# This file is the result of combining several RDB files, specifically # T0440.t04.str2.rdb (weight 1.54425) # T0440.t04.str4.rdb (weight 0.924988) # T0440.t04.pb.rdb (weight 0.789901) # T0440.t04.bys.rdb (weight 0.748322) # T0440.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 T0440.t04.str2.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1436 # # ============================================ # Comments from T0440.t04.str4.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1436 # # ============================================ # Comments from T0440.t04.pb.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1436 # # ============================================ # Comments from T0440.t04.bys.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1436 # # ============================================ # Comments from T0440.t04.alpha.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1436 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3030 0.0570 0.6400 2 K 0.3574 0.0616 0.5810 3 R 0.4478 0.1109 0.4414 4 D 0.3986 0.1243 0.4771 5 G 0.3688 0.1227 0.5084 6 H 0.4619 0.0920 0.4461 7 T 0.4729 0.0828 0.4443 8 H 0.3812 0.0799 0.5389 9 T 0.3429 0.1029 0.5541 10 E 0.2986 0.1678 0.5336 11 F 0.3008 0.1463 0.5530 12 C 0.2191 0.0884 0.6925 13 P 0.1009 0.3241 0.5750 14 H 0.0957 0.2636 0.6407 15 G 0.1229 0.2332 0.6439 16 T 0.1268 0.1806 0.6926 17 H 0.1217 0.1668 0.7115 18 D 0.1163 0.1694 0.7143 19 D 0.1494 0.0855 0.7651 20 V 0.0125 0.7255 0.2620 21 E 0.0091 0.8725 0.1184 22 E 0.0083 0.9217 0.0700 23 M 0.0083 0.9231 0.0686 24 V 0.0083 0.9234 0.0683 25 L 0.0083 0.9247 0.0670 26 K 0.0083 0.9237 0.0680 27 A 0.0084 0.9190 0.0725 28 I 0.0088 0.9022 0.0889 29 E 0.0122 0.8159 0.1719 30 L 0.0546 0.2271 0.7183 31 D 0.0526 0.0677 0.8797 32 F 0.1803 0.0466 0.7731 33 D 0.2822 0.0946 0.6232 34 E 0.7266 0.0305 0.2428 35 Y 0.7467 0.0154 0.2379 36 S 0.7903 0.0080 0.2017 37 I 0.7685 0.0205 0.2110 38 V 0.6678 0.0303 0.3019 39 E 0.3490 0.1107 0.5403 40 H 0.2013 0.1225 0.6762 41 A 0.2042 0.1034 0.6924 42 P 0.1420 0.2370 0.6211 43 L 0.1629 0.2481 0.5890 44 S 0.1508 0.2062 0.6430 45 S 0.0784 0.5603 0.3613 46 E 0.0267 0.7578 0.2155 47 F 0.0291 0.8081 0.1628 48 M 0.0365 0.7909 0.1726 49 K 0.0319 0.7888 0.1793 50 N 0.0351 0.7471 0.2178 51 T 0.0404 0.6930 0.2666 52 A 0.0665 0.5210 0.4125 53 G 0.0534 0.4099 0.5367 54 D 0.0836 0.3911 0.5253 55 K 0.0868 0.4116 0.5016 56 E 0.1217 0.3185 0.5598 57 A 0.1906 0.2824 0.5270 58 V 0.2424 0.3010 0.4565 59 T 0.2617 0.4061 0.3322 60 T 0.2188 0.4661 0.3151 61 A 0.1869 0.5072 0.3060 62 S 0.1354 0.5662 0.2985 63 M 0.1323 0.5747 0.2930 64 A 0.1112 0.5584 0.3304 65 M 0.0792 0.5744 0.3464 66 S 0.0640 0.5175 0.4185 67 D 0.0829 0.3593 0.5578 68 L 0.1731 0.2008 0.6260 69 P 0.1210 0.3185 0.5606 70 Y 0.2053 0.3054 0.4893 71 Y 0.3378 0.1983 0.4639 72 F 0.4174 0.1700 0.4126 73 K 0.4343 0.1504 0.4153 74 K 0.4388 0.1611 0.4001 75 M 0.3259 0.2806 0.3935 76 N 0.3408 0.3381 0.3211 77 H 0.4511 0.2728 0.2761 78 I 0.4387 0.2702 0.2911 79 K 0.3520 0.3170 0.3310 80 K 0.2548 0.4300 0.3152 81 K 0.2218 0.3822 0.3960 82 Y 0.2072 0.2923 0.5005 83 A 0.1506 0.2826 0.5668 84 S 0.1291 0.2704 0.6005 85 D 0.2373 0.1672 0.5955 86 L 0.5515 0.0546 0.3940 87 L 0.7067 0.0325 0.2609 88 I 0.7872 0.0166 0.1962 89 H 0.7460 0.0214 0.2327 90 I 0.6655 0.0366 0.2979 91 G 0.5554 0.0369 0.4077 92 F 0.6381 0.0293 0.3326 93 E 0.6460 0.0347 0.3193 94 V 0.5876 0.0514 0.3610 95 D 0.3730 0.0814 0.5456 96 Y 0.2584 0.2365 0.5050 97 L 0.1980 0.2609 0.5410 98 I 0.1248 0.3309 0.5443 99 G 0.0862 0.3067 0.6071 100 Y 0.0924 0.4799 0.4276 101 E 0.0397 0.7225 0.2379 102 D 0.0286 0.7953 0.1761 103 F 0.0250 0.8234 0.1517 104 T 0.0137 0.8717 0.1146 105 R 0.0092 0.9001 0.0907 106 D 0.0090 0.9062 0.0848 107 F 0.0103 0.8900 0.0998 108 L 0.0119 0.8512 0.1369 109 N 0.0136 0.7821 0.2043 110 E 0.0254 0.6184 0.3562 111 Y 0.0695 0.3570 0.5735 112 G 0.0959 0.2398 0.6643 113 P 0.0478 0.4964 0.4558 114 Q 0.0759 0.4071 0.5170 115 T 0.1193 0.3390 0.5417 116 D 0.1151 0.3764 0.5085 117 D 0.2279 0.3512 0.4209 118 G 0.3960 0.2881 0.3160 119 V 0.4979 0.2586 0.2434 120 L 0.5236 0.2227 0.2537 121 S 0.5098 0.1887 0.3015 122 L 0.4062 0.2635 0.3303 123 H 0.3523 0.2601 0.3876 124 F 0.2899 0.2612 0.4489 125 L 0.2455 0.2332 0.5213 126 E 0.1964 0.1608 0.6428 127 G 0.1342 0.1765 0.6892 128 Q 0.1569 0.2055 0.6376 129 G 0.1603 0.1664 0.6733 130 G 0.1904 0.1598 0.6498 131 F 0.2314 0.1541 0.6144 132 R 0.2306 0.1404 0.6290 133 S 0.2122 0.2031 0.5848 134 I 0.2348 0.2204 0.5447 135 D 0.2528 0.2019 0.5452 136 F 0.2477 0.2351 0.5172 137 S 0.2020 0.1592 0.6387 138 A 0.1124 0.3943 0.4933 139 E 0.0485 0.6260 0.3255 140 D 0.0430 0.6976 0.2593 141 Y 0.0385 0.7237 0.2377 142 N 0.0318 0.7673 0.2009 143 E 0.0198 0.7943 0.1859 144 G 0.0275 0.7772 0.1953 145 I 0.0449 0.7596 0.1955 146 V 0.0544 0.7444 0.2012 147 Q 0.0634 0.6775 0.2591 148 F 0.0874 0.4815 0.4311 149 Y 0.1015 0.3179 0.5805 150 G 0.0892 0.2386 0.6722 151 G 0.1093 0.2181 0.6726 152 F 0.0264 0.6696 0.3040 153 E 0.0108 0.8501 0.1391 154 Q 0.0094 0.9139 0.0767 155 A 0.0090 0.9180 0.0730 156 Q 0.0084 0.9182 0.0734 157 L 0.0083 0.9206 0.0711 158 A 0.0085 0.9146 0.0770 159 Y 0.0096 0.8940 0.0964 160 L 0.0097 0.8820 0.1083 161 E 0.0104 0.8520 0.1376 162 G 0.0149 0.8129 0.1721 163 V 0.0200 0.8396 0.1404 164 K 0.0172 0.8678 0.1150 165 Q 0.0236 0.8595 0.1169 166 S 0.0346 0.8294 0.1360 167 I 0.0502 0.7926 0.1573 168 E 0.0621 0.7493 0.1887 169 A 0.0929 0.6225 0.2846 170 D 0.0939 0.4552 0.4509 171 L 0.0988 0.3327 0.5686 172 G 0.0846 0.2511 0.6644 173 L 0.1512 0.2379 0.6109 174 F 0.2161 0.1457 0.6382 175 K 0.2019 0.1160 0.6822 176 P 0.1487 0.3345 0.5168 177 R 0.1916 0.3601 0.4483 178 R 0.2325 0.3482 0.4193 179 M 0.2160 0.3976 0.3865 180 G 0.2344 0.3618 0.4037 181 H 0.1993 0.3947 0.4060 182 I 0.0316 0.7360 0.2323 183 S 0.0187 0.8363 0.1450 184 L 0.0152 0.8860 0.0988 185 C 0.0135 0.8834 0.1031 186 Q 0.0122 0.8896 0.0982 187 K 0.0180 0.8313 0.1507 188 F 0.0478 0.6314 0.3208 189 Q 0.0603 0.3974 0.5424 190 Q 0.0814 0.3249 0.5937 191 F 0.1502 0.2469 0.6029 192 F 0.1846 0.2256 0.5897 193 G 0.1458 0.3556 0.4986 194 E 0.1107 0.4868 0.4025 195 D 0.1180 0.3529 0.5291 196 T 0.1471 0.2490 0.6039 197 S 0.0378 0.5816 0.3806 198 D 0.0283 0.6568 0.3149 199 F 0.0415 0.6712 0.2873 200 S 0.0396 0.7470 0.2134 201 E 0.0107 0.8404 0.1489 202 E 0.0112 0.8572 0.1316 203 V 0.0120 0.8784 0.1096 204 M 0.0090 0.9076 0.0834 205 E 0.0084 0.9176 0.0740 206 K 0.0085 0.9134 0.0780 207 F 0.0084 0.9180 0.0736 208 R 0.0083 0.9231 0.0686 209 V 0.0083 0.9242 0.0675 210 I 0.0083 0.9236 0.0681 211 L 0.0083 0.9222 0.0695 212 A 0.0083 0.9240 0.0677 213 L 0.0083 0.9231 0.0686 214 V 0.0085 0.9158 0.0757 215 K 0.0089 0.8794 0.1117 216 K 0.0128 0.7581 0.2291 217 R 0.0563 0.2239 0.7198 218 D 0.0603 0.0707 0.8690 219 Y 0.2422 0.0333 0.7245 220 E 0.6222 0.0337 0.3440 221 L 0.7657 0.0097 0.2246 222 D 0.7669 0.0115 0.2216 223 F 0.7458 0.0164 0.2379 224 N 0.5609 0.0571 0.3820 225 T 0.3133 0.1446 0.5421 226 A 0.1785 0.1868 0.6347 227 G 0.1269 0.2131 0.6599 228 L 0.1699 0.2412 0.5889 229 F 0.2246 0.1783 0.5970 230 K 0.2537 0.1293 0.6170 231 P 0.1814 0.2329 0.5857 232 L 0.1599 0.3077 0.5324 233 C 0.1487 0.2021 0.6492 234 G 0.1149 0.1350 0.7502 235 E 0.1898 0.0969 0.7133 236 T 0.2070 0.1197 0.6733 237 Y 0.2274 0.0540 0.7187 238 P 0.1641 0.0791 0.7568 239 P 0.0575 0.5537 0.3887 240 K 0.0134 0.8127 0.1740 241 K 0.0113 0.8815 0.1071 242 I 0.0093 0.9156 0.0750 243 V 0.0084 0.9206 0.0711 244 T 0.0083 0.9235 0.0682 245 L 0.0083 0.9213 0.0704 246 A 0.0087 0.9135 0.0778 247 S 0.0092 0.8880 0.1028 248 E 0.0148 0.7930 0.1921 249 L 0.0615 0.2914 0.6471 250 Q 0.0532 0.0741 0.8727 251 I 0.2098 0.0182 0.7720 252 P 0.3971 0.0378 0.5652 253 F 0.7722 0.0148 0.2130 254 V 0.7745 0.0121 0.2133 255 Y 0.7031 0.0273 0.2696 256 G 0.5025 0.0500 0.4475 257 S 0.2716 0.1077 0.6207 258 D 0.1849 0.1989 0.6163 259 S 0.1203 0.3088 0.5710 260 H 0.1412 0.2261 0.6327 261 G 0.1523 0.1967 0.6510 262 V 0.1053 0.4346 0.4602 263 Q 0.0999 0.4740 0.4261 264 D 0.1220 0.4573 0.4207 265 I 0.1091 0.4361 0.4549 266 G 0.0955 0.3403 0.5642 267 R 0.1076 0.3728 0.5196 268 G 0.1105 0.2752 0.6143 269 Y 0.1441 0.3927 0.4633 270 S 0.1224 0.5152 0.3624 271 T 0.1491 0.5263 0.3247 272 Y 0.1728 0.4708 0.3565 273 C 0.2013 0.3479 0.4508 274 Q 0.1616 0.3299 0.5085 275 K 0.1637 0.2621 0.5742