# This file is the result of combining several RDB files, specifically # T0407.t04.str2.rdb (weight 1.54425) # T0407.t04.str4.rdb (weight 0.924988) # T0407.t04.pb.rdb (weight 0.789901) # T0407.t04.bys.rdb (weight 0.748322) # T0407.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 T0407.t04.str2.rdb # ============================================ # TARGET T0407 # 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 T0407.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 1930 # # ============================================ # Comments from T0407.t04.str4.rdb # ============================================ # TARGET T0407 # 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 T0407.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 1930 # # ============================================ # Comments from T0407.t04.pb.rdb # ============================================ # TARGET T0407 # 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 T0407.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 1930 # # ============================================ # Comments from T0407.t04.bys.rdb # ============================================ # TARGET T0407 # 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 T0407.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 1930 # # ============================================ # Comments from T0407.t04.alpha.rdb # ============================================ # TARGET T0407 # 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 T0407.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 1930 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.6718 0.0199 0.3083 2 E 0.7209 0.0171 0.2619 3 V 0.6831 0.0220 0.2950 4 K 0.5728 0.0842 0.3430 5 K 0.5886 0.0745 0.3369 6 V 0.5519 0.0949 0.3531 7 L 0.4685 0.1333 0.3981 8 V 0.3287 0.2169 0.4544 9 S 0.1766 0.3392 0.4842 10 A 0.1466 0.4312 0.4222 11 F 0.2204 0.3321 0.4475 12 L 0.2022 0.3577 0.4401 13 L 0.1172 0.5886 0.2942 14 T 0.1573 0.5727 0.2700 15 T 0.2447 0.4991 0.2562 16 C 0.3306 0.4225 0.2469 17 L 0.3372 0.3788 0.2841 18 M 0.2371 0.3423 0.4207 19 S 0.1146 0.4059 0.4795 20 G 0.0780 0.4135 0.5085 21 Q 0.1106 0.5549 0.3345 22 A 0.1109 0.6615 0.2276 23 Q 0.0990 0.7000 0.2010 24 R 0.1466 0.5995 0.2539 25 R 0.1755 0.4519 0.3725 26 N 0.1829 0.2959 0.5212 27 E 0.2160 0.2502 0.5338 28 I 0.2569 0.1591 0.5840 29 Q 0.2747 0.0997 0.6256 30 V 0.2639 0.0598 0.6763 31 P 0.1786 0.1872 0.6342 32 D 0.1639 0.2044 0.6316 33 L 0.1669 0.2389 0.5942 34 D 0.1266 0.2257 0.6477 35 G 0.0943 0.1968 0.7089 36 Y 0.1988 0.1599 0.6414 37 T 0.2962 0.1283 0.5755 38 T 0.3653 0.1216 0.5132 39 L 0.4813 0.0967 0.4220 40 K 0.6395 0.0490 0.3115 41 C 0.7006 0.0316 0.2677 42 D 0.6602 0.0398 0.3000 43 F 0.6689 0.0525 0.2786 44 H 0.6349 0.0496 0.3155 45 M 0.6121 0.0513 0.3366 46 H 0.4906 0.0764 0.4329 47 S 0.4350 0.0864 0.4786 48 V 0.3424 0.1468 0.5108 49 F 0.2802 0.1538 0.5659 50 S 0.1990 0.1642 0.6368 51 D 0.1263 0.2371 0.6367 52 G 0.1234 0.1852 0.6914 53 L 0.1921 0.1867 0.6212 54 V 0.2322 0.1033 0.6645 55 W 0.1751 0.0385 0.7865 56 P 0.0208 0.6784 0.3008 57 T 0.0106 0.8417 0.1477 58 V 0.0094 0.9062 0.0844 59 R 0.0092 0.9111 0.0797 60 V 0.0085 0.9141 0.0775 61 D 0.0083 0.9226 0.0691 62 E 0.0083 0.9226 0.0691 63 A 0.0084 0.9190 0.0726 64 Y 0.0089 0.9021 0.0890 65 R 0.0106 0.8335 0.1559 66 D 0.0511 0.2164 0.7325 67 G 0.0470 0.0638 0.8892 68 L 0.1947 0.0299 0.7755 69 D 0.3283 0.0918 0.5798 70 A 0.7587 0.0212 0.2201 71 I 0.7644 0.0140 0.2216 72 S 0.7945 0.0073 0.1982 73 L 0.7461 0.0286 0.2253 74 T 0.5540 0.0451 0.4009 75 E 0.2474 0.1889 0.5638 76 H 0.1411 0.2384 0.6206 77 I 0.1296 0.3441 0.5263 78 E 0.0950 0.3607 0.5442 79 Y 0.1297 0.2644 0.6059 80 R 0.1702 0.1528 0.6770 81 P 0.0826 0.3984 0.5190 82 H 0.1007 0.3838 0.5155 83 K 0.1192 0.3654 0.5154 84 Q 0.1078 0.3510 0.5412 85 D 0.1230 0.3084 0.5687 86 V 0.1576 0.3272 0.5151 87 V 0.1034 0.5224 0.3742 88 S 0.0710 0.5967 0.3324 89 D 0.0647 0.5772 0.3581 90 H 0.0471 0.6925 0.2604 91 N 0.0208 0.8212 0.1580 92 R 0.0122 0.8564 0.1313 93 S 0.0132 0.8619 0.1249 94 F 0.0089 0.8966 0.0944 95 D 0.0085 0.9142 0.0773 96 L 0.0084 0.9165 0.0752 97 C 0.0085 0.9153 0.0762 98 R 0.0084 0.9176 0.0739 99 E 0.0083 0.9212 0.0705 100 Q 0.0085 0.9112 0.0803 101 A 0.0092 0.9000 0.0908 102 E 0.0092 0.8581 0.1327 103 K 0.0156 0.7824 0.2020 104 L 0.0582 0.2799 0.6619 105 G 0.0512 0.0668 0.8820 106 I 0.2475 0.0136 0.7389 107 L 0.5060 0.0187 0.4753 108 L 0.7166 0.0128 0.2706 109 I 0.6730 0.0210 0.3059 110 K 0.6531 0.0303 0.3166 111 G 0.6308 0.0260 0.3432 112 S 0.7009 0.0200 0.2791 113 E 0.7520 0.0154 0.2325 114 I 0.7391 0.0151 0.2458 115 T 0.6485 0.0267 0.3248 116 R 0.5935 0.0605 0.3459 117 A 0.3671 0.0913 0.5416 118 M 0.2444 0.1004 0.6552 119 A 0.2074 0.0611 0.7315 120 P 0.1637 0.1569 0.6794 121 G 0.2019 0.0934 0.7046 122 H 0.5159 0.0342 0.4500 123 F 0.7467 0.0082 0.2450 124 N 0.7928 0.0074 0.1998 125 A 0.7992 0.0052 0.1956 126 I 0.7792 0.0107 0.2100 127 F 0.6820 0.0131 0.3049 128 L 0.4377 0.0608 0.5015 129 S 0.2491 0.0797 0.6712 130 D 0.1228 0.2380 0.6392 131 S 0.1138 0.2194 0.6668 132 N 0.1736 0.1296 0.6968 133 P 0.0875 0.4113 0.5012 134 L 0.0830 0.5441 0.3729 135 E 0.0944 0.5109 0.3947 136 Q 0.0414 0.6949 0.2637 137 K 0.0320 0.7052 0.2627 138 D 0.0413 0.6535 0.3052 139 Y 0.0215 0.7578 0.2207 140 K 0.0103 0.8769 0.1128 141 D 0.0088 0.9148 0.0764 142 A 0.0086 0.9144 0.0770 143 F 0.0083 0.9206 0.0711 144 R 0.0083 0.9215 0.0702 145 E 0.0084 0.9207 0.0710 146 A 0.0088 0.9095 0.0818 147 K 0.0099 0.8682 0.1219 148 K 0.0118 0.7564 0.2318 149 Q 0.0556 0.2135 0.7308 150 G 0.0562 0.0675 0.8763 151 A 0.2576 0.0414 0.7010 152 F 0.6680 0.0196 0.3125 153 M 0.7780 0.0101 0.2120 154 F 0.7502 0.0187 0.2311 155 W 0.5872 0.0577 0.3551 156 N 0.3767 0.0872 0.5361 157 H 0.2161 0.0751 0.7088 158 P 0.0973 0.3372 0.5655 159 G 0.0756 0.1879 0.7365 160 W 0.1384 0.2162 0.6453 161 D 0.1326 0.2143 0.6530 162 S 0.1131 0.2488 0.6381 163 Q 0.1469 0.1426 0.7105 164 Q 0.2081 0.0573 0.7347 165 P 0.1518 0.2709 0.5774 166 D 0.1153 0.3478 0.5369 167 T 0.1138 0.4039 0.4822 168 T 0.1161 0.4265 0.4574 169 K 0.1021 0.4671 0.4307 170 W 0.1284 0.3381 0.5335 171 W 0.1427 0.2326 0.6248 172 P 0.0319 0.6134 0.3547 173 E 0.0375 0.6186 0.3439 174 H 0.0323 0.7384 0.2293 175 T 0.0196 0.8338 0.1466 176 A 0.0222 0.8654 0.1124 177 L 0.0249 0.8260 0.1491 178 Y 0.0460 0.7430 0.2109 179 Q 0.0437 0.6566 0.2998 180 E 0.0713 0.2816 0.6472 181 G 0.0737 0.1104 0.8159 182 C 0.2291 0.0928 0.6781 183 M 0.3597 0.0787 0.5616 184 H 0.5032 0.0644 0.4324 185 G 0.7115 0.0267 0.2618 186 I 0.7890 0.0118 0.1992 187 E 0.7982 0.0090 0.1927 188 V 0.7538 0.0240 0.2223 189 A 0.4936 0.0807 0.4258 190 N 0.2562 0.1087 0.6351 191 G 0.1297 0.1633 0.7070 192 H 0.1293 0.2403 0.6304 193 L 0.1328 0.2725 0.5948 194 Y 0.1328 0.2336 0.6336 195 M 0.1212 0.2725 0.6063 196 P 0.0229 0.7382 0.2388 197 E 0.0141 0.8495 0.1363 198 A 0.0108 0.8995 0.0897 199 I 0.0087 0.9159 0.0754 200 Q 0.0084 0.9219 0.0697 201 W 0.0084 0.9176 0.0740 202 C 0.0094 0.9062 0.0844 203 L 0.0095 0.8790 0.1115 204 D 0.0166 0.7541 0.2293 205 K 0.0614 0.2670 0.6716 206 N 0.0585 0.0697 0.8718 207 L 0.2277 0.0170 0.7553 208 T 0.4913 0.0330 0.4758 209 M 0.7709 0.0124 0.2167 210 I 0.7659 0.0152 0.2189 211 G 0.7151 0.0175 0.2674 212 T 0.5418 0.0528 0.4054 213 S 0.3043 0.1115 0.5842 214 D 0.2274 0.1678 0.6048 215 I 0.1636 0.2522 0.5842 216 H 0.1767 0.1635 0.6599 217 Q 0.2314 0.1086 0.6600 218 P 0.1896 0.1863 0.6241 219 I 0.1939 0.2005 0.6056 220 Q 0.1690 0.2829 0.5481 221 T 0.1569 0.3115 0.5316 222 D 0.1647 0.2652 0.5701 223 Y 0.1476 0.3572 0.4952 224 D 0.1443 0.3355 0.5202 225 F 0.1500 0.3468 0.5032 226 E 0.1440 0.2940 0.5620 227 K 0.1201 0.3550 0.5249 228 G 0.1100 0.3048 0.5852 229 E 0.1426 0.3845 0.4729 230 H 0.1295 0.4702 0.4003 231 R 0.1281 0.5043 0.3676 232 T 0.2127 0.4277 0.3596 233 M 0.3479 0.3253 0.3268 234 T 0.4396 0.3043 0.2561 235 F 0.5612 0.2428 0.1960 236 V 0.5591 0.2441 0.1969 237 F 0.4791 0.2786 0.2422 238 A 0.3074 0.3498 0.3428 239 K 0.1505 0.3666 0.4829 240 E 0.1035 0.3138 0.5827 241 R 0.1667 0.2241 0.6092 242 S 0.1853 0.1416 0.6731 243 L 0.0199 0.6862 0.2939 244 Q 0.0130 0.8256 0.1614 245 G 0.0186 0.8553 0.1261 246 I 0.0098 0.8983 0.0919 247 R 0.0095 0.9056 0.0849 248 E 0.0094 0.8969 0.0936 249 A 0.0123 0.8692 0.1185 250 L 0.0245 0.7630 0.2126 251 D 0.0336 0.5451 0.4212 252 N 0.0746 0.2696 0.6558 253 R 0.0932 0.2321 0.6747 254 R 0.1568 0.2340 0.6093 255 T 0.3398 0.1715 0.4887 256 A 0.4831 0.1328 0.3841 257 A 0.4955 0.1391 0.3653 258 Y 0.4475 0.1184 0.4341 259 F 0.2904 0.1232 0.5863 260 H 0.0728 0.5578 0.3695 261 E 0.0229 0.7636 0.2135 262 L 0.0207 0.8250 0.1543 263 L 0.0262 0.8131 0.1607 264 I 0.0265 0.8017 0.1718 265 G 0.0353 0.7220 0.2427 266 R 0.0407 0.6722 0.2871 267 E 0.0263 0.7385 0.2351 268 D 0.0137 0.7679 0.2184 269 L 0.0200 0.6876 0.2924 270 L 0.0361 0.6790 0.2849 271 R 0.0288 0.8133 0.1579 272 P 0.0090 0.9023 0.0887 273 F 0.0089 0.9083 0.0828 274 F 0.0093 0.9059 0.0849 275 E 0.0092 0.9040 0.0869 276 K 0.0134 0.8440 0.1425 277 C 0.0330 0.8401 0.1269 278 V 0.0421 0.8403 0.1177 279 K 0.0437 0.8511 0.1052 280 I 0.0240 0.8698 0.1062 281 E 0.0232 0.8667 0.1102 282 E 0.0303 0.8370 0.1327 283 V 0.0676 0.6802 0.2521 284 S 0.1306 0.4078 0.4616 285 R 0.0944 0.3263 0.5793 286 N 0.1343 0.2435 0.6222 287 E 0.1591 0.2437 0.5972 288 Q 0.2022 0.1722 0.6255 289 G 0.2849 0.0693 0.6458 290 V 0.3816 0.0519 0.5665 291 T 0.5460 0.0379 0.4162 292 L 0.6333 0.0166 0.3501 293 S 0.6177 0.0175 0.3649 294 I 0.4816 0.0328 0.4856 295 T 0.2656 0.1095 0.6249 296 N 0.1719 0.1299 0.6982 297 V 0.0919 0.3058 0.6023 298 T 0.0872 0.4715 0.4413 299 D 0.1063 0.5943 0.2994 300 L 0.0288 0.8082 0.1630 301 V 0.0131 0.8795 0.1074 302 L 0.0098 0.9131 0.0771 303 K 0.0113 0.9048 0.0840 304 L 0.0175 0.8799 0.1025 305 K 0.0160 0.8631 0.1209 306 K 0.0294 0.7968 0.1738 307 T 0.0963 0.5863 0.3174 308 A 0.1473 0.3617 0.4910 309 H 0.1064 0.4318 0.4617 310 D 0.0988 0.3911 0.5101 311 T 0.1218 0.3553 0.5230 312 L 0.1584 0.3944 0.4471 313 L 0.2849 0.3496 0.3656 314 V 0.4060 0.2526 0.3414 315 Y 0.4095 0.1665 0.4240 316 F 0.3074 0.1412 0.5514 317 R 0.1896 0.2979 0.5125 318 D 0.2110 0.2361 0.5529 319 M 0.2373 0.1686 0.5940 320 T 0.2143 0.1160 0.6697 321 L 0.2170 0.1128 0.6702 322 K 0.2099 0.0645 0.7256 323 P 0.1611 0.2721 0.5668 324 H 0.2262 0.2416 0.5321 325 T 0.4728 0.1277 0.3995 326 R 0.6497 0.0545 0.2958 327 Y 0.7477 0.0333 0.2190 328 T 0.7857 0.0161 0.1982 329 V 0.8057 0.0135 0.1808 330 R 0.7828 0.0199 0.1972 331 I 0.7317 0.0576 0.2106 332 G 0.6156 0.1079 0.2765 333 F 0.4344 0.2664 0.2992 334 K 0.2910 0.3781 0.3309 335 Q 0.1598 0.2955 0.5448 336 G 0.1279 0.1794 0.6927 337 I 0.2436 0.1512 0.6052 338 K 0.2763 0.1318 0.5919 339 G 0.2329 0.1074 0.6597 340 G 0.1904 0.1220 0.6875 341 D 0.2188 0.1366 0.6446 342 V 0.2881 0.1416 0.5703 343 N 0.3207 0.1645 0.5149 344 F 0.4473 0.2054 0.3473 345 E 0.5603 0.1561 0.2835 346 V 0.5455 0.1754 0.2791 347 T 0.4757 0.1930 0.3313 348 N 0.4492 0.1515 0.3993 349 F 0.5678 0.0892 0.3430 350 I 0.6257 0.0538 0.3205 351 V 0.6362 0.0410 0.3228 352 A 0.4166 0.0369 0.5465 353 P 0.1966 0.1935 0.6099 354 D 0.1192 0.1822 0.6987 355 K 0.1235 0.1629 0.7137 356 G 0.2208 0.1105 0.6686 357 L 0.4955 0.0902 0.4143 358 K 0.5832 0.1009 0.3159 359 Y 0.6644 0.0899 0.2457 360 T 0.6352 0.1204 0.2444 361 I 0.6093 0.1364 0.2543 362 S 0.4637 0.1524 0.3839 363 L 0.2331 0.2203 0.5466