# This file is the result of combining several RDB files, specifically # T0407.t06.str2.rdb (weight 1.54425) # T0407.t06.str4.rdb (weight 0.924988) # T0407.t06.pb.rdb (weight 0.789901) # T0407.t06.bys.rdb (weight 0.748322) # T0407.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 T0407.t06.str2.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2397 # # ============================================ # Comments from T0407.t06.str4.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2397 # # ============================================ # Comments from T0407.t06.pb.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2397 # # ============================================ # Comments from T0407.t06.bys.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2397 # # ============================================ # Comments from T0407.t06.alpha.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2397 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.6663 0.0190 0.3147 2 E 0.6853 0.0232 0.2915 3 V 0.6759 0.0374 0.2868 4 K 0.5716 0.1143 0.3141 5 K 0.5657 0.1380 0.2964 6 V 0.5449 0.1678 0.2873 7 L 0.5385 0.1837 0.2778 8 V 0.4309 0.2176 0.3515 9 S 0.2858 0.3191 0.3951 10 A 0.1561 0.4307 0.4132 11 F 0.1815 0.3829 0.4356 12 L 0.2616 0.2602 0.4782 13 L 0.2180 0.3196 0.4624 14 T 0.1436 0.5164 0.3400 15 T 0.2029 0.4878 0.3093 16 C 0.3092 0.3763 0.3145 17 L 0.3818 0.2871 0.3311 18 M 0.3857 0.1950 0.4192 19 S 0.2358 0.1295 0.6346 20 G 0.0940 0.4138 0.4922 21 Q 0.0912 0.4656 0.4432 22 A 0.1306 0.5061 0.3633 23 Q 0.1808 0.4741 0.3452 24 R 0.2197 0.4132 0.3672 25 R 0.2802 0.3028 0.4170 26 N 0.2625 0.2244 0.5132 27 E 0.2763 0.1845 0.5391 28 I 0.3282 0.1229 0.5489 29 Q 0.3229 0.0912 0.5858 30 V 0.2906 0.0405 0.6689 31 P 0.2206 0.1658 0.6136 32 D 0.1948 0.1598 0.6454 33 L 0.1635 0.2304 0.6060 34 D 0.1087 0.2193 0.6720 35 G 0.0832 0.1722 0.7446 36 Y 0.2033 0.1522 0.6445 37 T 0.2982 0.1478 0.5541 38 T 0.4121 0.1321 0.4558 39 L 0.4995 0.1223 0.3782 40 K 0.6341 0.0618 0.3042 41 C 0.6798 0.0421 0.2781 42 D 0.6307 0.0461 0.3232 43 F 0.6918 0.0453 0.2629 44 H 0.6554 0.0471 0.2975 45 M 0.6502 0.0449 0.3049 46 H 0.5246 0.0526 0.4228 47 S 0.3846 0.0597 0.5556 48 V 0.2756 0.1313 0.5930 49 F 0.2448 0.1561 0.5991 50 S 0.1818 0.1662 0.6520 51 D 0.1117 0.2229 0.6654 52 G 0.0972 0.2184 0.6844 53 L 0.1557 0.2222 0.6221 54 V 0.2092 0.1305 0.6602 55 W 0.1787 0.0725 0.7488 56 P 0.0203 0.7161 0.2635 57 T 0.0099 0.8597 0.1304 58 V 0.0087 0.9185 0.0728 59 R 0.0086 0.9199 0.0714 60 V 0.0084 0.9184 0.0732 61 D 0.0083 0.9227 0.0690 62 E 0.0083 0.9242 0.0676 63 A 0.0084 0.9231 0.0685 64 Y 0.0086 0.9146 0.0768 65 R 0.0119 0.8318 0.1563 66 D 0.0536 0.3082 0.6382 67 G 0.0420 0.0741 0.8839 68 L 0.1826 0.0232 0.7942 69 D 0.2977 0.0702 0.6321 70 A 0.7655 0.0228 0.2116 71 I 0.7614 0.0145 0.2241 72 S 0.8007 0.0101 0.1891 73 L 0.7557 0.0185 0.2257 74 T 0.5993 0.0308 0.3699 75 E 0.2646 0.1786 0.5568 76 H 0.1609 0.2341 0.6050 77 I 0.1511 0.3151 0.5338 78 E 0.1006 0.3624 0.5370 79 Y 0.1468 0.2790 0.5743 80 R 0.1789 0.1809 0.6401 81 P 0.1329 0.3044 0.5627 82 H 0.1279 0.3474 0.5247 83 K 0.1058 0.4067 0.4875 84 Q 0.1084 0.3778 0.5137 85 D 0.1292 0.2921 0.5787 86 V 0.1520 0.3423 0.5057 87 V 0.1208 0.4843 0.3950 88 S 0.0572 0.5972 0.3456 89 D 0.0547 0.5630 0.3824 90 H 0.0447 0.7116 0.2437 91 N 0.0126 0.8658 0.1216 92 R 0.0098 0.8972 0.0930 93 S 0.0097 0.9082 0.0821 94 F 0.0087 0.9079 0.0835 95 D 0.0083 0.9204 0.0713 96 L 0.0084 0.9199 0.0717 97 C 0.0084 0.9188 0.0728 98 R 0.0084 0.9175 0.0741 99 E 0.0086 0.9074 0.0841 100 Q 0.0115 0.8748 0.1137 101 A 0.0172 0.8152 0.1676 102 E 0.0238 0.7397 0.2365 103 K 0.0437 0.5072 0.4491 104 L 0.0744 0.1958 0.7298 105 G 0.0880 0.0755 0.8366 106 I 0.3977 0.0126 0.5897 107 L 0.6250 0.0172 0.3578 108 L 0.6963 0.0114 0.2923 109 I 0.6849 0.0177 0.2973 110 K 0.5977 0.0371 0.3652 111 G 0.5330 0.0419 0.4250 112 S 0.6257 0.0418 0.3325 113 E 0.7089 0.0317 0.2595 114 I 0.7030 0.0330 0.2639 115 T 0.6911 0.0293 0.2796 116 R 0.6258 0.0490 0.3252 117 A 0.4784 0.0753 0.4463 118 M 0.3277 0.0822 0.5901 119 A 0.2467 0.0510 0.7023 120 P 0.1658 0.1253 0.7089 121 G 0.2206 0.0897 0.6897 122 H 0.5167 0.0308 0.4525 123 F 0.7755 0.0075 0.2171 124 N 0.7851 0.0089 0.2060 125 A 0.8051 0.0070 0.1879 126 I 0.7775 0.0134 0.2091 127 F 0.6828 0.0152 0.3020 128 L 0.4423 0.0541 0.5036 129 S 0.2413 0.0832 0.6755 130 D 0.1065 0.2358 0.6576 131 S 0.0986 0.2298 0.6716 132 N 0.1733 0.1150 0.7117 133 P 0.1086 0.3514 0.5400 134 L 0.0766 0.5197 0.4038 135 E 0.0887 0.5169 0.3944 136 Q 0.0652 0.6249 0.3098 137 K 0.0468 0.6677 0.2855 138 D 0.0555 0.6091 0.3355 139 Y 0.0382 0.7027 0.2591 140 K 0.0167 0.8161 0.1672 141 D 0.0140 0.8587 0.1272 142 A 0.0110 0.9019 0.0871 143 F 0.0090 0.9154 0.0756 144 R 0.0088 0.9157 0.0755 145 E 0.0092 0.9059 0.0849 146 A 0.0124 0.8821 0.1056 147 K 0.0141 0.8498 0.1361 148 K 0.0273 0.6734 0.2993 149 Q 0.0659 0.2523 0.6817 150 G 0.0546 0.1016 0.8438 151 A 0.2447 0.0600 0.6954 152 F 0.5551 0.0400 0.4049 153 M 0.6654 0.0371 0.2975 154 F 0.6653 0.0526 0.2821 155 W 0.5001 0.1103 0.3896 156 N 0.3423 0.1077 0.5501 157 H 0.2366 0.0434 0.7200 158 P 0.0945 0.3052 0.6003 159 G 0.0768 0.2466 0.6766 160 W 0.1232 0.2630 0.6137 161 D 0.0985 0.2997 0.6018 162 S 0.0864 0.2947 0.6189 163 Q 0.1325 0.1737 0.6938 164 Q 0.1735 0.1076 0.7189 165 P 0.0541 0.4711 0.4748 166 D 0.0514 0.4999 0.4487 167 T 0.0530 0.5922 0.3548 168 T 0.0331 0.7411 0.2258 169 K 0.0245 0.7489 0.2266 170 W 0.0383 0.6735 0.2882 171 W 0.0318 0.7629 0.2053 172 P 0.0099 0.8765 0.1136 173 E 0.0090 0.8981 0.0929 174 H 0.0096 0.9065 0.0839 175 T 0.0090 0.9054 0.0855 176 A 0.0096 0.8821 0.1083 177 L 0.0146 0.7700 0.2154 178 Y 0.0337 0.6852 0.2811 179 Q 0.0261 0.6418 0.3321 180 E 0.0404 0.4472 0.5124 181 G 0.0395 0.1838 0.7767 182 C 0.1895 0.1605 0.6500 183 M 0.3751 0.1057 0.5192 184 H 0.5107 0.0877 0.4016 185 G 0.7124 0.0436 0.2440 186 I 0.7537 0.0245 0.2218 187 E 0.7678 0.0210 0.2112 188 V 0.7034 0.0306 0.2660 189 A 0.4590 0.0765 0.4646 190 N 0.2391 0.1148 0.6461 191 G 0.1247 0.1697 0.7056 192 H 0.1345 0.2483 0.6172 193 L 0.1454 0.2545 0.6001 194 Y 0.1530 0.2270 0.6200 195 M 0.1502 0.2826 0.5673 196 P 0.0307 0.6922 0.2771 197 E 0.0171 0.8408 0.1421 198 A 0.0128 0.8940 0.0932 199 I 0.0086 0.9169 0.0745 200 Q 0.0084 0.9207 0.0709 201 W 0.0085 0.9157 0.0759 202 C 0.0104 0.9072 0.0824 203 L 0.0098 0.8933 0.0969 204 D 0.0175 0.7591 0.2233 205 K 0.0606 0.2918 0.6476 206 N 0.0543 0.0782 0.8676 207 L 0.2268 0.0177 0.7555 208 T 0.4270 0.0278 0.5452 209 M 0.7444 0.0136 0.2421 210 I 0.7769 0.0124 0.2107 211 G 0.6876 0.0210 0.2913 212 T 0.5589 0.0658 0.3754 213 S 0.3164 0.1160 0.5676 214 D 0.2104 0.2085 0.5811 215 I 0.1477 0.2957 0.5566 216 H 0.1722 0.1875 0.6403 217 Q 0.2104 0.1067 0.6829 218 P 0.1690 0.2090 0.6220 219 I 0.1852 0.2328 0.5821 220 Q 0.1646 0.2774 0.5580 221 T 0.1422 0.3135 0.5443 222 D 0.1469 0.2937 0.5594 223 Y 0.1385 0.3633 0.4983 224 D 0.1307 0.3573 0.5120 225 F 0.1186 0.3759 0.5055 226 E 0.0962 0.3535 0.5503 227 K 0.0959 0.2567 0.6474 228 G 0.1010 0.1385 0.7605 229 E 0.1615 0.1631 0.6753 230 H 0.1704 0.2129 0.6167 231 R 0.1728 0.2684 0.5589 232 T 0.3101 0.2336 0.4563 233 M 0.4237 0.2660 0.3104 234 T 0.4334 0.3465 0.2202 235 F 0.5252 0.2888 0.1860 236 V 0.4471 0.3656 0.1874 237 F 0.3734 0.3940 0.2326 238 A 0.2667 0.3944 0.3389 239 K 0.1102 0.3564 0.5334 240 E 0.1064 0.2413 0.6522 241 R 0.1826 0.1655 0.6519 242 S 0.1811 0.1227 0.6961 243 L 0.0441 0.6536 0.3022 244 Q 0.0252 0.7656 0.2092 245 G 0.0278 0.8104 0.1618 246 I 0.0166 0.8695 0.1139 247 R 0.0124 0.8879 0.0996 248 E 0.0147 0.8728 0.1125 249 A 0.0254 0.8083 0.1663 250 L 0.0469 0.7145 0.2386 251 D 0.0508 0.5676 0.3817 252 N 0.0899 0.3335 0.5766 253 R 0.0840 0.3183 0.5977 254 R 0.1620 0.2562 0.5819 255 T 0.3766 0.1624 0.4610 256 A 0.4750 0.1637 0.3612 257 A 0.5122 0.1387 0.3491 258 Y 0.4656 0.1265 0.4079 259 F 0.3077 0.1233 0.5690 260 H 0.0892 0.5108 0.4000 261 E 0.0284 0.7697 0.2019 262 L 0.0355 0.7961 0.1685 263 L 0.0430 0.7839 0.1731 264 I 0.0340 0.7882 0.1778 265 G 0.0411 0.7248 0.2341 266 R 0.0521 0.6751 0.2728 267 E 0.0349 0.7167 0.2484 268 D 0.0207 0.7443 0.2351 269 L 0.0295 0.6527 0.3178 270 L 0.0773 0.5735 0.3491 271 R 0.0367 0.7608 0.2025 272 P 0.0127 0.8524 0.1348 273 F 0.0133 0.8642 0.1225 274 F 0.0144 0.8759 0.1097 275 E 0.0108 0.8675 0.1217 276 K 0.0177 0.7806 0.2017 277 C 0.0328 0.7883 0.1789 278 V 0.0303 0.8301 0.1396 279 K 0.0369 0.8443 0.1188 280 I 0.0200 0.8793 0.1007 281 E 0.0159 0.8830 0.1010 282 E 0.0197 0.8553 0.1250 283 V 0.0442 0.7359 0.2199 284 S 0.0754 0.4781 0.4465 285 R 0.0738 0.3075 0.6187 286 N 0.1150 0.2443 0.6407 287 E 0.1207 0.2898 0.5895 288 Q 0.1548 0.1858 0.6595 289 G 0.2267 0.0792 0.6941 290 V 0.3410 0.0603 0.5987 291 T 0.5293 0.0347 0.4360 292 L 0.6300 0.0184 0.3516 293 S 0.5781 0.0182 0.4038 294 I 0.4717 0.0258 0.5025 295 T 0.2577 0.0977 0.6446 296 N 0.1513 0.1378 0.7109 297 V 0.0918 0.3254 0.5827 298 T 0.1035 0.4789 0.4176 299 D 0.1018 0.5621 0.3361 300 L 0.0200 0.8204 0.1597 301 V 0.0099 0.8785 0.1116 302 L 0.0087 0.9148 0.0765 303 K 0.0099 0.9104 0.0796 304 L 0.0118 0.9034 0.0848 305 K 0.0099 0.8970 0.0931 306 K 0.0157 0.8558 0.1285 307 T 0.0477 0.7066 0.2457 308 A 0.0846 0.5805 0.3348 309 H 0.0657 0.6292 0.3051 310 D 0.0600 0.5877 0.3523 311 T 0.0772 0.5291 0.3937 312 L 0.0827 0.6305 0.2868 313 L 0.1297 0.6174 0.2529 314 V 0.1884 0.5131 0.2984 315 Y 0.2151 0.3324 0.4525 316 F 0.2071 0.2531 0.5398 317 R 0.1197 0.3992 0.4812 318 D 0.1309 0.3301 0.5391 319 M 0.1591 0.2038 0.6372 320 T 0.1856 0.1249 0.6896 321 L 0.1734 0.1662 0.6604 322 K 0.1846 0.1071 0.7084 323 P 0.1279 0.3990 0.4731 324 H 0.1204 0.5112 0.3684 325 T 0.2548 0.4616 0.2835 326 R 0.2994 0.4214 0.2793 327 Y 0.3498 0.3935 0.2567 328 T 0.5094 0.2475 0.2431 329 V 0.5854 0.2056 0.2090 330 R 0.5024 0.2768 0.2208 331 I 0.3868 0.3705 0.2427 332 G 0.2963 0.4401 0.2636 333 F 0.1989 0.5741 0.2270 334 K 0.1672 0.5888 0.2440 335 Q 0.0901 0.5372 0.3727 336 G 0.0815 0.3874 0.5311 337 I 0.1939 0.1674 0.6386 338 K 0.1688 0.1856 0.6456 339 G 0.1221 0.1221 0.7557 340 G 0.1526 0.1021 0.7453 341 D 0.1848 0.1529 0.6623 342 V 0.1522 0.2652 0.5826 343 N 0.1820 0.2745 0.5435 344 F 0.2239 0.3497 0.4264 345 E 0.2307 0.4335 0.3359 346 V 0.2310 0.5095 0.2595 347 T 0.1942 0.5446 0.2612 348 N 0.2315 0.4906 0.2779 349 F 0.2948 0.4316 0.2736 350 I 0.3504 0.3624 0.2872 351 V 0.3312 0.2843 0.3845 352 A 0.2667 0.1832 0.5501 353 P 0.0985 0.4132 0.4883 354 D 0.0704 0.3415 0.5881 355 K 0.0969 0.2207 0.6825 356 G 0.1621 0.1189 0.7190 357 L 0.4232 0.0628 0.5140 358 K 0.5480 0.0641 0.3879 359 Y 0.7444 0.0315 0.2241 360 T 0.7747 0.0144 0.2109 361 I 0.8075 0.0109 0.1815 362 S 0.7427 0.0201 0.2372 363 L 0.5774 0.0423 0.3803