# This file is the result of combining several RDB files, specifically # T0399.t06.str2.rdb (weight 1.54425) # T0399.t06.str4.rdb (weight 0.924988) # T0399.t06.pb.rdb (weight 0.789901) # T0399.t06.bys.rdb (weight 0.748322) # T0399.t06.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.t06.str2.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t06-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.t06-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 144 # # ============================================ # Comments from T0399.t06.str4.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t06-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.t06-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 144 # # ============================================ # Comments from T0399.t06.pb.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t06-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.t06-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 144 # # ============================================ # Comments from T0399.t06.bys.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t06-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.t06-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 144 # # ============================================ # Comments from T0399.t06.alpha.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t06-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.t06-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 144 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1594 0.4404 0.4001 2 S 0.1146 0.5309 0.3545 3 M 0.0793 0.6302 0.2905 4 K 0.0557 0.7104 0.2339 5 K 0.0443 0.6949 0.2609 6 T 0.0501 0.7216 0.2284 7 K 0.0379 0.7971 0.1649 8 N 0.0207 0.8598 0.1195 9 W 0.0164 0.8956 0.0880 10 L 0.0128 0.9130 0.0742 11 L 0.0118 0.9180 0.0702 12 V 0.0099 0.9209 0.0693 13 F 0.0085 0.9235 0.0680 14 L 0.0083 0.9243 0.0674 15 T 0.0083 0.9247 0.0670 16 V 0.0083 0.9248 0.0670 17 T 0.0083 0.9247 0.0670 18 F 0.0083 0.9242 0.0675 19 C 0.0083 0.9226 0.0691 20 F 0.0084 0.9181 0.0735 21 L 0.0094 0.9024 0.0882 22 M 0.0137 0.8422 0.1442 23 L 0.0320 0.6849 0.2831 24 G 0.0771 0.4468 0.4761 25 C 0.1546 0.2887 0.5567 26 Q 0.1939 0.1869 0.6192 27 S 0.1553 0.1816 0.6631 28 K 0.1037 0.2495 0.6468 29 E 0.0933 0.3047 0.6021 30 D 0.1315 0.2727 0.5958 31 K 0.1534 0.2849 0.5617 32 K 0.1938 0.2345 0.5717 33 G 0.1737 0.1480 0.6783 34 G 0.1906 0.1040 0.7054 35 T 0.2803 0.0730 0.6467 36 K 0.2808 0.0445 0.6747 37 P 0.1935 0.1649 0.6415 38 S 0.1345 0.2285 0.6370 39 N 0.1182 0.2467 0.6351 40 E 0.1427 0.3403 0.5170 41 A 0.1353 0.4859 0.3789 42 A 0.1073 0.5849 0.3079 43 L 0.1205 0.5637 0.3158 44 T 0.1439 0.5053 0.3508 45 K 0.1430 0.4625 0.3945 46 T 0.1760 0.3748 0.4491 47 E 0.0948 0.4308 0.4745 48 N 0.1020 0.3291 0.5689 49 L 0.1168 0.4582 0.4250 50 D 0.1669 0.4027 0.4303 51 F 0.2475 0.3297 0.4228 52 R 0.3311 0.2541 0.4149 53 L 0.4208 0.1442 0.4349 54 S 0.3475 0.1395 0.5130 55 F 0.2053 0.3996 0.3951 56 N 0.1296 0.4752 0.3952 57 K 0.1763 0.4258 0.3979 58 I 0.3079 0.2476 0.4446 59 K 0.3084 0.1923 0.4992 60 V 0.2895 0.2279 0.4826 61 T 0.2066 0.2657 0.5277 62 T 0.1756 0.3517 0.4728 63 D 0.1520 0.3359 0.5121 64 Q 0.1301 0.3605 0.5095 65 N 0.1039 0.2723 0.6238 66 H 0.1570 0.1969 0.6462 67 F 0.2606 0.0760 0.6634 68 S 0.2119 0.0923 0.6958 69 G 0.1870 0.1213 0.6917 70 G 0.1685 0.0926 0.7389 71 T 0.2261 0.0693 0.7046 72 S 0.1954 0.0526 0.7520 73 I 0.0124 0.7491 0.2386 74 E 0.0092 0.8687 0.1221 75 Q 0.0084 0.9206 0.0710 76 L 0.0086 0.9208 0.0706 77 K 0.0085 0.9100 0.0815 78 Q 0.0092 0.8924 0.0983 79 W 0.0176 0.7533 0.2291 80 F 0.0609 0.2623 0.6768 81 G 0.0491 0.1097 0.8412 82 D 0.1608 0.0387 0.8005 83 P 0.1523 0.1643 0.6834 84 N 0.1546 0.1691 0.6763 85 K 0.2268 0.1640 0.6092 86 S 0.3321 0.1704 0.4976 87 E 0.3967 0.1755 0.4278 88 Q 0.3973 0.1745 0.4283 89 R 0.3628 0.1704 0.4667 90 N 0.3049 0.1725 0.5225 91 A 0.1594 0.1491 0.6915 92 G 0.1243 0.0898 0.7859 93 N 0.3687 0.0434 0.5879 94 I 0.6304 0.0230 0.3466 95 T 0.7224 0.0191 0.2585 96 L 0.7347 0.0240 0.2413 97 D 0.7062 0.0406 0.2532 98 S 0.7250 0.0349 0.2401 99 Y 0.6603 0.0604 0.2793 100 T 0.6819 0.0443 0.2739 101 W 0.6405 0.0456 0.3139 102 V 0.4710 0.0826 0.4463 103 K 0.1907 0.1869 0.6225 104 D 0.1111 0.1189 0.7699 105 G 0.1867 0.0631 0.7503 106 A 0.5816 0.0223 0.3961 107 V 0.7535 0.0072 0.2393 108 I 0.8123 0.0058 0.1819 109 N 0.8202 0.0047 0.1751 110 A 0.8216 0.0049 0.1735 111 Q 0.8055 0.0062 0.1883 112 L 0.7458 0.0143 0.2400 113 Y 0.4902 0.0407 0.4691 114 K 0.1707 0.2326 0.5967 115 N 0.1150 0.1675 0.7175 116 S 0.1986 0.1466 0.6548 117 T 0.3985 0.1563 0.4452 118 V 0.5024 0.1658 0.3318 119 A 0.4849 0.1983 0.3168 120 R 0.5270 0.2036 0.2695 121 S 0.5159 0.2013 0.2828 122 I 0.5008 0.1855 0.3138 123 S 0.4030 0.2029 0.3941 124 N 0.3260 0.1823 0.4918 125 F 0.3471 0.1642 0.4886 126 S 0.3690 0.1936 0.4373 127 F 0.3479 0.2367 0.4154 128 S 0.2320 0.2870 0.4811 129 R 0.1736 0.2493 0.5771 130 E 0.1862 0.2421 0.5716 131 A 0.2110 0.2013 0.5878 132 K 0.2484 0.1324 0.6191 133 I 0.3169 0.0521 0.6311 134 G 0.1946 0.0269 0.7785 135 K 0.0366 0.6342 0.3292 136 E 0.0279 0.6962 0.2759 137 D 0.0518 0.6388 0.3094 138 Y 0.0669 0.6489 0.2842 139 D 0.0408 0.6411 0.3181 140 E 0.0650 0.5024 0.4326 141 L 0.1949 0.3077 0.4974 142 K 0.1897 0.2173 0.5929 143 I 0.1451 0.1708 0.6841 144 G 0.0879 0.1113 0.8009 145 E 0.1610 0.1257 0.7133 146 S 0.1815 0.0962 0.7224 147 Y 0.0152 0.7438 0.2410 148 K 0.0095 0.8683 0.1222 149 K 0.0087 0.9194 0.0719 150 V 0.0095 0.9191 0.0713 151 V 0.0088 0.9145 0.0767 152 E 0.0104 0.8964 0.0931 153 K 0.0193 0.7685 0.2122 154 L 0.0632 0.2897 0.6471 155 G 0.0491 0.0972 0.8538 156 E 0.1682 0.0393 0.7925 157 P 0.1794 0.0932 0.7274 158 D 0.1993 0.1816 0.6191 159 V 0.3859 0.1937 0.4204 160 L 0.4674 0.1611 0.3714 161 S 0.4872 0.1508 0.3620 162 Q 0.4465 0.1615 0.3920 163 S 0.3596 0.1480 0.4924 164 M 0.2549 0.1780 0.5671 165 S 0.1995 0.1542 0.6463 166 S 0.1423 0.1684 0.6893 167 D 0.1465 0.1349 0.7186 168 K 0.2948 0.1572 0.5481 169 E 0.4814 0.1356 0.3830 170 E 0.6058 0.0889 0.3053 171 M 0.6789 0.0654 0.2557 172 Q 0.7229 0.0470 0.2301 173 T 0.7743 0.0245 0.2012 174 V 0.7523 0.0326 0.2152 175 W 0.6853 0.0519 0.2628 176 S 0.5517 0.1212 0.3271 177 S 0.3254 0.1396 0.5350 178 G 0.2156 0.1146 0.6698 179 I 0.2549 0.1221 0.6230 180 K 0.2437 0.1213 0.6349 181 T 0.2359 0.1098 0.6544 182 K 0.2305 0.1161 0.6535 183 S 0.2735 0.1007 0.6258 184 S 0.2668 0.1338 0.5994 185 S 0.3498 0.0908 0.5594 186 A 0.6013 0.0502 0.3485 187 T 0.7625 0.0118 0.2256 188 I 0.8181 0.0050 0.1769 189 E 0.8206 0.0045 0.1748 190 L 0.8207 0.0046 0.1747 191 Y 0.8142 0.0055 0.1803 192 F 0.7193 0.0128 0.2679 193 E 0.4940 0.1302 0.3758 194 N 0.1539 0.0937 0.7524 195 G 0.1303 0.0564 0.8133 196 L 0.5148 0.0212 0.4640 197 L 0.6611 0.0163 0.3226 198 K 0.6321 0.0378 0.3302 199 N 0.6135 0.0422 0.3443 200 K 0.5404 0.0940 0.3656 201 T 0.4513 0.0979 0.4508 202 Q 0.2804 0.2395 0.4801 203 K 0.1722 0.3086 0.5191 204 D 0.1360 0.2351 0.6290 205 L 0.1682 0.2117 0.6200 206 E 0.1558 0.2188 0.6254