# This file is the result of combining several RDB files, specifically # T0581.t04.dssp-ebghstl.rdb (weight 1.53986) # T0581.t04.stride-ebghtl.rdb (weight 1.24869) # T0581.t04.str2.rdb (weight 1.54758) # T0581.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 T0581.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0581 # 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 T0581.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 3.21195 # # ============================================ # Comments from T0581.t04.stride-ebghtl.rdb # ============================================ # TARGET T0581 # 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 T0581.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 3.21195 # # ============================================ # Comments from T0581.t04.str2.rdb # ============================================ # TARGET T0581 # 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 T0581.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 3.21195 # # ============================================ # Comments from T0581.t04.alpha.rdb # ============================================ # TARGET T0581 # 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 T0581.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 3.21195 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0425 0.4242 0.5333 2 S 0.0693 0.5937 0.3370 3 R 0.0545 0.8013 0.1443 4 F 0.0569 0.8475 0.0956 5 M 0.0686 0.8557 0.0757 6 A 0.0615 0.8772 0.0613 7 L 0.0501 0.8906 0.0593 8 A 0.0462 0.8967 0.0571 9 L 0.0391 0.9023 0.0586 10 C 0.0432 0.8912 0.0656 11 F 0.0579 0.8482 0.0940 12 V 0.0518 0.8060 0.1422 13 L 0.0329 0.7157 0.2513 14 P 0.0157 0.7875 0.1968 15 T 0.0148 0.8434 0.1418 16 A 0.0156 0.8658 0.1187 17 A 0.0216 0.8455 0.1329 18 H 0.0253 0.7752 0.1995 19 A 0.0449 0.6709 0.2841 20 A 0.0839 0.4473 0.4689 21 S 0.0679 0.2557 0.6763 22 L 0.0062 0.8674 0.1264 23 K 0.0074 0.8689 0.1237 24 D 0.0086 0.8810 0.1104 25 F 0.0089 0.9052 0.0859 26 E 0.0133 0.8763 0.1104 27 L 0.0064 0.9122 0.0814 28 S 0.0056 0.9305 0.0639 29 K 0.0050 0.9428 0.0521 30 M 0.0050 0.9476 0.0474 31 L 0.0047 0.9578 0.0375 32 E 0.0047 0.9596 0.0357 33 K 0.0048 0.9573 0.0379 34 V 0.0048 0.9521 0.0431 35 A 0.0053 0.9337 0.0610 36 K 0.0067 0.8975 0.0959 37 E 0.0150 0.7805 0.2045 38 S 0.0661 0.3575 0.5764 39 S 0.0377 0.1556 0.8067 40 V 0.0561 0.0771 0.8669 41 G 0.0597 0.0532 0.8871 42 T 0.0885 0.0342 0.8773 43 P 0.1369 0.1640 0.6992 44 R 0.2017 0.3017 0.4967 45 A 0.2759 0.2844 0.4396 46 I 0.2912 0.2263 0.4826 47 N 0.1739 0.1555 0.6706 48 E 0.0183 0.7313 0.2504 49 D 0.0218 0.7722 0.2059 50 I 0.0380 0.7680 0.1940 51 L 0.1117 0.5600 0.3283 52 D 0.0957 0.5065 0.3978 53 Q 0.0934 0.3915 0.5151 54 G 0.1455 0.2017 0.6528 55 Y 0.4978 0.0423 0.4599 56 T 0.6925 0.0274 0.2800 57 V 0.5597 0.0671 0.3732 58 E 0.3166 0.0810 0.6024 59 G 0.1075 0.0964 0.7961 60 N 0.2096 0.1789 0.6115 61 Q 0.5117 0.1511 0.3372 62 L 0.7061 0.1074 0.1865 63 I 0.7207 0.0886 0.1907 64 N 0.6159 0.1180 0.2661 65 H 0.5511 0.1433 0.3056 66 L 0.5361 0.1354 0.3286 67 S 0.5114 0.1326 0.3559 68 V 0.3250 0.1723 0.5027 69 R 0.1828 0.1863 0.6308 70 A 0.0292 0.6932 0.2776 71 S 0.0133 0.7791 0.2076 72 H 0.0090 0.8414 0.1497 73 A 0.0062 0.9245 0.0693 74 E 0.0052 0.9298 0.0650 75 R 0.0061 0.8984 0.0954 76 M 0.0151 0.7712 0.2136 77 R 0.0189 0.5249 0.4562 78 S 0.0328 0.3688 0.5984 79 N 0.0870 0.0390 0.8740 80 P 0.0067 0.8989 0.0944 81 D 0.0052 0.9419 0.0529 82 S 0.0074 0.9417 0.0508 83 V 0.0069 0.9487 0.0444 84 R 0.0082 0.9379 0.0538 85 S 0.0110 0.9061 0.0830 86 Q 0.0150 0.8588 0.1263 87 L 0.0441 0.7257 0.2303 88 G 0.0365 0.5725 0.3910 89 D 0.0372 0.5350 0.4279 90 S 0.0623 0.5518 0.3859 91 V 0.0879 0.5445 0.3676 92 C 0.1167 0.4020 0.4813 93 S 0.0717 0.3429 0.5854 94 N 0.0610 0.2309 0.7082 95 T 0.0243 0.6066 0.3691 96 G 0.0164 0.7882 0.1955 97 Y 0.0066 0.9343 0.0590 98 R 0.0057 0.9497 0.0446 99 Q 0.0060 0.9509 0.0430 100 L 0.0077 0.9439 0.0484 101 L 0.0098 0.9052 0.0850 102 A 0.0227 0.7825 0.1948 103 R 0.0335 0.3493 0.6172 104 G 0.0511 0.0545 0.8944 105 A 0.2460 0.0280 0.7260 106 I 0.7560 0.0146 0.2294 107 L 0.8868 0.0071 0.1061 108 T 0.9009 0.0062 0.0929 109 Y 0.8841 0.0062 0.1098 110 S 0.8277 0.0070 0.1653 111 F 0.7473 0.0127 0.2401 112 T 0.6684 0.0256 0.3060 113 E 0.6248 0.0532 0.3220 114 Y 0.5825 0.0624 0.3552 115 K 0.4745 0.0804 0.4451 116 T 0.2693 0.0756 0.6551 117 N 0.1793 0.0754 0.7453 118 Q 0.3052 0.0790 0.6157 119 P 0.4117 0.1201 0.4681 120 V 0.3646 0.1809 0.4544 121 A 0.3755 0.1819 0.4426 122 T 0.2517 0.3419 0.4064 123 E 0.2279 0.4339 0.3381 124 R 0.3192 0.3729 0.3079 125 F 0.3443 0.3111 0.3447 126 D 0.2227 0.3096 0.4677 127 A 0.1171 0.4188 0.4641 128 G 0.1271 0.2607 0.6122 129 S 0.1403 0.1986 0.6611 130 C 0.1981 0.1306 0.6713 131 R 0.2242 0.1237 0.6521 132 I 0.1727 0.1454 0.6819 133 Q 0.1001 0.1247 0.7752 134 G 0.0673 0.0897 0.8430 135 K 0.1317 0.0460 0.8224 136 K 0.1227 0.0354 0.8419