# This file is the result of combining several RDB files, specifically # T0501.t06.str2.rdb (weight 1.54425) # T0501.t06.str4.rdb (weight 0.924988) # T0501.t06.pb.rdb (weight 0.789901) # T0501.t06.bys.rdb (weight 0.748322) # T0501.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 T0501.t06.str2.rdb # ============================================ # TARGET T0501 # 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 T0501.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 1807 # # ============================================ # Comments from T0501.t06.str4.rdb # ============================================ # TARGET T0501 # 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 T0501.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 1807 # # ============================================ # Comments from T0501.t06.pb.rdb # ============================================ # TARGET T0501 # 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 T0501.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 1807 # # ============================================ # Comments from T0501.t06.bys.rdb # ============================================ # TARGET T0501 # 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 T0501.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 1807 # # ============================================ # Comments from T0501.t06.alpha.rdb # ============================================ # TARGET T0501 # 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 T0501.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 1807 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1969 0.3032 0.4998 2 L 0.1596 0.3546 0.4857 3 T 0.1052 0.5274 0.3674 4 K 0.0303 0.7846 0.1851 5 V 0.0125 0.8839 0.1036 6 I 0.0100 0.9079 0.0821 7 A 0.0086 0.9172 0.0742 8 Q 0.0083 0.9200 0.0717 9 A 0.0083 0.9217 0.0700 10 H 0.0084 0.9194 0.0722 11 I 0.0084 0.9179 0.0737 12 D 0.0083 0.9218 0.0699 13 H 0.0083 0.9228 0.0689 14 F 0.0083 0.9218 0.0699 15 T 0.0084 0.9159 0.0757 16 K 0.0083 0.9201 0.0715 17 W 0.0086 0.9136 0.0778 18 F 0.0094 0.9033 0.0873 19 E 0.0109 0.8462 0.1430 20 R 0.0231 0.5401 0.4368 21 A 0.0932 0.2611 0.6457 22 D 0.1200 0.1454 0.7346 23 K 0.4186 0.0457 0.5358 24 I 0.7480 0.0081 0.2439 25 V 0.8068 0.0054 0.1878 26 I 0.8049 0.0055 0.1897 27 V 0.7808 0.0100 0.2093 28 S 0.6826 0.0209 0.2965 29 H 0.4577 0.0389 0.5035 30 V 0.3231 0.0715 0.6054 31 S 0.2465 0.0333 0.7202 32 P 0.0669 0.3063 0.6269 33 D 0.1119 0.2249 0.6631 34 G 0.0499 0.4466 0.5035 35 D 0.0558 0.6101 0.3341 36 A 0.0380 0.7855 0.1765 37 I 0.0164 0.8733 0.1104 38 G 0.0092 0.9153 0.0755 39 S 0.0083 0.9224 0.0693 40 S 0.0083 0.9236 0.0681 41 L 0.0083 0.9242 0.0675 42 G 0.0083 0.9248 0.0669 43 L 0.0083 0.9240 0.0677 44 Y 0.0083 0.9227 0.0690 45 H 0.0083 0.9219 0.0697 46 F 0.0086 0.9154 0.0760 47 L 0.0091 0.9017 0.0892 48 D 0.0106 0.8224 0.1670 49 S 0.0181 0.6092 0.3726 50 Q 0.0635 0.2593 0.6772 51 D 0.0639 0.1125 0.8236 52 K 0.1950 0.0900 0.7149 53 I 0.4031 0.0565 0.5404 54 V 0.6299 0.0164 0.3537 55 N 0.7096 0.0158 0.2746 56 V 0.7885 0.0067 0.2048 57 I 0.7608 0.0112 0.2280 58 V 0.5506 0.0111 0.4383 59 P 0.2425 0.1145 0.6430 60 N 0.1399 0.1373 0.7228 61 A 0.1810 0.1249 0.6941 62 F 0.2272 0.0719 0.7010 63 P 0.1312 0.2972 0.5716 64 D 0.0622 0.4559 0.4819 65 F 0.0812 0.4673 0.4515 66 L 0.1547 0.4155 0.4299 67 K 0.1727 0.3512 0.4761 68 W 0.2167 0.2521 0.5313 69 M 0.2040 0.1075 0.6885 70 P 0.0803 0.4135 0.5063 71 G 0.0530 0.3959 0.5511 72 S 0.0995 0.4977 0.4028 73 K 0.0832 0.6169 0.2999 74 D 0.0945 0.6400 0.2655 75 I 0.1230 0.6308 0.2462 76 L 0.1386 0.5538 0.3076 77 L 0.1295 0.5084 0.3622 78 Y 0.0859 0.5874 0.3267 79 D 0.0698 0.6033 0.3270 80 R 0.0645 0.6266 0.3089 81 Y 0.0714 0.6610 0.2676 82 Q 0.0347 0.7814 0.1838 83 E 0.0273 0.8112 0.1615 84 F 0.0315 0.7948 0.1737 85 A 0.0383 0.7912 0.1705 86 D 0.0291 0.8011 0.1698 87 K 0.0380 0.7702 0.1917 88 L 0.0640 0.6826 0.2534 89 I 0.0953 0.5530 0.3517 90 M 0.1056 0.4201 0.4742 91 E 0.1484 0.2200 0.6316 92 A 0.2828 0.0978 0.6194 93 D 0.3829 0.0543 0.5627 94 V 0.7792 0.0089 0.2119 95 I 0.7744 0.0066 0.2190 96 C 0.8046 0.0053 0.1900 97 C 0.7937 0.0062 0.2000 98 L 0.7426 0.0131 0.2444 99 D 0.4475 0.0331 0.5194 100 F 0.1644 0.1983 0.6373 101 N 0.1206 0.2352 0.6442 102 A 0.0854 0.4613 0.4533 103 L 0.0547 0.6262 0.3191 104 K 0.0466 0.6875 0.2659 105 R 0.0664 0.5864 0.3472 106 I 0.0946 0.5976 0.3078 107 D 0.0434 0.7338 0.2228 108 E 0.0194 0.8193 0.1613 109 M 0.0185 0.8470 0.1345 110 S 0.0122 0.8869 0.1009 111 D 0.0101 0.8977 0.0923 112 I 0.0108 0.8803 0.1089 113 V 0.0209 0.8383 0.1407 114 A 0.0212 0.7667 0.2122 115 A 0.0457 0.5205 0.4338 116 S 0.1421 0.1515 0.7064 117 P 0.1266 0.1429 0.7305 118 G 0.2105 0.0616 0.7279 119 R 0.4616 0.0270 0.5114 120 K 0.7710 0.0067 0.2223 121 I 0.7967 0.0060 0.1973 122 M 0.8021 0.0055 0.1924 123 I 0.7755 0.0112 0.2133 124 D 0.5892 0.0438 0.3669 125 H 0.3236 0.0948 0.5816 126 H 0.2710 0.0865 0.6425 127 L 0.2072 0.0893 0.7035 128 Y 0.1930 0.0484 0.7586 129 P 0.0636 0.4347 0.5016 130 E 0.0503 0.4556 0.4941 131 D 0.0959 0.4006 0.5035 132 F 0.1945 0.1856 0.6199 133 C 0.2337 0.1525 0.6138 134 R 0.2882 0.1628 0.5489 135 I 0.4858 0.0896 0.4246 136 T 0.5989 0.0604 0.3407 137 I 0.6695 0.0376 0.2929 138 S 0.5817 0.0444 0.3739 139 H 0.3200 0.0243 0.6557 140 P 0.1090 0.2884 0.6025 141 E 0.1108 0.2686 0.6206 142 I 0.1530 0.2334 0.6135 143 S 0.1127 0.3709 0.5164 144 S 0.0757 0.6297 0.2946 145 T 0.0286 0.8261 0.1454 146 S 0.0115 0.9041 0.0844 147 E 0.0092 0.9215 0.0693 148 L 0.0083 0.9243 0.0674 149 V 0.0083 0.9248 0.0670 150 F 0.0083 0.9242 0.0675 151 R 0.0083 0.9248 0.0669 152 L 0.0083 0.9247 0.0670 153 I 0.0083 0.9219 0.0698 154 C 0.0085 0.9141 0.0774 155 R 0.0116 0.8132 0.1752 156 M 0.0471 0.4438 0.5092 157 G 0.0415 0.1755 0.7830 158 Y 0.1016 0.2472 0.6512 159 F 0.1383 0.2648 0.5969 160 S 0.1491 0.2437 0.6072 161 D 0.1761 0.1449 0.6790 162 I 0.2289 0.1163 0.6549 163 S 0.1677 0.0825 0.7499 164 K 0.0157 0.7306 0.2537 165 E 0.0143 0.8078 0.1779 166 G 0.0153 0.8663 0.1183 167 A 0.0135 0.9006 0.0858 168 E 0.0171 0.8910 0.0919 169 C 0.0318 0.8805 0.0877 170 I 0.0355 0.8680 0.0965 171 Y 0.0963 0.7926 0.1110 172 T 0.1255 0.7117 0.1628 173 G 0.1869 0.6277 0.1854 174 M 0.2510 0.5446 0.2044 175 M 0.3516 0.3640 0.2844 176 T 0.2691 0.3017 0.4292 177 D 0.1934 0.2293 0.5772 178 T 0.1118 0.1960 0.6922 179 G 0.1101 0.1633 0.7266 180 G 0.1806 0.1476 0.6717 181 F 0.2935 0.1135 0.5930 182 T 0.3520 0.0891 0.5589 183 Y 0.3023 0.0836 0.6141 184 N 0.1721 0.1872 0.6407 185 S 0.1679 0.1992 0.6328 186 N 0.2003 0.1717 0.6280 187 N 0.1886 0.1728 0.6385 188 R 0.0469 0.6514 0.3017 189 E 0.0326 0.7659 0.2015 190 I 0.0275 0.8486 0.1239 191 Y 0.0144 0.8964 0.0892 192 F 0.0111 0.9092 0.0797 193 I 0.0124 0.8991 0.0885 194 I 0.0089 0.9130 0.0781 195 S 0.0085 0.9179 0.0736 196 E 0.0084 0.9189 0.0727 197 L 0.0094 0.9129 0.0777 198 L 0.0105 0.8863 0.1032 199 S 0.0134 0.7520 0.2346 200 K 0.0570 0.2661 0.6769 201 G 0.0491 0.0867 0.8641 202 I 0.1612 0.0510 0.7878 203 D 0.1682 0.0357 0.7961 204 K 0.0226 0.6955 0.2819 205 D 0.0157 0.8149 0.1693 206 D 0.0135 0.8894 0.0971 207 I 0.0110 0.9089 0.0801 208 Y 0.0091 0.9108 0.0801 209 R 0.0096 0.9066 0.0838 210 K 0.0131 0.8787 0.1082 211 V 0.0305 0.7769 0.1926 212 Y 0.0501 0.6316 0.3183 213 N 0.0635 0.4684 0.4682 214 T 0.0726 0.3257 0.6016 215 Y 0.1088 0.2311 0.6601 216 S 0.0871 0.4312 0.4818 217 E 0.0120 0.7840 0.2040 218 S 0.0096 0.8664 0.1239 219 R 0.0091 0.9130 0.0780 220 L 0.0086 0.9182 0.0732 221 R 0.0085 0.9173 0.0742 222 L 0.0088 0.9112 0.0800 223 M 0.0087 0.9087 0.0825 224 G 0.0085 0.9123 0.0793 225 Y 0.0087 0.9095 0.0817 226 V 0.0112 0.8846 0.1042 227 L 0.0117 0.8573 0.1310 228 S 0.0124 0.7697 0.2179 229 N 0.0222 0.6479 0.3299 230 M 0.0549 0.6264 0.3187 231 K 0.0740 0.6652 0.2608 232 V 0.1396 0.6126 0.2478 233 Y 0.1651 0.5471 0.2878 234 K 0.1461 0.5257 0.3282 235 D 0.1381 0.4266 0.4352 236 Y 0.1263 0.2788 0.5949 237 N 0.1778 0.2092 0.6131 238 S 0.3188 0.2773 0.4039 239 A 0.4385 0.2589 0.3026 240 L 0.5946 0.1793 0.2260 241 I 0.6570 0.1253 0.2177 242 S 0.6360 0.1341 0.2299 243 L 0.5828 0.1386 0.2786 244 T 0.4430 0.1425 0.4145 245 K 0.2533 0.3350 0.4117 246 E 0.2239 0.4289 0.3472 247 E 0.2131 0.4194 0.3675 248 Q 0.2036 0.3185 0.4779 249 G 0.1610 0.2396 0.5994 250 K 0.1876 0.2387 0.5737 251 F 0.1896 0.2387 0.5717 252 D 0.1890 0.2239 0.5871 253 Y 0.2408 0.2160 0.5432 254 I 0.2406 0.1759 0.5836 255 K 0.1550 0.2588 0.5862 256 G 0.1425 0.2090 0.6485 257 D 0.1752 0.2845 0.5403 258 S 0.1456 0.4398 0.4146 259 E 0.1077 0.5114 0.3810 260 G 0.1441 0.5224 0.3335 261 F 0.1966 0.5172 0.2861 262 V 0.2494 0.4098 0.3408 263 N 0.2328 0.3161 0.4511 264 I 0.2497 0.2306 0.5198 265 P 0.1865 0.3545 0.4590 266 L 0.1883 0.4098 0.4019 267 S 0.1865 0.3756 0.4379 268 I 0.1648 0.3964 0.4388 269 K 0.1060 0.3271 0.5670 270 N 0.1001 0.1856 0.7143 271 V 0.3057 0.0583 0.6360 272 C 0.3491 0.0421 0.6089 273 F 0.5724 0.0224 0.4052 274 S 0.6716 0.0191 0.3093 275 C 0.8150 0.0054 0.1796 276 F 0.8148 0.0057 0.1795 277 L 0.8043 0.0059 0.1898 278 R 0.7662 0.0105 0.2233 279 E 0.6150 0.0282 0.3569 280 D 0.3815 0.0718 0.5467 281 T 0.2026 0.1484 0.6491 282 E 0.1125 0.2135 0.6741 283 K 0.1440 0.1245 0.7316 284 K 0.3120 0.0708 0.6171 285 M 0.6733 0.0129 0.3138 286 I 0.7727 0.0074 0.2199 287 K 0.8155 0.0048 0.1796 288 I 0.8241 0.0046 0.1713 289 S 0.8003 0.0054 0.1943 290 L 0.7390 0.0160 0.2449 291 R 0.6304 0.0367 0.3329 292 S 0.4314 0.0434 0.5252 293 V 0.1704 0.1617 0.6679 294 G 0.0863 0.1519 0.7618 295 K 0.1416 0.1290 0.7294 296 F 0.2610 0.0435 0.6956 297 P 0.1725 0.0857 0.7418 298 C 0.0228 0.7337 0.2435 299 N 0.0165 0.8498 0.1337 300 R 0.0136 0.9080 0.0784 301 L 0.0096 0.9174 0.0730 302 A 0.0089 0.9130 0.0781 303 A 0.0090 0.9044 0.0866 304 E 0.0117 0.8491 0.1392 305 F 0.0322 0.6483 0.3195 306 F 0.0468 0.4702 0.4830 307 N 0.0527 0.3214 0.6260 308 G 0.0896 0.2224 0.6880 309 G 0.1314 0.2026 0.6660 310 G 0.1804 0.2295 0.5901 311 H 0.2076 0.2966 0.4958 312 L 0.1300 0.4980 0.3720 313 N 0.1793 0.4304 0.3903 314 A 0.2822 0.3410 0.3768 315 S 0.3382 0.2263 0.4355 316 G 0.4171 0.1480 0.4349 317 G 0.5073 0.0890 0.4037 318 E 0.5594 0.0666 0.3739 319 F 0.3831 0.0770 0.5399 320 Y 0.1884 0.1444 0.6672 321 G 0.1246 0.2075 0.6678 322 T 0.1435 0.2162 0.6403 323 M 0.0187 0.7523 0.2289 324 E 0.0092 0.8722 0.1186 325 E 0.0083 0.9230 0.0687 326 A 0.0083 0.9233 0.0684 327 V 0.0083 0.9216 0.0701 328 K 0.0083 0.9241 0.0677 329 V 0.0083 0.9243 0.0675 330 F 0.0083 0.9234 0.0684 331 E 0.0084 0.9195 0.0721 332 Q 0.0083 0.9216 0.0701 333 A 0.0087 0.9135 0.0778 334 L 0.0089 0.9011 0.0899 335 E 0.0091 0.8796 0.1113 336 K 0.0118 0.8137 0.1746 337 Y 0.0381 0.6302 0.3318 338 K 0.0697 0.4381 0.4922 339 P 0.0493 0.4749 0.4758 340 L 0.0665 0.3979 0.5356 341 L 0.1339 0.2624 0.6036 342 K 0.1464 0.2411 0.6125 343 E 0.1591 0.2062 0.6347