# This file is the result of combining several RDB files, specifically # T0167.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0167.t2k.stride-ebghtl.rdb (weight 1.24869) # T0167.t2k.str.rdb (weight 1.53983) # T0167.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 T0167.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0167 # 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 T0167.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 202 # # ============================================ # Comments from T0167.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0167 # 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 T0167.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 202 # # ============================================ # Comments from T0167.t2k.str.rdb # ============================================ # TARGET T0167 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0167.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 202 # # ============================================ # Comments from T0167.t2k.alpha.rdb # ============================================ # TARGET T0167 # 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 T0167.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 202 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0263 0.2567 0.7170 2 K 0.0571 0.6005 0.3424 3 T 0.0174 0.7807 0.2019 4 T 0.0120 0.8352 0.1528 5 E 0.0112 0.8415 0.1473 6 Y 0.0096 0.8502 0.1402 7 V 0.0063 0.8983 0.0954 8 A 0.0065 0.9139 0.0797 9 E 0.0059 0.9172 0.0769 10 I 0.0046 0.9376 0.0578 11 L 0.0046 0.9430 0.0524 12 N 0.0046 0.9407 0.0547 13 E 0.0045 0.9460 0.0495 14 L 0.0045 0.9470 0.0485 15 H 0.0046 0.9424 0.0530 16 N 0.0047 0.9344 0.0609 17 S 0.0049 0.9179 0.0772 18 A 0.0056 0.8642 0.1302 19 A 0.0075 0.6837 0.3088 20 Y 0.0154 0.5151 0.4695 21 I 0.0549 0.1777 0.7675 22 S 0.0553 0.0940 0.8507 23 N 0.0063 0.8612 0.1325 24 E 0.0049 0.9116 0.0835 25 E 0.0049 0.9330 0.0621 26 A 0.0045 0.9504 0.0452 27 D 0.0045 0.9523 0.0432 28 Q 0.0045 0.9517 0.0439 29 L 0.0045 0.9524 0.0431 30 A 0.0045 0.9549 0.0406 31 D 0.0046 0.9499 0.0455 32 H 0.0050 0.9429 0.0521 33 I 0.0062 0.9233 0.0705 34 L 0.0091 0.8181 0.1727 35 S 0.0175 0.5191 0.4635 36 S 0.0702 0.1513 0.7784 37 H 0.0279 0.0709 0.9012 38 Q 0.2935 0.0261 0.6805 39 I 0.8910 0.0039 0.1050 40 F 0.9261 0.0041 0.0699 41 T 0.9283 0.0035 0.0682 42 A 0.8666 0.0210 0.1124 43 G 0.6826 0.0171 0.3003 44 A 0.2786 0.0406 0.6808 45 G 0.0774 0.0668 0.8558 46 R 0.0349 0.3174 0.6477 47 S 0.0266 0.5580 0.4154 48 G 0.0103 0.8744 0.1154 49 L 0.0058 0.9457 0.0485 50 M 0.0046 0.9524 0.0430 51 A 0.0044 0.9583 0.0372 52 K 0.0044 0.9599 0.0357 53 S 0.0044 0.9590 0.0365 54 F 0.0044 0.9571 0.0384 55 A 0.0045 0.9552 0.0403 56 M 0.0049 0.9462 0.0489 57 R 0.0053 0.9263 0.0684 58 L 0.0082 0.8978 0.0940 59 M 0.0097 0.8561 0.1342 60 H 0.0157 0.7402 0.2441 61 M 0.0542 0.4051 0.5407 62 G 0.0604 0.0472 0.8924 63 F 0.1349 0.0242 0.8410 64 N 0.3941 0.0285 0.5774 65 A 0.7331 0.0311 0.2358 66 H 0.8236 0.0320 0.1444 67 I 0.8215 0.0305 0.1480 68 V 0.6384 0.0485 0.3130 69 G 0.3138 0.0676 0.6187 70 E 0.1764 0.0779 0.7457 71 I 0.2077 0.0661 0.7263 72 L 0.2975 0.0793 0.6232 73 T 0.3587 0.1267 0.5146 74 P 0.3001 0.1573 0.5426 75 P 0.3265 0.1313 0.5423 76 L 0.2553 0.0406 0.7041 77 A 0.1188 0.0294 0.8518 78 E 0.0286 0.1010 0.8704 79 G 0.0300 0.0449 0.9251 80 D 0.3055 0.0128 0.6817 81 L 0.8604 0.0037 0.1360 82 V 0.9233 0.0037 0.0730 83 I 0.9281 0.0035 0.0684 84 I 0.9149 0.0038 0.0813 85 G 0.8256 0.0051 0.1693 86 S 0.4494 0.0138 0.5369 87 G 0.1382 0.0550 0.8068 88 S 0.0655 0.0691 0.8654 89 G 0.0398 0.1228 0.8374 90 E 0.0594 0.1765 0.7640 91 T 0.0710 0.3233 0.6057 92 K 0.0049 0.9336 0.0615 93 S 0.0049 0.9422 0.0529 94 L 0.0047 0.9552 0.0401 95 I 0.0044 0.9581 0.0375 96 H 0.0044 0.9581 0.0375 97 T 0.0046 0.9536 0.0418 98 A 0.0046 0.9567 0.0386 99 A 0.0044 0.9590 0.0366 100 K 0.0044 0.9593 0.0364 101 A 0.0044 0.9578 0.0378 102 K 0.0047 0.9498 0.0455 103 S 0.0054 0.9107 0.0839 104 L 0.0416 0.2752 0.6832 105 H 0.0430 0.0139 0.9431 106 G 0.0900 0.0077 0.9023 107 I 0.5235 0.0080 0.4685 108 V 0.9275 0.0033 0.0692 109 A 0.9300 0.0039 0.0662 110 A 0.9286 0.0037 0.0677 111 L 0.9010 0.0066 0.0924 112 T 0.6834 0.0192 0.2974 113 I 0.2458 0.0249 0.7293 114 N 0.1181 0.0279 0.8540 115 P 0.0249 0.1104 0.8647 116 E 0.0245 0.0792 0.8963 117 S 0.0754 0.0644 0.8602 118 S 0.0680 0.4577 0.4743 119 I 0.0373 0.7296 0.2332 120 G 0.0447 0.7344 0.2209 121 K 0.0682 0.6320 0.2998 122 Q 0.1117 0.4510 0.4373 123 A 0.2387 0.1445 0.6168 124 D 0.1985 0.0790 0.7225 125 L 0.7766 0.0161 0.2073 126 I 0.9010 0.0064 0.0926 127 I 0.9058 0.0056 0.0886 128 R 0.8790 0.0072 0.1138 129 M 0.6362 0.0126 0.3513 130 P 0.3734 0.0249 0.6017 131 G 0.2591 0.0423 0.6985 132 S 0.2117 0.0554 0.7328 133 P 0.2065 0.1059 0.6876 134 K 0.1935 0.1519 0.6546 135 D 0.1611 0.1480 0.6909 136 Q 0.1216 0.1375 0.7409 137 S 0.0655 0.1742 0.7603 138 N 0.0711 0.1339 0.7950 139 G 0.0886 0.1208 0.7906 140 S 0.1455 0.1165 0.7380 141 Y 0.2807 0.1152 0.6041 142 K 0.2802 0.1230 0.5969 143 T 0.2388 0.1616 0.5995 144 I 0.2425 0.1720 0.5856 145 Q 0.2506 0.1655 0.5839 146 P 0.2535 0.2251 0.5214 147 M 0.1697 0.3092 0.5210 148 G 0.1147 0.4031 0.4822 149 S 0.0891 0.4781 0.4328 150 L 0.0602 0.5019 0.4379 151 F 0.0394 0.6298 0.3308 152 E 0.0122 0.8592 0.1286 153 Q 0.0072 0.9248 0.0680 154 T 0.0058 0.9400 0.0542 155 L 0.0053 0.9441 0.0506 156 L 0.0048 0.9485 0.0467 157 L 0.0044 0.9520 0.0435 158 F 0.0044 0.9582 0.0374 159 Y 0.0044 0.9600 0.0357 160 D 0.0044 0.9598 0.0358 161 A 0.0044 0.9605 0.0351 162 V 0.0043 0.9611 0.0346 163 I 0.0044 0.9606 0.0350 164 L 0.0044 0.9604 0.0353 165 K 0.0044 0.9598 0.0358 166 L 0.0044 0.9589 0.0368 167 M 0.0045 0.9564 0.0391 168 E 0.0052 0.9402 0.0546 169 K 0.0093 0.8530 0.1377 170 K 0.0437 0.4154 0.5409 171 G 0.0413 0.0385 0.9202 172 L 0.0752 0.0152 0.9095 173 D 0.0956 0.0187 0.8857 174 S 0.0114 0.6146 0.3740 175 E 0.0076 0.6659 0.3265 176 T 0.0200 0.6324 0.3476 177 M 0.0274 0.6496 0.3229 178 F 0.0496 0.6444 0.3059 179 T 0.0805 0.6160 0.3035 180 H 0.0827 0.5101 0.4072 181 H 0.0965 0.2709 0.6326 182 A 0.0626 0.2170 0.7204 183 N 0.0764 0.1982 0.7254 184 L 0.0585 0.1813 0.7602 185 E 0.0413 0.0992 0.8594