# This file is the result of combining several RDB files, specifically # T0338.t04.dssp-ebghstl.rdb (weight 1.53986) # T0338.t04.stride-ebghtl.rdb (weight 1.24869) # T0338.t04.str2.rdb (weight 1.54758) # T0338.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 T0338.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0338 # 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 T0338.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 989 # # ============================================ # Comments from T0338.t04.stride-ebghtl.rdb # ============================================ # TARGET T0338 # 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 T0338.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 989 # # ============================================ # Comments from T0338.t04.str2.rdb # ============================================ # TARGET T0338 # 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 T0338.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 989 # # ============================================ # Comments from T0338.t04.alpha.rdb # ============================================ # TARGET T0338 # 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 T0338.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 989 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0456 0.0978 0.8566 2 S 0.0751 0.1840 0.7409 3 S 0.0599 0.4963 0.4438 4 R 0.0479 0.5776 0.3745 5 W 0.0463 0.6347 0.3189 6 F 0.0568 0.6138 0.3294 7 F 0.0859 0.5154 0.3987 8 T 0.0636 0.5695 0.3669 9 R 0.0105 0.9095 0.0800 10 E 0.0087 0.9214 0.0700 11 Q 0.0077 0.9172 0.0751 12 L 0.0133 0.8728 0.1139 13 E 0.0153 0.7213 0.2635 14 N 0.0277 0.4584 0.5139 15 T 0.0677 0.0396 0.8926 16 P 0.0567 0.1021 0.8412 17 S 0.0731 0.1402 0.7866 18 R 0.0486 0.3246 0.6268 19 R 0.0610 0.2988 0.6402 20 C 0.0900 0.2101 0.6999 21 G 0.0800 0.1110 0.8090 22 V 0.1409 0.0967 0.7625 23 E 0.1322 0.1051 0.7628 24 A 0.0743 0.2901 0.6356 25 D 0.0739 0.3290 0.5971 26 K 0.0655 0.4077 0.5268 27 E 0.0462 0.4089 0.5449 28 L 0.0124 0.8362 0.1513 29 S 0.0108 0.8795 0.1097 30 C 0.0073 0.9240 0.0688 31 R 0.0048 0.9537 0.0415 32 Q 0.0047 0.9601 0.0352 33 Q 0.0046 0.9588 0.0365 34 A 0.0047 0.9581 0.0372 35 A 0.0047 0.9607 0.0346 36 N 0.0046 0.9613 0.0341 37 L 0.0046 0.9608 0.0346 38 I 0.0047 0.9600 0.0353 39 Q 0.0046 0.9608 0.0346 40 E 0.0046 0.9602 0.0352 41 M 0.0047 0.9590 0.0363 42 G 0.0048 0.9500 0.0452 43 Q 0.0052 0.9360 0.0588 44 R 0.0071 0.8949 0.0980 45 L 0.0490 0.5855 0.3655 46 N 0.0555 0.1102 0.8344 47 V 0.0564 0.0817 0.8619 48 S 0.0438 0.1969 0.7593 49 Q 0.0055 0.9088 0.0857 50 L 0.0049 0.9403 0.0548 51 T 0.0048 0.9517 0.0435 52 I 0.0047 0.9588 0.0365 53 N 0.0046 0.9614 0.0340 54 T 0.0046 0.9607 0.0346 55 A 0.0047 0.9606 0.0348 56 I 0.0047 0.9606 0.0347 57 V 0.0046 0.9594 0.0360 58 Y 0.0047 0.9505 0.0448 59 M 0.0047 0.9519 0.0433 60 H 0.0054 0.9502 0.0444 61 R 0.0056 0.9393 0.0550 62 F 0.0108 0.8976 0.0916 63 Y 0.0370 0.7801 0.1829 64 M 0.0740 0.6229 0.3031 65 H 0.0868 0.4508 0.4624 66 H 0.1092 0.1749 0.7159 67 S 0.1514 0.1066 0.7421 68 F 0.1877 0.0955 0.7168 69 T 0.1726 0.1237 0.7037 70 K 0.0990 0.3196 0.5814 71 F 0.0758 0.2885 0.6357 72 N 0.1078 0.2460 0.6462 73 K 0.0339 0.6820 0.2841 74 N 0.0324 0.8209 0.1467 75 I 0.0458 0.8941 0.0601 76 I 0.0159 0.9411 0.0430 77 S 0.0076 0.9547 0.0377 78 S 0.0047 0.9598 0.0355 79 T 0.0047 0.9601 0.0352 80 A 0.0047 0.9599 0.0354 81 L 0.0047 0.9596 0.0357 82 F 0.0047 0.9578 0.0375 83 L 0.0047 0.9552 0.0401 84 A 0.0049 0.9478 0.0474 85 A 0.0066 0.9336 0.0598 86 K 0.0090 0.9141 0.0769 87 V 0.0215 0.8561 0.1223 88 E 0.0292 0.8250 0.1457 89 E 0.0512 0.7299 0.2190 90 Q 0.0609 0.6254 0.3137 91 A 0.0575 0.5801 0.3624 92 R 0.0833 0.5425 0.3741 93 K 0.1069 0.4313 0.4619 94 L 0.0411 0.7364 0.2225 95 E 0.0297 0.7794 0.1909 96 H 0.0598 0.7600 0.1802 97 V 0.1045 0.7811 0.1145 98 I 0.1624 0.7312 0.1065 99 K 0.1882 0.6824 0.1294 100 V 0.1507 0.6961 0.1532 101 A 0.1584 0.6289 0.2127 102 H 0.1842 0.4721 0.3436 103 A 0.2324 0.2796 0.4880 104 C 0.2592 0.1421 0.5987 105 L 0.1746 0.0656 0.7598 106 H 0.1057 0.0522 0.8421 107 P 0.1129 0.1065 0.7807 108 L 0.0705 0.3687 0.5609 109 E 0.0582 0.4703 0.4715 110 P 0.0614 0.5691 0.3694 111 L 0.0977 0.5944 0.3078 112 L 0.1740 0.4743 0.3517 113 D 0.1962 0.3633 0.4405 114 T 0.1905 0.3008 0.5087 115 K 0.1646 0.2593 0.5762 116 C 0.0933 0.3423 0.5644 117 D 0.0491 0.4840 0.4668 118 A 0.0757 0.6031 0.3212 119 Y 0.1222 0.5950 0.2829 120 L 0.1121 0.5722 0.3157 121 Q 0.1002 0.4750 0.4248 122 Q 0.0614 0.4344 0.5042 123 T 0.0073 0.9411 0.0516 124 R 0.0052 0.9554 0.0394 125 E 0.0053 0.9556 0.0391 126 L 0.0051 0.9593 0.0355 127 V 0.0048 0.9599 0.0353 128 I 0.0047 0.9606 0.0348 129 L 0.0047 0.9604 0.0349 130 E 0.0047 0.9606 0.0347 131 T 0.0046 0.9617 0.0337 132 I 0.0046 0.9611 0.0342 133 M 0.0046 0.9612 0.0342 134 L 0.0047 0.9602 0.0351 135 Q 0.0049 0.9504 0.0448 136 T 0.0057 0.8957 0.0987 137 L 0.0498 0.4916 0.4586 138 G 0.0591 0.0595 0.8813 139 F 0.2059 0.0345 0.7596 140 E 0.6078 0.0279 0.3642 141 I 0.7004 0.0134 0.2862 142 T 0.6142 0.0161 0.3697 143 I 0.4624 0.0176 0.5199 144 E 0.2209 0.0374 0.7417 145 H 0.1030 0.0235 0.8736 146 P 0.0457 0.1646 0.7897 147 H 0.0446 0.3285 0.6269 148 T 0.0267 0.6843 0.2891 149 D 0.0176 0.8604 0.1220 150 V 0.0069 0.9438 0.0492 151 V 0.0064 0.9536 0.0400 152 K 0.0065 0.9531 0.0403 153 C 0.0069 0.9498 0.0433 154 T 0.0074 0.9431 0.0495 155 Q 0.0076 0.9228 0.0695 156 L 0.0087 0.8929 0.0984 157 V 0.0279 0.7438 0.2283 158 R 0.0311 0.5163 0.4526 159 A 0.0331 0.3882 0.5788 160 S 0.0507 0.3464 0.6029 161 K 0.0113 0.8255 0.1633 162 D 0.0131 0.8707 0.1162 163 L 0.0059 0.9338 0.0604 164 A 0.0050 0.9508 0.0442 165 Q 0.0047 0.9559 0.0393 166 T 0.0047 0.9573 0.0379 167 S 0.0047 0.9594 0.0359 168 Y 0.0047 0.9607 0.0346 169 F 0.0047 0.9605 0.0348 170 M 0.0047 0.9584 0.0369 171 A 0.0047 0.9543 0.0410 172 T 0.0054 0.9339 0.0607 173 N 0.0071 0.8783 0.1146 174 S 0.0136 0.7949 0.1915 175 L 0.0286 0.6412 0.3302 176 H 0.0488 0.4451 0.5060 177 L 0.0854 0.3386 0.5760 178 T 0.1169 0.2414 0.6417 179 T 0.1446 0.2783 0.5770 180 F 0.2468 0.3001 0.4531 181 C 0.3381 0.3280 0.3339 182 L 0.3477 0.2636 0.3888 183 Q 0.2763 0.1934 0.5304 184 Y 0.2075 0.1481 0.6444 185 K 0.0948 0.1963 0.7089 186 P 0.0140 0.8711 0.1150 187 T 0.0071 0.9275 0.0654 188 V 0.0049 0.9574 0.0377 189 I 0.0047 0.9599 0.0354 190 A 0.0047 0.9606 0.0348 191 C 0.0046 0.9612 0.0342 192 V 0.0046 0.9613 0.0340 193 C 0.0046 0.9610 0.0343 194 I 0.0046 0.9606 0.0347 195 H 0.0046 0.9606 0.0348 196 L 0.0047 0.9592 0.0361 197 A 0.0048 0.9553 0.0399 198 C 0.0052 0.9452 0.0497 199 K 0.0066 0.9100 0.0834 200 W 0.0122 0.8224 0.1654 201 S 0.0466 0.4368 0.5166 202 N 0.0353 0.0936 0.8712 203 W 0.0806 0.0486 0.8708 204 E 0.1204 0.0459 0.8337 205 I 0.1301 0.0213 0.8486 206 P 0.1256 0.0258 0.8486 207 V 0.1469 0.0566 0.7965 208 S 0.1108 0.0628 0.8264 209 T 0.0535 0.2600 0.6865 210 D 0.0813 0.2485 0.6702 211 G 0.1330 0.3268 0.5401 212 K 0.2030 0.3851 0.4118 213 H 0.2854 0.4187 0.2959 214 W 0.2371 0.4926 0.2704 215 W 0.1889 0.5129 0.2982 216 E 0.1591 0.4582 0.3827 217 Y 0.1677 0.3818 0.4504 218 V 0.1737 0.1650 0.6613 219 D 0.0908 0.0376 0.8717 220 P 0.0119 0.1541 0.8341 221 T 0.0295 0.0854 0.8851 222 V 0.1417 0.0296 0.8286 223 T 0.0852 0.0212 0.8936 224 L 0.0049 0.9337 0.0614 225 E 0.0047 0.9456 0.0497 226 L 0.0052 0.9465 0.0484 227 L 0.0053 0.9498 0.0449 228 D 0.0047 0.9570 0.0383 229 E 0.0047 0.9564 0.0389 230 L 0.0047 0.9556 0.0397 231 T 0.0047 0.9601 0.0353 232 H 0.0046 0.9608 0.0345 233 E 0.0046 0.9591 0.0362 234 F 0.0047 0.9575 0.0378 235 L 0.0047 0.9582 0.0371 236 Q 0.0048 0.9564 0.0388 237 I 0.0050 0.9484 0.0466 238 L 0.0059 0.9093 0.0848 239 E 0.0085 0.7649 0.2266 240 K 0.0194 0.4954 0.4852 241 T 0.0614 0.0463 0.8922 242 P 0.0181 0.4057 0.5762 243 N 0.0208 0.5020 0.4772 244 R 0.0315 0.6343 0.3342 245 L 0.0328 0.7226 0.2446 246 K 0.0415 0.7758 0.1827 247 K 0.0548 0.7812 0.1641 248 I 0.0633 0.7738 0.1629 249 R 0.0736 0.7417 0.1848 250 N 0.0815 0.6677 0.2508 251 W 0.1149 0.6179 0.2672 252 R 0.1123 0.6164 0.2713 253 A 0.0852 0.5212 0.3936 254 N 0.0488 0.3998 0.5514 255 Q 0.0489 0.1789 0.7722 256 A 0.0455 0.0491 0.9054