# This file is the result of combining several RDB files, specifically # T0578.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0578.t2k.stride-ebghtl.rdb (weight 1.24869) # T0578.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 T0578.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0578 # 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 T0578.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 28 # # ============================================ # Comments from T0578.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0578 # 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 T0578.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 28 # # ============================================ # Comments from T0578.t2k.str.rdb # ============================================ # TARGET T0578 # 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 T0578.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 28 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0125 0.1320 0.8554 2 N 0.0568 0.5079 0.4352 3 A 0.0462 0.6752 0.2786 4 M 0.0699 0.6753 0.2548 5 K 0.0420 0.7068 0.2512 6 K 0.0473 0.6226 0.3300 7 A 0.0100 0.6197 0.3702 8 T 0.0203 0.3261 0.6536 9 M 0.0108 0.7511 0.2381 10 L 0.0053 0.9206 0.0741 11 T 0.0039 0.9443 0.0518 12 Y 0.0038 0.9568 0.0394 13 L 0.0038 0.9593 0.0370 14 E 0.0037 0.9595 0.0367 15 E 0.0038 0.9596 0.0366 16 Q 0.0038 0.9523 0.0439 17 L 0.0061 0.9202 0.0737 18 E 0.0070 0.8326 0.1603 19 K 0.0080 0.6332 0.3588 20 H 0.0194 0.3217 0.6589 21 L 0.0464 0.1297 0.8239 22 G 0.0935 0.0608 0.8458 23 D 0.1103 0.0661 0.8236 24 Y 0.2400 0.0774 0.6826 25 E 0.4483 0.0706 0.4811 26 V 0.6962 0.0528 0.2510 27 G 0.7838 0.0364 0.1799 28 L 0.7065 0.0262 0.2673 29 D 0.5851 0.0274 0.3875 30 W 0.2266 0.1375 0.6359 31 D 0.1654 0.1307 0.7039 32 R 0.0772 0.1986 0.7241 33 K 0.0471 0.1421 0.8108 34 N 0.1142 0.0466 0.8392 35 H 0.3358 0.0143 0.6500 36 T 0.7683 0.0036 0.2281 37 I 0.9411 0.0025 0.0564 38 E 0.9648 0.0025 0.0327 39 V 0.9642 0.0024 0.0334 40 I 0.9743 0.0024 0.0233 41 V 0.9762 0.0024 0.0214 42 R 0.9776 0.0024 0.0200 43 L 0.9748 0.0025 0.0227 44 Y 0.9696 0.0025 0.0279 45 A 0.9246 0.0034 0.0720 46 E 0.7796 0.0030 0.2174 47 N 0.4867 0.0097 0.5036 48 N 0.0657 0.1791 0.7551 49 E 0.0345 0.1367 0.8289 50 Q 0.2408 0.1371 0.6221 51 V 0.6082 0.0114 0.3804 52 A 0.8929 0.0032 0.1039 53 I 0.9261 0.0038 0.0701 54 D 0.9235 0.0052 0.0714 55 D 0.5215 0.0128 0.4657 56 V 0.2093 0.0281 0.7626 57 D 0.1186 0.0199 0.8615 58 G 0.1780 0.0130 0.8090 59 T 0.4497 0.0083 0.5420 60 L 0.6433 0.0114 0.3453 61 S 0.2586 0.0180 0.7233 62 E 0.0867 0.0773 0.8360 63 E 0.0853 0.0854 0.8294 64 E 0.2143 0.0992 0.6865 65 F 0.5768 0.0653 0.3579 66 I 0.7706 0.0507 0.1787 67 E 0.8136 0.0463 0.1400 68 F 0.6522 0.1153 0.2326 69 E 0.5392 0.1152 0.3456 70 D 0.4940 0.1151 0.3909 71 G 0.7707 0.0304 0.1989 72 L 0.9055 0.0100 0.0846 73 L 0.9255 0.0100 0.0645 74 F 0.8437 0.0194 0.1369 75 Y 0.6362 0.0120 0.3519 76 N 0.1694 0.0149 0.8158 77 P 0.0187 0.1576 0.8237 78 Q 0.0131 0.2004 0.7865 79 K 0.0597 0.3121 0.6282 80 S 0.1048 0.1296 0.7657 81 V 0.2153 0.0757 0.7090 82 V 0.2575 0.0421 0.7004 83 D 0.1288 0.0347 0.8366 84 D 0.0246 0.5323 0.4431 85 E 0.0165 0.4232 0.5603 86 E 0.0508 0.3771 0.5721 87 Y 0.3922 0.0784 0.5295 88 L 0.7626 0.0145 0.2229 89 V 0.9045 0.0070 0.0885 90 T 0.8892 0.0076 0.1032 91 I 0.7659 0.0072 0.2269 92 P 0.5072 0.0122 0.4807 93 Y 0.1661 0.0408 0.7930 94 E 0.0701 0.0569 0.8730 95 G 0.0304 0.0859 0.8838 96 K 0.0360 0.1467 0.8173 97 K 0.0490 0.1550 0.7961 98 G 0.0406 0.1562 0.8032 99 L 0.0643 0.2635 0.6723 100 R 0.0346 0.4722 0.4932 101 K 0.0038 0.9537 0.0425 102 A 0.0037 0.9641 0.0322 103 V 0.0037 0.9707 0.0255 104 L 0.0037 0.9755 0.0208 105 D 0.0037 0.9759 0.0204 106 G 0.0037 0.9748 0.0214 107 F 0.0037 0.9766 0.0197 108 I 0.0037 0.9770 0.0193 109 H 0.0037 0.9763 0.0200 110 Y 0.0037 0.9745 0.0218 111 L 0.0037 0.9738 0.0225 112 K 0.0037 0.9720 0.0243 113 V 0.0037 0.9709 0.0254 114 V 0.0037 0.9660 0.0303 115 L 0.0037 0.9478 0.0485 116 D 0.0041 0.8549 0.1410 117 E 0.0040 0.5743 0.4217 118 G 0.0106 0.2477 0.7417 119 Q 0.0099 0.6356 0.3545 120 S 0.0121 0.7773 0.2105 121 D 0.0117 0.7975 0.1907 122 L 0.0103 0.8734 0.1163 123 L 0.0085 0.8826 0.1090 124 D 0.0072 0.8758 0.1170 125 F 0.0103 0.7761 0.2136 126 L 0.0447 0.4908 0.4645 127 S 0.0299 0.1684 0.8018 128 D 0.0252 0.0534 0.9214 129 E 0.0318 0.1031 0.8651 130 T 0.0419 0.1333 0.8248 131 A 0.0680 0.1619 0.7701 132 E 0.2557 0.0748 0.6695 133 V 0.6858 0.0192 0.2950 134 F 0.8889 0.0061 0.1050 135 E 0.9225 0.0064 0.0711 136 L 0.9033 0.0064 0.0903 137 H 0.8297 0.0053 0.1649 138 W 0.4920 0.0081 0.4999 139 E 0.0982 0.0114 0.8903 140 P 0.0048 0.8569 0.1383 141 A 0.0039 0.9279 0.0683 142 D 0.0038 0.9429 0.0533 143 F 0.0038 0.9549 0.0413 144 E 0.0044 0.9515 0.0441 145 A 0.0048 0.9353 0.0599 146 M 0.0046 0.9158 0.0796 147 I 0.0080 0.9049 0.0871 148 K 0.0061 0.8282 0.1657 149 K 0.0064 0.7342 0.2594 150 V 0.0102 0.6643 0.3256 151 A 0.0124 0.6987 0.2889 152 E 0.0116 0.7113 0.2771 153 T 0.0124 0.5906 0.3969 154 E 0.0172 0.4955 0.4873 155 K 0.0288 0.3019 0.6693 156 E 0.0652 0.2195 0.7152 157 Q 0.0811 0.1693 0.7495 158 W 0.0697 0.0945 0.8358 159 I 0.0448 0.0513 0.9039 160 A 0.0454 0.0498 0.9048 161 Y 0.0570 0.0439 0.8991 162 P 0.0523 0.0448 0.9028 163 S 0.0607 0.0287 0.9106 164 Y 0.0101 0.0047 0.9852