# This file is the result of combining several RDB files, specifically # T0405.t04.str2.rdb (weight 1.54425) # T0405.t04.str4.rdb (weight 0.924988) # T0405.t04.pb.rdb (weight 0.789901) # T0405.t04.bys.rdb (weight 0.748322) # T0405.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 T0405.t04.str2.rdb # ============================================ # TARGET T0405 # 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 T0405.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 3.05259 # # ============================================ # Comments from T0405.t04.str4.rdb # ============================================ # TARGET T0405 # 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 T0405.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 3.05259 # # ============================================ # Comments from T0405.t04.pb.rdb # ============================================ # TARGET T0405 # 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 T0405.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 3.05259 # # ============================================ # Comments from T0405.t04.bys.rdb # ============================================ # TARGET T0405 # 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 T0405.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 3.05259 # # ============================================ # Comments from T0405.t04.alpha.rdb # ============================================ # TARGET T0405 # 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 T0405.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 3.05259 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1676 0.2224 0.6100 2 N 0.1232 0.2785 0.5983 3 E 0.0483 0.6182 0.3334 4 T 0.0345 0.7430 0.2225 5 E 0.0136 0.8738 0.1125 6 K 0.0153 0.8990 0.0857 7 L 0.0110 0.9160 0.0730 8 V 0.0117 0.9165 0.0718 9 A 0.0090 0.9196 0.0714 10 A 0.0099 0.9183 0.0718 11 L 0.0118 0.9084 0.0798 12 L 0.0142 0.8916 0.0942 13 E 0.0207 0.8509 0.1284 14 R 0.0326 0.7659 0.2015 15 N 0.0618 0.5270 0.4112 16 F 0.0783 0.2788 0.6429 17 G 0.0950 0.1742 0.7308 18 K 0.1730 0.1954 0.6316 19 N 0.2062 0.1651 0.6286 20 I 0.2514 0.1517 0.5969 21 G 0.2421 0.1113 0.6466 22 T 0.3471 0.0939 0.5590 23 R 0.3650 0.0805 0.5545 24 Y 0.2785 0.0408 0.6806 25 P 0.1475 0.1328 0.7196 26 G 0.0876 0.1397 0.7727 27 N 0.1347 0.1835 0.6818 28 E 0.0838 0.5113 0.4048 29 A 0.0798 0.6696 0.2506 30 A 0.1025 0.6979 0.1997 31 Q 0.1464 0.6121 0.2415 32 M 0.2229 0.5060 0.2711 33 R 0.1920 0.4113 0.3967 34 A 0.0378 0.7366 0.2256 35 E 0.0170 0.8307 0.1523 36 E 0.0240 0.8689 0.1071 37 V 0.0412 0.8135 0.1453 38 I 0.0414 0.7701 0.1885 39 G 0.0496 0.7515 0.1990 40 E 0.1043 0.7025 0.1932 41 I 0.2469 0.5293 0.2238 42 A 0.3995 0.3668 0.2337 43 I 0.5837 0.2201 0.1963 44 V 0.5550 0.2054 0.2397 45 I 0.3566 0.3191 0.3243 46 A 0.2229 0.3880 0.3891 47 P 0.0780 0.6779 0.2441 48 L 0.0450 0.8015 0.1536 49 V 0.0294 0.8244 0.1462 50 E 0.0254 0.8402 0.1345 51 K 0.0389 0.7191 0.2421 52 L 0.0837 0.3827 0.5336 53 G 0.0909 0.1879 0.7212 54 I 0.1970 0.2196 0.5834 55 E 0.2045 0.2544 0.5411 56 N 0.2042 0.2487 0.5471 57 K 0.2239 0.2730 0.5031 58 T 0.3672 0.2051 0.4277 59 V 0.3196 0.2724 0.4080 60 K 0.2401 0.3682 0.3917 61 K 0.2348 0.3812 0.3840 62 T 0.2664 0.2773 0.4564 63 I 0.3054 0.2156 0.4790 64 P 0.2033 0.4344 0.3622 65 F 0.2087 0.5597 0.2316 66 L 0.2361 0.6037 0.1602 67 Y 0.2590 0.6149 0.1262 68 E 0.2630 0.6052 0.1318 69 L 0.1855 0.6227 0.1918 70 Q 0.1480 0.5479 0.3041 71 K 0.0736 0.5842 0.3422 72 N 0.0766 0.4228 0.5006 73 Q 0.1250 0.3839 0.4911 74 F 0.2062 0.2814 0.5124 75 C 0.2771 0.2073 0.5155 76 D 0.2156 0.1891 0.5954 77 M 0.1825 0.3089 0.5086 78 S 0.1945 0.2340 0.5716 79 A 0.2062 0.2190 0.5749 80 Y 0.2609 0.0986 0.6405 81 P 0.2609 0.1369 0.6022 82 Y 0.3532 0.0737 0.5731 83 P 0.3973 0.1346 0.4680 84 L 0.5933 0.0968 0.3100 85 L 0.7065 0.0553 0.2381 86 L 0.7146 0.0362 0.2492 87 V 0.6551 0.0558 0.2890 88 N 0.3757 0.0741 0.5502 89 G 0.1899 0.0980 0.7121 90 T 0.2319 0.0942 0.6739 91 S 0.2297 0.1169 0.6534 92 T 0.1522 0.2626 0.5852 93 D 0.1528 0.2570 0.5902 94 T 0.1425 0.3929 0.4646 95 E 0.1135 0.5768 0.3097 96 K 0.1429 0.6069 0.2502 97 Y 0.1804 0.5461 0.2735 98 W 0.1903 0.5128 0.2970 99 R 0.1956 0.4383 0.3662 100 D 0.2142 0.2488 0.5370 101 L 0.2456 0.1267 0.6277 102 P 0.1859 0.2045 0.6097 103 T 0.2431 0.2323 0.5246 104 Y 0.3195 0.1770 0.5035 105 W 0.3501 0.1564 0.4936 106 T 0.2869 0.1671 0.5459 107 D 0.1592 0.2962 0.5446 108 D 0.1299 0.3462 0.5238 109 A 0.0977 0.4356 0.4667 110 N 0.1161 0.2734 0.6106 111 K 0.2753 0.2236 0.5011 112 I 0.4307 0.1674 0.4019 113 V 0.4700 0.1510 0.3791 114 L 0.3702 0.1421 0.4878 115 P 0.2317 0.4310 0.3373 116 Y 0.2266 0.5290 0.2444 117 V 0.1807 0.6148 0.2045 118 L 0.0877 0.7554 0.1569 119 E 0.0489 0.8318 0.1193 120 H 0.0630 0.7888 0.1481 121 I 0.0713 0.7518 0.1769 122 K 0.0533 0.7034 0.2433 123 N 0.0544 0.5097 0.4359 124 N 0.0410 0.5225 0.4365 125 K 0.0572 0.6061 0.3367 126 V 0.0587 0.7512 0.1901 127 R 0.0262 0.8559 0.1178 128 Q 0.0164 0.8972 0.0864 129 K 0.0138 0.9056 0.0807 130 L 0.0143 0.9045 0.0812 131 L 0.0110 0.9095 0.0795 132 A 0.0109 0.9111 0.0780 133 F 0.0136 0.9050 0.0814 134 H 0.0192 0.8906 0.0901 135 A 0.0149 0.9021 0.0830 136 W 0.0177 0.8918 0.0905 137 L 0.0367 0.8065 0.1568 138 L 0.0389 0.6733 0.2878 139 G 0.0430 0.6358 0.3212 140 E 0.0699 0.7180 0.2121 141 V 0.0696 0.7560 0.1744 142 V 0.0748 0.7666 0.1586 143 E 0.0897 0.7274 0.1829 144 M 0.0853 0.6916 0.2231 145 N 0.0677 0.6651 0.2672 146 E 0.0192 0.7895 0.1913 147 A 0.0368 0.6727 0.2905 148 L 0.0720 0.3184 0.6096 149 G 0.0760 0.1284 0.7957 150 A 0.2011 0.1589 0.6401 151 D 0.3072 0.1205 0.5723 152 F 0.5464 0.0421 0.4115 153 R 0.6612 0.0237 0.3150 154 V 0.7658 0.0086 0.2256 155 K 0.7713 0.0139 0.2148 156 L 0.7928 0.0067 0.2005 157 V 0.7755 0.0146 0.2099 158 F 0.6667 0.0204 0.3129 159 E 0.4696 0.0848 0.4456 160 S 0.3082 0.1541 0.5377 161 D 0.2914 0.1305 0.5780 162 M 0.4760 0.0872 0.4368 163 R 0.6612 0.0403 0.2985 164 I 0.7582 0.0196 0.2222 165 R 0.7680 0.0170 0.2150 166 L 0.7847 0.0102 0.2051 167 R 0.7621 0.0139 0.2240 168 V 0.7264 0.0188 0.2548 169 Y 0.6509 0.0413 0.3079 170 E 0.5945 0.0574 0.3481 171 V 0.4125 0.2361 0.3514 172 E 0.3015 0.3872 0.3113 173 Q 0.4930 0.2673 0.2397 174 I 0.4712 0.2771 0.2517 175 A 0.6531 0.1196 0.2273 176 I 0.7429 0.0517 0.2055 177 E 0.7500 0.0397 0.2102 178 V 0.7457 0.0329 0.2214 179 H 0.6874 0.0445 0.2681 180 F 0.6093 0.0720 0.3186 181 L 0.4103 0.1241 0.4657 182 D 0.2452 0.1389 0.6159 183 N 0.1332 0.1807 0.6861 184 H 0.1314 0.2041 0.6644 185 D 0.1518 0.2327 0.6154 186 T 0.1175 0.4386 0.4439 187 E 0.0936 0.6258 0.2806 188 Q 0.1151 0.6328 0.2522 189 Q 0.1704 0.5336 0.2960 190 H 0.2230 0.3472 0.4298 191 L 0.2089 0.2083 0.5828 192 G 0.2252 0.1164 0.6584 193 Y 0.3759 0.0725 0.5517 194 D 0.4283 0.0633 0.5083 195 V 0.5416 0.0621 0.3963 196 S 0.4939 0.0589 0.4472 197 L 0.4332 0.1273 0.4394 198 D 0.3054 0.1303 0.5643 199 A 0.1894 0.3740 0.4366 200 D 0.1490 0.3893 0.4617 201 F 0.0770 0.6019 0.3211 202 T 0.0363 0.7504 0.2134 203 E 0.0132 0.8575 0.1294 204 K 0.0145 0.8713 0.1142 205 A 0.0127 0.9043 0.0830 206 R 0.0168 0.9059 0.0773 207 L 0.0210 0.8977 0.0813 208 L 0.0187 0.8946 0.0867 209 L 0.0228 0.8616 0.1156 210 R 0.0302 0.7698 0.1999 211 Q 0.0631 0.5152 0.4217 212 G 0.0826 0.3584 0.5590 213 I 0.1252 0.4742 0.4007 214 L 0.1371 0.5451 0.3177 215 T 0.1315 0.5540 0.3145 216 E 0.0569 0.6681 0.2750 217 N 0.0577 0.5680 0.3744 218 L 0.0613 0.4707 0.4680 219 G 0.0423 0.5983 0.3594 220 L 0.0175 0.8206 0.1620 221 E 0.0097 0.9004 0.0899 222 A 0.0106 0.9109 0.0785 223 L 0.0094 0.9162 0.0745 224 K 0.0088 0.9180 0.0732 225 A 0.0090 0.9169 0.0741 226 Y 0.0134 0.8917 0.0949 227 M 0.0150 0.8689 0.1161 228 K 0.0132 0.8570 0.1298 229 S 0.0306 0.7507 0.2187 230 V 0.0634 0.6393 0.2973 231 L 0.1070 0.5605 0.3326 232 P 0.0702 0.6796 0.2502 233 I 0.0615 0.7248 0.2137 234 A 0.0511 0.7291 0.2198 235 H 0.0635 0.6347 0.3019 236 S 0.0938 0.5582 0.3481 237 L 0.0471 0.6549 0.2979 238 K 0.0511 0.6202 0.3287 239 N 0.0666 0.5487 0.3847 240 L 0.0553 0.6090 0.3356 241 E 0.0574 0.6444 0.2982 242 H 0.1147 0.4810 0.4044 243 L 0.2328 0.2816 0.4856 244 T 0.2202 0.2084 0.5714 245 F 0.0722 0.6192 0.3085 246 E 0.0372 0.7635 0.1992 247 E 0.0541 0.7418 0.2042 248 T 0.0401 0.7492 0.2107 249 K 0.0205 0.8167 0.1628 250 K 0.0259 0.8256 0.1485 251 L 0.0198 0.8410 0.1392 252 T 0.0204 0.8465 0.1331 253 K 0.0272 0.8438 0.1290 254 L 0.0533 0.7782 0.1685 255 L 0.0953 0.6311 0.2736 256 T 0.1038 0.5042 0.3920 257 Q 0.1141 0.3889 0.4970 258 E 0.1378 0.2523 0.6100 259 E 0.2231 0.1106 0.6663 260 P 0.1810 0.1978 0.6212 261 K 0.2678 0.2332 0.4989 262 I 0.3994 0.1975 0.4032 263 M 0.3692 0.1867 0.4441 264 E 0.2499 0.2533 0.4968 265 D 0.1689 0.2308 0.6002 266 T 0.1281 0.2714 0.6004 267 D 0.1253 0.2872 0.5876 268 L 0.0878 0.4224 0.4898 269 T 0.0568 0.5404 0.4028 270 S 0.0208 0.7701 0.2091 271 K 0.0113 0.8253 0.1634 272 A 0.0109 0.8861 0.1030 273 L 0.0089 0.9068 0.0843 274 D 0.0086 0.9109 0.0805 275 F 0.0084 0.9140 0.0775 276 L 0.0086 0.9140 0.0774 277 Q 0.0088 0.9123 0.0789 278 K 0.0097 0.8977 0.0926 279 A 0.0153 0.8545 0.1302 280 A 0.0281 0.7520 0.2198 281 Q 0.0333 0.6337 0.3330 282 Q 0.0694 0.4266 0.5040