# This file is the result of combining several RDB files, specifically # T0398.t04.str2.rdb (weight 1.54425) # T0398.t04.str4.rdb (weight 0.924988) # T0398.t04.pb.rdb (weight 0.789901) # T0398.t04.bys.rdb (weight 0.748322) # T0398.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 T0398.t04.str2.rdb # ============================================ # TARGET T0398 # 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 T0398.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 944.963 # # ============================================ # Comments from T0398.t04.str4.rdb # ============================================ # TARGET T0398 # 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 T0398.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 944.963 # # ============================================ # Comments from T0398.t04.pb.rdb # ============================================ # TARGET T0398 # 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 T0398.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 944.963 # # ============================================ # Comments from T0398.t04.bys.rdb # ============================================ # TARGET T0398 # 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 T0398.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 944.963 # # ============================================ # Comments from T0398.t04.alpha.rdb # ============================================ # TARGET T0398 # 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 T0398.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 944.963 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3615 0.1253 0.5132 2 L 0.3340 0.1247 0.5413 3 T 0.2815 0.1223 0.5962 4 G 0.2357 0.0782 0.6861 5 K 0.3909 0.0455 0.5637 6 H 0.5167 0.0559 0.4274 7 V 0.5589 0.1304 0.3107 8 V 0.6339 0.1163 0.2498 9 I 0.5835 0.1085 0.3080 10 I 0.4006 0.1200 0.4794 11 G 0.1769 0.1652 0.6580 12 G 0.0978 0.2154 0.6868 13 D 0.1321 0.4000 0.4679 14 A 0.1572 0.5275 0.3153 15 R 0.1319 0.6660 0.2020 16 Q 0.0844 0.7870 0.1286 17 L 0.0268 0.8886 0.0845 18 E 0.0252 0.8982 0.0766 19 I 0.0181 0.9058 0.0761 20 I 0.0191 0.8941 0.0868 21 R 0.0176 0.8783 0.1041 22 K 0.0267 0.7947 0.1786 23 L 0.0675 0.6025 0.3300 24 S 0.1300 0.3495 0.5205 25 T 0.1824 0.1803 0.6373 26 F 0.1309 0.1811 0.6880 27 D 0.1401 0.0803 0.7796 28 A 0.3755 0.0215 0.6030 29 K 0.6816 0.0144 0.3040 30 I 0.7959 0.0048 0.1994 31 S 0.7894 0.0079 0.2027 32 L 0.7685 0.0071 0.2244 33 V 0.6264 0.0306 0.3430 34 G 0.3580 0.0342 0.6077 35 F 0.2373 0.0763 0.6865 36 D 0.1928 0.0725 0.7347 37 Q 0.0897 0.3845 0.5258 38 L 0.0626 0.5185 0.4189 39 D 0.0789 0.5100 0.4111 40 D 0.0716 0.5822 0.3462 41 G 0.0838 0.6371 0.2792 42 F 0.1257 0.5970 0.2772 43 I 0.1815 0.4932 0.3253 44 G 0.1747 0.4338 0.3915 45 V 0.2613 0.4270 0.3117 46 T 0.3074 0.4110 0.2816 47 K 0.3927 0.3007 0.3066 48 M 0.3385 0.2554 0.4061 49 R 0.2608 0.2132 0.5260 50 I 0.1792 0.3665 0.4543 51 D 0.1234 0.4688 0.4078 52 E 0.1819 0.3979 0.4203 53 V 0.3192 0.2581 0.4227 54 D 0.4031 0.1855 0.4114 55 W 0.4286 0.1896 0.3818 56 N 0.4008 0.1805 0.4188 57 T 0.4467 0.1126 0.4407 58 V 0.3974 0.1592 0.4434 59 D 0.3689 0.1228 0.5083 60 A 0.5504 0.0607 0.3888 61 I 0.6374 0.0304 0.3323 62 L 0.6563 0.0192 0.3245 63 L 0.5763 0.0173 0.4064 64 P 0.4082 0.0290 0.5627 65 I 0.2850 0.1602 0.5548 66 S 0.2054 0.1429 0.6518 67 G 0.1780 0.1857 0.6362 68 T 0.1149 0.3598 0.5253 69 N 0.0672 0.5686 0.3642 70 E 0.0627 0.5899 0.3474 71 A 0.0643 0.5676 0.3681 72 G 0.0493 0.5999 0.3508 73 K 0.0856 0.6096 0.3048 74 V 0.1303 0.6420 0.2278 75 D 0.1221 0.6886 0.1893 76 T 0.1785 0.6544 0.1671 77 I 0.2099 0.5597 0.2303 78 F 0.2957 0.3550 0.3493 79 S 0.2129 0.2232 0.5639 80 N 0.1078 0.2622 0.6300 81 E 0.1292 0.1691 0.7017 82 S 0.2619 0.1504 0.5877 83 I 0.4671 0.1318 0.4010 84 V 0.5627 0.1016 0.3357 85 L 0.4507 0.1382 0.4111 86 T 0.3961 0.1765 0.4273 87 E 0.2785 0.3670 0.3545 88 E 0.2479 0.4294 0.3227 89 M 0.1826 0.5112 0.3062 90 I 0.1408 0.5128 0.3465 91 E 0.1609 0.4332 0.4059 92 K 0.1750 0.3021 0.5229 93 T 0.1676 0.1024 0.7300 94 P 0.0606 0.4385 0.5009 95 N 0.0638 0.3038 0.6325 96 H 0.1285 0.1716 0.6999 97 C 0.3962 0.0760 0.5278 98 V 0.5313 0.0821 0.3867 99 V 0.5595 0.1152 0.3254 100 Y 0.4605 0.1474 0.3921 101 S 0.4059 0.1293 0.4647 102 G 0.3422 0.1056 0.5522 103 I 0.3426 0.1295 0.5279 104 S 0.3237 0.1841 0.4922 105 N 0.3761 0.2351 0.3887 106 T 0.3953 0.1764 0.4283 107 Y 0.2784 0.1216 0.6000 108 L 0.0866 0.5192 0.3942 109 N 0.0592 0.6130 0.3278 110 Q 0.0691 0.6523 0.2786 111 C 0.0784 0.6004 0.3211 112 M 0.0561 0.6315 0.3124 113 K 0.0540 0.5965 0.3495 114 K 0.0766 0.5712 0.3522 115 T 0.1083 0.4505 0.4412 116 N 0.0434 0.6747 0.2819 117 R 0.0291 0.7879 0.1831 118 T 0.0296 0.8339 0.1365 119 L 0.0237 0.8601 0.1162 120 V 0.0176 0.8816 0.1007 121 K 0.0179 0.8685 0.1136 122 L 0.0295 0.8048 0.1657 123 M 0.0645 0.6611 0.2744 124 E 0.0665 0.5155 0.4180 125 R 0.0624 0.4458 0.4918 126 D 0.0808 0.3535 0.5657 127 D 0.1284 0.3699 0.5017 128 I 0.1630 0.4275 0.4095 129 A 0.2125 0.4449 0.3425 130 I 0.2807 0.3678 0.3516 131 Y 0.2367 0.3345 0.4288 132 N 0.1826 0.3150 0.5024 133 S 0.2073 0.2310 0.5618 134 I 0.2447 0.1207 0.6346 135 P 0.1724 0.2396 0.5880 136 T 0.1131 0.3804 0.5064 137 A 0.1244 0.3446 0.5311 138 E 0.0937 0.3280 0.5783 139 G 0.0952 0.2252 0.6796 140 T 0.2266 0.2437 0.5297 141 I 0.3875 0.2620 0.3505 142 M 0.4408 0.2746 0.2846 143 M 0.4478 0.2656 0.2866 144 A 0.3553 0.3014 0.3433 145 I 0.2943 0.2872 0.4185 146 Q 0.2069 0.2905 0.5025 147 H 0.1926 0.1976 0.6099 148 T 0.2307 0.1316 0.6376 149 D 0.2225 0.1046 0.6729 150 F 0.3702 0.0591 0.5707 151 T 0.4326 0.0513 0.5161 152 I 0.4500 0.0637 0.4863 153 H 0.2773 0.0815 0.6411 154 G 0.1891 0.0557 0.7553 155 A 0.3346 0.0387 0.6266 156 N 0.5797 0.0203 0.3999 157 V 0.8049 0.0054 0.1897 158 A 0.7922 0.0054 0.2025 159 V 0.7785 0.0043 0.2171 160 L 0.7155 0.0222 0.2623 161 G 0.5646 0.0296 0.4058 162 L 0.4077 0.0928 0.4995 163 G 0.2384 0.1500 0.6116 164 R 0.1722 0.3353 0.4926 165 V 0.1054 0.3893 0.5054 166 G 0.0507 0.5663 0.3830 167 M 0.0141 0.8451 0.1408 168 S 0.0091 0.9083 0.0825 169 V 0.0084 0.9204 0.0712 170 A 0.0083 0.9214 0.0702 171 R 0.0083 0.9218 0.0699 172 K 0.0084 0.9180 0.0736 173 F 0.0090 0.8993 0.0916 174 A 0.0107 0.8592 0.1301 175 A 0.0173 0.7850 0.1977 176 L 0.0546 0.1869 0.7584 177 G 0.0483 0.0644 0.8872 178 A 0.2485 0.0127 0.7388 179 K 0.5360 0.0154 0.4485 180 V 0.7741 0.0058 0.2201 181 K 0.7808 0.0085 0.2107 182 V 0.7578 0.0076 0.2346 183 G 0.6532 0.0284 0.3184 184 A 0.3542 0.0343 0.6115 185 R 0.1721 0.1623 0.6656 186 E 0.1406 0.1794 0.6801 187 S 0.0267 0.6823 0.2909 188 D 0.0213 0.7762 0.2025 189 L 0.0135 0.8804 0.1061 190 L 0.0091 0.9062 0.0847 191 A 0.0085 0.9227 0.0689 192 R 0.0089 0.9193 0.0717 193 I 0.0086 0.9156 0.0759 194 A 0.0095 0.9033 0.0873 195 E 0.0135 0.8015 0.1850 196 M 0.0578 0.3173 0.6249 197 G 0.0483 0.0806 0.8711 198 M 0.1786 0.0402 0.7812 199 E 0.2739 0.0398 0.6864 200 P 0.3723 0.0775 0.5503 201 F 0.4653 0.0569 0.4779 202 H 0.4122 0.0443 0.5435 203 I 0.1614 0.3565 0.4821 204 S 0.0469 0.6421 0.3111 205 K 0.0391 0.6945 0.2663 206 A 0.0144 0.8467 0.1388 207 A 0.0095 0.8884 0.1021 208 Q 0.0086 0.9041 0.0873 209 E 0.0104 0.8789 0.1107 210 L 0.0166 0.7821 0.2013 211 R 0.0203 0.6140 0.3657 212 D 0.0534 0.3440 0.6025 213 V 0.1863 0.1999 0.6138 214 D 0.3701 0.1220 0.5079 215 V 0.7806 0.0315 0.1879 216 C 0.7413 0.0208 0.2379 217 I 0.7775 0.0189 0.2037 218 N 0.7021 0.0560 0.2419 219 T 0.5088 0.0498 0.4414 220 I 0.3372 0.0440 0.6187 221 P 0.2224 0.0626 0.7150 222 A 0.1508 0.2702 0.5790 223 L 0.1875 0.2873 0.5251 224 V 0.3271 0.2075 0.4654 225 V 0.3333 0.1284 0.5383 226 T 0.1851 0.1029 0.7120 227 A 0.0132 0.7200 0.2668 228 N 0.0098 0.8427 0.1476 229 V 0.0096 0.8943 0.0961 230 L 0.0129 0.8338 0.1533 231 A 0.0156 0.7153 0.2690 232 E 0.0324 0.4191 0.5484 233 M 0.1667 0.1170 0.7163 234 P 0.1252 0.1082 0.7666 235 S 0.1088 0.2355 0.6557 236 H 0.1660 0.0812 0.7528 237 T 0.6101 0.0170 0.3729 238 F 0.7416 0.0114 0.2470 239 V 0.8001 0.0058 0.1941 240 I 0.7944 0.0100 0.1956 241 D 0.7037 0.0119 0.2844 242 L 0.6420 0.0747 0.2832 243 A 0.6091 0.0645 0.3264 244 S 0.4901 0.0800 0.4300 245 K 0.2823 0.0656 0.6521 246 P 0.1420 0.1714 0.6866 247 G 0.1096 0.1077 0.7827 248 G 0.1372 0.1059 0.7568 249 T 0.2555 0.1153 0.6292 250 D 0.2369 0.1767 0.5864 251 F 0.1207 0.4868 0.3924 252 R 0.0978 0.6078 0.2944 253 Y 0.1151 0.6714 0.2135 254 A 0.0496 0.7900 0.1604 255 E 0.0374 0.7944 0.1682 256 K 0.0476 0.6788 0.2736 257 R 0.0826 0.2395 0.6778 258 G 0.0660 0.0811 0.8529 259 I 0.2644 0.0353 0.7003 260 K 0.5226 0.0581 0.4194 261 A 0.7426 0.0261 0.2313 262 L 0.7469 0.0229 0.2302 263 L 0.7152 0.0262 0.2586 264 V 0.5673 0.0364 0.3963 265 P 0.2754 0.0831 0.6415 266 G 0.1492 0.0824 0.7684 267 L 0.2281 0.0420 0.7299 268 P 0.2579 0.0813 0.6608 269 G 0.3814 0.1028 0.5158 270 I 0.5095 0.0891 0.4014 271 V 0.5348 0.0522 0.4130 272 A 0.4505 0.0386 0.5109 273 P 0.3046 0.0936 0.6018 274 K 0.2631 0.1727 0.5642 275 T 0.1993 0.2205 0.5803 276 A 0.0652 0.6010 0.3338 277 G 0.0244 0.7944 0.1812 278 R 0.0139 0.8825 0.1036 279 I 0.0128 0.8862 0.1010 280 L 0.0158 0.8563 0.1279 281 A 0.0163 0.8422 0.1415 282 D 0.0242 0.7651 0.2107 283 V 0.0584 0.7307 0.2109 284 L 0.0654 0.7288 0.2057 285 V 0.0858 0.7077 0.2066 286 K 0.1269 0.6022 0.2709 287 L 0.1195 0.4938 0.3867 288 L 0.1622 0.2717 0.5661 289 A 0.2047 0.1592 0.6361 290 E 0.2194 0.0554 0.7251 291 P 0.1522 0.1759 0.6719 292 S 0.1331 0.1807 0.6862