# This file is the result of combining several RDB files, specifically # T0356.t06.dssp-ebghstl.rdb (weight 1.53986) # T0356.t06.stride-ebghtl.rdb (weight 1.24869) # T0356.t06.str2.rdb (weight 1.54758) # T0356.t06.alpha.rdb (weight 0.659012) # T0356.t04.dssp-ebghstl.rdb (weight 1.53986) # T0356.t04.stride-ebghtl.rdb (weight 1.24869) # T0356.t04.str2.rdb (weight 1.54758) # T0356.t04.alpha.rdb (weight 0.659012) # T0356.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0356.t2k.stride-ebghtl.rdb (weight 1.24869) # T0356.t2k.str2.rdb (weight 1.54758) # T0356.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 T0356.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 177.873 # # ============================================ # Comments from T0356.t06.stride-ebghtl.rdb # ============================================ # TARGET T0356 # Using neural net t06-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 T0356.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 177.873 # # ============================================ # Comments from T0356.t06.str2.rdb # ============================================ # TARGET T0356 # Using neural net t06-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 T0356.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 177.873 # # ============================================ # Comments from T0356.t06.alpha.rdb # ============================================ # TARGET T0356 # Using neural net t06-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 T0356.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 177.873 # # ============================================ # Comments from T0356.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 202.306 # # ============================================ # Comments from T0356.t04.stride-ebghtl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 202.306 # # ============================================ # Comments from T0356.t04.str2.rdb # ============================================ # TARGET T0356 # 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 T0356.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 202.306 # # ============================================ # Comments from T0356.t04.alpha.rdb # ============================================ # TARGET T0356 # 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 T0356.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 202.306 # # ============================================ # Comments from T0356.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 231 # # ============================================ # Comments from T0356.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 231 # # ============================================ # Comments from T0356.t2k.str2.rdb # ============================================ # TARGET T0356 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0356.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 231 # # ============================================ # Comments from T0356.t2k.alpha.rdb # ============================================ # TARGET T0356 # 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 T0356.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 231 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.2840 0.0438 0.6722 2 Y 0.3420 0.0409 0.6171 3 T 0.2126 0.0503 0.7371 4 G 0.1057 0.0395 0.8548 5 R 0.0918 0.0352 0.8730 6 P 0.0790 0.0625 0.8585 7 P 0.0444 0.3262 0.6294 8 D 0.0341 0.4453 0.5206 9 E 0.0468 0.5037 0.4495 10 P 0.0297 0.6423 0.3280 11 A 0.0339 0.7047 0.2614 12 V 0.0386 0.7621 0.1993 13 L 0.0306 0.7666 0.2028 14 G 0.0213 0.7767 0.2019 15 V 0.0144 0.8407 0.1450 16 A 0.0125 0.8446 0.1429 17 L 0.0139 0.8406 0.1455 18 N 0.0145 0.8429 0.1427 19 E 0.0110 0.8763 0.1127 20 V 0.0133 0.8670 0.1197 21 F 0.0101 0.8695 0.1204 22 V 0.0095 0.9125 0.0780 23 P 0.0056 0.9328 0.0617 24 I 0.0051 0.9420 0.0529 25 L 0.0058 0.9288 0.0654 26 Q 0.0055 0.9092 0.0853 27 K 0.0085 0.8367 0.1548 28 Q 0.0213 0.6949 0.2838 29 F 0.0690 0.2024 0.7286 30 P 0.0353 0.1886 0.7761 31 E 0.1241 0.1473 0.7286 32 I 0.5195 0.0641 0.4164 33 V 0.6856 0.0499 0.2645 34 D 0.7965 0.0260 0.1775 35 F 0.7842 0.0250 0.1908 36 Y 0.7449 0.0170 0.2381 37 L 0.5701 0.0133 0.4167 38 P 0.2595 0.0238 0.7168 39 P 0.0566 0.2616 0.6818 40 E 0.0506 0.2486 0.7009 41 G 0.0857 0.2454 0.6689 42 C 0.1933 0.1455 0.6612 43 S 0.4344 0.0854 0.4802 44 Y 0.5162 0.0502 0.4336 45 R 0.6444 0.0318 0.3238 46 L 0.8447 0.0092 0.1461 47 A 0.9096 0.0051 0.0852 48 V 0.9291 0.0033 0.0675 49 V 0.9217 0.0049 0.0734 50 T 0.9107 0.0041 0.0851 51 I 0.8341 0.0223 0.1436 52 K 0.6197 0.0485 0.3319 53 K 0.3768 0.0973 0.5258 54 Q 0.2100 0.0999 0.6901 55 Y 0.0938 0.0490 0.8572 56 A 0.0141 0.3993 0.5866 57 G 0.0122 0.6322 0.3556 58 H 0.0091 0.8563 0.1345 59 A 0.0048 0.9457 0.0495 60 K 0.0047 0.9555 0.0398 61 R 0.0047 0.9570 0.0383 62 V 0.0047 0.9577 0.0376 63 M 0.0047 0.9575 0.0378 64 M 0.0048 0.9552 0.0399 65 G 0.0050 0.9480 0.0470 66 V 0.0055 0.9343 0.0603 67 W 0.0074 0.8586 0.1340 68 S 0.0125 0.6269 0.3607 69 F 0.0254 0.4304 0.5442 70 L 0.0398 0.3799 0.5803 71 R 0.0297 0.3466 0.6238 72 Q 0.0502 0.3437 0.6061 73 F 0.0770 0.2404 0.6826 74 M 0.1109 0.2209 0.6682 75 Y 0.2665 0.1164 0.6171 76 T 0.4800 0.0175 0.5025 77 K 0.6293 0.0374 0.3333 78 F 0.9202 0.0037 0.0762 79 V 0.9298 0.0033 0.0669 80 I 0.9287 0.0034 0.0679 81 V 0.9023 0.0037 0.0940 82 C 0.7298 0.0174 0.2528 83 D 0.2403 0.0360 0.7237 84 D 0.0501 0.1103 0.8397 85 D 0.0897 0.0853 0.8250 86 V 0.1597 0.0608 0.7794 87 N 0.1255 0.0266 0.8478 88 A 0.0272 0.1917 0.7811 89 R 0.0266 0.1262 0.8472 90 D 0.1022 0.0968 0.8011 91 W 0.0054 0.9127 0.0819 92 N 0.0059 0.9346 0.0595 93 D 0.0063 0.9409 0.0528 94 V 0.0065 0.9516 0.0419 95 I 0.0063 0.9520 0.0417 96 W 0.0122 0.9451 0.0427 97 A 0.0129 0.9357 0.0515 98 I 0.0232 0.9087 0.0682 99 T 0.0209 0.8376 0.1415 100 T 0.0370 0.6127 0.3503 101 R 0.0745 0.2345 0.6910 102 M 0.1581 0.0794 0.7625 103 D 0.1269 0.0413 0.8317 104 P 0.0197 0.4313 0.5491 105 A 0.0184 0.3661 0.6155 106 R 0.0687 0.3077 0.6236 107 D 0.1979 0.0859 0.7162 108 T 0.6750 0.0350 0.2901 109 V 0.8504 0.0200 0.1295 110 L 0.8065 0.0297 0.1638 111 V 0.6095 0.0371 0.3534 112 E 0.1745 0.0982 0.7272 113 N 0.0712 0.0470 0.8818 114 T 0.1624 0.0230 0.8146 115 P 0.1911 0.0467 0.7622 116 I 0.2196 0.0594 0.7209 117 D 0.1630 0.0743 0.7627 118 Y 0.1713 0.1340 0.6947 119 L 0.2310 0.1055 0.6635 120 D 0.2145 0.0772 0.7084 121 F 0.0989 0.1870 0.7141 122 A 0.0758 0.1561 0.7680 123 S 0.1048 0.0998 0.7954 124 P 0.1092 0.1105 0.7803 125 V 0.1259 0.1253 0.7489 126 S 0.0848 0.1676 0.7475 127 G 0.0846 0.1412 0.7742 128 L 0.1449 0.1249 0.7301 129 G 0.1811 0.0723 0.7466 130 S 0.3168 0.0380 0.6453 131 K 0.5614 0.0310 0.4076 132 M 0.8697 0.0137 0.1166 133 G 0.8998 0.0104 0.0898 134 L 0.8794 0.0137 0.1069 135 D 0.8039 0.0214 0.1747 136 A 0.5167 0.0733 0.4100 137 T 0.3491 0.0903 0.5606 138 N 0.2674 0.0493 0.6833 139 K 0.1855 0.0650 0.7495 140 W 0.1755 0.0612 0.7633 141 P 0.0887 0.1156 0.7957 142 G 0.0592 0.2197 0.7210 143 E 0.0723 0.2582 0.6695 144 T 0.0995 0.2148 0.6858 145 Q 0.1221 0.1912 0.6867 146 R 0.1705 0.1735 0.6560 147 E 0.2049 0.1723 0.6228 148 W 0.1720 0.1091 0.7189 149 G 0.1269 0.0872 0.7859 150 R 0.1407 0.1031 0.7562 151 P 0.1656 0.0898 0.7447 152 I 0.1748 0.1084 0.7168 153 K 0.1628 0.0649 0.7723 154 K 0.0934 0.0302 0.8764 155 D 0.0587 0.0253 0.9160 156 P 0.0051 0.9244 0.0705 157 D 0.0048 0.9413 0.0539 158 V 0.0049 0.9505 0.0446 159 V 0.0047 0.9575 0.0377 160 A 0.0048 0.9522 0.0429 161 H 0.0049 0.9467 0.0484 162 I 0.0057 0.9482 0.0461 163 D 0.0053 0.9525 0.0422 164 A 0.0051 0.9494 0.0455 165 I 0.0055 0.9440 0.0505 166 W 0.0075 0.9381 0.0543 167 D 0.0068 0.9224 0.0708 168 E 0.0068 0.9018 0.0914 169 L 0.0428 0.5464 0.4108 170 A 0.0522 0.0902 0.8576 171 I 0.0703 0.0649 0.8648 172 F 0.0483 0.1820 0.7698 173 N 0.0630 0.1535 0.7834 174 N 0.0758 0.1336 0.7906 175 G 0.0964 0.1009 0.8027 176 K 0.0620 0.1981 0.7399 177 S 0.0547 0.1746 0.7707 178 A 0.0949 0.2066 0.6985 179 L 0.1262 0.1895 0.6843 180 E 0.1046 0.1427 0.7527 181 H 0.0723 0.3566 0.5712 182 H 0.0943 0.3779 0.5279 183 H 0.1272 0.3451 0.5277 184 H 0.1428 0.2157 0.6415 185 H 0.1149 0.1011 0.7841 186 H 0.0468 0.0356 0.9175