# This file is the result of combining several RDB files, specifically # T0489.t2k.str2.rdb (weight 1.54425) # T0489.t2k.str4.rdb (weight 0.924988) # T0489.t2k.pb.rdb (weight 0.789901) # T0489.t2k.bys.rdb (weight 0.748322) # T0489.t2k.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 T0489.t2k.str2.rdb # ============================================ # TARGET T0489 # Using neural net dunbrack-40pc-3157-t2k-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 T0489.t2k-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 47.711 # # ============================================ # Comments from T0489.t2k.str4.rdb # ============================================ # TARGET T0489 # Using neural net dunbrack-40pc-3157-t2k-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 T0489.t2k-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 47.711 # # ============================================ # Comments from T0489.t2k.pb.rdb # ============================================ # TARGET T0489 # Using neural net dunbrack-40pc-3157-t2k-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 T0489.t2k-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 47.711 # # ============================================ # Comments from T0489.t2k.bys.rdb # ============================================ # TARGET T0489 # Using neural net dunbrack-40pc-3157-t2k-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 T0489.t2k-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 47.711 # # ============================================ # Comments from T0489.t2k.alpha.rdb # ============================================ # TARGET T0489 # Using neural net dunbrack-40pc-3157-t2k-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 T0489.t2k-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 47.711 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3373 0.2123 0.4504 2 M 0.3374 0.1901 0.4724 3 F 0.3458 0.1764 0.4778 4 K 0.3313 0.1258 0.5429 5 W 0.3255 0.0672 0.6073 6 P 0.2380 0.1916 0.5704 7 W 0.2807 0.2353 0.4840 8 K 0.2690 0.2292 0.5018 9 A 0.2347 0.2781 0.4871 10 D 0.1765 0.2530 0.5705 11 D 0.1352 0.2923 0.5725 12 E 0.1479 0.2457 0.6064 13 S 0.1350 0.2101 0.6549 14 G 0.1421 0.1117 0.7462 15 N 0.1294 0.1539 0.7167 16 A 0.0324 0.5344 0.4333 17 E 0.0425 0.5205 0.4370 18 M 0.0960 0.4837 0.4203 19 P 0.0314 0.7795 0.1891 20 W 0.0147 0.8793 0.1060 21 E 0.0092 0.9129 0.0779 22 Q 0.0099 0.9031 0.0870 23 A 0.0145 0.8519 0.1336 24 L 0.0155 0.7699 0.2145 25 A 0.0364 0.5765 0.3871 26 I 0.0916 0.4487 0.4596 27 P 0.0632 0.6157 0.3211 28 V 0.0551 0.6908 0.2541 29 L 0.0458 0.7545 0.1997 30 A 0.0524 0.6535 0.2941 31 H 0.0811 0.3036 0.6153 32 L 0.1859 0.0830 0.7311 33 S 0.1553 0.0368 0.8080 34 S 0.0164 0.6450 0.3386 35 T 0.0105 0.8168 0.1727 36 E 0.0099 0.8925 0.0976 37 Q 0.0087 0.9129 0.0784 38 H 0.0084 0.9176 0.0740 39 K 0.0084 0.9202 0.0714 40 L 0.0084 0.9200 0.0716 41 T 0.0083 0.9222 0.0695 42 Q 0.0083 0.9240 0.0678 43 M 0.0083 0.9236 0.0681 44 A 0.0083 0.9220 0.0697 45 A 0.0083 0.9230 0.0687 46 R 0.0085 0.9208 0.0707 47 F 0.0104 0.9071 0.0824 48 L 0.0107 0.8835 0.1058 49 Q 0.0133 0.8144 0.1723 50 Q 0.0404 0.6604 0.2992 51 K 0.1197 0.4691 0.4112 52 R 0.2412 0.2835 0.4753 53 L 0.3882 0.1638 0.4480 54 V 0.4411 0.1264 0.4325 55 A 0.3804 0.1207 0.4990 56 L 0.2617 0.1743 0.5640 57 Q 0.1634 0.1225 0.7141 58 G 0.1228 0.0871 0.7901 59 L 0.4156 0.0355 0.5489 60 E 0.5668 0.0303 0.4029 61 L 0.4789 0.0590 0.4621 62 T 0.2087 0.0470 0.7443 63 P 0.0344 0.6014 0.3641 64 L 0.0192 0.7399 0.2409 65 H 0.0196 0.8696 0.1108 66 Q 0.0134 0.8892 0.0974 67 A 0.0115 0.9173 0.0711 68 R 0.0091 0.9234 0.0675 69 I 0.0108 0.9185 0.0707 70 A 0.0109 0.9153 0.0738 71 M 0.0107 0.9047 0.0846 72 L 0.0138 0.8794 0.1068 73 F 0.0238 0.8267 0.1495 74 C 0.0385 0.7580 0.2036 75 L 0.0827 0.6799 0.2374 76 P 0.0662 0.7192 0.2146 77 V 0.0702 0.6928 0.2371 78 L 0.0975 0.5749 0.3276 79 E 0.1056 0.4291 0.4653 80 L 0.1184 0.2675 0.6141 81 G 0.1068 0.1862 0.7070 82 I 0.1015 0.4444 0.4541 83 E 0.1079 0.5469 0.3452 84 W 0.1380 0.5030 0.3590 85 L 0.2030 0.3278 0.4693 86 D 0.1303 0.1933 0.6764 87 G 0.0801 0.1216 0.7984 88 F 0.2627 0.0726 0.6646 89 H 0.3219 0.0683 0.6098 90 E 0.7023 0.0183 0.2794 91 V 0.7628 0.0072 0.2300 92 L 0.7874 0.0059 0.2067 93 I 0.7539 0.0132 0.2329 94 Y 0.5411 0.0133 0.4456 95 P 0.2567 0.0678 0.6756 96 A 0.2265 0.0652 0.7084 97 P 0.2060 0.2142 0.5798 98 F 0.3285 0.1518 0.5197 99 I 0.4405 0.0931 0.4665 100 V 0.3967 0.0695 0.5338 101 D 0.3001 0.0992 0.6008 102 D 0.2288 0.2580 0.5132 103 E 0.2793 0.2700 0.4506 104 W 0.3564 0.2263 0.4173 105 E 0.3079 0.2501 0.4420 106 D 0.2337 0.2502 0.5161 107 D 0.1655 0.3430 0.4914 108 I 0.1504 0.2045 0.6451 109 G 0.2181 0.1130 0.6689 110 L 0.4397 0.0760 0.4843 111 V 0.5291 0.0711 0.3998 112 H 0.4212 0.0814 0.4975 113 N 0.3134 0.1929 0.4937 114 Q 0.2910 0.2206 0.4884 115 R 0.3885 0.1792 0.4323 116 V 0.4800 0.1691 0.3509 117 V 0.4669 0.1970 0.3361 118 Q 0.4689 0.1718 0.3593 119 S 0.3585 0.1915 0.4500 120 G 0.2723 0.1712 0.5565 121 Q 0.3437 0.2216 0.4347 122 S 0.3388 0.2830 0.3782 123 W 0.2517 0.3473 0.4009 124 Q 0.2023 0.3303 0.4674 125 Q 0.1873 0.1576 0.6552 126 G 0.2783 0.0608 0.6608 127 P 0.4518 0.0336 0.5146 128 V 0.7494 0.0123 0.2383 129 V 0.7639 0.0150 0.2211 130 L 0.7531 0.0199 0.2270 131 N 0.4506 0.0203 0.5291 132 W 0.1282 0.4201 0.4517 133 L 0.0508 0.6853 0.2639 134 D 0.0462 0.7406 0.2132 135 I 0.0314 0.7903 0.1783 136 Q 0.0410 0.7041 0.2549 137 D 0.0490 0.5423 0.4087 138 S 0.0839 0.2900 0.6262 139 F 0.1491 0.1779 0.6731 140 D 0.1383 0.1876 0.6741 141 A 0.0587 0.3554 0.5858 142 S 0.0723 0.2228 0.7049 143 G 0.0891 0.1475 0.7634 144 F 0.2650 0.1327 0.6024 145 N 0.4222 0.1561 0.4217 146 L 0.5186 0.2108 0.2706 147 V 0.5084 0.2794 0.2122 148 V 0.3241 0.5066 0.1693 149 H 0.2115 0.6316 0.1570 150 E 0.1200 0.7305 0.1495 151 V 0.0594 0.7894 0.1511 152 A 0.0446 0.7966 0.1588 153 H 0.0368 0.7969 0.1663 154 K 0.0541 0.7301 0.2158 155 L 0.1253 0.5754 0.2993 156 D 0.1077 0.4352 0.4571 157 T 0.0669 0.5475 0.3856 158 R 0.0565 0.4826 0.4609 159 N 0.0824 0.2258 0.6918 160 G 0.0774 0.1538 0.7688 161 D 0.1663 0.1917 0.6421 162 R 0.1463 0.2993 0.5544 163 A 0.1316 0.2136 0.6548 164 S 0.1355 0.1335 0.7310 165 G 0.2000 0.0675 0.7325 166 V 0.2419 0.0646 0.6935 167 P 0.2287 0.1288 0.6425 168 L 0.2493 0.1274 0.6232 169 I 0.2311 0.0732 0.6958 170 P 0.1441 0.2053 0.6506 171 L 0.0813 0.4085 0.5102 172 R 0.0885 0.5168 0.3946 173 E 0.0953 0.5474 0.3573 174 V 0.0719 0.6630 0.2651 175 A 0.0398 0.7284 0.2318 176 G 0.0271 0.7721 0.2008 177 W 0.0167 0.8637 0.1197 178 E 0.0111 0.8991 0.0898 179 H 0.0088 0.9142 0.0771 180 D 0.0089 0.9128 0.0783 181 L 0.0103 0.9074 0.0823 182 H 0.0084 0.9176 0.0740 183 A 0.0083 0.9199 0.0717 184 A 0.0085 0.9136 0.0779 185 M 0.0088 0.9116 0.0796 186 N 0.0085 0.9064 0.0851 187 N 0.0089 0.8873 0.1038 188 I 0.0108 0.8782 0.1110 189 Q 0.0092 0.8892 0.1016 190 D 0.0087 0.9021 0.0892 191 E 0.0112 0.8817 0.1071 192 I 0.0169 0.8719 0.1112 193 D 0.0192 0.8425 0.1383 194 L 0.0357 0.7031 0.2612 195 V 0.0710 0.3986 0.5304 196 G 0.0640 0.2531 0.6829 197 E 0.0978 0.2391 0.6631 198 S 0.1431 0.2106 0.6463 199 A 0.1356 0.3532 0.5112 200 A 0.1617 0.3397 0.4986 201 S 0.2031 0.2564 0.5405 202 I 0.2961 0.1781 0.5259 203 D 0.2324 0.1202 0.6474 204 A 0.0528 0.5794 0.3678 205 Y 0.0524 0.4968 0.4507 206 A 0.1246 0.4098 0.4656 207 A 0.1840 0.3394 0.4766 208 T 0.2099 0.1995 0.5906 209 D 0.1750 0.0636 0.7614 210 P 0.0179 0.7258 0.2563 211 A 0.0185 0.7816 0.2000 212 E 0.0324 0.8237 0.1439 213 C 0.0338 0.8565 0.1096 214 F 0.0586 0.8270 0.1144 215 A 0.0845 0.8075 0.1080 216 V 0.0854 0.7967 0.1179 217 L 0.0987 0.7423 0.1589 218 S 0.0659 0.7557 0.1784 219 E 0.0526 0.7760 0.1714 220 Y 0.0591 0.7238 0.2171 221 F 0.0903 0.5753 0.3343 222 F 0.0999 0.5122 0.3879 223 S 0.1136 0.3744 0.5119 224 A 0.1606 0.2044 0.6351 225 P 0.0577 0.5690 0.3733 226 E 0.0183 0.7448 0.2369 227 L 0.0199 0.7641 0.2160 228 F 0.0370 0.6762 0.2867 229 A 0.0517 0.6590 0.2893 230 P 0.0189 0.7390 0.2422 231 R 0.0226 0.6946 0.2828 232 F 0.0322 0.7485 0.2193 233 P 0.0101 0.8720 0.1179 234 A 0.0086 0.9087 0.0827 235 L 0.0083 0.9211 0.0705 236 W 0.0083 0.9229 0.0688 237 Q 0.0083 0.9242 0.0675 238 R 0.0083 0.9239 0.0678 239 F 0.0084 0.9176 0.0739 240 C 0.0085 0.9161 0.0754 241 H 0.0092 0.9086 0.0822 242 F 0.0159 0.8606 0.1234 243 Y 0.0289 0.7617 0.2095 244 R 0.0406 0.6261 0.3333 245 Q 0.0821 0.4953 0.4226 246 D 0.1543 0.1761 0.6696 247 P 0.0232 0.6782 0.2986 248 L 0.0159 0.7617 0.2224 249 A 0.0185 0.8226 0.1589 250 R 0.0374 0.7503 0.2123 251 R 0.0671 0.6871 0.2458 252 R 0.0715 0.6176 0.3110 253 E 0.0654 0.5948 0.3398 254 N 0.0770 0.3620 0.5610 255 G 0.1018 0.2323 0.6659 256 L 0.2061 0.2001 0.5938 257 Q 0.2169 0.1772 0.6059 258 D 0.1899 0.1397 0.6704 259 E 0.0958 0.2898 0.6144 260 G 0.0954 0.1976 0.7070 261 D 0.2203 0.1869 0.5928 262 R 0.3675 0.1488 0.4837 263 R 0.5217 0.1130 0.3653 264 I 0.6015 0.0736 0.3248 265 V 0.5781 0.0664 0.3554 266 H 0.3613 0.0603 0.5785