# This file is the result of combining several RDB files, specifically # T0520.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0520.t2k.stride-ebghtl.rdb (weight 1.24869) # T0520.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 T0520.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0520 # 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 T0520.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 1499 # # ============================================ # Comments from T0520.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0520 # 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 T0520.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 1499 # # ============================================ # Comments from T0520.t2k.str.rdb # ============================================ # TARGET T0520 # 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 T0520.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 1499 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0251 0.0184 0.9565 2 N 0.0564 0.0373 0.9063 3 A 0.0829 0.0620 0.8551 4 E 0.1825 0.1258 0.6916 5 R 0.3830 0.1088 0.5082 6 R 0.5690 0.0985 0.3325 7 L 0.7020 0.1074 0.1907 8 C 0.8312 0.0863 0.0825 9 A 0.8431 0.1012 0.0557 10 I 0.8719 0.0928 0.0353 11 L 0.7840 0.1535 0.0626 12 A 0.6472 0.2530 0.0998 13 A 0.4784 0.3037 0.2179 14 D 0.3019 0.2990 0.3991 15 M 0.1175 0.5303 0.3522 16 A 0.0451 0.5969 0.3580 17 G 0.0346 0.5368 0.4286 18 Y 0.0426 0.6387 0.3187 19 S 0.0373 0.7428 0.2198 20 R 0.0173 0.8347 0.1480 21 L 0.0119 0.8452 0.1428 22 M 0.0115 0.8305 0.1579 23 E 0.0109 0.7052 0.2839 24 R 0.0114 0.4878 0.5008 25 N 0.0257 0.2019 0.7724 26 E 0.0122 0.0671 0.9207 27 T 0.0040 0.9136 0.0824 28 D 0.0039 0.9547 0.0415 29 V 0.0038 0.9657 0.0305 30 L 0.0038 0.9726 0.0236 31 N 0.0037 0.9753 0.0210 32 R 0.0037 0.9734 0.0228 33 Q 0.0038 0.9711 0.0251 34 K 0.0037 0.9726 0.0236 35 L 0.0038 0.9685 0.0278 36 Y 0.0038 0.9601 0.0361 37 R 0.0038 0.9575 0.0387 38 R 0.0038 0.9576 0.0386 39 E 0.0038 0.9533 0.0429 40 L 0.0038 0.9473 0.0488 41 I 0.0038 0.9608 0.0355 42 D 0.0037 0.9682 0.0280 43 P 0.0041 0.9710 0.0249 44 A 0.0037 0.9721 0.0242 45 I 0.0048 0.9662 0.0290 46 A 0.0066 0.9371 0.0563 47 Q 0.0067 0.8028 0.1905 48 A 0.0096 0.4201 0.5702 49 G 0.0186 0.0232 0.9583 50 G 0.1398 0.0214 0.8388 51 Q 0.7344 0.0151 0.2506 52 I 0.9011 0.0099 0.0890 53 V 0.8979 0.0126 0.0895 54 K 0.8744 0.0128 0.1129 55 T 0.8276 0.0153 0.1570 56 T 0.6577 0.0349 0.3074 57 G 0.2578 0.0683 0.6738 58 D 0.2310 0.0689 0.7001 59 G 0.7454 0.0753 0.1794 60 M 0.8247 0.0980 0.0773 61 L 0.8379 0.0990 0.0631 62 A 0.8248 0.0939 0.0814 63 R 0.6971 0.0904 0.2125 64 F 0.2972 0.0532 0.6496 65 D 0.0995 0.0341 0.8664 66 T 0.0484 0.0522 0.8994 67 A 0.0233 0.1995 0.7772 68 Q 0.0122 0.4258 0.5620 69 A 0.0096 0.5346 0.4558 70 A 0.0059 0.7517 0.2424 71 L 0.0049 0.8778 0.1172 72 R 0.0046 0.9068 0.0886 73 C 0.0041 0.9417 0.0542 74 A 0.0038 0.9670 0.0292 75 L 0.0037 0.9722 0.0241 76 E 0.0037 0.9725 0.0238 77 I 0.0037 0.9742 0.0221 78 Q 0.0037 0.9752 0.0211 79 Q 0.0037 0.9721 0.0242 80 A 0.0037 0.9655 0.0308 81 M 0.0037 0.9629 0.0334 82 Q 0.0038 0.9514 0.0448 83 Q 0.0038 0.9222 0.0740 84 R 0.0043 0.8840 0.1118 85 E 0.0055 0.8458 0.1487 86 E 0.0062 0.7491 0.2447 87 D 0.0094 0.6423 0.3483 88 T 0.0145 0.3859 0.5995 89 P 0.0151 0.2483 0.7366 90 R 0.0166 0.1635 0.8199 91 K 0.0303 0.0927 0.8770 92 E 0.0669 0.0499 0.8832 93 R 0.1928 0.0283 0.7789 94 I 0.4631 0.0130 0.5239 95 Q 0.7913 0.0043 0.2044 96 Y 0.9373 0.0026 0.0601 97 R 0.9462 0.0025 0.0513 98 I 0.9460 0.0025 0.0514 99 G 0.8922 0.0030 0.1048 100 I 0.8198 0.0074 0.1727 101 N 0.6367 0.0165 0.3468 102 I 0.4546 0.0209 0.5245 103 G 0.3650 0.0247 0.6103 104 D 0.4693 0.0315 0.4992 105 I 0.6797 0.0268 0.2936 106 V 0.7952 0.0297 0.1751 107 L 0.7279 0.0405 0.2316 108 E 0.4925 0.0423 0.4652 109 D 0.3184 0.0376 0.6440 110 G 0.2030 0.0551 0.7419 111 D 0.1808 0.0558 0.7634 112 I 0.3218 0.0636 0.6147 113 F 0.2699 0.0990 0.6311 114 G 0.0973 0.2082 0.6945 115 D 0.0306 0.7261 0.2432 116 A 0.0259 0.8650 0.1091 117 V 0.0081 0.9507 0.0412 118 N 0.0077 0.9567 0.0356 119 V 0.0047 0.9702 0.0252 120 A 0.0047 0.9703 0.0249 121 A 0.0047 0.9678 0.0275 122 R 0.0048 0.9581 0.0372 123 L 0.0045 0.9530 0.0426 124 E 0.0041 0.9461 0.0497 125 A 0.0045 0.8789 0.1165 126 I 0.0071 0.7624 0.2304 127 S 0.0267 0.4687 0.5046 128 E 0.0384 0.1181 0.8436 129 P 0.0267 0.0870 0.8863 130 G 0.0483 0.0447 0.9070 131 A 0.4321 0.0258 0.5422 132 I 0.8892 0.0069 0.1039 133 C 0.9057 0.0061 0.0881 134 V 0.7943 0.0114 0.1943 135 S 0.2938 0.0238 0.6825 136 D 0.0054 0.8947 0.0999 137 I 0.0038 0.9368 0.0594 138 V 0.0038 0.9566 0.0396 139 H 0.0038 0.9560 0.0402 140 Q 0.0042 0.9412 0.0546 141 I 0.0046 0.9039 0.0915 142 T 0.0107 0.7539 0.2353 143 Q 0.0131 0.5965 0.3904 144 D 0.0127 0.4353 0.5520 145 R 0.0192 0.3584 0.6224 146 V 0.0496 0.2142 0.7362 147 S 0.0859 0.1271 0.7870 148 E 0.2048 0.0933 0.7019 149 P 0.3756 0.0631 0.5613 150 F 0.5738 0.0564 0.3698 151 T 0.5987 0.0568 0.3445 152 D 0.5383 0.0613 0.4005 153 L 0.3445 0.0661 0.5894 154 G 0.2233 0.0384 0.7383 155 L 0.4339 0.0295 0.5366 156 Q 0.7544 0.0090 0.2366 157 K 0.8189 0.0091 0.1720 158 V 0.6942 0.0162 0.2895 159 K 0.3776 0.0289 0.5935 160 N 0.1420 0.0263 0.8317 161 I 0.1407 0.0233 0.8360 162 T 0.1259 0.0160 0.8582 163 R 0.1937 0.0078 0.7985 164 P 0.3169 0.0056 0.6775 165 I 0.7219 0.0036 0.2745 166 R 0.9226 0.0025 0.0748 167 V 0.9551 0.0024 0.0424 168 W 0.9582 0.0025 0.0393 169 Q 0.9403 0.0028 0.0569 170 W 0.8097 0.0045 0.1858 171 V 0.3970 0.0101 0.5929 172 P 0.1035 0.0294 0.8671 173 D 0.0388 0.0830 0.8781 174 A 0.0321 0.1233 0.8446 175 D 0.0253 0.1736 0.8010 176 R 0.0311 0.1836 0.7853 177 D 0.0500 0.1422 0.8078 178 Q 0.0594 0.0827 0.8579 179 S 0.0566 0.0536 0.8898 180 H 0.0458 0.0439 0.9103 181 D 0.0344 0.0293 0.9363 182 P 0.0385 0.0339 0.9276 183 Q 0.0397 0.0377 0.9226 184 P 0.0448 0.1591 0.7961 185 S 0.0498 0.1998 0.7504 186 H 0.1179 0.2829 0.5992 187 V 0.2403 0.1617 0.5980 188 Q 0.1755 0.0936 0.7309 189 H 0.0191 0.0113 0.9697