# This file is the result of combining several RDB files, specifically # YGR030C.t2k.dssp-ebghstl.rdb (weight 1.53986) # YGR030C.t2k.stride-ebghtl.rdb (weight 1.24869) # YGR030C.t2k.str2.rdb (weight 1.54758) # YGR030C.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 YGR030C.t2k.dssp-ebghstl.rdb # ============================================ # TARGET YGR030C # 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 YGR030C.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 1 # # ============================================ # Comments from YGR030C.t2k.stride-ebghtl.rdb # ============================================ # TARGET YGR030C # 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 YGR030C.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 1 # # ============================================ # Comments from YGR030C.t2k.str2.rdb # ============================================ # TARGET YGR030C # 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 YGR030C.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 1 # # ============================================ # Comments from YGR030C.t2k.alpha.rdb # ============================================ # TARGET YGR030C # 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 YGR030C.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0813 0.0675 0.8512 2 I 0.2002 0.1150 0.6848 3 N 0.1989 0.1460 0.6551 4 G 0.2501 0.1656 0.5843 5 V 0.4604 0.1580 0.3816 6 Y 0.5595 0.1359 0.3047 7 Y 0.3918 0.2377 0.3704 8 N 0.2795 0.3047 0.4159 9 E 0.2336 0.3768 0.3896 10 I 0.2473 0.3678 0.3848 11 S 0.2137 0.3488 0.4375 12 R 0.1438 0.3801 0.4762 13 D 0.1418 0.3373 0.5209 14 L 0.1815 0.2716 0.5469 15 D 0.1853 0.1689 0.6458 16 I 0.1422 0.2536 0.6042 17 S 0.1036 0.2294 0.6669 18 S 0.0710 0.3400 0.5890 19 S 0.0624 0.4701 0.4676 20 T 0.0574 0.6690 0.2736 21 Q 0.0664 0.7383 0.1952 22 C 0.0674 0.7788 0.1538 23 L 0.0507 0.8328 0.1164 24 R 0.0647 0.8135 0.1218 25 F 0.0668 0.7704 0.1628 26 L 0.0911 0.7056 0.2033 27 K 0.0826 0.6795 0.2378 28 E 0.0814 0.6521 0.2665 29 T 0.1438 0.5426 0.3136 30 V 0.2158 0.4116 0.3726 31 I 0.2010 0.3387 0.4603 32 P 0.1380 0.4556 0.4064 33 S 0.1186 0.5038 0.3777 34 L 0.1212 0.4987 0.3801 35 A 0.1139 0.4126 0.4735 36 N 0.0890 0.2842 0.6267 37 N 0.0742 0.1443 0.7816 38 G 0.0680 0.0957 0.8362 39 N 0.1007 0.0891 0.8101 40 N 0.1434 0.0862 0.7703 41 S 0.2266 0.1185 0.6549 42 T 0.3636 0.1371 0.4992 43 S 0.5082 0.1168 0.3750 44 I 0.6221 0.0947 0.2832 45 Q 0.6325 0.0955 0.2720 46 Y 0.5900 0.1151 0.2949 47 H 0.4190 0.1281 0.4529 48 G 0.3812 0.0911 0.5277 49 I 0.4104 0.0792 0.5104 50 S 0.3160 0.0926 0.5914 51 K 0.1309 0.2262 0.6429 52 N 0.0877 0.2480 0.6642 53 D 0.0748 0.3154 0.6099 54 N 0.1108 0.3352 0.5540 55 I 0.1393 0.4366 0.4242 56 K 0.1305 0.4853 0.3841 57 K 0.1049 0.5677 0.3274 58 S 0.1124 0.5527 0.3349 59 V 0.0871 0.6110 0.3019 60 N 0.0848 0.5757 0.3395 61 K 0.0660 0.6178 0.3162 62 L 0.0564 0.6417 0.3019 63 D 0.0616 0.6050 0.3334 64 K 0.0538 0.6157 0.3306 65 Q 0.0824 0.5885 0.3291 66 I 0.1382 0.4725 0.3894 67 N 0.1448 0.3801 0.4750 68 M 0.0836 0.5537 0.3627 69 A 0.0638 0.5608 0.3755 70 D 0.0720 0.5096 0.4184 71 R 0.0685 0.4785 0.4530 72 S 0.0957 0.3909 0.5134 73 L 0.1103 0.2982 0.5915 74 G 0.1357 0.1666 0.6977 75 L 0.2652 0.1738 0.5610 76 Q 0.4167 0.1638 0.4195 77 Q 0.5907 0.1116 0.2978 78 V 0.7808 0.0619 0.1573 79 V 0.8210 0.0537 0.1253 80 C 0.8439 0.0448 0.1113 81 I 0.7699 0.0851 0.1449 82 F 0.6521 0.0970 0.2509 83 S 0.3841 0.1230 0.4928 84 Y 0.1556 0.1214 0.7229 85 G 0.0655 0.1896 0.7449 86 P 0.0327 0.4981 0.4692 87 H 0.0351 0.6347 0.3303 88 I 0.0216 0.8234 0.1549 89 Q 0.0193 0.8621 0.1186 90 K 0.0230 0.8591 0.1180 91 M 0.0252 0.8821 0.0927 92 L 0.0274 0.8782 0.0944 93 S 0.0288 0.8755 0.0957 94 I 0.0199 0.9053 0.0748 95 L 0.0283 0.8999 0.0718 96 E 0.0353 0.8751 0.0895 97 I 0.0413 0.8276 0.1311 98 F 0.0612 0.7552 0.1836 99 K 0.0613 0.6819 0.2568 100 K 0.0521 0.4949 0.4530 101 G 0.0772 0.2497 0.6731 102 Y 0.2056 0.2137 0.5807 103 I 0.2988 0.1960 0.5052 104 K 0.1929 0.2108 0.5963 105 N 0.1322 0.1841 0.6837 106 N 0.1223 0.1759 0.7017 107 K 0.2176 0.2146 0.5678 108 K 0.3899 0.2015 0.4086 109 I 0.4793 0.2180 0.3027 110 Y 0.4897 0.2150 0.2954 111 Q 0.4777 0.2143 0.3080 112 W 0.3498 0.2886 0.3617 113 N 0.2966 0.2651 0.4383 114 K 0.3100 0.2586 0.4314 115 L 0.3437 0.2019 0.4544 116 T 0.3537 0.1726 0.4737 117 S 0.3689 0.1956 0.4355 118 F 0.4008 0.1958 0.4035 119 D 0.4054 0.1787 0.4159 120 I 0.3444 0.2559 0.3996 121 K 0.2447 0.2838 0.4716 122 R 0.1488 0.3711 0.4801 123 E 0.0759 0.3759 0.5482 124 G 0.0703 0.2739 0.6558 125 R 0.0709 0.3535 0.5756 126 N 0.0813 0.4490 0.4697 127 E 0.0686 0.5668 0.3646 128 L 0.0731 0.5873 0.3396 129 Q 0.0633 0.6041 0.3326 130 E 0.0563 0.6449 0.2988 131 E 0.0592 0.5902 0.3506 132 R 0.1027 0.4727 0.4247 133 L 0.1669 0.3066 0.5265 134 K 0.1986 0.2278 0.5736 135 V 0.2633 0.1216 0.6151 136 P 0.3698 0.0853 0.5449 137 I 0.7265 0.0694 0.2040 138 L 0.8355 0.0465 0.1180 139 V 0.8489 0.0364 0.1147 140 T 0.8367 0.0308 0.1325 141 L 0.7908 0.0314 0.1778 142 V 0.5840 0.0515 0.3645 143 S 0.3484 0.0558 0.5958 144 D 0.1531 0.1642 0.6826 145 S 0.1251 0.2653 0.6095 146 E 0.2351 0.2960 0.4689 147 I 0.4375 0.2399 0.3225 148 I 0.4967 0.2182 0.2850 149 D 0.5063 0.2031 0.2907 150 L 0.3479 0.2902 0.3619 151 N 0.3143 0.2479 0.4378 152 L 0.2245 0.3547 0.4208 153 H 0.1875 0.3463 0.4662 154 S 0.1969 0.3447 0.4584 155 F 0.1865 0.2927 0.5208 156 T 0.1708 0.2063 0.6229 157 K 0.0998 0.1349 0.7653 158 Q 0.0426 0.0407 0.9167