# This file is the result of combining several RDB files, specifically # T0501.t04.str2.rdb (weight 1.54425) # T0501.t04.str4.rdb (weight 0.924988) # T0501.t04.pb.rdb (weight 0.789901) # T0501.t04.bys.rdb (weight 0.748322) # T0501.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 T0501.t04.str2.rdb # ============================================ # TARGET T0501 # 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 T0501.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 1757 # # ============================================ # Comments from T0501.t04.str4.rdb # ============================================ # TARGET T0501 # 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 T0501.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 1757 # # ============================================ # Comments from T0501.t04.pb.rdb # ============================================ # TARGET T0501 # 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 T0501.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 1757 # # ============================================ # Comments from T0501.t04.bys.rdb # ============================================ # TARGET T0501 # 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 T0501.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 1757 # # ============================================ # Comments from T0501.t04.alpha.rdb # ============================================ # TARGET T0501 # 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 T0501.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 1757 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1801 0.2959 0.5240 2 L 0.1665 0.3148 0.5187 3 T 0.0920 0.5334 0.3746 4 K 0.0327 0.7773 0.1900 5 V 0.0199 0.8500 0.1301 6 I 0.0124 0.8836 0.1040 7 A 0.0096 0.8952 0.0952 8 Q 0.0094 0.9017 0.0890 9 A 0.0104 0.9033 0.0863 10 H 0.0143 0.8834 0.1023 11 I 0.0086 0.9059 0.0855 12 D 0.0084 0.9183 0.0734 13 H 0.0084 0.9199 0.0717 14 F 0.0085 0.9148 0.0767 15 T 0.0083 0.9209 0.0707 16 K 0.0083 0.9198 0.0719 17 W 0.0084 0.9185 0.0731 18 F 0.0089 0.9017 0.0894 19 E 0.0105 0.8209 0.1686 20 R 0.0232 0.5923 0.3845 21 A 0.0932 0.2634 0.6434 22 D 0.1550 0.1517 0.6934 23 K 0.4449 0.0434 0.5117 24 I 0.7419 0.0093 0.2488 25 V 0.7955 0.0058 0.1986 26 I 0.8011 0.0062 0.1926 27 V 0.7736 0.0141 0.2124 28 S 0.6538 0.0242 0.3220 29 H 0.4800 0.0336 0.4864 30 V 0.3217 0.0822 0.5961 31 S 0.2279 0.0482 0.7239 32 P 0.0765 0.3107 0.6128 33 D 0.0998 0.2026 0.6976 34 G 0.0525 0.3888 0.5587 35 D 0.0761 0.4813 0.4426 36 A 0.0736 0.7361 0.1903 37 I 0.0323 0.8566 0.1111 38 G 0.0189 0.8971 0.0840 39 S 0.0112 0.9161 0.0727 40 S 0.0083 0.9234 0.0683 41 L 0.0083 0.9245 0.0672 42 G 0.0083 0.9239 0.0678 43 L 0.0083 0.9235 0.0682 44 Y 0.0083 0.9229 0.0688 45 H 0.0083 0.9214 0.0703 46 F 0.0085 0.9167 0.0748 47 L 0.0090 0.8974 0.0936 48 D 0.0109 0.8335 0.1556 49 S 0.0223 0.7118 0.2659 50 Q 0.0624 0.2785 0.6590 51 D 0.0750 0.0931 0.8318 52 K 0.1836 0.0709 0.7455 53 I 0.3267 0.0611 0.6122 54 V 0.6369 0.0153 0.3478 55 N 0.7030 0.0137 0.2833 56 V 0.7750 0.0067 0.2183 57 I 0.7282 0.0164 0.2555 58 V 0.5835 0.0127 0.4038 59 P 0.2929 0.0869 0.6203 60 N 0.1474 0.1388 0.7138 61 A 0.1898 0.1159 0.6943 62 F 0.2252 0.0570 0.7178 63 P 0.1325 0.3091 0.5584 64 D 0.0636 0.5380 0.3985 65 F 0.0757 0.5023 0.4220 66 L 0.1510 0.3900 0.4590 67 K 0.1780 0.3006 0.5214 68 W 0.2310 0.2013 0.5677 69 M 0.2046 0.0946 0.7008 70 P 0.0980 0.3377 0.5643 71 G 0.0700 0.3012 0.6288 72 S 0.1307 0.3243 0.5450 73 K 0.1109 0.3743 0.5148 74 D 0.1294 0.3570 0.5136 75 I 0.1633 0.4111 0.4257 76 L 0.1750 0.4153 0.4097 77 L 0.1500 0.4593 0.3906 78 Y 0.0807 0.6289 0.2904 79 D 0.0625 0.6928 0.2447 80 R 0.0656 0.6946 0.2398 81 Y 0.0434 0.7726 0.1840 82 Q 0.0203 0.8445 0.1351 83 E 0.0179 0.8721 0.1100 84 F 0.0198 0.8555 0.1247 85 A 0.0171 0.8629 0.1200 86 D 0.0123 0.8668 0.1209 87 K 0.0161 0.8481 0.1358 88 L 0.0333 0.7704 0.1964 89 I 0.0625 0.6219 0.3156 90 M 0.0847 0.4159 0.4994 91 E 0.1345 0.1641 0.7014 92 A 0.2882 0.0542 0.6576 93 D 0.4226 0.0436 0.5338 94 V 0.7957 0.0062 0.1982 95 I 0.7729 0.0061 0.2210 96 C 0.8178 0.0043 0.1779 97 C 0.8087 0.0044 0.1869 98 L 0.7662 0.0142 0.2195 99 D 0.5012 0.0210 0.4778 100 F 0.2051 0.2089 0.5860 101 N 0.1127 0.2950 0.5923 102 A 0.0913 0.4540 0.4547 103 L 0.0558 0.6266 0.3176 104 K 0.0398 0.7017 0.2584 105 R 0.0680 0.6150 0.3170 106 I 0.0533 0.6985 0.2482 107 D 0.0298 0.7821 0.1880 108 E 0.0198 0.8376 0.1425 109 M 0.0149 0.8637 0.1214 110 S 0.0107 0.8925 0.0967 111 D 0.0105 0.8967 0.0928 112 I 0.0122 0.8779 0.1099 113 V 0.0218 0.8363 0.1419 114 A 0.0403 0.6792 0.2805 115 A 0.0889 0.4682 0.4428 116 S 0.1548 0.1410 0.7042 117 P 0.1259 0.1416 0.7325 118 G 0.2167 0.0637 0.7196 119 R 0.4580 0.0288 0.5132 120 K 0.7752 0.0059 0.2189 121 I 0.7929 0.0063 0.2008 122 M 0.7945 0.0059 0.1996 123 I 0.7712 0.0117 0.2172 124 D 0.6385 0.0284 0.3330 125 H 0.3992 0.0889 0.5119 126 H 0.2867 0.0917 0.6216 127 L 0.2253 0.1163 0.6583 128 Y 0.1824 0.0638 0.7539 129 P 0.0919 0.3578 0.5504 130 E 0.0546 0.4675 0.4780 131 D 0.0804 0.4395 0.4801 132 F 0.1537 0.3011 0.5452 133 C 0.1887 0.2174 0.5939 134 R 0.2175 0.2235 0.5589 135 I 0.3228 0.1475 0.5297 136 T 0.4678 0.1080 0.4242 137 I 0.6351 0.0558 0.3091 138 S 0.5947 0.0451 0.3602 139 H 0.3202 0.0254 0.6544 140 P 0.0969 0.3361 0.5670 141 E 0.0876 0.2991 0.6133 142 I 0.1333 0.3083 0.5584 143 S 0.0987 0.5006 0.4007 144 S 0.0610 0.6931 0.2458 145 T 0.0250 0.8229 0.1521 146 S 0.0104 0.9024 0.0873 147 E 0.0084 0.9228 0.0688 148 L 0.0083 0.9248 0.0669 149 V 0.0082 0.9252 0.0665 150 F 0.0082 0.9251 0.0666 151 R 0.0082 0.9253 0.0665 152 L 0.0083 0.9249 0.0668 153 I 0.0083 0.9226 0.0691 154 C 0.0085 0.9160 0.0754 155 R 0.0113 0.8327 0.1560 156 M 0.0544 0.4350 0.5106 157 G 0.0454 0.1532 0.8014 158 Y 0.1019 0.2062 0.6919 159 F 0.1410 0.2144 0.6446 160 S 0.1702 0.2555 0.5744 161 D 0.1844 0.1591 0.6565 162 I 0.2119 0.1316 0.6565 163 S 0.1677 0.0777 0.7547 164 K 0.0143 0.7331 0.2526 165 E 0.0123 0.8132 0.1745 166 G 0.0149 0.8672 0.1179 167 A 0.0141 0.9005 0.0854 168 E 0.0119 0.9109 0.0771 169 C 0.0170 0.9044 0.0786 170 I 0.0215 0.8958 0.0827 171 Y 0.0426 0.8507 0.1066 172 T 0.1023 0.7460 0.1517 173 G 0.2303 0.5409 0.2287 174 M 0.3109 0.4269 0.2622 175 M 0.3767 0.3006 0.3227 176 T 0.3678 0.2105 0.4217 177 D 0.2340 0.1851 0.5810 178 T 0.1453 0.1880 0.6667 179 G 0.1253 0.1399 0.7348 180 G 0.1800 0.1320 0.6881 181 F 0.3054 0.0931 0.6015 182 T 0.3497 0.0927 0.5576 183 Y 0.3128 0.0986 0.5885 184 N 0.2073 0.1957 0.5969 185 S 0.1825 0.1932 0.6243 186 N 0.1877 0.1721 0.6402 187 N 0.1820 0.1616 0.6564 188 R 0.0597 0.6057 0.3346 189 E 0.0369 0.7605 0.2026 190 I 0.0367 0.8278 0.1355 191 Y 0.0229 0.8811 0.0960 192 F 0.0199 0.8955 0.0847 193 I 0.0216 0.8886 0.0898 194 I 0.0104 0.8984 0.0912 195 S 0.0087 0.9115 0.0799 196 E 0.0087 0.9124 0.0789 197 L 0.0089 0.8989 0.0922 198 L 0.0107 0.8449 0.1443 199 S 0.0138 0.7435 0.2427 200 K 0.0522 0.2588 0.6890 201 G 0.0507 0.0788 0.8705 202 I 0.1457 0.0828 0.7716 203 D 0.1760 0.0295 0.7945 204 K 0.0204 0.6857 0.2938 205 D 0.0114 0.8353 0.1533 206 D 0.0103 0.8985 0.0912 207 I 0.0094 0.9143 0.0763 208 Y 0.0090 0.9145 0.0765 209 R 0.0097 0.9098 0.0806 210 K 0.0127 0.8873 0.0999 211 V 0.0262 0.8120 0.1619 212 Y 0.0420 0.6660 0.2920 213 N 0.0539 0.4851 0.4610 214 T 0.0669 0.3310 0.6020 215 Y 0.0997 0.2475 0.6527 216 S 0.0867 0.4369 0.4764 217 E 0.0115 0.7882 0.2003 218 S 0.0094 0.8693 0.1213 219 R 0.0088 0.9137 0.0775 220 L 0.0085 0.9217 0.0699 221 R 0.0083 0.9206 0.0711 222 L 0.0086 0.9126 0.0788 223 M 0.0087 0.9119 0.0793 224 G 0.0084 0.9151 0.0765 225 Y 0.0085 0.9142 0.0774 226 V 0.0101 0.9045 0.0854 227 L 0.0150 0.8506 0.1344 228 S 0.0226 0.7141 0.2633 229 N 0.0505 0.3809 0.5686 230 M 0.1166 0.3569 0.5265 231 K 0.2082 0.4107 0.3811 232 V 0.3896 0.3209 0.2895 233 Y 0.3821 0.2674 0.3505 234 K 0.3176 0.3096 0.3728 235 D 0.2080 0.3129 0.4792 236 Y 0.1524 0.2392 0.6084 237 N 0.2163 0.1801 0.6036 238 S 0.4419 0.1692 0.3888 239 A 0.6301 0.1137 0.2562 240 L 0.7110 0.0938 0.1952 241 I 0.7238 0.0995 0.1766 242 S 0.7043 0.1062 0.1895 243 L 0.6661 0.1120 0.2219 244 T 0.5065 0.1820 0.3114 245 K 0.2516 0.4640 0.2844 246 E 0.1462 0.5869 0.2669 247 E 0.1277 0.5660 0.3063 248 Q 0.1258 0.4345 0.4396 249 G 0.1110 0.3262 0.5629 250 K 0.1757 0.2779 0.5464 251 F 0.2286 0.2326 0.5389 252 D 0.2309 0.2251 0.5440 253 Y 0.2712 0.2220 0.5068 254 I 0.2639 0.1705 0.5656 255 K 0.1845 0.1867 0.6288 256 G 0.1169 0.1730 0.7101 257 D 0.1484 0.2203 0.6313 258 S 0.1548 0.2919 0.5533 259 E 0.1156 0.4081 0.4763 260 G 0.1376 0.3772 0.4853 261 F 0.2134 0.3943 0.3923 262 V 0.2772 0.3258 0.3970 263 N 0.2898 0.2558 0.4544 264 I 0.3323 0.2175 0.4502 265 P 0.2735 0.3162 0.4103 266 L 0.2894 0.3396 0.3710 267 S 0.2609 0.2743 0.4648 268 I 0.1970 0.3826 0.4204 269 K 0.1175 0.3031 0.5794 270 N 0.1097 0.1609 0.7294 271 V 0.2878 0.0514 0.6609 272 C 0.3781 0.0448 0.5771 273 F 0.6124 0.0249 0.3627 274 S 0.7066 0.0150 0.2784 275 C 0.8072 0.0060 0.1868 276 F 0.8147 0.0052 0.1801 277 L 0.8073 0.0062 0.1866 278 R 0.7678 0.0107 0.2215 279 E 0.6707 0.0292 0.3001 280 D 0.4651 0.0723 0.4626 281 T 0.2572 0.1683 0.5746 282 E 0.1283 0.2058 0.6659 283 K 0.1487 0.1323 0.7191 284 K 0.4071 0.0511 0.5418 285 M 0.6971 0.0122 0.2907 286 I 0.7775 0.0074 0.2150 287 K 0.8202 0.0047 0.1752 288 I 0.8218 0.0045 0.1736 289 S 0.7966 0.0062 0.1972 290 L 0.7608 0.0123 0.2270 291 R 0.6853 0.0285 0.2862 292 S 0.4870 0.0375 0.4755 293 V 0.1917 0.1714 0.6369 294 G 0.0993 0.1602 0.7405 295 K 0.1407 0.1386 0.7207 296 F 0.2692 0.0705 0.6603 297 P 0.2273 0.0757 0.6970 298 C 0.0353 0.6790 0.2857 299 N 0.0114 0.8516 0.1370 300 R 0.0095 0.9119 0.0786 301 L 0.0091 0.9160 0.0750 302 A 0.0090 0.9065 0.0845 303 A 0.0090 0.9027 0.0883 304 E 0.0101 0.8684 0.1215 305 F 0.0273 0.7447 0.2280 306 F 0.0453 0.5771 0.3776 307 N 0.0669 0.3779 0.5552 308 G 0.0751 0.2376 0.6874 309 G 0.1070 0.2101 0.6830 310 G 0.1455 0.2757 0.5788 311 H 0.1775 0.3448 0.4777 312 L 0.1019 0.5407 0.3573 313 N 0.1446 0.4401 0.4154 314 A 0.2027 0.3407 0.4566 315 S 0.2425 0.2054 0.5521 316 G 0.3242 0.1390 0.5369 317 G 0.4079 0.0998 0.4924 318 E 0.4953 0.0953 0.4094 319 F 0.4188 0.0988 0.4824 320 Y 0.2290 0.1413 0.6297 321 G 0.1489 0.1478 0.7033 322 T 0.1547 0.0920 0.7533 323 M 0.0145 0.7303 0.2552 324 E 0.0094 0.8664 0.1242 325 E 0.0083 0.9219 0.0698 326 A 0.0084 0.9223 0.0694 327 V 0.0083 0.9237 0.0680 328 K 0.0083 0.9248 0.0670 329 V 0.0083 0.9246 0.0672 330 F 0.0083 0.9223 0.0694 331 E 0.0083 0.9227 0.0690 332 Q 0.0083 0.9232 0.0685 333 A 0.0084 0.9187 0.0729 334 L 0.0086 0.9013 0.0900 335 E 0.0087 0.8730 0.1183 336 K 0.0110 0.7904 0.1986 337 Y 0.0303 0.5921 0.3776 338 K 0.0694 0.4085 0.5221 339 P 0.0495 0.4529 0.4976 340 L 0.0826 0.4007 0.5167 341 L 0.1335 0.3121 0.5545 342 K 0.1270 0.3163 0.5567 343 E 0.1462 0.2557 0.5981