0047 0.9560 0.0393 147 E 0.0047 0.9588 0.0365 148 A 0.0047 0.9596 0.0357 149 I 0.0047 0.9601 0.0352 150 E 0.0047 0.9604 0.0350 151 L 0.0049 0.9532 0.0418 152 F 0.0052 0.9498 0.0450 153 N 0.0063 0.9303 0.0634 154 S 0.0092 0.8910 0.0998 155 L 0.0176 0.8757 0.1068 156 N 0.0334 0.8199 0.1467 157 Q 0.0919 0.7319 0.1762 158 L 0.1324 0.5979 0.2697 159 H 0.1180 0.2199 0.6621 160 P 0.0802 0.1625 0.7573 161 F 0.1255 0.1289 0.7457 162 R 0.0958 0.1704 0.7338 163 E 0.0534 0.1945 0.7520 164 G 0.0353 0.2623 0.7024 165 N 0.0372 0.2961 0.6667 166 G 0.0166 0.5950 0.3884 167 R 0.0065 0.9284 0.0651 168 T 0.0053 0.9545 0.0402 169 Q 0.0047 0.9595 0.0358 170 R 0.0046 0.9615 0.0339 171 L 0.0046 0.9615 0.0338 172 F 0.0047 0.9607 0.0347 173 F 0.0047 0.9606 0.0347 174 E 0.0046 0.9605 0.0348 175 N 0.0047 0.9594 0.0359 176 L 0.0047 0.9587 0.0366 177 A 0.0047 0.9593 0.0360 178 K 0.0049 0.9539 0.0412 179 A 0.0068 0.9126 0.0806 180 A 0.0443 0.4010 0.5547 181 G 0.0350 0.0195 0.9455 182 H 0.0629 0.0091 0.9280 183 Q 0.2313 0.0110 0.7577 184 L 0.3999 0.0118 0.5883 185 N 0.3966 0.0143 0.5890 186 F 0.3644 0.2329 0.4026 187 S 0.3434 0.1986 0.4580 188 L 0.3875 0.2029 0.4096 189 I 0.2852 0.0778 0.6371 190 T 0.1364 0.0402 0.8233 191 K 0.0088 0.9375 0.0537 192 E 0.0056 0.9550 0.0394 193 R 0.0047 0.9587 0.0365 194 M 0.0047 0.9604 0.0349 195 M 0.0047 0.9604 0.0349 196 V 0.0047 0.9590 0.0363 197 A 0.0048 0.9555 0.0397 198 S 0.0051 0.9486 0.0462 199 V 0.0054 0.9391 0.0554 200 A 0.0069 0.9199 0.0731 201 V 0.0151 0.8707 0.1141 202 A 0.0228 0.7390 0.2382 203 E 0.0240 0.5658 0.4102 204 N 0.0495 0.2021 0.7484 205 G 0.0291 0.0703 0.9006 206 D 0.0793 0.0506 0.8700 207 L 0.0652 0.4647 0.4700 208 E 0.0136 0.8778 0.1085 209 P 0.0072 0.9371 0.0557 210 M 0.0049 0.9521 0.0430 211 Q 0.0051 0.9569 0.0380 212 H 0.0051 0.9527 0.0421 213 L 0.0054 0.9462 0.0484 214 F 0.0053 0.9434 0.0513 215 E 0.0061 0.9263 0.0675 216 D 0.0072 0.8697 0.1231 217 I 0.0128 0.7495 0.2377 218 S 0.0312 0.5424 0.4264 219 N 0.0459 0.3532 0.6010 220 P 0.0049 0.9069 0.0881 221 E 0.0049 0.9304 0.0647 222 K 0.0048 0.9517 0.0435 223 I 0.0047 0.9576 0.0377 224 R 0.0048 0.9531 0.0422 225 L 0.0047 0.9514 0.0438 226 L 0.0047 0.9579 0.0374 227 K 0.0047 0.9589 0.0363 228 E 0.0048 0.9585 0.0368 229 F 0.0047 0.9572 0.0381 230 M 0.0048 0.9582 0.0370 231 H 0.0048 0.9547 0.0405 232 T 0.0051 0.9511 0.0439 233 M 0.0061 0.9432 0.0506 234 K 0.0078 0.9057 0.0865 235 N 0.0099 0.8292 0.1609 236 T 0.0413 0.5722 0.3864 237 G 0.0379 0.2417 0.7204 238 R 0.0792 0.2303 0.6905 239 N 0.1269 0.2434 0.6298 240 V 0.0901 0.3664 0.5435 241 N 0.0629 0.2303 0.7068 242 D 0.0775 0.1764 0.7461 243 R 0.1578 0.1991 0.6432 244 P 0.2114 0.3343 0.4543 245 V 0.2624 0.3976 0.3400 246 M 0.3866 0.3564 0.2570 247 V 0.3568 0.3498 0.2934 248 A 0.2383 0.3846 0.3771 249 K 0.1305 0.5748 0.2947 250 E 0.1287 0.5797 0.2916 251 G 0.1446 0.5422 0.3132 252 E 0.1898 0.5784 0.2317 253 T 0.2479 0.5824 0.1697 254 Y 0.2013 0.6380 0.1607 255 T 0.1314 0.6513 0.2173 256 G 0.1234 0.5245 0.3521 257 T 0.1217 0.5339 0.3444 258 Y 0.1652 0.4877 0.3471 259 R 0.1041 0.4005 0.4953 260 G 0.0746 0.2897 0.6356 261 A 0.0760 0.1876 0.7365 262 G 0.0966 0.1547 0.7487 263 L 0.2058 0.2249 0.5693 264 E 0.2441 0.2544 0.5015 265 G 0.2994 0.2025 0.4981 266 F 0.4580 0.1339 0.4081 267 A 0.4879 0.1370 0.3751 268 L 0.4055 0.1548 0.4397 269 N 0.3050 0.1144 0.5806 270 V 0.3198 0.1179 0.5623 271 K 0.2420 0.1656 0.5924 272 G 0.1636 0.4310 0.4054 273 A 0.2387 0.4262 0.3351 274 Y 0.4370 0.3962 0.1667 275 I 0.5327 0.3493 0.1180 276 I 0.5272 0.3103 0.1625 277 G 0.4424 0.2713 0.2864 278 N 0.3720 0.2693 0.3587 279 I 0.2233 0.3661 0.4106 280 D 0.0797 0.3171 0.6032 281 H 0.0491 0.1969 0.7540 282 L 0.0934 0.0245 0.8821 283 P 0.0778 0.0143 0.9079 284 P 0.0096 0.7894 0.2010 285 E 0.0126 0.7926 0.1947 286 Q 0.0205 0.8236 0.1559 287 L 0.1753 0.5284 0.2964 288 K 0.2763 0.4409 0.2828 289 I 0.4252 0.3263 0.2485 290 L 0.3333 0.1956 0.4711 291 K 0.1785 0.0433 0.7782 292 P 0.0906 0.0873 0.8221 293 G 0.0777 0.0741 0.8482 294 D 0.1784 0.0844 0.7371 295 K 0.4349 0.0453 0.5197 296 I 0.6264 0.0157 0.3579 297 T 0.7194 0.0129 0.2677 298 F 0.6097 0.0131 0.3772 299 T 0.2915 0.0209 0.6875