# This file is the result of combining several RDB files, specifically # T0360.t04.dssp-ebghstl.rdb (weight 1.53986) # T0360.t04.stride-ebghtl.rdb (weight 1.24869) # T0360.t04.str2.rdb (weight 1.54758) # T0360.t04.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 T0360.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0360 # 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 T0360.t04-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 48.0141 # # ============================================ # Comments from T0360.t04.stride-ebghtl.rdb # ============================================ # TARGET T0360 # Using neural net t04-2621-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 T0360.t04-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 48.0141 # # ============================================ # Comments from T0360.t04.str2.rdb # ============================================ # TARGET T0360 # Using neural net t04-2621-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 T0360.t04-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 48.0141 # # ============================================ # Comments from T0360.t04.alpha.rdb # ============================================ # TARGET T0360 # Using neural net t04-2621-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 T0360.t04-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 48.0141 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0473 0.0777 0.8750 2 T 0.0469 0.1886 0.7645 3 Q 0.0203 0.6835 0.2962 4 E 0.0213 0.7825 0.1961 5 T 0.0317 0.7952 0.1731 6 A 0.0430 0.7438 0.2132 7 L 0.0419 0.6981 0.2600 8 G 0.0310 0.5577 0.4113 9 A 0.0528 0.5025 0.4448 10 A 0.0740 0.5173 0.4087 11 L 0.0676 0.4845 0.4479 12 K 0.0595 0.4871 0.4534 13 S 0.0758 0.4755 0.4486 14 A 0.0854 0.4670 0.4476 15 V 0.1357 0.4078 0.4566 16 Q 0.1740 0.3754 0.4506 17 T 0.1249 0.2858 0.5893 18 M 0.0693 0.2346 0.6961 19 S 0.0577 0.2463 0.6960 20 K 0.0099 0.8356 0.1545 21 K 0.0069 0.9326 0.0605 22 K 0.0075 0.9376 0.0549 23 Q 0.0053 0.9512 0.0435 24 T 0.0052 0.9565 0.0383 25 E 0.0047 0.9587 0.0366 26 M 0.0047 0.9579 0.0374 27 I 0.0049 0.9537 0.0414 28 A 0.0049 0.9506 0.0446 29 D 0.0059 0.9275 0.0667 30 H 0.0104 0.8448 0.1448 31 I 0.0289 0.6287 0.3424 32 Y 0.0219 0.5611 0.4170 33 G 0.0213 0.4341 0.5446 34 K 0.0449 0.4360 0.5191 35 Y 0.1188 0.1893 0.6919 36 D 0.0787 0.1625 0.7588 37 V 0.0377 0.3015 0.6608 38 F 0.0600 0.2439 0.6961 39 K 0.0542 0.2178 0.7279 40 R 0.1021 0.1169 0.7810 41 F 0.1747 0.0528 0.7724 42 K 0.2134 0.0494 0.7373 43 P 0.2402 0.1659 0.5940 44 L 0.1682 0.2742 0.5576 45 A 0.2083 0.3487 0.4430 46 L 0.2077 0.3522 0.4401 47 G 0.1923 0.2860 0.5218 48 I 0.1143 0.5530 0.3327 49 D 0.0436 0.7554 0.2009 50 Q 0.0081 0.9108 0.0811 51 D 0.0067 0.9324 0.0610 52 L 0.0057 0.9363 0.0580 53 I 0.0064 0.9199 0.0737 54 A 0.0064 0.8321 0.1614 55 A 0.0107 0.6184 0.3709 56 L 0.0595 0.0889 0.8517 57 P 0.0132 0.1704 0.8165 58 Q 0.0233 0.1037 0.8730 59 Y 0.0835 0.0379 0.8786 60 D 0.0683 0.0261 0.9056 61 A 0.0049 0.9495 0.0456 62 A 0.0047 0.9602 0.0352 63 L 0.0047 0.9611 0.0342 64 I 0.0046 0.9615 0.0339 65 A 0.0046 0.9613 0.0340 66 R 0.0046 0.9605 0.0349 67 V 0.0047 0.9590 0.0363 68 L 0.0048 0.9543 0.0409 69 A 0.0051 0.9435 0.0514 70 N 0.0075 0.8679 0.1246 71 H 0.0111 0.6681 0.3208 72 C 0.0446 0.3356 0.6198 73 R 0.0391 0.1541 0.8068 74 R 0.0627 0.1738 0.7635 75 P 0.0084 0.8863 0.1054 76 R 0.0083 0.9209 0.0709 77 Y 0.0096 0.9272 0.0632 78 L 0.0102 0.9300 0.0598 79 K 0.0098 0.9161 0.0741 80 A 0.0168 0.8929 0.0903 81 L 0.0384 0.8535 0.1081 82 A 0.0660 0.7214 0.2126 83 R 0.0346 0.3143 0.6511 84 G 0.0274 0.0355 0.9371 85 G 0.1019 0.0167 0.8814 86 K 0.3682 0.0124 0.6194 87 R 0.8056 0.0095 0.1849 88 F 0.8469 0.0077 0.1454 89 D 0.6486 0.0105 0.3409 90 L 0.2636 0.1182 0.6182 91 N 0.0769 0.0336 0.8895 92 N 0.0761 0.0362 0.8876 93 R 0.2282 0.0288 0.7430 94 F 0.4930 0.0282 0.4788 95 K 0.3755 0.0502 0.5743 96 G 0.2927 0.0466 0.6607 97 E 0.4078 0.0298 0.5624 98 V 0.3445 0.0116 0.6439 99 T 0.1207 0.0142 0.8651 100 P 0.0051 0.9437 0.0512 101 E 0.0052 0.9522 0.0426 102 E 0.0048 0.9563 0.0389 103 Q 0.0049 0.9570 0.0381 104 A 0.0047 0.9482 0.0471 105 I 0.0049 0.9212 0.0738 106 A 0.0055 0.8682 0.1263 107 Q 0.0063 0.7030 0.2907 108 N 0.0106 0.5379 0.4515 109 H 0.0395 0.2596 0.7010 110 P 0.0093 0.5639 0.4267 111 F 0.0083 0.8309 0.1608 112 V 0.0104 0.8941 0.0955 113 Q 0.0059 0.9269 0.0673 114 Q 0.0047 0.9458 0.0495 115 A 0.0047 0.9463 0.0491 116 L 0.0047 0.9430 0.0523 117 Q 0.0047 0.9430 0.0524 118 Q 0.0047 0.9371 0.0582 119 Q 0.0047 0.9173 0.0780 120 S 0.0047 0.8937 0.1015 121 A 0.0047 0.9116 0.0837 122 Q 0.0047 0.9209 0.0745 123 A 0.0047 0.9152 0.0801 124 A 0.0050 0.9077 0.0872 125 A 0.0055 0.8734 0.1211 126 E 0.0057 0.7860 0.2083 127 T 0.0075 0.6548 0.3377 128 L 0.0325 0.4458 0.5217 129 S 0.0334 0.3497 0.6169 130 V 0.0137 0.6249 0.3613 131 E 0.0165 0.6863 0.2972 132 A 0.0116 0.7865 0.2019 133 E 0.0123 0.8225 0.1652 134 A 0.0146 0.8015 0.1839 135 A 0.0241 0.6969 0.2790 136 E 0.0343 0.5625 0.4033 137 S 0.0377 0.4300 0.5323 138 S 0.0326 0.3020 0.6654 139 A 0.0432 0.1932 0.7635 140 A 0.0473 0.1219 0.8308 141 E 0.0490 0.0849 0.8662