# This file is the result of combining several RDB files, specifically # T0399.t04.str2.rdb (weight 1.54425) # T0399.t04.str4.rdb (weight 0.924988) # T0399.t04.pb.rdb (weight 0.789901) # T0399.t04.bys.rdb (weight 0.748322) # T0399.t04.alpha.rdb (weight 0.678173) # 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 T0399.t04.str2.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t04-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 T0399.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 132 # # ============================================ # Comments from T0399.t04.str4.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0399.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 132 # # ============================================ # Comments from T0399.t04.pb.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0399.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 132 # # ============================================ # Comments from T0399.t04.bys.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0399.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 132 # # ============================================ # Comments from T0399.t04.alpha.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t04-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 T0399.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 132 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1494 0.3368 0.5138 2 S 0.1078 0.3691 0.5231 3 M 0.0337 0.6947 0.2716 4 K 0.0334 0.7271 0.2396 5 K 0.0533 0.6809 0.2658 6 T 0.0645 0.6318 0.3037 7 K 0.0409 0.7357 0.2234 8 N 0.0303 0.8043 0.1654 9 W 0.0365 0.8443 0.1191 10 L 0.0380 0.8694 0.0925 11 L 0.0442 0.8779 0.0780 12 V 0.0408 0.8880 0.0712 13 F 0.0198 0.9085 0.0717 14 L 0.0204 0.9092 0.0704 15 T 0.0133 0.9179 0.0688 16 V 0.0096 0.9234 0.0670 17 T 0.0112 0.9222 0.0666 18 F 0.0092 0.9234 0.0673 19 C 0.0093 0.9229 0.0678 20 F 0.0132 0.9172 0.0696 21 L 0.0128 0.9116 0.0756 22 M 0.0175 0.8806 0.1019 23 L 0.0324 0.8077 0.1599 24 G 0.0668 0.6587 0.2745 25 C 0.1043 0.5245 0.3712 26 Q 0.1284 0.3841 0.4875 27 S 0.1373 0.3140 0.5487 28 K 0.1066 0.3433 0.5501 29 E 0.1081 0.3263 0.5656 30 D 0.1348 0.2781 0.5870 31 K 0.1152 0.3550 0.5298 32 K 0.1403 0.2635 0.5962 33 G 0.1559 0.1508 0.6934 34 G 0.1843 0.0925 0.7231 35 T 0.2452 0.0787 0.6761 36 K 0.2521 0.0509 0.6969 37 P 0.1612 0.2146 0.6242 38 S 0.1051 0.3591 0.5358 39 N 0.0788 0.4877 0.4335 40 E 0.0894 0.6110 0.2996 41 A 0.0633 0.7453 0.1914 42 A 0.0560 0.7598 0.1843 43 L 0.0715 0.7029 0.2256 44 T 0.1010 0.5954 0.3036 45 K 0.1249 0.4775 0.3976 46 T 0.1382 0.4043 0.4576 47 E 0.0871 0.4561 0.4568 48 N 0.1102 0.3375 0.5523 49 L 0.1113 0.4573 0.4314 50 D 0.1870 0.3900 0.4230 51 F 0.3338 0.2966 0.3696 52 R 0.4130 0.2537 0.3333 53 L 0.5302 0.1835 0.2863 54 S 0.4382 0.1780 0.3838 55 F 0.2768 0.3237 0.3994 56 N 0.1663 0.3757 0.4579 57 K 0.2274 0.3109 0.4618 58 I 0.4184 0.1383 0.4434 59 K 0.4117 0.1007 0.4875 60 V 0.3698 0.1301 0.5002 61 T 0.2178 0.1455 0.6367 62 T 0.1711 0.2722 0.5567 63 D 0.1599 0.2752 0.5648 64 Q 0.1296 0.3483 0.5221 65 N 0.1297 0.2495 0.6208 66 H 0.2002 0.1620 0.6377 67 F 0.2822 0.0794 0.6384 68 S 0.2492 0.0948 0.6559 69 G 0.1644 0.1690 0.6666 70 G 0.1352 0.1205 0.7443 71 T 0.1940 0.0641 0.7419 72 S 0.1840 0.0370 0.7790 73 I 0.0149 0.7360 0.2491 74 E 0.0095 0.8642 0.1263 75 Q 0.0086 0.9144 0.0770 76 L 0.0085 0.9163 0.0752 77 K 0.0085 0.9113 0.0802 78 Q 0.0098 0.8798 0.1104 79 W 0.0169 0.7775 0.2056 80 F 0.0628 0.3068 0.6304 81 G 0.0521 0.1239 0.8240 82 D 0.1604 0.0362 0.8033 83 P 0.1417 0.1816 0.6767 84 N 0.1491 0.1937 0.6572 85 K 0.2381 0.1849 0.5770 86 S 0.3054 0.2091 0.4854 87 E 0.3335 0.2528 0.4136 88 Q 0.3402 0.2622 0.3975 89 R 0.2869 0.2366 0.4765 90 N 0.2137 0.2154 0.5708 91 A 0.1442 0.1546 0.7012 92 G 0.1123 0.1001 0.7877 93 N 0.2900 0.0553 0.6547 94 I 0.5738 0.0244 0.4018 95 T 0.6834 0.0206 0.2960 96 L 0.7290 0.0217 0.2493 97 D 0.6714 0.0419 0.2866 98 S 0.6600 0.0394 0.3006 99 Y 0.5794 0.0655 0.3550 100 T 0.5837 0.0618 0.3544 101 W 0.5009 0.0510 0.4482 102 V 0.3320 0.0707 0.5974 103 K 0.1825 0.1707 0.6468 104 D 0.1206 0.1113 0.7681 105 G 0.1785 0.0607 0.7609 106 A 0.5565 0.0174 0.4261 107 V 0.7499 0.0071 0.2430 108 I 0.8027 0.0061 0.1911 109 N 0.8206 0.0044 0.1750 110 A 0.8162 0.0052 0.1787 111 Q 0.8030 0.0052 0.1918 112 L 0.7376 0.0179 0.2445 113 Y 0.4704 0.0406 0.4891 114 K 0.1791 0.2278 0.5931 115 N 0.1086 0.1756 0.7158 116 S 0.1721 0.1964 0.6315 117 T 0.3219 0.2259 0.4521 118 V 0.3821 0.2769 0.3410 119 A 0.3433 0.3431 0.3136 120 R 0.3041 0.3984 0.2975 121 S 0.3109 0.3729 0.3163 122 I 0.3031 0.3131 0.3838 123 S 0.2467 0.2732 0.4801 124 N 0.2262 0.2420 0.5319 125 F 0.2803 0.2059 0.5139 126 S 0.3024 0.2299 0.4677 127 F 0.3311 0.2359 0.4330 128 S 0.2598 0.2384 0.5018 129 R 0.1610 0.3322 0.5068 130 E 0.1431 0.3311 0.5258 131 A 0.2196 0.2487 0.5317 132 K 0.2469 0.1796 0.5736 133 I 0.3187 0.1123 0.5690 134 G 0.1854 0.0564 0.7582 135 K 0.0337 0.6581 0.3083 136 E 0.0238 0.7589 0.2173 137 D 0.0495 0.6506 0.2998 138 Y 0.0487 0.6808 0.2705 139 D 0.0505 0.6474 0.3021 140 E 0.1311 0.4869 0.3820 141 L 0.2500 0.2988 0.4512 142 K 0.2616 0.2190 0.5194 143 I 0.1676 0.2262 0.6062 144 G 0.0879 0.1552 0.7570 145 E 0.1633 0.1568 0.6799 146 S 0.1870 0.1792 0.6338 147 Y 0.0204 0.7194 0.2602 148 K 0.0103 0.8557 0.1339 149 K 0.0107 0.9096 0.0797 150 V 0.0101 0.9178 0.0721 151 V 0.0100 0.9111 0.0788 152 E 0.0125 0.8838 0.1037 153 K 0.0207 0.7733 0.2060 154 L 0.0690 0.3282 0.6029 155 G 0.0637 0.1244 0.8119 156 E 0.1648 0.0404 0.7948 157 P 0.1949 0.1134 0.6917 158 D 0.2468 0.1867 0.5665 159 V 0.3961 0.1942 0.4096 160 L 0.4437 0.1901 0.3662 161 S 0.4546 0.1861 0.3594 162 Q 0.4291 0.1992 0.3717 163 S 0.3892 0.1411 0.4696 164 M 0.2823 0.1583 0.5595 165 S 0.2005 0.1509 0.6486 166 S 0.1430 0.1856 0.6713 167 D 0.1261 0.1395 0.7343 168 K 0.2475 0.1275 0.6250 169 E 0.4448 0.1088 0.4464 170 E 0.6217 0.0671 0.3111 171 M 0.6940 0.0483 0.2577 172 Q 0.7296 0.0475 0.2229 173 T 0.7693 0.0272 0.2036 174 V 0.7656 0.0271 0.2073 175 W 0.6663 0.0453 0.2884 176 S 0.4774 0.1436 0.3790 177 S 0.1865 0.1457 0.6678 178 G 0.1113 0.0980 0.7908 179 I 0.2621 0.0788 0.6591 180 K 0.3321 0.0950 0.5729 181 T 0.2884 0.0835 0.6281 182 K 0.2226 0.1252 0.6522 183 S 0.2331 0.1101 0.6569 184 S 0.2471 0.1160 0.6369 185 S 0.3393 0.0571 0.6036 186 A 0.6061 0.0208 0.3731 187 T 0.7690 0.0086 0.2224 188 I 0.8216 0.0047 0.1737 189 E 0.8288 0.0043 0.1669 190 L 0.8223 0.0045 0.1732 191 Y 0.8141 0.0059 0.1800 192 F 0.7286 0.0093 0.2622 193 E 0.4583 0.0729 0.4687 194 N 0.1748 0.0706 0.7546 195 G 0.1191 0.0721 0.8088 196 L 0.4792 0.0243 0.4965 197 L 0.6764 0.0188 0.3048 198 K 0.6508 0.0359 0.3133 199 N 0.6803 0.0381 0.2816 200 K 0.5974 0.0748 0.3278 201 T 0.5118 0.1040 0.3842 202 Q 0.3582 0.1797 0.4621 203 K 0.2265 0.1887 0.5848 204 D 0.1805 0.1415 0.6780 205 L 0.1980 0.1554 0.6467 206 E 0.1758 0.1718 0.6523