# This file is the result of combining several RDB files, specifically # T0627.t04.str2.rdb (weight 1.54425) # T0627.t04.str4.rdb (weight 0.924988) # T0627.t04.pb.rdb (weight 0.789901) # T0627.t04.bys.rdb (weight 0.748322) # T0627.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 T0627.t04.str2.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1052 # # ============================================ # Comments from T0627.t04.str4.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1052 # # ============================================ # Comments from T0627.t04.pb.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1052 # # ============================================ # Comments from T0627.t04.bys.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1052 # # ============================================ # Comments from T0627.t04.alpha.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1052 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3302 0.1270 0.5428 2 I 0.3193 0.1402 0.5405 3 D 0.2916 0.1496 0.5588 4 T 0.2154 0.2769 0.5078 5 F 0.1785 0.3677 0.4538 6 E 0.1772 0.3535 0.4693 7 R 0.1589 0.3026 0.5385 8 T 0.1809 0.1879 0.6312 9 G 0.1967 0.1054 0.6979 10 P 0.1737 0.1895 0.6368 11 L 0.1820 0.3104 0.5076 12 M 0.2103 0.2616 0.5281 13 E 0.1868 0.2326 0.5805 14 A 0.1320 0.3569 0.5111 15 S 0.1169 0.3018 0.5814 16 S 0.1082 0.2702 0.6216 17 Y 0.1280 0.2559 0.6161 18 P 0.0406 0.6353 0.3241 19 A 0.0178 0.8160 0.1662 20 W 0.0122 0.8698 0.1181 21 A 0.0086 0.9116 0.0798 22 Q 0.0084 0.9186 0.0731 23 Q 0.0084 0.9188 0.0728 24 L 0.0085 0.9163 0.0752 25 I 0.0087 0.8952 0.0961 26 N 0.0094 0.8314 0.1593 27 D 0.0148 0.6851 0.3001 28 C 0.0343 0.5585 0.4072 29 S 0.0470 0.5366 0.4164 30 P 0.0147 0.8062 0.1791 31 A 0.0111 0.8562 0.1327 32 K 0.0095 0.8973 0.0932 33 A 0.0097 0.9005 0.0899 34 R 0.0108 0.8868 0.1025 35 V 0.0182 0.8399 0.1419 36 V 0.0267 0.7781 0.1952 37 E 0.0345 0.6713 0.2942 38 H 0.0658 0.6134 0.3208 39 E 0.0174 0.7808 0.2018 40 L 0.0131 0.8586 0.1283 41 Y 0.0125 0.9057 0.0818 42 Q 0.0113 0.9118 0.0770 43 Q 0.0135 0.8921 0.0944 44 M 0.0210 0.8379 0.1411 45 R 0.0265 0.7067 0.2669 46 D 0.0407 0.3435 0.6158 47 A 0.0742 0.1514 0.7744 48 K 0.1673 0.0845 0.7482 49 L 0.2313 0.0439 0.7248 50 S 0.1709 0.0180 0.8112 51 P 0.0115 0.7411 0.2474 52 Q 0.0093 0.8712 0.1194 53 I 0.0084 0.9193 0.0723 54 M 0.0083 0.9222 0.0695 55 R 0.0083 0.9223 0.0694 56 Q 0.0091 0.9209 0.0700 57 Y 0.0111 0.9118 0.0771 58 L 0.0181 0.8816 0.1002 59 I 0.0196 0.8230 0.1575 60 G 0.0318 0.5569 0.4113 61 G 0.0507 0.3261 0.6232 62 W 0.0889 0.4064 0.5047 63 P 0.0682 0.6649 0.2669 64 V 0.0667 0.7836 0.1497 65 V 0.0206 0.8775 0.1019 66 E 0.0101 0.9061 0.0838 67 Q 0.0087 0.9070 0.0843 68 F 0.0088 0.9114 0.0797 69 A 0.0084 0.9184 0.0733 70 V 0.0083 0.9230 0.0687 71 Y 0.0083 0.9220 0.0697 72 M 0.0084 0.9206 0.0710 73 A 0.0084 0.9164 0.0752 74 K 0.0086 0.9047 0.0867 75 N 0.0097 0.8741 0.1162 76 L 0.0163 0.8016 0.1821 77 T 0.0245 0.7405 0.2350 78 K 0.0510 0.5458 0.4033 79 T 0.1295 0.3115 0.5590 80 R 0.1404 0.2674 0.5922 81 F 0.1584 0.2618 0.5797 82 G 0.1208 0.2042 0.6750 83 R 0.1373 0.1600 0.7027 84 H 0.1655 0.0972 0.7374 85 P 0.0845 0.2966 0.6189 86 G 0.0590 0.2638 0.6772 87 E 0.0396 0.6177 0.3427 88 D 0.0120 0.8412 0.1468 89 M 0.0091 0.8963 0.0946 90 A 0.0085 0.9190 0.0725 91 R 0.0083 0.9225 0.0692 92 R 0.0083 0.9239 0.0678 93 W 0.0083 0.9229 0.0688 94 L 0.0084 0.9174 0.0742 95 M 0.0087 0.9088 0.0825 96 R 0.0102 0.8920 0.0978 97 N 0.0253 0.7614 0.2132 98 I 0.0529 0.7290 0.2181 99 R 0.0507 0.7325 0.2168 100 V 0.0535 0.7121 0.2344 101 E 0.0673 0.6389 0.2938 102 L 0.0733 0.5385 0.3881 103 N 0.0643 0.4468 0.4889 104 H 0.0688 0.5733 0.3578 105 A 0.0172 0.7928 0.1900 106 D 0.0110 0.8867 0.1023 107 Y 0.0109 0.9079 0.0813 108 W 0.0092 0.9171 0.0737 109 V 0.0086 0.9188 0.0726 110 N 0.0085 0.9212 0.0703 111 W 0.0085 0.9173 0.0742 112 C 0.0089 0.9103 0.0808 113 A 0.0095 0.8939 0.0966 114 A 0.0151 0.7805 0.2044 115 H 0.0576 0.2601 0.6823 116 D 0.0481 0.0742 0.8778 117 V 0.1773 0.0318 0.7909 118 T 0.1822 0.0171 0.8007 119 L 0.0184 0.6990 0.2826 120 E 0.0124 0.8109 0.1767 121 D 0.0209 0.8118 0.1673 122 L 0.0270 0.7915 0.1815 123 H 0.0286 0.6254 0.3460 124 D 0.0426 0.4168 0.5406 125 Q 0.1010 0.3047 0.5943 126 R 0.1269 0.1949 0.6782 127 V 0.1379 0.2190 0.6431 128 A 0.1499 0.1049 0.7452 129 P 0.0182 0.7251 0.2567 130 E 0.0149 0.8298 0.1553 131 L 0.0098 0.9091 0.0810 132 H 0.0088 0.9197 0.0716 133 A 0.0086 0.9211 0.0703 134 L 0.0086 0.9198 0.0717 135 S 0.0085 0.9211 0.0704 136 H 0.0085 0.9207 0.0709 137 W 0.0092 0.9166 0.0742 138 C 0.0097 0.9114 0.0789 139 W 0.0096 0.9101 0.0803 140 Q 0.0118 0.8881 0.1001 141 T 0.0234 0.8137 0.1629 142 S 0.0442 0.6537 0.3021 143 S 0.0576 0.4586 0.4838 144 S 0.0682 0.3903 0.5414 145 D 0.0573 0.4093 0.5333 146 S 0.0860 0.4663 0.4477 147 L 0.0210 0.7520 0.2270 148 A 0.0134 0.8610 0.1255 149 V 0.0127 0.9107 0.0766 150 A 0.0183 0.9034 0.0782 151 M 0.0216 0.8982 0.0802 152 A 0.0245 0.8901 0.0854 153 A 0.0294 0.8667 0.1039 154 T 0.0450 0.7817 0.1732 155 N 0.0607 0.7081 0.2312 156 Y 0.0607 0.6609 0.2784 157 A 0.0685 0.6845 0.2471 158 I 0.0858 0.6446 0.2696 159 E 0.0923 0.5691 0.3386 160 G 0.0997 0.4235 0.4768 161 A 0.1265 0.3479 0.5256 162 T 0.1387 0.2763 0.5849 163 G 0.0748 0.4681 0.4571 164 E 0.0729 0.6246 0.3025 165 W 0.0945 0.6734 0.2321 166 S 0.1026 0.7007 0.1967 167 A 0.1092 0.7387 0.1521 168 V 0.0946 0.7831 0.1223 169 V 0.0887 0.7733 0.1380 170 C 0.0749 0.7488 0.1762 171 S 0.0510 0.7133 0.2356 172 T 0.0375 0.6850 0.2775 173 G 0.0339 0.7023 0.2639 174 V 0.0416 0.7540 0.2043 175 Y 0.0326 0.7940 0.1734 176 A 0.0260 0.8199 0.1541 177 E 0.0261 0.7923 0.1816 178 A 0.0477 0.6487 0.3036 179 F 0.1069 0.4254 0.4677 180 A 0.0920 0.4163 0.4917 181 E 0.0522 0.5857 0.3621 182 E 0.0608 0.5702 0.3690 183 T 0.0800 0.5201 0.3999 184 R 0.0925 0.4459 0.4616 185 K 0.0692 0.6162 0.3146 186 K 0.0341 0.7395 0.2265 187 S 0.0431 0.7524 0.2045 188 M 0.0585 0.7883 0.1532 189 K 0.0562 0.8178 0.1260 190 W 0.0888 0.7741 0.1371 191 L 0.1295 0.7215 0.1490 192 K 0.1310 0.6862 0.1829 193 M 0.1580 0.5679 0.2741 194 H 0.1918 0.3687 0.4395 195 A 0.1812 0.2911 0.5278 196 Q 0.1700 0.2241 0.6059 197 Y 0.1244 0.3049 0.5707 198 D 0.1151 0.2757 0.6091 199 D 0.0615 0.4045 0.5340 200 A 0.0746 0.3428 0.5826 201 H 0.1515 0.2669 0.5816 202 P 0.0242 0.7465 0.2293 203 W 0.0116 0.8652 0.1232 204 E 0.0091 0.9135 0.0774 205 A 0.0085 0.9184 0.0731 206 L 0.0083 0.9207 0.0710 207 E 0.0083 0.9238 0.0679 208 I 0.0083 0.9232 0.0685 209 I 0.0084 0.9175 0.0740 210 C 0.0085 0.9140 0.0775 211 T 0.0094 0.8896 0.1010 212 L 0.0170 0.7902 0.1928 213 V 0.0346 0.5927 0.3727 214 G 0.0441 0.3757 0.5802 215 N 0.0683 0.2123 0.7194 216 K 0.1422 0.1248 0.7329 217 P 0.1107 0.2182 0.6711 218 S 0.1492 0.1074 0.7434 219 L 0.0120 0.7376 0.2504 220 Q 0.0094 0.8670 0.1237 221 L 0.0089 0.9130 0.0781 222 Q 0.0083 0.9236 0.0681 223 A 0.0083 0.9241 0.0676 224 E 0.0083 0.9250 0.0667 225 L 0.0083 0.9239 0.0678 226 R 0.0083 0.9239 0.0678 227 Q 0.0083 0.9246 0.0671 228 A 0.0083 0.9236 0.0681 229 V 0.0084 0.9203 0.0713 230 T 0.0083 0.9218 0.0698 231 K 0.0085 0.9201 0.0715 232 S 0.0087 0.9184 0.0729 233 Y 0.0086 0.9186 0.0728 234 D 0.0083 0.9231 0.0685 235 Y 0.0083 0.9231 0.0686 236 M 0.0083 0.9235 0.0682 237 Y 0.0083 0.9233 0.0684 238 L 0.0083 0.9227 0.0690 239 F 0.0084 0.9198 0.0718 240 L 0.0085 0.9148 0.0767 241 E 0.0084 0.9156 0.0759 242 R 0.0090 0.9046 0.0864 243 C 0.0102 0.8917 0.0980 244 I 0.0123 0.8538 0.1339 245 Q 0.0206 0.7788 0.2006 246 L 0.0478 0.6448 0.3074 247 D 0.0719 0.4641 0.4640 248 K 0.1131 0.3470 0.5399 249 V 0.2221 0.1610 0.6169 250 K 0.2203 0.1253 0.6544 251 S 0.2413 0.0564 0.7022 252 P 0.1859 0.0779 0.7362 253 R 0.1179 0.2500 0.6321 254 G 0.0979 0.1691 0.7329 255 R 0.3087 0.1133 0.5779 256 V 0.4928 0.0862 0.4210 257 A 0.5329 0.0876 0.3795 258 A 0.4532 0.1281 0.4187 259 L 0.3767 0.1814 0.4419 260 E 0.2990 0.1921 0.5088 261 M 0.2454 0.1823 0.5723