# This file is the result of combining several RDB files, specifically # T0427.t06.str2.rdb (weight 1.54425) # T0427.t06.str4.rdb (weight 0.924988) # T0427.t06.pb.rdb (weight 0.789901) # T0427.t06.bys.rdb (weight 0.748322) # T0427.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 T0427.t06.str2.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2886 # # ============================================ # Comments from T0427.t06.str4.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2886 # # ============================================ # Comments from T0427.t06.pb.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2886 # # ============================================ # Comments from T0427.t06.bys.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2886 # # ============================================ # Comments from T0427.t06.alpha.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2886 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.5405 0.0280 0.4315 2 S 0.6621 0.0149 0.3231 3 V 0.7656 0.0097 0.2247 4 Q 0.7574 0.0093 0.2333 5 L 0.6541 0.0193 0.3266 6 V 0.3526 0.1510 0.4964 7 K 0.1523 0.1195 0.7281 8 G 0.1920 0.0604 0.7476 9 V 0.5360 0.0098 0.4542 10 N 0.6985 0.0103 0.2912 11 L 0.7949 0.0054 0.1997 12 H 0.7900 0.0082 0.2018 13 V 0.7627 0.0074 0.2299 14 I 0.7036 0.0107 0.2857 15 P 0.4172 0.0247 0.5582 16 T 0.2404 0.0748 0.6848 17 E 0.0699 0.3179 0.6123 18 K 0.1026 0.2572 0.6402 19 Y 0.2344 0.1074 0.6582 20 K 0.2930 0.1037 0.6034 21 T 0.6520 0.0251 0.3229 22 V 0.7777 0.0083 0.2140 23 R 0.8149 0.0055 0.1796 24 L 0.8274 0.0046 0.1680 25 L 0.8297 0.0043 0.1660 26 V 0.8266 0.0046 0.1688 27 R 0.8137 0.0052 0.1811 28 F 0.7508 0.0120 0.2372 29 N 0.5399 0.0358 0.4243 30 T 0.3038 0.0964 0.5997 31 R 0.2048 0.1016 0.6936 32 L 0.2078 0.1650 0.6272 33 N 0.1443 0.2430 0.6127 34 H 0.1550 0.2302 0.6148 35 E 0.1514 0.2499 0.5987 36 T 0.1393 0.3312 0.5296 37 I 0.0788 0.5250 0.3962 38 T 0.0784 0.6016 0.3200 39 K 0.0164 0.8384 0.1451 40 R 0.0092 0.8950 0.0958 41 T 0.0086 0.9195 0.0719 42 L 0.0085 0.9193 0.0722 43 L 0.0084 0.9180 0.0736 44 S 0.0083 0.9215 0.0702 45 S 0.0084 0.9182 0.0734 46 L 0.0089 0.9094 0.0817 47 M 0.0106 0.8850 0.1044 48 E 0.0182 0.7603 0.2215 49 T 0.0527 0.4126 0.5347 50 N 0.0493 0.1975 0.7533 51 S 0.1379 0.1884 0.6737 52 L 0.0860 0.3244 0.5895 53 N 0.1139 0.1948 0.6912 54 Y 0.2088 0.0775 0.7137 55 P 0.1499 0.1602 0.6898 56 N 0.1293 0.1662 0.7044 57 Q 0.0293 0.6886 0.2822 58 V 0.0146 0.8428 0.1425 59 K 0.0137 0.8874 0.0989 60 L 0.0111 0.8999 0.0890 61 S 0.0086 0.9159 0.0755 62 E 0.0083 0.9202 0.0715 63 R 0.0086 0.9165 0.0749 64 L 0.0089 0.9093 0.0818 65 A 0.0086 0.9059 0.0855 66 E 0.0106 0.8724 0.1170 67 L 0.0311 0.7166 0.2523 68 Y 0.0632 0.3995 0.5373 69 G 0.0891 0.2431 0.6678 70 A 0.2286 0.2582 0.5132 71 S 0.3611 0.2125 0.4264 72 F 0.3667 0.1583 0.4751 73 G 0.3285 0.1114 0.5601 74 I 0.3927 0.1002 0.5071 75 G 0.3954 0.0895 0.5151 76 V 0.3894 0.0810 0.5297 77 S 0.2838 0.0785 0.6376 78 K 0.1675 0.2747 0.5579 79 K 0.1530 0.1898 0.6571 80 G 0.1381 0.1092 0.7527 81 N 0.2065 0.1031 0.6904 82 Q 0.1867 0.2332 0.5801 83 H 0.3050 0.1699 0.5251 84 W 0.5618 0.0762 0.3619 85 F 0.6932 0.0382 0.2686 86 N 0.7684 0.0149 0.2167 87 I 0.7970 0.0095 0.1934 88 S 0.7839 0.0124 0.2037 89 M 0.7655 0.0148 0.2197 90 N 0.6968 0.0312 0.2719 91 I 0.6001 0.0461 0.3537 92 V 0.4235 0.0887 0.4878 93 N 0.2330 0.1273 0.6396 94 D 0.0783 0.3614 0.5603 95 H 0.0794 0.4311 0.4895 96 Y 0.1089 0.4323 0.4588 97 L 0.1031 0.4174 0.4795 98 Q 0.0957 0.3432 0.5611 99 D 0.1164 0.3188 0.5649 100 S 0.0303 0.6779 0.2919 101 Q 0.0244 0.7576 0.2181 102 V 0.0276 0.7937 0.1787 103 L 0.0140 0.8789 0.1071 104 A 0.0085 0.9158 0.0756 105 E 0.0083 0.9199 0.0718 106 A 0.0084 0.9180 0.0736 107 V 0.0084 0.9178 0.0738 108 D 0.0083 0.9226 0.0691 109 F 0.0083 0.9211 0.0705 110 L 0.0084 0.9208 0.0709 111 K 0.0085 0.9120 0.0795 112 E 0.0089 0.8966 0.0945 113 I 0.0136 0.8442 0.1421 114 I 0.0289 0.7363 0.2349 115 F 0.0688 0.5646 0.3666 116 A 0.1436 0.2879 0.5684 117 P 0.0730 0.4576 0.4693 118 N 0.0764 0.4956 0.4280 119 I 0.0842 0.5398 0.3760 120 Q 0.0861 0.4515 0.4624 121 A 0.0694 0.2815 0.6492 122 G 0.0543 0.1674 0.7783 123 Q 0.1975 0.0974 0.7050 124 F 0.2578 0.0552 0.6870 125 E 0.1732 0.0495 0.7773 126 A 0.0209 0.7179 0.2612 127 E 0.0127 0.8240 0.1633 128 T 0.0150 0.8831 0.1019 129 F 0.0138 0.8993 0.0869 130 Q 0.0096 0.9117 0.0787 131 R 0.0094 0.9124 0.0782 132 E 0.0097 0.9069 0.0834 133 K 0.0087 0.9134 0.0779 134 E 0.0084 0.9181 0.0736 135 N 0.0083 0.9213 0.0704 136 L 0.0084 0.9199 0.0717 137 K 0.0084 0.9185 0.0731 138 A 0.0085 0.9170 0.0746 139 Y 0.0091 0.9104 0.0805 140 L 0.0113 0.8977 0.0910 141 E 0.0098 0.8808 0.1093 142 S 0.0156 0.8122 0.1722 143 I 0.0407 0.7058 0.2534 144 V 0.0517 0.5989 0.3494 145 E 0.0687 0.4169 0.5144 146 D 0.1363 0.2352 0.6286 147 K 0.0147 0.7405 0.2449 148 Q 0.0109 0.8378 0.1513 149 T 0.0109 0.9069 0.0822 150 Y 0.0093 0.9154 0.0753 151 A 0.0087 0.9145 0.0768 152 S 0.0084 0.9187 0.0729 153 L 0.0084 0.9205 0.0712 154 A 0.0084 0.9183 0.0733 155 L 0.0089 0.9130 0.0781 156 Q 0.0089 0.9008 0.0904 157 S 0.0110 0.8657 0.1233 158 V 0.0211 0.7630 0.2160 159 Y 0.0530 0.5308 0.4162 160 F 0.1185 0.2840 0.5975 161 N 0.1150 0.2462 0.6389 162 Q 0.0508 0.3879 0.5613 163 S 0.0810 0.2703 0.6487 164 E 0.1583 0.1788 0.6629 165 D 0.1210 0.2941 0.5849 166 Q 0.1359 0.2644 0.5997 167 K 0.2188 0.1423 0.6389 168 I 0.2808 0.0532 0.6660 169 P 0.2104 0.1035 0.6861 170 S 0.1697 0.2321 0.5983 171 F 0.1602 0.2031 0.6368 172 G 0.1869 0.1085 0.7047 173 T 0.1956 0.0917 0.7126 174 V 0.0293 0.6938 0.2769 175 A 0.0178 0.8000 0.1822 176 A 0.0259 0.7974 0.1767 177 L 0.0381 0.7612 0.2007 178 A 0.0222 0.6951 0.2828 179 E 0.0358 0.6133 0.3508 180 E 0.1141 0.3278 0.5581 181 T 0.1508 0.0995 0.7497 182 A 0.0125 0.7507 0.2368 183 A 0.0093 0.8693 0.1214 184 S 0.0086 0.9193 0.0721 185 L 0.0083 0.9223 0.0694 186 A 0.0084 0.9198 0.0719 187 A 0.0083 0.9220 0.0697 188 Y 0.0084 0.9213 0.0704 189 Y 0.0084 0.9167 0.0749 190 Q 0.0086 0.9101 0.0813 191 K 0.0111 0.8528 0.1361 192 M 0.0286 0.7106 0.2608 193 L 0.0872 0.4780 0.4348 194 A 0.1374 0.2689 0.5937 195 E 0.0360 0.4698 0.4942 196 D 0.0476 0.3099 0.6426 197 Q 0.1318 0.1419 0.7263 198 V 0.4735 0.0192 0.5073 199 D 0.6996 0.0116 0.2887 200 I 0.8168 0.0048 0.1784 201 F 0.8090 0.0061 0.1849 202 V 0.7839 0.0077 0.2084 203 L 0.6994 0.0255 0.2750 204 G 0.4193 0.0415 0.5392 205 D 0.2630 0.0572 0.6798 206 V 0.2372 0.0755 0.6873 207 N 0.1782 0.0243 0.7975 208 E 0.0142 0.7230 0.2628 209 A 0.0097 0.8282 0.1621 210 E 0.0098 0.8991 0.0911 211 L 0.0106 0.9036 0.0857 212 V 0.0091 0.9065 0.0844 213 P 0.0089 0.9047 0.0864 214 L 0.0099 0.8961 0.0940 215 F 0.0149 0.8692 0.1158 216 K 0.0158 0.7379 0.2462 217 Q 0.0385 0.4376 0.5239 218 L 0.1335 0.1478 0.7187 219 P 0.0862 0.2692 0.6447 220 F 0.1307 0.1750 0.6942 221 T 0.2059 0.0557 0.7384 222 P 0.1777 0.1102 0.7121 223 R 0.1548 0.1949 0.6503 224 E 0.1375 0.2392 0.6233 225 E 0.1278 0.2143 0.6580 226 G 0.1466 0.1476 0.7058 227 K 0.1990 0.1496 0.6513 228 A 0.2607 0.1763 0.5630 229 A 0.2858 0.1893 0.5248 230 I 0.3135 0.1670 0.5194 231 F 0.2891 0.1331 0.5778 232 Y 0.2495 0.1413 0.6092 233 N 0.2263 0.1107 0.6630 234 Q 0.2601 0.0601 0.6798 235 P 0.2294 0.0916 0.6791 236 I 0.2171 0.1844 0.5985 237 R 0.2111 0.1900 0.5989 238 N 0.2263 0.1705 0.6032 239 V 0.3209 0.1466 0.5325 240 I 0.4084 0.1519 0.4397 241 E 0.5261 0.1374 0.3365 242 E 0.6105 0.1049 0.2846 243 R 0.6001 0.1044 0.2955 244 T 0.6122 0.0885 0.2993 245 E 0.5311 0.1098 0.3591 246 R 0.4568 0.1331 0.4102 247 E 0.3251 0.1760 0.4989 248 V 0.2392 0.2701 0.4907 249 L 0.2287 0.2589 0.5125 250 A 0.2131 0.2890 0.4979 251 Q 0.2427 0.3068 0.4505 252 S 0.3264 0.2471 0.4265 253 K 0.5722 0.1362 0.2916 254 L 0.7248 0.0582 0.2170 255 N 0.7358 0.0566 0.2076 256 L 0.7372 0.0552 0.2076 257 A 0.6864 0.0632 0.2504 258 Y 0.6064 0.0537 0.3399 259 N 0.4075 0.0720 0.5205 260 T 0.2811 0.0943 0.6246 261 D 0.2127 0.1208 0.6665 262 I 0.1996 0.2165 0.5839 263 Y 0.1884 0.2354 0.5761 264 Y 0.1746 0.1827 0.6428 265 G 0.1312 0.1284 0.7404 266 D 0.1505 0.1970 0.6525 267 S 0.0286 0.6369 0.3345 268 Y 0.0241 0.7281 0.2478 269 Y 0.0288 0.8238 0.1474 270 F 0.0155 0.8931 0.0914 271 A 0.0090 0.9160 0.0749 272 L 0.0083 0.9217 0.0700 273 Q 0.0083 0.9233 0.0684 274 V 0.0085 0.9213 0.0702 275 F 0.0089 0.9158 0.0753 276 N 0.0099 0.8971 0.0930 277 G 0.0140 0.8640 0.1220 278 I 0.0289 0.7759 0.1952 279 F 0.0502 0.5854 0.3644 280 G 0.0574 0.2653 0.6773 281 G 0.0711 0.2050 0.7239 282 F 0.1596 0.1271 0.7134 283 P 0.0810 0.3591 0.5599 284 H 0.0792 0.4244 0.4964 285 S 0.0646 0.6422 0.2932 286 K 0.0296 0.7782 0.1922 287 L 0.0262 0.8273 0.1465 288 F 0.0215 0.8708 0.1077 289 M 0.0171 0.8875 0.0953 290 N 0.0213 0.8806 0.0981 291 V 0.0316 0.8632 0.1053 292 R 0.0437 0.8268 0.1295 293 E 0.0499 0.7830 0.1672 294 K 0.0589 0.6637 0.2774 295 E 0.0731 0.3980 0.5290 296 H 0.1153 0.2997 0.5851 297 L 0.2871 0.2592 0.4536 298 A 0.4098 0.2166 0.3736 299 Y 0.5050 0.1646 0.3304 300 Y 0.5194 0.1313 0.3493 301 A 0.4855 0.1667 0.3477 302 S 0.4623 0.1499 0.3878 303 S 0.4054 0.1734 0.4212 304 S 0.3183 0.1840 0.4976 305 I 0.3018 0.2050 0.4932 306 D 0.2591 0.1999 0.5409 307 T 0.1956 0.2785 0.5259 308 F 0.1851 0.2272 0.5877 309 R 0.2202 0.1391 0.6407 310 G 0.3250 0.0845 0.5905 311 F 0.5879 0.0450 0.3672 312 M 0.7556 0.0157 0.2287 313 T 0.7964 0.0096 0.1940 314 V 0.7958 0.0090 0.1952 315 Q 0.7686 0.0143 0.2170 316 T 0.6920 0.0270 0.2810 317 G 0.4614 0.0439 0.4947 318 I 0.3563 0.0657 0.5780 319 D 0.1921 0.0546 0.7534 320 G 0.0503 0.3917 0.5580 321 K 0.0444 0.4451 0.5106 322 N 0.0799 0.4167 0.5033 323 R 0.0161 0.7977 0.1862 324 N 0.0089 0.8965 0.0947 325 Q 0.0084 0.9220 0.0696 326 V 0.0083 0.9231 0.0686 327 L 0.0083 0.9233 0.0684 328 R 0.0083 0.9243 0.0674 329 L 0.0083 0.9236 0.0681 330 I 0.0083 0.9210 0.0707 331 S 0.0084 0.9178 0.0738 332 T 0.0084 0.9221 0.0695 333 E 0.0085 0.9200 0.0716 334 L 0.0084 0.9195 0.0721 335 E 0.0085 0.9131 0.0784 336 N 0.0087 0.9075 0.0838 337 I 0.0136 0.8849 0.1015 338 R 0.0178 0.8139 0.1684 339 L 0.0408 0.5144 0.4448 340 G 0.0497 0.1940 0.7563 341 K 0.0926 0.1189 0.7884 342 I 0.1793 0.0652 0.7556 343 R 0.1625 0.0461 0.7914 344 E 0.0145 0.7341 0.2514 345 L 0.0096 0.8665 0.1238 346 E 0.0093 0.9170 0.0737 347 I 0.0087 0.9201 0.0712 348 E 0.0083 0.9218 0.0699 349 Q 0.0083 0.9233 0.0684 350 T 0.0083 0.9237 0.0681 351 K 0.0083 0.9221 0.0696 352 A 0.0083 0.9210 0.0707 353 M 0.0084 0.9161 0.0754 354 L 0.0087 0.9159 0.0754 355 K 0.0090 0.9065 0.0845 356 N 0.0104 0.8703 0.1193 357 Q 0.0141 0.8470 0.1389 358 Y 0.0215 0.8426 0.1359 359 I 0.0355 0.8099 0.1546 360 L 0.0546 0.7334 0.2120 361 A 0.0837 0.5745 0.3417 362 L 0.0931 0.4573 0.4496 363 D 0.0898 0.3754 0.5347 364 N 0.1234 0.2459 0.6307 365 A 0.0389 0.6507 0.3105 366 G 0.0270 0.7460 0.2269 367 A 0.0225 0.8499 0.1276 368 W 0.0160 0.8859 0.0981 369 L 0.0149 0.8878 0.0973 370 E 0.0114 0.9006 0.0880 371 K 0.0106 0.9025 0.0869 372 E 0.0122 0.8895 0.0983 373 Y 0.0161 0.8653 0.1187 374 L 0.0166 0.8534 0.1300 375 N 0.0205 0.8205 0.1589 376 E 0.0329 0.7437 0.2235 377 L 0.0787 0.5502 0.3711 378 M 0.1554 0.2600 0.5846 379 P 0.0957 0.2742 0.6301 380 Q 0.1282 0.1965 0.6753 381 T 0.1552 0.1751 0.6697 382 M 0.0760 0.4846 0.4394 383 L 0.0680 0.5570 0.3750 384 T 0.0863 0.5712 0.3425 385 A 0.0147 0.8156 0.1697 386 E 0.0089 0.8896 0.1015 387 E 0.0084 0.9211 0.0706 388 W 0.0084 0.9211 0.0706 389 I 0.0084 0.9183 0.0734 390 A 0.0085 0.9151 0.0764 391 R 0.0094 0.8964 0.0942 392 I 0.0196 0.8420 0.1384 393 N 0.0185 0.6368 0.3447 394 A 0.0367 0.3328 0.6305 395 V 0.2041 0.0806 0.7154 396 T 0.1633 0.0266 0.8101 397 I 0.0256 0.6885 0.2859 398 P 0.0096 0.8592 0.1312 399 E 0.0086 0.9135 0.0779 400 I 0.0084 0.9198 0.0717 401 Q 0.0084 0.9184 0.0733 402 E 0.0083 0.9240 0.0677 403 V 0.0085 0.9211 0.0704 404 A 0.0086 0.9098 0.0816 405 K 0.0096 0.8803 0.1101 406 R 0.0206 0.6698 0.3096 407 L 0.1190 0.2489 0.6320 408 E 0.1151 0.1616 0.7233 409 L 0.2163 0.1072 0.6765 410 Q 0.4357 0.0650 0.4992 411 A 0.7315 0.0182 0.2503 412 I 0.7890 0.0077 0.2034 413 F 0.7948 0.0071 0.1980 414 F 0.7472 0.0101 0.2427 415 L 0.5684 0.0214 0.4102 416 E 0.2690 0.0579 0.6732 417 G 0.1382 0.0757 0.7861 418 E 0.1595 0.1915 0.6490 419 T 0.1764 0.2420 0.5815 420 E 0.1709 0.2571 0.5720 421 N 0.1704 0.2099 0.6197 422 D 0.1557 0.1964 0.6479