# This file is the result of combining several RDB files, specifically # T0321.t04.dssp-ebghstl.rdb (weight 1.53986) # T0321.t04.stride-ebghtl.rdb (weight 1.24869) # T0321.t04.str2.rdb (weight 1.54758) # T0321.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 T0321.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-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 T0321.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 28 # # ============================================ # Comments from T0321.t04.stride-ebghtl.rdb # ============================================ # TARGET T0321 # 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 T0321.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 28 # # ============================================ # Comments from T0321.t04.str2.rdb # ============================================ # TARGET T0321 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0321.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 28 # # ============================================ # Comments from T0321.t04.alpha.rdb # ============================================ # TARGET T0321 # 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 T0321.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 28 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0153 0.3604 0.6243 2 W 0.0225 0.6262 0.3513 3 E 0.0356 0.7309 0.2335 4 I 0.0136 0.9027 0.0837 5 Y 0.0053 0.9464 0.0483 6 D 0.0048 0.9543 0.0409 7 A 0.0077 0.9441 0.0482 8 M 0.0070 0.9264 0.0666 9 I 0.0126 0.8396 0.1478 10 N 0.0215 0.5149 0.4636 11 G 0.0212 0.2571 0.7217 12 I 0.0622 0.0406 0.8972 13 P 0.0514 0.1960 0.7526 14 E 0.0270 0.3047 0.6683 15 D 0.0673 0.2873 0.6453 16 F 0.2372 0.0678 0.6950 17 L 0.4632 0.0281 0.5087 18 V 0.6114 0.0476 0.3410 19 D 0.5245 0.0787 0.3968 20 E 0.8338 0.0267 0.1395 21 L 0.9033 0.0103 0.0864 22 V 0.9088 0.0087 0.0825 23 C 0.8465 0.0194 0.1341 24 G 0.6073 0.0237 0.3690 25 T 0.4769 0.0225 0.5006 26 T 0.5423 0.0361 0.4216 27 H 0.7698 0.0224 0.2077 28 S 0.8775 0.0094 0.1131 29 V 0.9070 0.0068 0.0862 30 I 0.9092 0.0062 0.0846 31 R 0.8842 0.0090 0.1068 32 S 0.5756 0.0286 0.3958 33 G 0.1238 0.0587 0.8174 34 N 0.0649 0.0357 0.8994 35 G 0.2033 0.0529 0.7438 36 V 0.3826 0.0637 0.5537 37 G 0.5940 0.0527 0.3534 38 L 0.6348 0.0565 0.3087 39 G 0.5188 0.0375 0.4437 40 P 0.3660 0.0346 0.5994 41 N 0.1987 0.0280 0.7732 42 R 0.0986 0.0296 0.8718 43 P 0.0659 0.1196 0.8145 44 F 0.0725 0.1369 0.7905 45 E 0.1075 0.1276 0.7649 46 T 0.1377 0.0963 0.7660 47 R 0.1447 0.0957 0.7595 48 M 0.1167 0.0724 0.8109 49 P 0.1073 0.1727 0.7199 50 M 0.0541 0.3686 0.5773 51 L 0.0515 0.4216 0.5269 52 T 0.0489 0.5169 0.4342 53 Q 0.0501 0.4928 0.4571 54 N 0.0656 0.4487 0.4857 55 L 0.0689 0.3991 0.5320 56 L 0.0409 0.2059 0.7532 57 G 0.0232 0.0953 0.8815 58 L 0.0650 0.0846 0.8504 59 P 0.0959 0.1270 0.7770 60 L 0.0093 0.9303 0.0603 61 R 0.0152 0.9353 0.0495 62 V 0.0136 0.9417 0.0447 63 A 0.0183 0.9211 0.0606 64 A 0.0116 0.9170 0.0713 65 G 0.0132 0.8941 0.0926 66 C 0.0180 0.8630 0.1190 67 V 0.0396 0.7503 0.2101 68 K 0.0383 0.6126 0.3491 69 S 0.0521 0.4902 0.4576 70 W 0.0251 0.4933 0.4816 71 N 0.0328 0.6179 0.3493 72 Y 0.0049 0.9348 0.0604 73 V 0.0047 0.9576 0.0377 74 E 0.0047 0.9602 0.0351 75 A 0.0047 0.9603 0.0350 76 S 0.0047 0.9600 0.0353 77 I 0.0047 0.9601 0.0352 78 G 0.0047 0.9609 0.0344 79 L 0.0047 0.9606 0.0347 80 A 0.0047 0.9609 0.0344 81 A 0.0047 0.9597 0.0356 82 I 0.0047 0.9580 0.0373 83 N 0.0053 0.9470 0.0477 84 A 0.0068 0.9166 0.0766 85 Y 0.0166 0.7565 0.2269 86 Y 0.0645 0.4636 0.4718 87 N 0.0514 0.2056 0.7430 88 N 0.0780 0.0698 0.8522 89 P 0.0248 0.4241 0.5511 90 Q 0.0343 0.5199 0.4457 91 V 0.0517 0.5765 0.3718 92 A 0.0886 0.4840 0.4274 93 R 0.0454 0.4568 0.4978 94 E 0.0361 0.4710 0.4929 95 H 0.0603 0.2524 0.6873 96 G 0.0498 0.0821 0.8681 97 V 0.2209 0.0412 0.7379 98 I 0.5192 0.0424 0.4384 99 F 0.5136 0.0871 0.3993 100 S 0.4005 0.1154 0.4841 101 D 0.2727 0.1356 0.5917 102 A 0.1635 0.1893 0.6472 103 K 0.1137 0.2315 0.6548 104 R 0.1397 0.1716 0.6887 105 V 0.2000 0.1457 0.6544 106 E 0.3085 0.1259 0.5656 107 D 0.4212 0.1677 0.4112 108 R 0.4831 0.1471 0.3698 109 M 0.5317 0.1121 0.3562 110 N 0.3981 0.1267 0.4753 111 D 0.1778 0.1080 0.7142 112 P 0.1263 0.2154 0.6582 113 F 0.1848 0.2649 0.5503 114 I 0.1897 0.3232 0.4871 115 M 0.1393 0.3960 0.4648 116 S 0.1376 0.4092 0.4532 117 Q 0.0401 0.7547 0.2053 118 N 0.0188 0.7967 0.1845 119 E 0.0214 0.7709 0.2076 120 V 0.0592 0.6164 0.3244 121 K 0.0488 0.3540 0.5973 122 G 0.0418 0.1204 0.8377 123 K 0.0510 0.0453 0.9037