# This file is the result of combining several RDB files, specifically # T0295.t06.dssp-ebghstl.rdb (weight 1.53986) # T0295.t06.stride-ebghtl.rdb (weight 1.24869) # T0295.t06.str2.rdb (weight 1.54758) # T0295.t06.alpha.rdb (weight 0.659012) # T0295.t04.dssp-ebghstl.rdb (weight 1.53986) # T0295.t04.stride-ebghtl.rdb (weight 1.24869) # T0295.t04.str2.rdb (weight 1.54758) # T0295.t04.alpha.rdb (weight 0.659012) # T0295.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0295.t2k.stride-ebghtl.rdb (weight 1.24869) # T0295.t2k.str2.rdb (weight 1.54758) # T0295.t2k.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 T0295.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0295 # 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 T0295.t06-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 3565 # # ============================================ # Comments from T0295.t06.stride-ebghtl.rdb # ============================================ # TARGET T0295 # 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 T0295.t06-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 3565 # # ============================================ # Comments from T0295.t06.str2.rdb # ============================================ # TARGET T0295 # 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 T0295.t06-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 3565 # # ============================================ # Comments from T0295.t06.alpha.rdb # ============================================ # TARGET T0295 # 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 T0295.t06-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 3565 # # ============================================ # Comments from T0295.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0295 # 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 T0295.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 2108 # # ============================================ # Comments from T0295.t04.stride-ebghtl.rdb # ============================================ # TARGET T0295 # 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 T0295.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 2108 # # ============================================ # Comments from T0295.t04.str2.rdb # ============================================ # TARGET T0295 # 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 T0295.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 2108 # # ============================================ # Comments from T0295.t04.alpha.rdb # ============================================ # TARGET T0295 # 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 T0295.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 2108 # # ============================================ # Comments from T0295.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0295 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0295.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 3085 # # ============================================ # Comments from T0295.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0295 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0295.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 3085 # # ============================================ # Comments from T0295.t2k.str2.rdb # ============================================ # TARGET T0295 # 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 T0295.t2k-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 3085 # # ============================================ # Comments from T0295.t2k.alpha.rdb # ============================================ # TARGET T0295 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0295.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 3085 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 H 0.0968 0.1395 0.7637 2 L 0.1056 0.2079 0.6866 3 L 0.1283 0.2009 0.6708 4 K 0.0936 0.1360 0.7704 5 N 0.0689 0.0677 0.8634 6 P 0.0050 0.9172 0.0778 7 G 0.0049 0.9402 0.0549 8 I 0.0048 0.9555 0.0397 9 L 0.0047 0.9599 0.0354 10 D 0.0047 0.9593 0.0361 11 K 0.0047 0.9589 0.0364 12 I 0.0047 0.9566 0.0386 13 I 0.0049 0.9503 0.0448 14 Y 0.0057 0.9181 0.0762 15 A 0.0090 0.8461 0.1449 16 A 0.0638 0.5273 0.4088 17 K 0.0627 0.2143 0.7230 18 I 0.0919 0.1667 0.7414 19 K 0.0608 0.0649 0.8743 20 S 0.0266 0.1098 0.8636 21 S 0.0331 0.0650 0.9020 22 D 0.2224 0.0295 0.7482 23 I 0.7658 0.0066 0.2276 24 V 0.8930 0.0059 0.1011 25 L 0.8972 0.0076 0.0952 26 E 0.8810 0.0072 0.1118 27 I 0.5877 0.0389 0.3734 28 G 0.3086 0.0306 0.6608 29 C 0.1371 0.0716 0.7913 30 G 0.0732 0.1019 0.8250 31 T 0.0500 0.2801 0.6699 32 G 0.0339 0.4853 0.4808 33 N 0.0141 0.9023 0.0836 34 L 0.0072 0.9387 0.0541 35 T 0.0057 0.9477 0.0466 36 V 0.0052 0.9512 0.0436 37 K 0.0054 0.9405 0.0542 38 L 0.0056 0.9187 0.0757 39 L 0.0077 0.8875 0.1048 40 P 0.0070 0.7625 0.2305 41 L 0.0159 0.5229 0.4612 42 A 0.0722 0.1310 0.7967 43 K 0.0776 0.0954 0.8270 44 K 0.4609 0.0408 0.4984 45 V 0.8264 0.0102 0.1634 46 I 0.8778 0.0172 0.1050 47 T 0.8972 0.0086 0.0941 48 I 0.8600 0.0116 0.1284 49 D 0.6542 0.0167 0.3291 50 I 0.1425 0.0376 0.8198 51 D 0.0796 0.0180 0.9024 52 S 0.0056 0.8740 0.1204 53 R 0.0052 0.9144 0.0804 54 M 0.0051 0.9399 0.0550 55 I 0.0047 0.9565 0.0388 56 S 0.0047 0.9570 0.0382 57 E 0.0047 0.9562 0.0391 58 V 0.0048 0.9546 0.0406 59 K 0.0049 0.9531 0.0420 60 K 0.0056 0.9415 0.0528 61 R 0.0072 0.9181 0.0747 62 C 0.0104 0.8943 0.0954 63 L 0.0077 0.8768 0.1156 64 Y 0.0134 0.7898 0.1969 65 E 0.0473 0.3755 0.5772 66 G 0.0513 0.0625 0.8861 67 Y 0.1050 0.0312 0.8639 68 N 0.1186 0.0787 0.8028 69 N 0.3896 0.0449 0.5655 70 L 0.8083 0.0077 0.1841 71 E 0.8983 0.0056 0.0961 72 V 0.9148 0.0041 0.0811 73 Y 0.8705 0.0134 0.1161 74 E 0.7607 0.0198 0.2195 75 G 0.3704 0.0510 0.5786 76 D 0.2448 0.0807 0.6745 77 A 0.1195 0.3607 0.5198 78 I 0.1315 0.3783 0.4902 79 K 0.1204 0.3281 0.5516 80 T 0.0855 0.1342 0.7803 81 V 0.0753 0.1120 0.8128 82 F 0.0591 0.1531 0.7877 83 P 0.0490 0.1133 0.8377 84 K 0.1054 0.0950 0.7996 85 F 0.2615 0.0280 0.7105 86 D 0.4325 0.0420 0.5256 87 V 0.9057 0.0049 0.0893 88 C 0.9259 0.0043 0.0699 89 T 0.9132 0.0078 0.0790 90 A 0.8380 0.0149 0.1471 91 N 0.4793 0.0305 0.4901 92 I 0.1986 0.0680 0.7334 93 P 0.1424 0.2186 0.6391 94 Y 0.1663 0.3491 0.4846 95 K 0.1356 0.3557 0.5087 96 I 0.0877 0.2938 0.6185 97 S 0.0811 0.1583 0.7605 98 S 0.0429 0.2616 0.6955 99 P 0.0505 0.5308 0.4187 100 L 0.0116 0.8689 0.1194 101 I 0.0069 0.9236 0.0695 102 F 0.0076 0.9336 0.0588 103 K 0.0079 0.9354 0.0567 104 L 0.0082 0.9306 0.0612 105 I 0.0110 0.8936 0.0954 106 S 0.0134 0.7938 0.1927 107 H 0.0199 0.7415 0.2385 108 R 0.0274 0.5377 0.4350 109 P 0.0303 0.5188 0.4509 110 L 0.0519 0.4293 0.5188 111 F 0.1277 0.2389 0.6334 112 K 0.1369 0.1092 0.7540 113 C 0.0848 0.1921 0.7231 114 A 0.0966 0.1125 0.7909 115 V 0.4453 0.1241 0.4306 116 L 0.6857 0.1305 0.1838 117 M 0.7079 0.1626 0.1295 118 F 0.6927 0.1834 0.1239 119 Q 0.6028 0.2438 0.1534 120 K 0.4948 0.2999 0.2052 121 E 0.4281 0.3034 0.2685 122 F 0.3389 0.2911 0.3700 123 A 0.2923 0.2149 0.4929 124 E 0.2787 0.2559 0.4654 125 R 0.3674 0.2257 0.4069 126 M 0.4777 0.1749 0.3474 127 L 0.4618 0.1568 0.3814 128 A 0.3846 0.1035 0.5119 129 N 0.2481 0.0744 0.6775 130 V 0.1337 0.1282 0.7381 131 G 0.0828 0.0712 0.8460 132 D 0.0863 0.0898 0.8239 133 S 0.0745 0.1319 0.7936 134 N 0.0635 0.2840 0.6525 135 Y 0.1810 0.3425 0.4765 136 S 0.3423 0.3642 0.2936 137 R 0.3931 0.4587 0.1482 138 L 0.4057 0.5013 0.0930 139 T 0.4219 0.4992 0.0789 140 I 0.4358 0.4981 0.0661 141 N 0.4132 0.5170 0.0698 142 V 0.3990 0.5204 0.0806 143 K 0.4125 0.4706 0.1169 144 L 0.3615 0.4505 0.1880 145 F 0.3574 0.3588 0.2839 146 C 0.3040 0.2691 0.4269 147 K 0.3756 0.1519 0.4726 148 V 0.5617 0.0990 0.3393 149 T 0.6742 0.0761 0.2497 150 K 0.7555 0.0596 0.1850 151 V 0.7387 0.0595 0.2019 152 C 0.7411 0.0386 0.2203 153 N 0.7129 0.0247 0.2624 154 V 0.4356 0.0191 0.5453 155 N 0.1719 0.0264 0.8018 156 R 0.0489 0.3650 0.5862 157 S 0.0430 0.4010 0.5560 158 S 0.1142 0.2919 0.5940 159 F 0.2264 0.0590 0.7146 160 N 0.1380 0.0261 0.8358 161 P 0.1586 0.0205 0.8209 162 P 0.1040 0.0215 0.8745 163 P 0.1052 0.0317 0.8631 164 K 0.1955 0.0355 0.7690 165 V 0.4100 0.0206 0.5694 166 D 0.4652 0.0336 0.5012 167 S 0.7331 0.0139 0.2531 168 V 0.8536 0.0068 0.1396 169 I 0.9150 0.0033 0.0818 170 V 0.9130 0.0035 0.0834 171 K 0.9069 0.0038 0.0894 172 L 0.8772 0.0051 0.1177 173 I 0.7680 0.0062 0.2258 174 P 0.5021 0.0152 0.4827 175 K 0.1953 0.0245 0.7802 176 E 0.1163 0.0320 0.8517 177 S 0.0811 0.0246 0.8943 178 S 0.0735 0.0287 0.8978 179 F 0.0994 0.0343 0.8663 180 L 0.0907 0.0221 0.8873 181 T 0.0548 0.0266 0.9186