# This file is the result of combining several RDB files, specifically # T0380.t04.dssp-ebghstl.rdb (weight 1.53986) # T0380.t04.stride-ebghtl.rdb (weight 1.24869) # T0380.t04.str2.rdb (weight 1.54758) # T0380.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 T0380.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0380 # 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 T0380.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 1009 # # ============================================ # Comments from T0380.t04.stride-ebghtl.rdb # ============================================ # TARGET T0380 # 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 T0380.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 1009 # # ============================================ # Comments from T0380.t04.str2.rdb # ============================================ # TARGET T0380 # 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 T0380.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 1009 # # ============================================ # Comments from T0380.t04.alpha.rdb # ============================================ # TARGET T0380 # 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 T0380.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 1009 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0634 0.0383 0.8983 2 I 0.0785 0.0725 0.8490 3 D 0.0553 0.1683 0.7764 4 E 0.0055 0.8952 0.0993 5 K 0.0055 0.9153 0.0793 6 F 0.0057 0.9098 0.0844 7 L 0.0057 0.9143 0.0800 8 I 0.0061 0.9141 0.0798 9 E 0.0072 0.8743 0.1185 10 S 0.0070 0.8983 0.0948 11 N 0.0065 0.8940 0.0995 12 E 0.0071 0.8695 0.1234 13 L 0.0089 0.8667 0.1244 14 V 0.0169 0.7955 0.1876 15 E 0.0157 0.6808 0.3034 16 S 0.0273 0.3335 0.6392 17 S 0.0796 0.0633 0.8571 18 K 0.1107 0.0567 0.8326 19 I 0.8341 0.0069 0.1589 20 V 0.9174 0.0036 0.0790 21 M 0.9294 0.0032 0.0674 22 V 0.9184 0.0053 0.0763 23 G 0.8595 0.0065 0.1340 24 T 0.7798 0.0078 0.2124 25 N 0.6044 0.0205 0.3751 26 G 0.1354 0.0248 0.8398 27 E 0.0200 0.1046 0.8754 28 N 0.0447 0.0350 0.9203 29 G 0.0480 0.0385 0.9135 30 Y 0.1501 0.0168 0.8331 31 P 0.4489 0.0277 0.5234 32 N 0.5608 0.0327 0.4064 33 I 0.6976 0.0272 0.2752 34 K 0.7780 0.0213 0.2007 35 A 0.8460 0.0163 0.1377 36 M 0.8399 0.0199 0.1401 37 M 0.8537 0.0148 0.1315 38 R 0.8475 0.0182 0.1342 39 L 0.8551 0.0167 0.1281 40 K 0.8445 0.0160 0.1395 41 H 0.6793 0.0307 0.2899 42 D 0.2199 0.0581 0.7220 43 G 0.0626 0.0739 0.8635 44 L 0.1057 0.0374 0.8568 45 K 0.2046 0.0270 0.7684 46 K 0.7801 0.0051 0.2148 47 F 0.9198 0.0035 0.0767 48 W 0.9291 0.0033 0.0676 49 L 0.9198 0.0038 0.0763 50 S 0.8600 0.0050 0.1350 51 T 0.5296 0.0174 0.4530 52 N 0.1480 0.0459 0.8061 53 T 0.0293 0.1885 0.7821 54 S 0.0318 0.2393 0.7289 55 T 0.0488 0.4475 0.5038 56 R 0.0397 0.7762 0.1842 57 M 0.0322 0.8765 0.0913 58 V 0.0116 0.9331 0.0553 59 E 0.0083 0.9466 0.0452 60 R 0.0074 0.9450 0.0476 61 L 0.0078 0.9257 0.0665 62 K 0.0093 0.8597 0.1310 63 K 0.0150 0.5581 0.4269 64 N 0.0847 0.0393 0.8760 65 N 0.0425 0.0872 0.8703 66 K 0.1759 0.0558 0.7683 67 I 0.7619 0.0103 0.2279 68 C 0.9021 0.0039 0.0940 69 L 0.9279 0.0032 0.0690 70 Y 0.9244 0.0036 0.0720 71 F 0.9106 0.0042 0.0852 72 V 0.7854 0.0078 0.2068 73 D 0.4148 0.0154 0.5699 74 D 0.0733 0.1144 0.8123 75 N 0.0449 0.1198 0.8352 76 K 0.1071 0.1387 0.7542 77 F 0.3875 0.0585 0.5540 78 A 0.6153 0.0280 0.3567 79 G 0.8381 0.0089 0.1529 80 L 0.9147 0.0038 0.0815 81 M 0.9269 0.0034 0.0697 82 L 0.9254 0.0035 0.0710 83 V 0.8762 0.0158 0.1080 84 G 0.8747 0.0064 0.1189 85 T 0.8983 0.0042 0.0975 86 I 0.9027 0.0043 0.0930 87 E 0.8952 0.0052 0.0996 88 I 0.8884 0.0046 0.1069 89 L 0.5773 0.0181 0.4047 90 H 0.2399 0.0223 0.7378 91 D 0.0884 0.0625 0.8491 92 R 0.0084 0.7943 0.1973 93 A 0.0095 0.8539 0.1366 94 S 0.0078 0.9008 0.0914 95 K 0.0057 0.9335 0.0608 96 E 0.0057 0.9364 0.0578 97 M 0.0059 0.9256 0.0685 98 L 0.0074 0.9059 0.0867 99 W 0.0121 0.8589 0.1289 100 T 0.0157 0.7927 0.1915 101 D 0.0266 0.5836 0.3898 102 G 0.0279 0.4485 0.5236 103 C 0.0527 0.5101 0.4373 104 E 0.0683 0.5905 0.3412 105 I 0.0872 0.5415 0.3713 106 Y 0.1326 0.3628 0.5047 107 Y 0.1288 0.1009 0.7703 108 P 0.0779 0.1200 0.8020 109 L 0.0734 0.1052 0.8213 110 G 0.0876 0.0606 0.8518 111 I 0.1184 0.0574 0.8242 112 D 0.1661 0.0379 0.7959 113 D 0.0914 0.0297 0.8790 114 P 0.0264 0.1261 0.8475 115 D 0.0645 0.0693 0.8662 116 Y 0.4013 0.0237 0.5750 117 T 0.7566 0.0103 0.2331 118 A 0.9216 0.0034 0.0750 119 L 0.9220 0.0036 0.0745 120 C 0.9258 0.0034 0.0708 121 F 0.9088 0.0047 0.0865 122 T 0.8368 0.0068 0.1564 123 A 0.6753 0.0257 0.2990 124 E 0.5342 0.0812 0.3846 125 W 0.6992 0.0774 0.2234 126 G 0.7587 0.0565 0.1848 127 N 0.8100 0.0505 0.1395 128 Y 0.7891 0.0570 0.1539 129 Y 0.6243 0.0798 0.2959 130 R 0.4300 0.1102 0.4598 131 H 0.2808 0.1673 0.5519 132 L 0.2551 0.1597 0.5852 133 K 0.2797 0.1332 0.5871 134 N 0.5311 0.0720 0.3969 135 I 0.7615 0.0238 0.2148 136 T 0.8500 0.0154 0.1345 137 F 0.8645 0.0107 0.1247 138 K 0.8205 0.0132 0.1663 139 I 0.6809 0.0466 0.2725 140 D 0.3579 0.0938 0.5482 141 E 0.2442 0.1126 0.6432 142 I 0.2992 0.1166 0.5843 143 Y 0.2611 0.0821 0.6567 144 N 0.1592 0.0435 0.7972 145 Y 0.0641 0.0516 0.8843