# This file is the result of combining several RDB files, specifically # T0289.t04.dssp-ebghstl.rdb (weight 1.53986) # T0289.t04.stride-ebghtl.rdb (weight 1.24869) # T0289.t04.str2.rdb (weight 1.54758) # T0289.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 T0289.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 925 # # ============================================ # Comments from T0289.t04.stride-ebghtl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 925 # # ============================================ # Comments from T0289.t04.str2.rdb # ============================================ # TARGET T0289 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0289.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 925 # # ============================================ # Comments from T0289.t04.alpha.rdb # ============================================ # TARGET T0289 # 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 T0289.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 925 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1220 0.0320 0.8459 2 T 0.3595 0.0212 0.6192 3 S 0.6355 0.0190 0.3454 4 C 0.6869 0.0235 0.2896 5 V 0.5752 0.0308 0.3940 6 A 0.2870 0.0577 0.6553 7 E 0.1067 0.0609 0.8325 8 E 0.0856 0.0494 0.8650 9 P 0.1053 0.0648 0.8299 10 I 0.1889 0.0180 0.7932 11 K 0.3081 0.0105 0.6814 12 K 0.8000 0.0050 0.1950 13 I 0.9275 0.0033 0.0691 14 A 0.9332 0.0032 0.0635 15 I 0.9291 0.0033 0.0675 16 F 0.8872 0.0053 0.1074 17 G 0.6347 0.0195 0.3458 18 G 0.3171 0.0308 0.6521 19 T 0.3083 0.0493 0.6424 20 H 0.1918 0.0617 0.7466 21 G 0.0507 0.2231 0.7262 22 N 0.0463 0.2341 0.7196 23 E 0.0650 0.4766 0.4584 24 L 0.0532 0.6880 0.2587 25 T 0.0259 0.7787 0.1955 26 G 0.0060 0.9428 0.0512 27 V 0.0047 0.9594 0.0359 28 F 0.0046 0.9613 0.0341 29 L 0.0046 0.9614 0.0340 30 V 0.0046 0.9613 0.0341 31 T 0.0046 0.9614 0.0339 32 H 0.0046 0.9607 0.0347 33 W 0.0047 0.9579 0.0374 34 L 0.0048 0.9512 0.0441 35 K 0.0054 0.8978 0.0969 36 N 0.0204 0.7044 0.2752 37 G 0.0203 0.4602 0.5195 38 A 0.0322 0.4179 0.5499 39 E 0.0365 0.5715 0.3920 40 V 0.0739 0.4996 0.4265 41 H 0.0938 0.4162 0.4900 42 R 0.1123 0.3041 0.5836 43 A 0.0494 0.1911 0.7595 44 G 0.0820 0.0556 0.8624 45 L 0.3735 0.0100 0.6165 46 E 0.8498 0.0041 0.1461 47 V 0.9265 0.0033 0.0702 48 K 0.9245 0.0038 0.0717 49 P 0.9274 0.0031 0.0695 50 F 0.8683 0.0173 0.1144 51 I 0.7873 0.0064 0.2062 52 T 0.3978 0.0170 0.5852 53 N 0.1995 0.0185 0.7820 54 P 0.0433 0.5445 0.4122 55 R 0.0215 0.7116 0.2669 56 A 0.0345 0.8250 0.1404 57 V 0.0767 0.8019 0.1213 58 E 0.0851 0.7615 0.1534 59 K 0.1021 0.6072 0.2907 60 C 0.1565 0.3429 0.5006 61 T 0.1618 0.1836 0.6546 62 R 0.1890 0.1503 0.6607 63 Y 0.2232 0.1278 0.6491 64 I 0.1552 0.1195 0.7254 65 D 0.1373 0.0718 0.7909 66 C 0.2147 0.0854 0.7000 67 D 0.3305 0.0839 0.5856 68 L 0.1374 0.3446 0.5180 69 N 0.1433 0.3634 0.4933 70 R 0.1867 0.3686 0.4448 71 V 0.1953 0.1732 0.6315 72 F 0.1718 0.0613 0.7669 73 D 0.1187 0.0557 0.8257 74 L 0.0493 0.4875 0.4632 75 E 0.0228 0.6054 0.3718 76 N 0.0449 0.6139 0.3412 77 L 0.0547 0.5012 0.4441 78 S 0.0625 0.3841 0.5534 79 K 0.0997 0.3107 0.5897 80 E 0.1170 0.1729 0.7102 81 M 0.1081 0.1622 0.7298 82 S 0.0882 0.1287 0.7831 83 E 0.0546 0.1514 0.7940 84 D 0.0736 0.0912 0.8352 85 L 0.0649 0.2253 0.7097 86 P 0.0437 0.4210 0.5353 87 Y 0.0245 0.7102 0.2654 88 E 0.0173 0.8224 0.1603 89 V 0.0160 0.9023 0.0817 90 R 0.0143 0.9217 0.0640 91 R 0.0156 0.9168 0.0676 92 A 0.0091 0.9367 0.0542 93 Q 0.0094 0.9387 0.0519 94 E 0.0103 0.9333 0.0564 95 I 0.0124 0.9160 0.0716 96 N 0.0146 0.8833 0.1021 97 H 0.0228 0.8181 0.1591 98 L 0.0349 0.6848 0.2802 99 F 0.0793 0.3736 0.5470 100 G 0.0605 0.0923 0.8472 101 P 0.0634 0.1633 0.7734 102 K 0.0661 0.2481 0.6858 103 N 0.0725 0.2272 0.7002 104 S 0.0634 0.2123 0.7243 105 D 0.0496 0.1998 0.7505 106 D 0.0715 0.1070 0.8215 107 A 0.1932 0.0367 0.7701 108 Y 0.5034 0.0081 0.4884 109 D 0.7204 0.0109 0.2687 110 V 0.9259 0.0033 0.0707 111 V 0.9327 0.0032 0.0641 112 F 0.9275 0.0039 0.0686 113 D 0.8875 0.0037 0.1088 114 L 0.5419 0.0328 0.4253 115 H 0.2582 0.0573 0.6845 116 N 0.1464 0.0960 0.7576 117 T 0.1043 0.1327 0.7630 118 T 0.1010 0.1826 0.7164 119 S 0.0610 0.2962 0.6428 120 N 0.0869 0.2922 0.6209 121 M 0.1384 0.2112 0.6504 122 G 0.1571 0.0947 0.7482 123 C 0.2559 0.0639 0.6801 124 T 0.4283 0.0931 0.4787 125 L 0.5496 0.1122 0.3382 126 I 0.5693 0.1152 0.3155 127 L 0.4861 0.1327 0.3811 128 E 0.3394 0.1163 0.5443 129 D 0.1398 0.1428 0.7174 130 S 0.0725 0.1830 0.7445 131 R 0.0578 0.1597 0.7826 132 N 0.0698 0.1582 0.7720 133 D 0.0117 0.6979 0.2904 134 F 0.0109 0.8076 0.1815 135 L 0.0074 0.9135 0.0791 136 I 0.0059 0.9391 0.0550 137 Q 0.0060 0.9417 0.0523 138 M 0.0054 0.9412 0.0533 139 F 0.0053 0.9280 0.0666 140 H 0.0049 0.9291 0.0660 141 Y 0.0050 0.9195 0.0755 142 I 0.0095 0.8918 0.0987 143 K 0.0101 0.8789 0.1110 144 T 0.0174 0.8339 0.1487 145 C 0.0346 0.7017 0.2636 146 M 0.0621 0.4235 0.5144 147 A 0.0601 0.1700 0.7699 148 P 0.0555 0.0791 0.8654 149 L 0.1029 0.0279 0.8692 150 P 0.1631 0.0454 0.7915 151 C 0.3695 0.0659 0.5647 152 S 0.5041 0.0637 0.4322 153 V 0.5551 0.0903 0.3545 154 Y 0.5673 0.0803 0.3524 155 L 0.4543 0.0926 0.4531 156 I 0.2843 0.1089 0.6068 157 E 0.1517 0.0889 0.7594 158 H 0.1013 0.0655 0.8332 159 P 0.0484 0.1872 0.7644 160 S 0.0794 0.2329 0.6877 161 L 0.0890 0.4680 0.4430 162 K 0.0673 0.5561 0.3766 163 Y 0.0760 0.6456 0.2785 164 A 0.0730 0.7204 0.2067 165 T 0.0809 0.7238 0.1953 166 T 0.0700 0.7457 0.1843 167 R 0.0550 0.7367 0.2082 168 S 0.0571 0.6325 0.3104 169 I 0.0688 0.3951 0.5361 170 A 0.1124 0.1634 0.7242 171 K 0.1438 0.0800 0.7761 172 Y 0.2005 0.0248 0.7747 173 P 0.4789 0.0306 0.4905 174 V 0.8388 0.0180 0.1433 175 G 0.9008 0.0113 0.0878 176 I 0.9048 0.0110 0.0843 177 E 0.8642 0.0110 0.1248 178 V 0.5202 0.0275 0.4523 179 G 0.2204 0.0174 0.7623 180 P 0.1214 0.0476 0.8310 181 Q 0.0903 0.0260 0.8837 182 P 0.0677 0.0649 0.8674 183 H 0.0547 0.1267 0.8187 184 G 0.0482 0.1395 0.8123 185 V 0.1094 0.2656 0.6250 186 L 0.1487 0.2154 0.6358 187 R 0.0572 0.4204 0.5224 188 A 0.0069 0.9217 0.0714 189 D 0.0061 0.9307 0.0632 190 I 0.0048 0.9504 0.0448 191 L 0.0047 0.9582 0.0371 192 D 0.0047 0.9597 0.0356 193 Q 0.0047 0.9583 0.0370 194 M 0.0047 0.9593 0.0361 195 R 0.0047 0.9595 0.0358 196 R 0.0047 0.9483 0.0470 197 M 0.0051 0.9246 0.0703 198 L 0.0073 0.8296 0.1631 199 K 0.0148 0.5450 0.4401 200 H 0.0263 0.2128 0.7609