# This file is the result of combining several RDB files, specifically # T0475.t04.dssp-ebghstl.rdb (weight 1.53986) # T0475.t04.stride-ebghtl.rdb (weight 1.24869) # T0475.t04.str2.rdb (weight 1.54758) # T0475.t04.alpha.rdb (weight 0.659012) # T0475.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0475.t2k.stride-ebghtl.rdb (weight 1.24869) # T0475.t2k.str2.rdb (weight 1.54758) # T0475.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 T0475.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0475 # Using neural net t04-2621-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 T0475.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 1280 # # ============================================ # Comments from T0475.t04.stride-ebghtl.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1280 # # ============================================ # Comments from T0475.t04.str2.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1280 # # ============================================ # Comments from T0475.t04.alpha.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1280 # # ============================================ # Comments from T0475.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0475 # 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 T0475.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 87 # # ============================================ # Comments from T0475.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0475 # 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 T0475.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 87 # # ============================================ # Comments from T0475.t2k.str2.rdb # ============================================ # TARGET T0475 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0475.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 87 # # ============================================ # Comments from T0475.t2k.alpha.rdb # ============================================ # TARGET T0475 # 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 T0475.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 87 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0466 0.1256 0.8278 2 N 0.0656 0.1403 0.7941 3 S 0.0452 0.3053 0.6494 4 E 0.0488 0.2839 0.6673 5 I 0.0075 0.8282 0.1643 6 E 0.0050 0.9280 0.0670 7 L 0.0047 0.9505 0.0448 8 P 0.0047 0.9561 0.0392 9 V 0.0047 0.9571 0.0381 10 Q 0.0047 0.9577 0.0377 11 K 0.0047 0.9558 0.0395 12 Q 0.0047 0.9529 0.0423 13 L 0.0047 0.9518 0.0435 14 E 0.0047 0.9392 0.0560 15 A 0.0049 0.9131 0.0820 16 Y 0.0079 0.8249 0.1672 17 N 0.0114 0.6460 0.3425 18 A 0.0470 0.4119 0.5411 19 R 0.0415 0.2656 0.6928 20 D 0.0932 0.2008 0.7060 21 I 0.0050 0.9368 0.0582 22 D 0.0048 0.9540 0.0412 23 A 0.0048 0.9561 0.0392 24 F 0.0047 0.9568 0.0385 25 M 0.0049 0.9477 0.0474 26 A 0.0068 0.8658 0.1274 27 W 0.0155 0.6887 0.2958 28 W 0.1251 0.4116 0.4633 29 A 0.0851 0.3204 0.5945 30 D 0.0499 0.3184 0.6317 31 D 0.1195 0.2407 0.6399 32 C 0.5760 0.1335 0.2905 33 Q 0.7481 0.0994 0.1525 34 Y 0.7813 0.0563 0.1625 35 Y 0.6648 0.0421 0.2931 36 A 0.3842 0.0307 0.5851 37 F 0.1486 0.0449 0.8065 38 P 0.0815 0.0786 0.8400 39 A 0.0661 0.1218 0.8122 40 T 0.0853 0.1772 0.7376 41 L 0.1661 0.2155 0.6184 42 L 0.1844 0.2535 0.5621 43 A 0.1399 0.2829 0.5772 44 G 0.0773 0.2436 0.6791 45 N 0.0592 0.2925 0.6482 46 A 0.0197 0.8082 0.1721 47 A 0.0130 0.9077 0.0794 48 E 0.0087 0.9304 0.0609 49 I 0.0091 0.9333 0.0575 50 R 0.0070 0.9461 0.0469 51 V 0.0059 0.9481 0.0460 52 R 0.0056 0.9422 0.0522 53 H 0.0062 0.9143 0.0795 54 I 0.0067 0.8898 0.1036 55 E 0.0093 0.8063 0.1844 56 R 0.0161 0.6725 0.3114 57 F 0.0496 0.3948 0.5556 58 K 0.0408 0.2258 0.7334 59 E 0.0596 0.1243 0.8161 60 P 0.0473 0.1883 0.7644 61 D 0.0854 0.2155 0.6990 62 L 0.1319 0.2707 0.5974 63 Y 0.3122 0.1810 0.5068 64 G 0.5982 0.0858 0.3161 65 E 0.7675 0.0527 0.1798 66 L 0.8050 0.0536 0.1414 67 L 0.7734 0.0781 0.1485 68 T 0.7781 0.0692 0.1527 69 R 0.8028 0.0622 0.1350 70 V 0.8315 0.0506 0.1179 71 I 0.7794 0.0627 0.1579 72 V 0.5042 0.0705 0.4252 73 G 0.1532 0.0466 0.8003 74 N 0.1932 0.0498 0.7570 75 V 0.7922 0.0135 0.1943 76 V 0.8822 0.0079 0.1099 77 I 0.8754 0.0107 0.1140 78 D 0.8451 0.0134 0.1414 79 H 0.7987 0.0293 0.1721 80 E 0.8165 0.0288 0.1547 81 T 0.8136 0.0303 0.1561 82 V 0.8269 0.0227 0.1504 83 T 0.7275 0.0338 0.2387 84 R 0.5948 0.0356 0.3696 85 N 0.3645 0.0354 0.6000 86 F 0.1277 0.0813 0.7911 87 P 0.0564 0.0537 0.8898 88 E 0.0637 0.0548 0.8815 89 G 0.3297 0.0394 0.6309 90 K 0.7057 0.0139 0.2804 91 G 0.7918 0.0095 0.1987 92 E 0.8223 0.0071 0.1706 93 V 0.8239 0.0072 0.1689 94 D 0.8658 0.0068 0.1274 95 V 0.9071 0.0043 0.0886 96 A 0.9192 0.0036 0.0772 97 C 0.9230 0.0035 0.0735 98 I 0.9210 0.0037 0.0752 99 Y 0.9118 0.0042 0.0840 100 E 0.9054 0.0039 0.0907 101 V 0.8100 0.0071 0.1829 102 E 0.4806 0.0482 0.4712 103 N 0.0626 0.0200 0.9174 104 G 0.0981 0.0312 0.8707 105 R 0.7065 0.0130 0.2805 106 I 0.9079 0.0051 0.0870 107 A 0.8469 0.0250 0.1281 108 K 0.8570 0.0271 0.1159 109 A 0.7495 0.0932 0.1573 110 W 0.6131 0.1663 0.2206 111 F 0.5090 0.2556 0.2354 112 K 0.4111 0.3090 0.2799 113 I 0.2270 0.2927 0.4802 114 G 0.0853 0.1929 0.7218 115 E 0.0889 0.0641 0.8470 116 P 0.1379 0.0436 0.8186 117 R 0.1150 0.0409 0.8441 118 I 0.1443 0.0889 0.7668 119 V 0.1612 0.0741 0.7647 120 S 0.1368 0.0607 0.8025 121 Q 0.1120 0.0467 0.8413 122 K 0.0469 0.0308 0.9223