# This file is the result of combining several RDB files, specifically # T0632.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0632.t2k.stride-ebghtl.rdb (weight 1.24869) # T0632.t2k.str.rdb (weight 1.53983) # 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 T0632.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0632 # 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 T0632.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 1373 # # ============================================ # Comments from T0632.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0632 # 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 T0632.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 1373 # # ============================================ # Comments from T0632.t2k.str.rdb # ============================================ # TARGET T0632 # 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 T0632.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 1373 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0105 0.0564 0.9331 2 D 0.0616 0.2779 0.6605 3 K 0.0856 0.4378 0.4766 4 R 0.0667 0.5664 0.3670 5 L 0.0493 0.5757 0.3751 6 Q 0.0367 0.5466 0.4167 7 Q 0.0242 0.4416 0.5341 8 D 0.0254 0.2611 0.7136 9 R 0.0530 0.4735 0.4735 10 I 0.1005 0.6528 0.2467 11 V 0.1095 0.6941 0.1965 12 D 0.0749 0.7507 0.1744 13 K 0.0882 0.7028 0.2090 14 M 0.0792 0.6537 0.2672 15 E 0.0524 0.5346 0.4130 16 R 0.0336 0.3996 0.5667 17 F 0.0227 0.1135 0.8637 18 L 0.0148 0.2432 0.7420 19 S 0.0191 0.2815 0.6993 20 T 0.0254 0.4123 0.5623 21 A 0.0330 0.4636 0.5034 22 N 0.0371 0.4980 0.4650 23 E 0.0374 0.4988 0.4638 24 E 0.0300 0.5118 0.4582 25 E 0.0244 0.5842 0.3914 26 K 0.0249 0.5918 0.3833 27 D 0.0198 0.4672 0.5130 28 V 0.0195 0.3435 0.6370 29 L 0.0188 0.2083 0.7729 30 S 0.0161 0.2020 0.7818 31 S 0.0070 0.6975 0.2954 32 I 0.0068 0.8263 0.1669 33 V 0.0074 0.8552 0.1375 34 D 0.0084 0.8824 0.1093 35 G 0.0080 0.9003 0.0917 36 L 0.0084 0.8968 0.0948 37 L 0.0096 0.8664 0.1240 38 A 0.0097 0.8645 0.1258 39 K 0.0146 0.7871 0.1984 40 Q 0.0135 0.6336 0.3529 41 E 0.0250 0.4275 0.5475 42 R 0.0525 0.3481 0.5995 43 R 0.0646 0.2723 0.6630 44 Y 0.0416 0.2147 0.7437 45 A 0.0256 0.1882 0.7862 46 T 0.0277 0.2327 0.7397 47 Y 0.0359 0.3924 0.5717 48 L 0.0405 0.6057 0.3539 49 A 0.0591 0.6435 0.2973 50 S 0.0756 0.6135 0.3109 51 L 0.1046 0.4621 0.4333 52 T 0.1004 0.1737 0.7259 53 Q 0.1294 0.0173 0.8533 54 I 0.5302 0.0065 0.4632 55 E 0.8961 0.0031 0.1008 56 S 0.9506 0.0024 0.0469 57 Q 0.9580 0.0025 0.0395 58 E 0.9454 0.0026 0.0520 59 R 0.8142 0.0052 0.1806 60 E 0.5227 0.0179 0.4594 61 D 0.0438 0.0266 0.9296 62 G 0.0293 0.0198 0.9509 63 R 0.7597 0.0053 0.2349 64 F 0.9548 0.0025 0.0427 65 E 0.9728 0.0024 0.0248 66 V 0.9776 0.0024 0.0200 67 R 0.9673 0.0025 0.0302 68 L 0.8724 0.0030 0.1246 69 P 0.6264 0.0050 0.3686 70 I 0.3336 0.0091 0.6573 71 G 0.0802 0.0292 0.8906 72 P 0.0156 0.4562 0.5282 73 L 0.0122 0.5519 0.4360 74 V 0.0262 0.5566 0.4172 75 N 0.0366 0.2998 0.6636 76 N 0.0295 0.1287 0.8419 77 P 0.0388 0.1376 0.8236 78 L 0.0277 0.2340 0.7383 79 N 0.0647 0.3027 0.6327 80 M 0.2014 0.4692 0.3294 81 V 0.2710 0.5517 0.1773 82 H 0.1288 0.7413 0.1299 83 G 0.0138 0.8599 0.1263 84 G 0.0061 0.9446 0.0493 85 I 0.0038 0.9710 0.0252 86 T 0.0038 0.9741 0.0221 87 A 0.0038 0.9730 0.0233 88 T 0.0038 0.9668 0.0294 89 L 0.0037 0.9719 0.0244 90 L 0.0038 0.9672 0.0290 91 D 0.0039 0.9599 0.0362 92 T 0.0038 0.9621 0.0341 93 A 0.0039 0.9499 0.0462 94 M 0.0043 0.9355 0.0602 95 G 0.0043 0.9370 0.0588 96 Q 0.0057 0.9453 0.0491 97 M 0.0088 0.9438 0.0474 98 V 0.0134 0.9111 0.0755 99 N 0.0207 0.8562 0.1230 100 R 0.0421 0.6826 0.2753 101 Q 0.0716 0.4088 0.5196 102 L 0.0743 0.0576 0.8681 103 P 0.0352 0.0506 0.9142 104 D 0.0134 0.0716 0.9150 105 G 0.0204 0.0522 0.9275 106 Q 0.1919 0.0250 0.7831 107 S 0.5462 0.0059 0.4479 108 A 0.8436 0.0031 0.1533 109 V 0.8977 0.0034 0.0990 110 T 0.9285 0.0025 0.0690 111 S 0.9355 0.0029 0.0616 112 E 0.9567 0.0025 0.0408 113 L 0.9356 0.0025 0.0618 114 N 0.9316 0.0026 0.0658 115 I 0.9339 0.0032 0.0630 116 H 0.9047 0.0052 0.0901 117 Y 0.9178 0.0073 0.0750 118 V 0.8879 0.0063 0.1059 119 K 0.8485 0.0063 0.1452 120 P 0.6829 0.0097 0.3074 121 G 0.3839 0.0175 0.5986 122 M 0.1342 0.0273 0.8385 123 G 0.0220 0.0229 0.9551 124 T 0.1372 0.0191 0.8437 125 Y 0.6897 0.0037 0.3066 126 L 0.9377 0.0025 0.0598 127 R 0.9667 0.0024 0.0309 128 A 0.9779 0.0024 0.0197 129 V 0.9784 0.0024 0.0192 130 A 0.9755 0.0024 0.0221 131 S 0.9753 0.0024 0.0223 132 I 0.9612 0.0024 0.0364 133 V 0.9414 0.0026 0.0561 134 H 0.8276 0.0045 0.1678 135 Q 0.3389 0.0212 0.6399 136 G 0.2360 0.0190 0.7450 137 K 0.3602 0.0160 0.6238 138 Q 0.6830 0.0040 0.3130 139 R 0.9465 0.0025 0.0510 140 I 0.9698 0.0024 0.0278 141 V 0.9768 0.0024 0.0209 142 V 0.9778 0.0024 0.0198 143 E 0.9784 0.0024 0.0192 144 G 0.9754 0.0024 0.0222 145 K 0.9765 0.0024 0.0211 146 V 0.9665 0.0025 0.0310 147 Y 0.9539 0.0026 0.0435 148 T 0.6193 0.0094 0.3713 149 D 0.0180 0.0171 0.9648 150 Q 0.0074 0.0152 0.9774 151 G 0.0708 0.0158 0.9133 152 E 0.5556 0.0043 0.4401 153 T 0.9521 0.0025 0.0454 154 V 0.9674 0.0024 0.0302 155 A 0.9774 0.0024 0.0203 156 M 0.9766 0.0024 0.0210 157 G 0.9764 0.0024 0.0212 158 T 0.9766 0.0024 0.0210 159 G 0.9700 0.0024 0.0275 160 S 0.9698 0.0024 0.0278 161 F 0.9692 0.0024 0.0283 162 F 0.9621 0.0025 0.0354 163 V 0.9250 0.0026 0.0724 164 L 0.7074 0.0040 0.2886 165 R 0.3176 0.0097 0.6727 166 S 0.1234 0.0216 0.8550 167 R 0.0612 0.0242 0.9146 168 G 0.0127 0.0119 0.9754