# This file is the result of combining several RDB files, specifically # T0493.t2k.str2.rdb (weight 1.54425) # T0493.t2k.str4.rdb (weight 0.924988) # T0493.t2k.pb.rdb (weight 0.789901) # T0493.t2k.bys.rdb (weight 0.748322) # T0493.t2k.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 T0493.t2k.str2.rdb # ============================================ # TARGET T0493 # Using neural net dunbrack-40pc-3157-t2k-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 T0493.t2k-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 528 # # ============================================ # Comments from T0493.t2k.str4.rdb # ============================================ # TARGET T0493 # Using neural net dunbrack-40pc-3157-t2k-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 T0493.t2k-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 528 # # ============================================ # Comments from T0493.t2k.pb.rdb # ============================================ # TARGET T0493 # Using neural net dunbrack-40pc-3157-t2k-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 T0493.t2k-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 528 # # ============================================ # Comments from T0493.t2k.bys.rdb # ============================================ # TARGET T0493 # Using neural net dunbrack-40pc-3157-t2k-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 T0493.t2k-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 528 # # ============================================ # Comments from T0493.t2k.alpha.rdb # ============================================ # TARGET T0493 # Using neural net dunbrack-40pc-3157-t2k-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 T0493.t2k-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 528 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.3061 0.1437 0.5501 2 N 0.2774 0.1238 0.5989 3 A 0.2828 0.1758 0.5414 4 S 0.2958 0.1431 0.5611 5 Y 0.2939 0.2007 0.5054 6 R 0.2629 0.2090 0.5281 7 S 0.1816 0.1691 0.6493 8 T 0.0301 0.6537 0.3162 9 Q 0.0120 0.8248 0.1632 10 Q 0.0095 0.9074 0.0831 11 I 0.0085 0.9176 0.0739 12 T 0.0084 0.9189 0.0728 13 D 0.0083 0.9233 0.0684 14 F 0.0083 0.9220 0.0697 15 T 0.0085 0.9135 0.0780 16 K 0.0087 0.9124 0.0789 17 E 0.0094 0.9017 0.0889 18 I 0.0189 0.8436 0.1375 19 L 0.0394 0.7464 0.2142 20 V 0.0499 0.6011 0.3489 21 N 0.0650 0.2182 0.7169 22 G 0.0503 0.1537 0.7960 23 E 0.1649 0.1380 0.6971 24 A 0.2515 0.1331 0.6155 25 V 0.3240 0.1642 0.5117 26 T 0.3613 0.1501 0.4886 27 A 0.3305 0.2481 0.4214 28 F 0.3256 0.2314 0.4430 29 D 0.2580 0.2128 0.5293 30 R 0.1483 0.3248 0.5270 31 Q 0.1256 0.1805 0.6939 32 G 0.1169 0.0982 0.7849 33 D 0.2249 0.0697 0.7054 34 L 0.3046 0.0346 0.6609 35 P 0.3135 0.0618 0.6247 36 N 0.5660 0.0469 0.3871 37 V 0.6886 0.0290 0.2825 38 V 0.6905 0.0225 0.2870 39 V 0.6169 0.0221 0.3610 40 T 0.2718 0.0194 0.7088 41 P 0.1236 0.2081 0.6683 42 N 0.1319 0.1642 0.7039 43 F 0.0228 0.6557 0.3215 44 E 0.0129 0.8165 0.1706 45 A 0.0110 0.8747 0.1143 46 G 0.0098 0.8913 0.0989 47 V 0.0088 0.9105 0.0807 48 D 0.0084 0.9209 0.0706 49 Q 0.0083 0.9235 0.0681 50 V 0.0083 0.9211 0.0705 51 V 0.0083 0.9211 0.0705 52 D 0.0083 0.9221 0.0696 53 Q 0.0086 0.9153 0.0762 54 L 0.0094 0.9038 0.0868 55 A 0.0118 0.8591 0.1292 56 M 0.0245 0.7402 0.2353 57 N 0.0696 0.4941 0.4363 58 D 0.0602 0.4858 0.4540 59 S 0.0462 0.4626 0.4912 60 E 0.0737 0.3361 0.5902 61 R 0.1119 0.2796 0.6085 62 D 0.1465 0.2787 0.5747 63 T 0.2406 0.2915 0.4679 64 T 0.4155 0.2696 0.3150 65 A 0.5242 0.2483 0.2275 66 I 0.5338 0.2488 0.2174 67 I 0.5043 0.2683 0.2274 68 G 0.3661 0.3385 0.2954 69 K 0.2126 0.4694 0.3180 70 S 0.1311 0.4879 0.3810 71 L 0.0413 0.7124 0.2463 72 A 0.0151 0.8312 0.1537 73 E 0.0127 0.8700 0.1173 74 C 0.0117 0.8965 0.0918 75 E 0.0086 0.9130 0.0784 76 A 0.0084 0.9174 0.0742 77 L 0.0084 0.9172 0.0744 78 T 0.0084 0.9193 0.0724 79 K 0.0083 0.9207 0.0709 80 A 0.0084 0.9200 0.0716 81 L 0.0085 0.9119 0.0795 82 K 0.0089 0.8907 0.1004 83 A 0.0131 0.7977 0.1893 84 R 0.0430 0.4741 0.4828 85 G 0.0534 0.2869 0.6598 86 E 0.1102 0.3800 0.5098 87 Q 0.1804 0.3894 0.4301 88 V 0.2654 0.4216 0.3130 89 T 0.3314 0.3855 0.2831 90 L 0.3519 0.3565 0.2916 91 I 0.3004 0.3259 0.3738 92 Q 0.2125 0.3158 0.4717 93 T 0.1227 0.3930 0.4843 94 E 0.0827 0.4413 0.4760 95 N 0.1029 0.3883 0.5089 96 Q 0.1539 0.3356 0.5105 97 R 0.1767 0.2976 0.5258 98 L 0.1878 0.2100 0.6023 99 A 0.2021 0.0905 0.7074 100 P 0.1447 0.1500 0.7054 101 G 0.2343 0.0811 0.6846 102 V 0.5027 0.0136 0.4837 103 I 0.7202 0.0126 0.2672 104 V 0.7593 0.0155 0.2252 105 V 0.6701 0.0220 0.3078 106 P 0.4677 0.1032 0.4291 107 S 0.2522 0.4459 0.3019 108 F 0.1483 0.5834 0.2683 109 L 0.1125 0.5771 0.3104 110 A 0.1375 0.4877 0.3748 111 K 0.0954 0.3003 0.6043 112 G 0.0930 0.1445 0.7624 113 L 0.2429 0.0889 0.6681 114 E 0.4056 0.0646 0.5298 115 F 0.4995 0.0316 0.4689 116 D 0.4738 0.0449 0.4813 117 A 0.7492 0.0151 0.2357 118 V 0.7737 0.0065 0.2199 119 I 0.8098 0.0048 0.1854 120 V 0.7691 0.0070 0.2238 121 W 0.6715 0.0205 0.3079 122 N 0.3446 0.0257 0.6296 123 A 0.1169 0.3675 0.5156 124 N 0.0954 0.3686 0.5360 125 Q 0.0933 0.4068 0.4999 126 E 0.0738 0.3494 0.5768 127 N 0.1059 0.2166 0.6775 128 Y 0.2018 0.0755 0.7228 129 Q 0.1789 0.0907 0.7304 130 R 0.1171 0.2641 0.6188 131 E 0.0305 0.6623 0.3072 132 D 0.0318 0.7509 0.2173 133 E 0.0473 0.7796 0.1731 134 R 0.0566 0.7742 0.1692 135 Q 0.1100 0.6964 0.1936 136 L 0.1836 0.6254 0.1910 137 L 0.2433 0.5844 0.1723 138 Y 0.3480 0.5100 0.1420 139 T 0.3560 0.5040 0.1400 140 I 0.3189 0.5146 0.1665 141 C 0.1832 0.6040 0.2128 142 S 0.1004 0.6569 0.2426 143 R 0.0395 0.7483 0.2123 144 A 0.0252 0.7540 0.2207 145 M 0.0461 0.6908 0.2631 146 H 0.0806 0.5814 0.3380 147 E 0.2546 0.3546 0.3908 148 L 0.5691 0.1213 0.3097 149 T 0.7088 0.0650 0.2262 150 L 0.7460 0.0413 0.2127 151 V 0.7289 0.0463 0.2248 152 A 0.6054 0.0640 0.3307 153 V 0.3276 0.1190 0.5534 154 G 0.1828 0.1039 0.7133 155 S 0.1924 0.1352 0.6724 156 L 0.1993 0.1412 0.6595 157 S 0.1500 0.1358 0.7141 158 P 0.0328 0.5894 0.3778 159 L 0.0361 0.6287 0.3352 160 L 0.0626 0.6728 0.2646 161 A 0.0803 0.5565 0.3632 162 R 0.1163 0.3462 0.5375 163 V 0.1703 0.2258 0.6039 164 N 0.1568 0.1902 0.6530 165 H 0.0291 0.6601 0.3109 166 A 0.0431 0.6586 0.2983 167 L 0.0976 0.6530 0.2494 168 Y 0.1655 0.5849 0.2496 169 T 0.2667 0.4275 0.3058 170 L 0.2092 0.4299 0.3608 171 N 0.1245 0.5027 0.3728 172 E 0.0696 0.6013 0.3291 173 A 0.0755 0.4906 0.4339 174 K 0.1119 0.3831 0.5050