# This file is the result of combining several RDB files, specifically # T0337.t06.dssp-ebghstl.rdb (weight 1.53986) # T0337.t06.stride-ebghtl.rdb (weight 1.24869) # T0337.t06.str2.rdb (weight 1.54758) # T0337.t06.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 T0337.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0337 # 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 T0337.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 1361 # # ============================================ # Comments from T0337.t06.stride-ebghtl.rdb # ============================================ # TARGET T0337 # 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 T0337.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 1361 # # ============================================ # Comments from T0337.t06.str2.rdb # ============================================ # TARGET T0337 # 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 T0337.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 1361 # # ============================================ # Comments from T0337.t06.alpha.rdb # ============================================ # TARGET T0337 # 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 T0337.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 1361 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0577 0.0441 0.8982 2 D 0.0787 0.1529 0.7683 3 C 0.0663 0.3022 0.6315 4 M 0.0676 0.3396 0.5928 5 R 0.0754 0.3361 0.5885 6 K 0.1028 0.2094 0.6878 7 L 0.0707 0.1536 0.7757 8 D 0.0533 0.1061 0.8406 9 R 0.0048 0.9523 0.0430 10 V 0.0047 0.9583 0.0370 11 D 0.0047 0.9598 0.0355 12 M 0.0047 0.9611 0.0343 13 Q 0.0046 0.9610 0.0344 14 L 0.0046 0.9605 0.0348 15 V 0.0047 0.9606 0.0347 16 K 0.0047 0.9601 0.0352 17 I 0.0048 0.9555 0.0397 18 L 0.0051 0.9403 0.0546 19 S 0.0065 0.8893 0.1043 20 E 0.0162 0.7104 0.2734 21 N 0.0420 0.2577 0.7003 22 S 0.0486 0.1879 0.7636 23 R 0.0524 0.1585 0.7891 24 L 0.0976 0.0557 0.8467 25 T 0.0822 0.0524 0.8655 26 Y 0.0048 0.9478 0.0474 27 R 0.0047 0.9586 0.0367 28 E 0.0047 0.9580 0.0373 29 L 0.0047 0.9589 0.0364 30 A 0.0047 0.9560 0.0393 31 D 0.0049 0.9413 0.0538 32 I 0.0057 0.9050 0.0893 33 L 0.0518 0.5651 0.3832 34 N 0.0424 0.0991 0.8585 35 T 0.0652 0.0546 0.8802 36 T 0.0669 0.0483 0.8847 37 R 0.0063 0.8897 0.1040 38 Q 0.0047 0.9522 0.0430 39 R 0.0047 0.9570 0.0383 40 I 0.0047 0.9595 0.0358 41 A 0.0047 0.9603 0.0351 42 R 0.0047 0.9589 0.0364 43 R 0.0047 0.9569 0.0384 44 I 0.0047 0.9601 0.0352 45 D 0.0047 0.9603 0.0351 46 K 0.0047 0.9594 0.0360 47 L 0.0047 0.9583 0.0371 48 K 0.0047 0.9515 0.0438 49 K 0.0054 0.9133 0.0813 50 L 0.0442 0.4054 0.5504 51 G 0.0357 0.0236 0.9407 52 I 0.1347 0.0507 0.8146 53 I 0.5881 0.0318 0.3801 54 R 0.6706 0.0511 0.2783 55 K 0.7055 0.0371 0.2574 56 F 0.7860 0.0186 0.1954 57 T 0.8594 0.0097 0.1309 58 I 0.8684 0.0075 0.1241 59 I 0.7726 0.0098 0.2176 60 P 0.4399 0.0350 0.5251 61 D 0.1905 0.0207 0.7888 62 I 0.0083 0.8128 0.1789 63 D 0.0081 0.8295 0.1623 64 K 0.0123 0.8192 0.1685 65 L 0.0846 0.3945 0.5210 66 G 0.0892 0.0555 0.8552 67 Y 0.3804 0.0347 0.5850 68 M 0.6825 0.0094 0.3081 69 Y 0.8334 0.0075 0.1591 70 A 0.9196 0.0033 0.0770 71 I 0.9313 0.0031 0.0656 72 V 0.9280 0.0040 0.0680 73 L 0.9238 0.0041 0.0722 74 I 0.9081 0.0042 0.0876 75 K 0.8598 0.0056 0.1346 76 S 0.6054 0.0159 0.3787 77 K 0.1924 0.0340 0.7736 78 V 0.0953 0.0174 0.8873 79 P 0.0246 0.3008 0.6746 80 S 0.0172 0.4121 0.5707 81 D 0.0244 0.5553 0.4203 82 A 0.0056 0.8738 0.1206 83 D 0.0048 0.9439 0.0513 84 K 0.0047 0.9534 0.0419 85 V 0.0047 0.9569 0.0384 86 I 0.0047 0.9562 0.0391 87 S 0.0048 0.9545 0.0406 88 E 0.0052 0.9413 0.0534 89 I 0.0058 0.8981 0.0960 90 S 0.0065 0.7072 0.2863 91 D 0.0124 0.4164 0.5711 92 I 0.0663 0.1072 0.8264 93 E 0.0237 0.3372 0.6391 94 Y 0.1140 0.4034 0.4826 95 V 0.3762 0.4202 0.2037 96 K 0.4227 0.4387 0.1386 97 S 0.4888 0.3931 0.1181 98 V 0.4643 0.3956 0.1401 99 E 0.5146 0.3010 0.1844 100 K 0.3948 0.2869 0.3182 101 G 0.2254 0.1677 0.6069 102 V 0.1199 0.0915 0.7886 103 G 0.0929 0.0506 0.8565 104 R 0.1488 0.0977 0.7536 105 Y 0.2420 0.0649 0.6931 106 N 0.3310 0.0475 0.6215 107 I 0.8819 0.0067 0.1114 108 I 0.9258 0.0047 0.0695 109 V 0.9238 0.0064 0.0699 110 R 0.9244 0.0076 0.0680 111 L 0.9098 0.0093 0.0808 112 L 0.8447 0.0147 0.1407 113 L 0.6062 0.0120 0.3818 114 P 0.2212 0.0270 0.7518 115 K 0.0844 0.0572 0.8584 116 D 0.0924 0.0226 0.8850 117 I 0.0056 0.9057 0.0887 118 K 0.0050 0.9408 0.0542 119 D 0.0052 0.9439 0.0509 120 A 0.0048 0.9537 0.0415 121 E 0.0047 0.9578 0.0376 122 N 0.0047 0.9562 0.0391 123 L 0.0047 0.9535 0.0417 124 I 0.0048 0.9533 0.0419 125 S 0.0048 0.9553 0.0399 126 E 0.0050 0.9508 0.0443 127 F 0.0052 0.9392 0.0556 128 L 0.0058 0.9233 0.0710 129 Q 0.0061 0.8307 0.1631 130 R 0.0115 0.6633 0.3252 131 I 0.0743 0.2588 0.6669 132 K 0.0236 0.2826 0.6938 133 N 0.0411 0.1601 0.7988 134 A 0.1414 0.2017 0.6568 135 E 0.2109 0.1738 0.6153 136 N 0.4054 0.0838 0.5108 137 V 0.6138 0.0327 0.3535 138 E 0.7818 0.0183 0.1999 139 V 0.8680 0.0100 0.1220 140 I 0.8777 0.0136 0.1087 141 L 0.8986 0.0124 0.0890 142 I 0.8765 0.0186 0.1048 143 S 0.8169 0.0290 0.1541 144 E 0.7779 0.0351 0.1869 145 V 0.7541 0.0413 0.2046 146 R 0.7274 0.0605 0.2121 147 K 0.6579 0.0987 0.2435 148 F 0.5134 0.1138 0.3728 149 E 0.3801 0.1030 0.5168 150 I 0.2204 0.0880 0.6917 151 I 0.0729 0.0389 0.8882