# This file is the result of combining several RDB files, specifically # T0634.t04.dssp-ebghstl.rdb (weight 1.53986) # T0634.t04.stride-ebghtl.rdb (weight 1.24869) # T0634.t04.str2.rdb (weight 1.54758) # T0634.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 T0634.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0634 # 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 T0634.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 13.1379 # # ============================================ # Comments from T0634.t04.stride-ebghtl.rdb # ============================================ # TARGET T0634 # 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 T0634.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 13.1379 # # ============================================ # Comments from T0634.t04.str2.rdb # ============================================ # TARGET T0634 # 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 T0634.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 13.1379 # # ============================================ # Comments from T0634.t04.alpha.rdb # ============================================ # TARGET T0634 # 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 T0634.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 13.1379 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1039 0.0744 0.8217 2 S 0.1536 0.0808 0.7656 3 L 0.2124 0.0867 0.7009 4 K 0.2852 0.0433 0.6715 5 K 0.7733 0.0122 0.2145 6 I 0.9212 0.0036 0.0752 7 L 0.9309 0.0033 0.0658 8 I 0.9288 0.0034 0.0679 9 I 0.8755 0.0085 0.1161 10 D 0.4886 0.0085 0.5029 11 Q 0.1107 0.0553 0.8340 12 Q 0.0370 0.1722 0.7908 13 D 0.0437 0.2552 0.7011 14 F 0.0207 0.6876 0.2917 15 S 0.0201 0.8075 0.1724 16 R 0.0255 0.8665 0.1080 17 I 0.0430 0.8661 0.0908 18 E 0.0563 0.8540 0.0896 19 L 0.0423 0.8769 0.0808 20 K 0.0356 0.8559 0.1086 21 N 0.0455 0.7799 0.1747 22 F 0.0749 0.6624 0.2626 23 L 0.0719 0.5742 0.3538 24 D 0.0675 0.4040 0.5286 25 S 0.0628 0.2004 0.7368 26 E 0.0966 0.0738 0.8296 27 Y 0.4617 0.0230 0.5152 28 L 0.7988 0.0118 0.1893 29 V 0.8926 0.0085 0.0990 30 I 0.8500 0.0228 0.1272 31 E 0.8405 0.0176 0.1419 32 S 0.5530 0.0557 0.3913 33 K 0.2589 0.0850 0.6561 34 N 0.1100 0.0528 0.8372 35 E 0.0173 0.7884 0.1942 36 K 0.0120 0.9294 0.0586 37 E 0.0089 0.9422 0.0488 38 A 0.0065 0.9495 0.0440 39 L 0.0057 0.9549 0.0394 40 E 0.0056 0.9494 0.0451 41 Q 0.0055 0.9392 0.0552 42 I 0.0091 0.9080 0.0828 43 D 0.0105 0.7999 0.1896 44 H 0.0124 0.6257 0.3619 45 H 0.0390 0.3625 0.5985 46 H 0.0758 0.0353 0.8889 47 P 0.0857 0.0393 0.8750 48 D 0.1468 0.0726 0.7806 49 L 0.8790 0.0102 0.1108 50 V 0.9290 0.0046 0.0664 51 I 0.9319 0.0048 0.0633 52 L 0.8957 0.0099 0.0944 53 D 0.6001 0.0300 0.3699 54 M 0.2509 0.2039 0.5452 55 D 0.1496 0.2886 0.5618 56 I 0.0935 0.3097 0.5968 57 I 0.0646 0.3165 0.6190 58 G 0.0386 0.2024 0.7590 59 E 0.0529 0.1771 0.7700 60 N 0.0613 0.1444 0.7943 61 S 0.0417 0.5019 0.4564 62 P 0.0090 0.9053 0.0857 63 N 0.0088 0.9420 0.0491 64 L 0.0089 0.9461 0.0450 65 C 0.0094 0.9497 0.0409 66 L 0.0086 0.9505 0.0409 67 K 0.0110 0.9401 0.0489 68 L 0.0161 0.9057 0.0782 69 K 0.0264 0.8266 0.1470 70 R 0.0386 0.6621 0.2992 71 S 0.0431 0.3444 0.6125 72 K 0.0434 0.2663 0.6903 73 G 0.0397 0.1862 0.7741 74 L 0.0923 0.2167 0.6910 75 K 0.0701 0.1410 0.7889 76 N 0.1093 0.0570 0.8337 77 V 0.1971 0.0137 0.7891 78 P 0.4226 0.0090 0.5684 79 L 0.9135 0.0040 0.0825 80 I 0.9286 0.0039 0.0675 81 L 0.9243 0.0050 0.0708 82 L 0.8542 0.0117 0.1341 83 F 0.5709 0.0233 0.4058 84 S 0.2662 0.0425 0.6913 85 S 0.1288 0.1410 0.7303 86 E 0.0937 0.2020 0.7043 87 H 0.0843 0.2135 0.7022 88 K 0.0795 0.2972 0.6233 89 E 0.1717 0.2913 0.5370 90 A 0.3303 0.1801 0.4896 91 I 0.4717 0.1333 0.3950 92 V 0.5576 0.1565 0.2858 93 N 0.4822 0.1601 0.3578 94 G 0.4479 0.1357 0.4164 95 L 0.4480 0.1606 0.3914 96 H 0.3774 0.1788 0.4438 97 S 0.2500 0.1381 0.6119 98 G 0.1617 0.0571 0.7812 99 A 0.1543 0.0708 0.7749 100 D 0.2131 0.1389 0.6480 101 D 0.4361 0.1445 0.4195 102 Y 0.6086 0.1063 0.2851 103 L 0.7001 0.0454 0.2545 104 T 0.5208 0.0391 0.4401 105 K 0.2341 0.0208 0.7452 106 P 0.1485 0.0248 0.8267 107 F 0.1355 0.0214 0.8430 108 N 0.1095 0.0164 0.8741 109 R 0.0057 0.8037 0.1906 110 N 0.0058 0.8681 0.1261 111 D 0.0137 0.9180 0.0683 112 L 0.0269 0.9135 0.0596 113 L 0.0381 0.9104 0.0515 114 S 0.0612 0.8877 0.0511 115 R 0.0652 0.8812 0.0536 116 I 0.0898 0.8532 0.0570 117 E 0.0786 0.8610 0.0604 118 I 0.1302 0.8084 0.0613 119 H 0.1210 0.8115 0.0675 120 L 0.1597 0.7224 0.1179 121 R 0.1885 0.5995 0.2120 122 T 0.1621 0.4738 0.3641 123 Q 0.0966 0.4302 0.4732 124 N 0.1116 0.2898 0.5986 125 Y 0.1307 0.3326 0.5367 126 Y 0.1328 0.3509 0.5163 127 S 0.1133 0.3745 0.5121 128 D 0.1319 0.3691 0.4990 129 L 0.1448 0.3484 0.5068 130 R 0.1524 0.2619 0.5857 131 K 0.1327 0.3184 0.5489 132 N 0.1276 0.2074 0.6649 133 E 0.1228 0.1308 0.7464 134 G 0.1458 0.0663 0.7879 135 H 0.3626 0.0691 0.5683 136 H 0.3956 0.0711 0.5332 137 H 0.2390 0.0636 0.6974 138 H 0.1538 0.1066 0.7396 139 H 0.1227 0.0779 0.7994 140 H 0.0709 0.0474 0.8817