# This file is the result of combining several RDB files, specifically # T0395.t06.str2.rdb (weight 1.54425) # T0395.t06.str4.rdb (weight 0.924988) # T0395.t06.pb.rdb (weight 0.789901) # T0395.t06.bys.rdb (weight 0.748322) # T0395.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 T0395.t06.str2.rdb # ============================================ # TARGET T0395 # 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 T0395.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 3830 # # ============================================ # Comments from T0395.t06.str4.rdb # ============================================ # TARGET T0395 # 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 T0395.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 3830 # # ============================================ # Comments from T0395.t06.pb.rdb # ============================================ # TARGET T0395 # 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 T0395.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 3830 # # ============================================ # Comments from T0395.t06.bys.rdb # ============================================ # TARGET T0395 # 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 T0395.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 3830 # # ============================================ # Comments from T0395.t06.alpha.rdb # ============================================ # TARGET T0395 # 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 T0395.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 3830 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3835 0.0684 0.5481 2 R 0.2969 0.0675 0.6355 3 L 0.1633 0.2777 0.5590 4 G 0.0873 0.4826 0.4302 5 D 0.0693 0.6352 0.2954 6 A 0.0472 0.7721 0.1807 7 A 0.0282 0.8496 0.1221 8 E 0.0272 0.8515 0.1213 9 L 0.0321 0.8139 0.1540 10 C 0.0464 0.7502 0.2034 11 Y 0.0370 0.7209 0.2421 12 N 0.0520 0.6086 0.3393 13 L 0.0910 0.5245 0.3845 14 T 0.1145 0.4371 0.4485 15 S 0.0953 0.4911 0.4136 16 S 0.0855 0.5276 0.3870 17 Y 0.1284 0.5731 0.2985 18 L 0.2135 0.5100 0.2765 19 Q 0.2199 0.5118 0.2683 20 I 0.2016 0.5357 0.2627 21 A 0.1716 0.5057 0.3227 22 A 0.1291 0.4654 0.4054 23 E 0.1098 0.3333 0.5570 24 S 0.1590 0.1927 0.6483 25 D 0.0848 0.3961 0.5191 26 S 0.0929 0.4547 0.4524 27 I 0.1290 0.4968 0.3742 28 I 0.1545 0.4860 0.3595 29 A 0.1587 0.4893 0.3520 30 Q 0.1388 0.4412 0.4200 31 T 0.0487 0.7059 0.2454 32 Q 0.0220 0.8225 0.1555 33 R 0.0249 0.8417 0.1334 34 A 0.0411 0.8190 0.1399 35 I 0.0571 0.7894 0.1535 36 N 0.0560 0.7351 0.2089 37 T 0.0530 0.6726 0.2745 38 T 0.0733 0.5740 0.3527 39 K 0.0469 0.7221 0.2310 40 S 0.0704 0.7057 0.2239 41 I 0.1590 0.6281 0.2129 42 L 0.1670 0.6153 0.2177 43 I 0.1268 0.7035 0.1697 44 N 0.0560 0.7933 0.1507 45 E 0.0509 0.7568 0.1923 46 T 0.0673 0.6740 0.2587 47 F 0.0957 0.5538 0.3504 48 P 0.0441 0.6094 0.3465 49 K 0.0591 0.4678 0.4730 50 W 0.1446 0.2290 0.6263 51 S 0.1764 0.1455 0.6780 52 P 0.1290 0.2429 0.6282 53 L 0.0750 0.3034 0.6216 54 N 0.0748 0.1559 0.7693 55 G 0.1388 0.0736 0.7876 56 E 0.3957 0.0207 0.5836 57 I 0.7454 0.0075 0.2471 58 S 0.8022 0.0067 0.1911 59 F 0.8123 0.0051 0.1826 60 S 0.7893 0.0076 0.2031 61 Y 0.6969 0.0144 0.2887 62 N 0.3967 0.0401 0.5631 63 G 0.1593 0.1017 0.7390 64 G 0.1217 0.2543 0.6240 65 K 0.0857 0.5574 0.3569 66 D 0.0469 0.7131 0.2400 67 C 0.0145 0.8558 0.1298 68 Q 0.0098 0.9081 0.0821 69 V 0.0084 0.9235 0.0681 70 L 0.0083 0.9251 0.0667 71 L 0.0083 0.9248 0.0670 72 L 0.0083 0.9244 0.0673 73 L 0.0083 0.9237 0.0680 74 Y 0.0083 0.9205 0.0711 75 L 0.0085 0.9138 0.0778 76 S 0.0092 0.8724 0.1184 77 C 0.0133 0.7994 0.1874 78 L 0.0238 0.7191 0.2571 79 W 0.0343 0.7387 0.2270 80 E 0.0420 0.6715 0.2865 81 Y 0.0817 0.5525 0.3658 82 Y 0.1113 0.4977 0.3910 83 I 0.1494 0.4722 0.3784 84 V 0.1460 0.4611 0.3929 85 K 0.1579 0.4147 0.4274 86 L 0.1796 0.3441 0.4763 87 S 0.1712 0.2638 0.5649 88 Q 0.1527 0.2921 0.5552 89 S 0.1487 0.3243 0.5270 90 Q 0.1334 0.3301 0.5365 91 F 0.1554 0.2683 0.5763 92 D 0.1269 0.1826 0.6906 93 G 0.1262 0.1468 0.7270 94 K 0.2242 0.1563 0.6195 95 F 0.2699 0.1550 0.5752 96 H 0.2784 0.1251 0.5965 97 R 0.3196 0.1064 0.5740 98 F 0.2996 0.0596 0.6408 99 P 0.2112 0.1214 0.6674 100 L 0.1745 0.1801 0.6454 101 T 0.1920 0.1462 0.6618 102 K 0.2857 0.0732 0.6411 103 L 0.4077 0.0136 0.5787 104 P 0.4855 0.0241 0.4904 105 T 0.7865 0.0064 0.2071 106 V 0.7983 0.0071 0.1947 107 F 0.7813 0.0063 0.2124 108 I 0.7228 0.0144 0.2628 109 D 0.3858 0.0310 0.5832 110 H 0.1455 0.1789 0.6757 111 D 0.0784 0.2161 0.7055 112 D 0.1088 0.2557 0.6355 113 T 0.1308 0.2744 0.5947 114 F 0.1309 0.3959 0.4732 115 K 0.0337 0.7083 0.2580 116 T 0.0309 0.7801 0.1890 117 L 0.0237 0.8419 0.1343 118 E 0.0091 0.8982 0.0927 119 N 0.0084 0.9169 0.0747 120 F 0.0086 0.9190 0.0724 121 I 0.0083 0.9210 0.0707 122 E 0.0083 0.9216 0.0701 123 E 0.0083 0.9230 0.0687 124 T 0.0084 0.9207 0.0709 125 S 0.0085 0.9114 0.0800 126 L 0.0093 0.8920 0.0987 127 R 0.0209 0.7613 0.2177 128 Y 0.0655 0.3002 0.6343 129 S 0.0702 0.0804 0.8493 130 L 0.2410 0.0160 0.7429 131 S 0.3785 0.0254 0.5961 132 L 0.6771 0.0154 0.3075 133 Y 0.7229 0.0212 0.2559 134 E 0.7018 0.0153 0.2829 135 S 0.6131 0.0315 0.3554 136 D 0.3017 0.0330 0.6653 137 R 0.1077 0.2910 0.6014 138 D 0.1111 0.2701 0.6188 139 K 0.1385 0.2407 0.6209 140 C 0.1325 0.3245 0.5430 141 E 0.1391 0.4693 0.3916 142 T 0.1700 0.5406 0.2894 143 M 0.1118 0.7020 0.1862 144 A 0.0353 0.8459 0.1188 145 E 0.0224 0.8781 0.0995 146 A 0.0117 0.9009 0.0874 147 F 0.0086 0.9169 0.0745 148 E 0.0084 0.9192 0.0725 149 T 0.0084 0.9200 0.0716 150 F 0.0089 0.9115 0.0796 151 L 0.0107 0.8740 0.1153 152 Q 0.0114 0.7855 0.2031 153 V 0.0264 0.6469 0.3267 154 F 0.1483 0.1195 0.7322 155 P 0.0461 0.3910 0.5630 156 E 0.0487 0.1741 0.7773 157 T 0.2139 0.0988 0.6873 158 K 0.3983 0.0793 0.5224 159 A 0.7926 0.0117 0.1958 160 I 0.7608 0.0141 0.2251 161 V 0.7917 0.0124 0.1959 162 I 0.7428 0.0261 0.2311 163 G 0.5810 0.0367 0.3823 164 I 0.4344 0.0619 0.5037 165 R 0.3393 0.0874 0.5734 166 H 0.2063 0.1649 0.6288 167 T 0.1497 0.1707 0.6796 168 D 0.2030 0.0972 0.6999 169 P 0.1189 0.3491 0.5319 170 F 0.1220 0.3588 0.5192 171 G 0.1459 0.3502 0.5039 172 E 0.1889 0.3441 0.4670 173 H 0.2340 0.2875 0.4784 174 L 0.2368 0.2140 0.5492 175 K 0.2840 0.1163 0.5998 176 P 0.2502 0.1879 0.5618 177 I 0.2567 0.2669 0.4763 178 Q 0.2897 0.2418 0.4685 179 K 0.2739 0.2153 0.5108 180 T 0.2241 0.2022 0.5738 181 D 0.1775 0.1623 0.6603 182 A 0.0804 0.3533 0.5663 183 N 0.0964 0.2368 0.6668 184 W 0.1967 0.0843 0.7190 185 P 0.1010 0.3000 0.5991 186 D 0.1188 0.2204 0.6608 187 F 0.3111 0.1140 0.5749 188 Y 0.4520 0.0927 0.4552 189 R 0.6215 0.0678 0.3107 190 L 0.5454 0.0901 0.3645 191 Q 0.4786 0.0506 0.4708 192 P 0.3269 0.1527 0.5204 193 L 0.2274 0.3261 0.4465 194 L 0.1904 0.3465 0.4631 195 H 0.1865 0.2392 0.5743 196 W 0.2198 0.1529 0.6273 197 N 0.1758 0.0627 0.7615 198 L 0.0126 0.7250 0.2624 199 A 0.0093 0.8624 0.1283 200 N 0.0085 0.9200 0.0716 201 I 0.0083 0.9218 0.0699 202 W 0.0083 0.9215 0.0702 203 S 0.0083 0.9231 0.0686 204 F 0.0083 0.9204 0.0713 205 L 0.0085 0.9152 0.0763 206 L 0.0086 0.9082 0.0831 207 Y 0.0138 0.8023 0.1839 208 S 0.0577 0.2500 0.6923 209 N 0.0396 0.0805 0.8799 210 E 0.1711 0.0184 0.8104 211 P 0.2197 0.0608 0.7194 212 I 0.3092 0.1322 0.5586 213 C 0.3130 0.1777 0.5092 214 E 0.2780 0.2963 0.4257 215 L 0.2197 0.3809 0.3995 216 Y 0.1593 0.4359 0.4048 217 R 0.1462 0.3509 0.5029 218 Y 0.1449 0.1866 0.6685 219 G 0.1170 0.1138 0.7692 220 F 0.2512 0.0734 0.6754 221 T 0.2723 0.1076 0.6201 222 S 0.2565 0.0878 0.6557 223 L 0.1559 0.2335 0.6105 224 G 0.1543 0.1496 0.6961 225 N 0.2406 0.1195 0.6399 226 V 0.2991 0.1133 0.5875 227 E 0.2815 0.1643 0.5542 228 E 0.3613 0.1211 0.5176 229 T 0.3643 0.0964 0.5394 230 L 0.3528 0.0580 0.5891 231 P 0.2633 0.0769 0.6597 232 N 0.2048 0.0637 0.7315 233 P 0.0473 0.5723 0.3804 234 H 0.0544 0.6152 0.3305 235 L 0.0901 0.6435 0.2664 236 R 0.1235 0.5929 0.2837 237 K 0.1285 0.5375 0.3340 238 D 0.1049 0.4506 0.4445 239 K 0.0614 0.4812 0.4574 240 N 0.0740 0.3509 0.5751 241 S 0.1202 0.2510 0.6288 242 T 0.1139 0.3455 0.5406 243 P 0.0697 0.5421 0.3882 244 L 0.0782 0.5875 0.3343 245 K 0.0920 0.6122 0.2958 246 L 0.0997 0.5779 0.3225 247 N 0.1034 0.4449 0.4516 248 F 0.1081 0.5238 0.3682 249 E 0.0483 0.7081 0.2435 250 W 0.0497 0.7792 0.1711 251 E 0.0590 0.7596 0.1814 252 I 0.0658 0.7500 0.1842 253 E 0.0435 0.7560 0.2005 254 N 0.0440 0.7232 0.2329 255 R 0.0627 0.7014 0.2360 256 Y 0.0923 0.6411 0.2666 257 K 0.0997 0.5697 0.3306 258 H 0.1223 0.4757 0.4020 259 N 0.1333 0.3714 0.4953 260 E 0.1714 0.3186 0.5100 261 V 0.2321 0.2690 0.4989 262 T 0.2036 0.2629 0.5334 263 K 0.1971 0.2160 0.5869 264 A 0.2449 0.1385 0.6166 265 E 0.3280 0.0493 0.6227 266 P 0.3383 0.0554 0.6063 267 I 0.3648 0.0511 0.5841 268 P 0.2979 0.1025 0.5996 269 I 0.2715 0.2226 0.5058 270 A 0.2330 0.2502 0.5168 271 D 0.1764 0.2841 0.5395 272 E 0.1091 0.4592 0.4317 273 D 0.1222 0.4863 0.3915 274 L 0.1387 0.5726 0.2887 275 V 0.1505 0.5529 0.2966 276 K 0.1916 0.4727 0.3357 277 I 0.2396 0.3340 0.4265 278 E 0.1923 0.2832 0.5245 279 N 0.2091 0.1498 0.6410 280 L 0.1185 0.3137 0.5678 281 H 0.1314 0.2728 0.5958 282 E 0.1678 0.2659 0.5662 283 D 0.1899 0.2012 0.6089 284 Y 0.2249 0.1543 0.6208 285 Y 0.2610 0.0585 0.6805 286 P 0.1731 0.1965 0.6304 287 G 0.1539 0.2695 0.5766 288 W 0.2599 0.3130 0.4271 289 Y 0.3460 0.2595 0.3945 290 L 0.2947 0.2899 0.4154 291 V 0.1979 0.3570 0.4452 292 D 0.1364 0.4690 0.3946 293 D 0.1357 0.4986 0.3657 294 K 0.1528 0.5643 0.2829 295 L 0.1788 0.5596 0.2616 296 E 0.2448 0.4557 0.2995 297 R 0.2872 0.3548 0.3579 298 A 0.3269 0.2454 0.4276 299 G 0.4262 0.1714 0.4024 300 R 0.5273 0.1098 0.3629 301 I 0.5026 0.0886 0.4088 302 K 0.4178 0.0811 0.5011 303 K 0.3252 0.0977 0.5770 304 K 0.2539 0.1281 0.6180