# This file is the result of combining several RDB files, specifically # T0443.t06.str2.rdb (weight 1.54425) # T0443.t06.str4.rdb (weight 0.924988) # T0443.t06.pb.rdb (weight 0.789901) # T0443.t06.bys.rdb (weight 0.748322) # T0443.t06.alpha.rdb (weight 0.678173) # T0443.t04.str2.rdb (weight 1.54425) # T0443.t04.str4.rdb (weight 0.924988) # T0443.t04.pb.rdb (weight 0.789901) # T0443.t04.bys.rdb (weight 0.748322) # T0443.t04.alpha.rdb (weight 0.678173) # T0443.t2k.str2.rdb (weight 1.54425) # T0443.t2k.str4.rdb (weight 0.924988) # T0443.t2k.pb.rdb (weight 0.789901) # T0443.t2k.bys.rdb (weight 0.748322) # T0443.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 T0443.t06.str2.rdb # ============================================ # TARGET T0443 # 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 T0443.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 209 # # ============================================ # Comments from T0443.t06.str4.rdb # ============================================ # TARGET T0443 # 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 T0443.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 209 # # ============================================ # Comments from T0443.t06.pb.rdb # ============================================ # TARGET T0443 # 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 T0443.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 209 # # ============================================ # Comments from T0443.t06.bys.rdb # ============================================ # TARGET T0443 # 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 T0443.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 209 # # ============================================ # Comments from T0443.t06.alpha.rdb # ============================================ # TARGET T0443 # 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 T0443.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 209 # # ============================================ # Comments from T0443.t04.str2.rdb # ============================================ # TARGET T0443 # 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 T0443.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 208 # # ============================================ # Comments from T0443.t04.str4.rdb # ============================================ # TARGET T0443 # 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 T0443.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 208 # # ============================================ # Comments from T0443.t04.pb.rdb # ============================================ # TARGET T0443 # 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 T0443.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 208 # # ============================================ # Comments from T0443.t04.bys.rdb # ============================================ # TARGET T0443 # 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 T0443.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 208 # # ============================================ # Comments from T0443.t04.alpha.rdb # ============================================ # TARGET T0443 # 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 T0443.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 208 # # ============================================ # Comments from T0443.t2k.str2.rdb # ============================================ # TARGET T0443 # 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 T0443.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 37.1723 # # ============================================ # Comments from T0443.t2k.str4.rdb # ============================================ # TARGET T0443 # 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 T0443.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 37.1723 # # ============================================ # Comments from T0443.t2k.pb.rdb # ============================================ # TARGET T0443 # 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 T0443.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 37.1723 # # ============================================ # Comments from T0443.t2k.bys.rdb # ============================================ # TARGET T0443 # 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 T0443.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 37.1723 # # ============================================ # Comments from T0443.t2k.alpha.rdb # ============================================ # TARGET T0443 # 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 T0443.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 37.1723 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2398 0.0640 0.6962 2 Q 0.1926 0.0266 0.7808 3 P 0.1173 0.2676 0.6150 4 E 0.0285 0.6192 0.3523 5 T 0.0338 0.6547 0.3115 6 S 0.0251 0.8141 0.1608 7 A 0.0113 0.8855 0.1031 8 Q 0.0090 0.9143 0.0768 9 Y 0.0093 0.9177 0.0730 10 Q 0.0085 0.9207 0.0708 11 H 0.0083 0.9219 0.0698 12 R 0.0083 0.9216 0.0701 13 F 0.0085 0.9122 0.0793 14 S 0.0085 0.9139 0.0777 15 Q 0.0087 0.9052 0.0861 16 A 0.0116 0.8552 0.1332 17 I 0.0370 0.7402 0.2229 18 R 0.0632 0.5226 0.4141 19 G 0.0892 0.2203 0.6905 20 G 0.0694 0.2569 0.6737 21 E 0.1483 0.1763 0.6754 22 A 0.1597 0.1298 0.7106 23 A 0.1216 0.2288 0.6496 24 D 0.0917 0.1685 0.7399 25 G 0.0542 0.0955 0.8503 26 L 0.1741 0.0255 0.8004 27 P 0.1755 0.1015 0.7230 28 Q 0.0468 0.6281 0.3251 29 D 0.0300 0.7641 0.2058 30 R 0.0575 0.7712 0.1713 31 L 0.0673 0.8050 0.1277 32 N 0.0522 0.8485 0.0993 33 V 0.0321 0.8793 0.0886 34 Y 0.0239 0.8930 0.0831 35 I 0.0129 0.9113 0.0758 36 R 0.0125 0.9117 0.0759 37 L 0.0158 0.8978 0.0864 38 I 0.0215 0.8537 0.1248 39 R 0.0229 0.7877 0.1894 40 N 0.0225 0.6629 0.3147 41 N 0.0448 0.5936 0.3617 42 I 0.0324 0.7477 0.2199 43 H 0.0372 0.7773 0.1855 44 S 0.0445 0.7995 0.1560 45 F 0.0505 0.7901 0.1594 46 I 0.0515 0.7324 0.2161 47 D 0.0370 0.6547 0.3083 48 R 0.0385 0.4904 0.4711 49 C 0.0813 0.3830 0.5357 50 Y 0.1515 0.3250 0.5235 51 T 0.0963 0.5743 0.3295 52 E 0.0875 0.6383 0.2742 53 T 0.0735 0.6972 0.2294 54 R 0.0388 0.7646 0.1966 55 Q 0.0353 0.7055 0.2591 56 Y 0.0612 0.4823 0.4565 57 F 0.1257 0.2759 0.5984 58 D 0.1390 0.1918 0.6692 59 S 0.0142 0.7049 0.2809 60 K 0.0103 0.8411 0.1486 61 E 0.0105 0.8985 0.0910 62 W 0.0091 0.9109 0.0800 63 S 0.0084 0.9150 0.0766 64 R 0.0085 0.9113 0.0803 65 L 0.0098 0.8995 0.0907 66 K 0.0117 0.8842 0.1041 67 E 0.0129 0.8749 0.1122 68 G 0.0215 0.8349 0.1436 69 F 0.0647 0.7598 0.1754 70 V 0.1023 0.7085 0.1892 71 R 0.1094 0.6641 0.2265 72 D 0.1480 0.5102 0.3418 73 A 0.1307 0.4166 0.4527 74 R 0.1252 0.3502 0.5246 75 A 0.1575 0.2865 0.5560 76 Q 0.1687 0.2012 0.6301 77 T 0.2230 0.1180 0.6590 78 P 0.1301 0.3875 0.4823 79 Y 0.1360 0.4354 0.4286 80 F 0.1201 0.5675 0.3124 81 Q 0.1087 0.5653 0.3260 82 E 0.1509 0.4344 0.4146 83 I 0.1680 0.2503 0.5817 84 P 0.0447 0.6636 0.2917 85 G 0.0215 0.7354 0.2430 86 E 0.0233 0.8325 0.1443 87 F 0.0238 0.8734 0.1028 88 L 0.0224 0.8830 0.0946 89 Q 0.0199 0.8748 0.1053 90 Y 0.0311 0.7708 0.1982 91 C 0.0744 0.5424 0.3832 92 Q 0.0895 0.3211 0.5894 93 S 0.1528 0.1273 0.7199 94 P 0.1162 0.1786 0.7052 95 P 0.1239 0.1844 0.6916 96 L 0.1345 0.1495 0.7160 97 S 0.1050 0.3565 0.5385 98 D 0.0251 0.7471 0.2278 99 G 0.0203 0.8224 0.1572 100 I 0.0135 0.8960 0.0905 101 L 0.0112 0.9069 0.0820 102 A 0.0097 0.9144 0.0758 103 L 0.0129 0.8955 0.0916 104 M 0.0271 0.8527 0.1202 105 D 0.0237 0.8537 0.1227 106 F 0.0304 0.8551 0.1145 107 E 0.0173 0.8832 0.0995 108 Y 0.0172 0.8949 0.0879 109 T 0.0154 0.9015 0.0831 110 Q 0.0215 0.8905 0.0880 111 L 0.0388 0.8638 0.0974 112 L 0.0503 0.8415 0.1082 113 A 0.0875 0.7872 0.1253 114 E 0.1447 0.6888 0.1666 115 V 0.1870 0.5582 0.2548 116 A 0.1746 0.4097 0.4156 117 Q 0.1441 0.2259 0.6299 118 I 0.1963 0.0919 0.7117 119 P 0.1402 0.1467 0.7131 120 D 0.1881 0.1003 0.7116 121 I 0.1929 0.0843 0.7228 122 P 0.1370 0.2064 0.6566 123 D 0.1750 0.1655 0.6594 124 I 0.1431 0.3387 0.5182 125 H 0.1699 0.2933 0.5368 126 Y 0.1918 0.2547 0.5535 127 S 0.1408 0.2791 0.5801 128 N 0.0958 0.3099 0.5943 129 D 0.0952 0.2364 0.6683 130 S 0.1706 0.1733 0.6561 131 K 0.2228 0.1326 0.6446 132 Y 0.2733 0.1086 0.6182 133 T 0.2614 0.0641 0.6745 134 P 0.2115 0.1373 0.6512 135 S 0.1862 0.0764 0.7374 136 P 0.0325 0.6477 0.3198 137 A 0.0509 0.7058 0.2433 138 A 0.1223 0.6891 0.1886 139 F 0.1591 0.6732 0.1677 140 I 0.1689 0.6419 0.1892 141 R 0.1704 0.5712 0.2585 142 Q 0.2134 0.3785 0.4082 143 Y 0.2874 0.1791 0.5335 144 R 0.3154 0.1160 0.5687 145 Y 0.3722 0.0681 0.5597 146 D 0.3494 0.1126 0.5380 147 V 0.3057 0.2616 0.4326 148 T 0.2646 0.2705 0.4648 149 H 0.2487 0.2735 0.4778 150 D 0.2001 0.2308 0.5690 151 L 0.1737 0.2317 0.5946 152 Q 0.1062 0.3839 0.5099 153 E 0.1390 0.2581 0.6029 154 A 0.2652 0.0923 0.6425 155 E 0.2987 0.0996 0.6017 156 T 0.5117 0.0490 0.4394 157 A 0.7418 0.0115 0.2467 158 L 0.8025 0.0059 0.1916 159 L 0.8155 0.0049 0.1796 160 I 0.8116 0.0058 0.1826 161 W 0.7621 0.0088 0.2292 162 R 0.6165 0.0252 0.3583 163 N 0.3486 0.0232 0.6283 164 A 0.1232 0.3457 0.5311 165 E 0.0746 0.3535 0.5719 166 D 0.1297 0.2805 0.5897 167 D 0.3121 0.1744 0.5135 168 V 0.5871 0.1021 0.3108 169 M 0.5951 0.1281 0.2768 170 Y 0.6243 0.1465 0.2292 171 Q 0.5276 0.1856 0.2868 172 T 0.3924 0.1694 0.4382 173 L 0.2610 0.1625 0.5766 174 D 0.1344 0.1521 0.7135 175 G 0.0296 0.6616 0.3087 176 F 0.0219 0.8179 0.1603 177 D 0.0245 0.8730 0.1025 178 M 0.0171 0.8953 0.0876 179 M 0.0118 0.9045 0.0837 180 L 0.0100 0.9196 0.0704 181 L 0.0087 0.9163 0.0751 182 E 0.0087 0.9111 0.0802 183 I 0.0119 0.8648 0.1233 184 M 0.0235 0.7575 0.2190 185 G 0.0280 0.6369 0.3350 186 S 0.0436 0.5680 0.3883 187 S 0.0648 0.4296 0.5056 188 A 0.0596 0.5186 0.4218 189 L 0.0846 0.4967 0.4188 190 S 0.0921 0.4964 0.4116 191 F 0.0332 0.7402 0.2266 192 D 0.0133 0.8579 0.1287 193 T 0.0095 0.9093 0.0812 194 L 0.0088 0.9159 0.0753 195 A 0.0084 0.9190 0.0726 196 Q 0.0083 0.9209 0.0708 197 T 0.0084 0.9203 0.0714 198 L 0.0090 0.9108 0.0803 199 V 0.0088 0.8995 0.0916 200 E 0.0108 0.8410 0.1482 201 F 0.0321 0.6331 0.3348 202 M 0.1335 0.2863 0.5801 203 P 0.0905 0.4028 0.5067 204 K 0.0614 0.4314 0.5072 205 A 0.0627 0.4809 0.4564 206 D 0.0443 0.5656 0.3901 207 N 0.0531 0.5533 0.3936 208 W 0.0299 0.7641 0.2060 209 K 0.0200 0.8707 0.1093 210 N 0.0174 0.8898 0.0928 211 I 0.0173 0.8937 0.0890 212 L 0.0236 0.8572 0.1192 213 L 0.0414 0.7591 0.1995 214 G 0.0422 0.6374 0.3204 215 K 0.0566 0.6729 0.2705 216 W 0.0786 0.5956 0.3258 217 S 0.0627 0.5872 0.3501 218 G 0.0647 0.5621 0.3732 219 W 0.1183 0.5559 0.3258 220 I 0.2137 0.4910 0.2953 221 E 0.2568 0.3986 0.3445 222 Q 0.3093 0.2895 0.4011 223 R 0.4467 0.1493 0.4039 224 I 0.6301 0.0576 0.3123 225 I 0.6374 0.0391 0.3235 226 I 0.4729 0.0311 0.4961 227 P 0.2922 0.1344 0.5734 228 S 0.2222 0.1445 0.6333 229 L 0.2004 0.2306 0.5690 230 S 0.1676 0.3557 0.4767 231 A 0.1566 0.4183 0.4251 232 I 0.1752 0.3307 0.4941 233 S 0.1584 0.2729 0.5687 234 E 0.1035 0.3148 0.5817 235 N 0.1039 0.1828 0.7133 236 M 0.1402 0.1940 0.6658 237 E 0.1460 0.1809 0.6732 238 G 0.1139 0.1387 0.7473 239 N 0.1712 0.1140 0.7148 240 S 0.1938 0.0740 0.7322 241 P 0.1107 0.2880 0.6014 242 S 0.1240 0.2695 0.6066 243 Q 0.1392 0.3814 0.4795 244 N 0.1596 0.3323 0.5081 245 H 0.2326 0.2573 0.5101 246 L 0.3074 0.1764 0.5162 247 S 0.2860 0.1405 0.5735 248 A 0.2064 0.2836 0.5100