# This file is the result of combining several RDB files, specifically # T0517.t04.dssp-ebghstl.rdb (weight 1.53986) # T0517.t04.stride-ebghtl.rdb (weight 1.24869) # T0517.t04.str2.rdb (weight 1.54758) # T0517.t04.alpha.rdb (weight 0.659012) # T0517.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0517.t2k.stride-ebghtl.rdb (weight 1.24869) # T0517.t2k.str2.rdb (weight 1.54758) # T0517.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 T0517.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0517 # 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 T0517.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 156.387 # # ============================================ # Comments from T0517.t04.stride-ebghtl.rdb # ============================================ # TARGET T0517 # 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 T0517.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 156.387 # # ============================================ # Comments from T0517.t04.str2.rdb # ============================================ # TARGET T0517 # 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 T0517.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 156.387 # # ============================================ # Comments from T0517.t04.alpha.rdb # ============================================ # TARGET T0517 # 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 T0517.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 156.387 # # ============================================ # Comments from T0517.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0517 # 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 T0517.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 223 # # ============================================ # Comments from T0517.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0517 # 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 T0517.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 223 # # ============================================ # Comments from T0517.t2k.str2.rdb # ============================================ # TARGET T0517 # 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 T0517.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 223 # # ============================================ # Comments from T0517.t2k.alpha.rdb # ============================================ # TARGET T0517 # 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 T0517.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 223 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0629 0.0837 0.8534 2 E 0.1136 0.0869 0.7995 3 N 0.1185 0.1096 0.7719 4 K 0.1781 0.0740 0.7479 5 K 0.2901 0.0372 0.6727 6 M 0.6925 0.0093 0.2982 7 N 0.8849 0.0045 0.1106 8 L 0.9251 0.0033 0.0716 9 L 0.9243 0.0032 0.0725 10 L 0.8684 0.0055 0.1261 11 F 0.6290 0.0130 0.3580 12 S 0.1641 0.0520 0.7839 13 G 0.0508 0.0458 0.9034 14 D 0.0741 0.0851 0.8408 15 Y 0.0070 0.8428 0.1501 16 D 0.0053 0.8837 0.1110 17 K 0.0050 0.9098 0.0852 18 A 0.0050 0.9250 0.0700 19 L 0.0048 0.9391 0.0561 20 A 0.0047 0.9522 0.0431 21 S 0.0047 0.9581 0.0372 22 L 0.0047 0.9605 0.0348 23 I 0.0047 0.9612 0.0341 24 I 0.0047 0.9604 0.0349 25 A 0.0047 0.9600 0.0353 26 N 0.0047 0.9589 0.0363 27 A 0.0047 0.9589 0.0364 28 A 0.0049 0.9567 0.0383 29 R 0.0055 0.9418 0.0527 30 E 0.0056 0.8886 0.1057 31 M 0.0444 0.3107 0.6449 32 E 0.0367 0.0180 0.9454 33 I 0.0769 0.0100 0.9132 34 E 0.5127 0.0055 0.4819 35 V 0.8388 0.0037 0.1576 36 T 0.9136 0.0041 0.0823 37 I 0.9316 0.0033 0.0651 38 F 0.9256 0.0043 0.0702 39 C 0.8882 0.0087 0.1031 40 A 0.6324 0.0540 0.3135 41 F 0.1927 0.2962 0.5111 42 W 0.0571 0.5941 0.3487 43 G 0.0367 0.7304 0.2329 44 L 0.0198 0.8573 0.1229 45 L 0.0201 0.8657 0.1141 46 L 0.0219 0.8391 0.1390 47 L 0.0380 0.7728 0.1892 48 R 0.0519 0.6381 0.3099 49 D 0.0539 0.4392 0.5068 50 P 0.0394 0.2913 0.6693 51 E 0.0582 0.2846 0.6572 52 K 0.0732 0.3139 0.6129 53 A 0.0712 0.3476 0.5812 54 S 0.1030 0.2518 0.6453 55 Q 0.1543 0.1566 0.6891 56 E 0.1734 0.1287 0.6979 57 D 0.1532 0.1623 0.6844 58 K 0.0922 0.2150 0.6929 59 S 0.0685 0.2509 0.6806 60 L 0.0560 0.3472 0.5968 61 Y 0.0425 0.3867 0.5708 62 E 0.0414 0.4507 0.5079 63 Q 0.0344 0.5879 0.3777 64 A 0.0417 0.5802 0.3781 65 F 0.0544 0.5484 0.3973 66 S 0.0464 0.5289 0.4247 67 S 0.0516 0.4824 0.4660 68 L 0.0800 0.3631 0.5569 69 T 0.0917 0.1737 0.7347 70 P 0.0637 0.1504 0.7858 71 R 0.0510 0.1800 0.7690 72 E 0.0568 0.1598 0.7835 73 A 0.0606 0.2291 0.7103 74 E 0.0445 0.3190 0.6365 75 E 0.0619 0.3433 0.5949 76 L 0.0940 0.2517 0.6543 77 P 0.0681 0.3108 0.6211 78 L 0.0744 0.3394 0.5862 79 S 0.0817 0.3361 0.5822 80 K 0.0762 0.2505 0.6733 81 M 0.0428 0.2831 0.6742 82 N 0.0484 0.1838 0.7678 83 L 0.0572 0.2789 0.6639 84 G 0.0366 0.3641 0.5993 85 G 0.0250 0.5536 0.4214 86 I 0.0275 0.6725 0.3001 87 G 0.0112 0.7835 0.2053 88 K 0.0053 0.9459 0.0489 89 K 0.0047 0.9574 0.0379 90 M 0.0047 0.9586 0.0368 91 L 0.0047 0.9582 0.0370 92 L 0.0048 0.9578 0.0374 93 E 0.0049 0.9555 0.0396 94 M 0.0048 0.9518 0.0433 95 M 0.0049 0.9430 0.0521 96 K 0.0052 0.9303 0.0645 97 E 0.0092 0.8445 0.1464 98 E 0.0422 0.3899 0.5680 99 K 0.0351 0.0458 0.9191 100 A 0.0683 0.0157 0.9160 101 P 0.0842 0.0300 0.8858 102 K 0.1365 0.0249 0.8386 103 L 0.0106 0.9030 0.0863 104 S 0.0051 0.9481 0.0467 105 D 0.0053 0.9539 0.0408 106 L 0.0051 0.9519 0.0430 107 L 0.0049 0.9568 0.0383 108 S 0.0052 0.9559 0.0389 109 G 0.0051 0.9555 0.0394 110 A 0.0051 0.9529 0.0420 111 R 0.0049 0.9396 0.0555 112 K 0.0053 0.8734 0.1213 113 K 0.0414 0.2989 0.6597 114 E 0.0382 0.0208 0.9410 115 V 0.1066 0.0120 0.8813 116 K 0.6462 0.0102 0.3436 117 F 0.9101 0.0051 0.0848 118 Y 0.9073 0.0100 0.0827 119 A 0.8652 0.0173 0.1174 120 C 0.5096 0.0810 0.4094 121 Q 0.1670 0.3896 0.4434 122 L 0.0619 0.5626 0.3755 123 S 0.0784 0.6671 0.2546 124 V 0.0533 0.7736 0.1731 125 E 0.0402 0.8056 0.1542 126 I 0.0286 0.7514 0.2200 127 M 0.0484 0.3465 0.6050 128 G 0.0440 0.0448 0.9112 129 F 0.0714 0.0207 0.9079 130 K 0.0780 0.0160 0.9059 131 K 0.0075 0.8123 0.1803 132 E 0.0068 0.8542 0.1389 133 E 0.0112 0.8502 0.1386 134 L 0.0656 0.6286 0.3057 135 F 0.0719 0.4878 0.4402 136 P 0.0364 0.4547 0.5090 137 E 0.0521 0.2736 0.6743 138 V 0.1644 0.0964 0.7392 139 Q 0.3154 0.0899 0.5947 140 I 0.5523 0.1185 0.3293 141 M 0.4358 0.1800 0.3841 142 D 0.3083 0.2608 0.4309 143 V 0.0252 0.8648 0.1100 144 K 0.0069 0.9288 0.0643 145 E 0.0065 0.9372 0.0563 146 Y 0.0064 0.9327 0.0608 147 L 0.0065 0.9349 0.0585 148 K 0.0074 0.9091 0.0835 149 N 0.0073 0.8741 0.1186 150 A 0.0192 0.8152 0.1656 151 L 0.0118 0.6542 0.3340 152 E 0.0183 0.3802 0.6015 153 S 0.0661 0.1513 0.7825 154 D 0.0776 0.0471 0.8753 155 L 0.4816 0.0160 0.5024 156 Q 0.8005 0.0096 0.1899 157 L 0.8591 0.0069 0.1340 158 F 0.7810 0.0066 0.2124 159 I 0.2987 0.0103 0.6910