# This file is the result of combining several RDB files, specifically # TR461.t04.str2.rdb (weight 1.54425) # TR461.t04.str4.rdb (weight 0.924988) # TR461.t04.pb.rdb (weight 0.789901) # TR461.t04.bys.rdb (weight 0.748322) # TR461.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 TR461.t04.str2.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2123 # # ============================================ # Comments from TR461.t04.str4.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2123 # # ============================================ # Comments from TR461.t04.pb.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2123 # # ============================================ # Comments from TR461.t04.bys.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2123 # # ============================================ # Comments from TR461.t04.alpha.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2123 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 F 0.2249 0.1409 0.6342 2 Q 0.2055 0.1436 0.6510 3 S 0.1997 0.1326 0.6677 4 M 0.1389 0.2327 0.6283 5 E 0.0888 0.4060 0.5053 6 E 0.0484 0.5914 0.3602 7 T 0.0383 0.7357 0.2260 8 E 0.0094 0.8725 0.1181 9 K 0.0087 0.8976 0.0937 10 W 0.0085 0.9191 0.0724 11 M 0.0083 0.9226 0.0691 12 E 0.0083 0.9241 0.0677 13 E 0.0083 0.9239 0.0678 14 A 0.0083 0.9241 0.0676 15 M 0.0083 0.9233 0.0684 16 H 0.0083 0.9232 0.0685 17 M 0.0084 0.9214 0.0703 18 A 0.0085 0.9188 0.0728 19 K 0.0085 0.9140 0.0775 20 E 0.0095 0.8813 0.1092 21 A 0.0210 0.7904 0.1885 22 L 0.0326 0.6269 0.3405 23 E 0.0502 0.4646 0.4851 24 N 0.0857 0.2397 0.6746 25 T 0.1343 0.1254 0.7402 26 E 0.1869 0.0908 0.7223 27 V 0.3487 0.0266 0.6248 28 P 0.4186 0.0228 0.5585 29 V 0.6046 0.0279 0.3676 30 G 0.7390 0.0164 0.2446 31 C 0.7996 0.0056 0.1948 32 L 0.8218 0.0049 0.1734 33 M 0.8144 0.0045 0.1810 34 V 0.7658 0.0107 0.2235 35 Y 0.5961 0.0369 0.3670 36 N 0.2032 0.0548 0.7420 37 N 0.1387 0.0639 0.7974 38 E 0.5188 0.0204 0.4608 39 V 0.6598 0.0126 0.3275 40 V 0.6283 0.0405 0.3312 41 G 0.7232 0.0275 0.2493 42 K 0.6412 0.0492 0.3095 43 G 0.5652 0.0575 0.3773 44 R 0.4417 0.1088 0.4495 45 N 0.2981 0.1222 0.5797 46 E 0.2266 0.2181 0.5553 47 V 0.2430 0.2158 0.5412 48 N 0.1827 0.2269 0.5904 49 Q 0.1600 0.2545 0.5855 50 T 0.1616 0.2029 0.6355 51 K 0.1536 0.2143 0.6321 52 N 0.1878 0.1611 0.6512 53 A 0.0918 0.4504 0.4578 54 T 0.0884 0.4948 0.4168 55 R 0.0609 0.6721 0.2669 56 H 0.0392 0.8074 0.1533 57 A 0.0229 0.8911 0.0860 58 E 0.0136 0.9136 0.0728 59 M 0.0090 0.9230 0.0679 60 V 0.0087 0.9235 0.0678 61 A 0.0085 0.9230 0.0686 62 I 0.0084 0.9197 0.0719 63 D 0.0084 0.9193 0.0724 64 Q 0.0085 0.9125 0.0790 65 V 0.0089 0.8966 0.0944 66 L 0.0091 0.8934 0.0975 67 D 0.0092 0.8433 0.1475 68 W 0.0133 0.7972 0.1896 69 C 0.0304 0.7393 0.2303 70 R 0.0223 0.7444 0.2333 71 Q 0.0332 0.6375 0.3293 72 S 0.0798 0.3606 0.5596 73 G 0.0688 0.1879 0.7433 74 K 0.1527 0.1260 0.7213 75 S 0.1887 0.0552 0.7560 76 P 0.1316 0.2113 0.6571 77 S 0.1309 0.2670 0.6021 78 E 0.1863 0.2987 0.5150 79 V 0.2578 0.2771 0.4651 80 F 0.2839 0.2211 0.4949 81 E 0.2327 0.1734 0.5939 82 H 0.2343 0.0870 0.6787 83 T 0.5235 0.0148 0.4617 84 V 0.7437 0.0100 0.2464 85 L 0.8102 0.0056 0.1843 86 Y 0.8038 0.0062 0.1901 87 V 0.7712 0.0100 0.2188 88 T 0.6260 0.0246 0.3494 89 V 0.4160 0.0910 0.4930 90 E 0.3044 0.0972 0.5984 91 P 0.1569 0.2319 0.6112 92 C 0.0814 0.3414 0.5772 93 I 0.0195 0.7579 0.2226 94 M 0.0132 0.8467 0.1401 95 C 0.0094 0.9023 0.0884 96 A 0.0084 0.9161 0.0754 97 A 0.0083 0.9224 0.0693 98 A 0.0083 0.9227 0.0690 99 L 0.0085 0.9192 0.0723 100 R 0.0088 0.9090 0.0822 101 L 0.0158 0.8103 0.1739 102 M 0.0627 0.3849 0.5524 103 K 0.0569 0.1268 0.8163 104 I 0.1864 0.0578 0.7558 105 P 0.2578 0.1163 0.6259 106 L 0.7178 0.0394 0.2428 107 V 0.7386 0.0239 0.2376 108 V 0.7713 0.0243 0.2044 109 Y 0.7696 0.0162 0.2142 110 G 0.6840 0.0260 0.2900 111 C 0.5479 0.0384 0.4137 112 Q 0.3293 0.0828 0.5879 113 N 0.2489 0.0607 0.6905 114 E 0.0608 0.4160 0.5232 115 R 0.0762 0.3319 0.5919 116 F 0.1206 0.2463 0.6331 117 G 0.1291 0.1767 0.6942 118 G 0.1797 0.2312 0.5891 119 C 0.1755 0.2447 0.5798 120 G 0.1453 0.2437 0.6110 121 S 0.1718 0.3820 0.4462 122 V 0.1525 0.5394 0.3081 123 L 0.1239 0.6321 0.2441 124 N 0.0985 0.6725 0.2290 125 I 0.0964 0.6586 0.2451 126 A 0.0936 0.5839 0.3224 127 S 0.0679 0.5658 0.3663 128 A 0.0724 0.5065 0.4211 129 D 0.1106 0.3453 0.5441 130 L 0.1859 0.2213 0.5928 131 P 0.1115 0.3222 0.5663 132 N 0.1084 0.3256 0.5660 133 T 0.1152 0.1853 0.6995 134 G 0.0911 0.0814 0.8275 135 R 0.2259 0.0288 0.7453 136 P 0.3040 0.0389 0.6571 137 F 0.5976 0.0216 0.3808 138 Q 0.6902 0.0174 0.2924 139 C 0.6865 0.0148 0.2986 140 I 0.4825 0.0291 0.4884 141 P 0.2398 0.1173 0.6430 142 G 0.1105 0.1311 0.7584 143 Y 0.1762 0.1788 0.6450 144 R 0.1404 0.2200 0.6395 145 A 0.0180 0.7668 0.2152 146 E 0.0094 0.8812 0.1094 147 E 0.0088 0.9135 0.0777 148 A 0.0084 0.9192 0.0723 149 V 0.0083 0.9208 0.0708 150 E 0.0083 0.9185 0.0732 151 M 0.0085 0.9160 0.0755 152 L 0.0088 0.9027 0.0885 153 K 0.0091 0.8909 0.1000 154 T 0.0125 0.8353 0.1522 155 F 0.0320 0.6899 0.2781 156 Y 0.0548 0.5506 0.3945 157 K 0.0783 0.4204 0.5013