# This file is the result of combining several RDB files, specifically # T0487.t06.str2.rdb (weight 1.54425) # T0487.t06.str4.rdb (weight 0.924988) # T0487.t06.pb.rdb (weight 0.789901) # T0487.t06.bys.rdb (weight 0.748322) # T0487.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 T0487.t06.str2.rdb # ============================================ # TARGET T0487 # 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 T0487.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 6.70837 # # ============================================ # Comments from T0487.t06.str4.rdb # ============================================ # TARGET T0487 # 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 T0487.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 6.70837 # # ============================================ # Comments from T0487.t06.pb.rdb # ============================================ # TARGET T0487 # 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 T0487.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 6.70837 # # ============================================ # Comments from T0487.t06.bys.rdb # ============================================ # TARGET T0487 # 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 T0487.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 6.70837 # # ============================================ # Comments from T0487.t06.alpha.rdb # ============================================ # TARGET T0487 # 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 T0487.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 6.70837 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 N 0.2400 0.1125 0.6475 2 R 0.3303 0.2025 0.4672 3 F 0.4752 0.1923 0.3324 4 A 0.4968 0.1336 0.3697 5 L 0.5380 0.0782 0.3838 6 R 0.4459 0.0445 0.5096 7 P 0.3142 0.0822 0.6035 8 L 0.2998 0.0651 0.6351 9 N 0.2002 0.0161 0.7837 10 P 0.0235 0.6558 0.3207 11 E 0.0182 0.6580 0.3238 12 E 0.0493 0.5267 0.4240 13 L 0.2203 0.1102 0.6695 14 R 0.2171 0.0788 0.7042 15 P 0.2886 0.2223 0.4891 16 W 0.4088 0.1856 0.4056 17 R 0.6372 0.0742 0.2886 18 L 0.7191 0.0314 0.2495 19 E 0.7668 0.0198 0.2135 20 V 0.7782 0.0119 0.2099 21 V 0.7271 0.0150 0.2579 22 L 0.6254 0.0234 0.3512 23 D 0.3895 0.0204 0.5901 24 P 0.2377 0.0845 0.6777 25 P 0.2062 0.0523 0.7415 26 P 0.1279 0.1650 0.7071 27 G 0.0782 0.1600 0.7618 28 R 0.1291 0.2077 0.6633 29 E 0.1170 0.2986 0.5843 30 E 0.1737 0.3080 0.5183 31 V 0.1474 0.4480 0.4046 32 Y 0.0688 0.6997 0.2315 33 P 0.0179 0.8842 0.0980 34 L 0.0108 0.9082 0.0811 35 L 0.0085 0.9189 0.0726 36 A 0.0085 0.9197 0.0718 37 Q 0.0083 0.9229 0.0688 38 V 0.0084 0.9216 0.0700 39 A 0.0087 0.9104 0.0809 40 R 0.0101 0.8902 0.0996 41 R 0.0210 0.7674 0.2116 42 A 0.0655 0.3723 0.5622 43 G 0.0662 0.1078 0.8260 44 G 0.2677 0.0658 0.6665 45 V 0.6034 0.0459 0.3507 46 T 0.7229 0.0382 0.2389 47 V 0.7379 0.0325 0.2297 48 R 0.6524 0.0447 0.3029 49 M 0.3819 0.1106 0.5074 50 G 0.1928 0.0861 0.7211 51 D 0.1869 0.1403 0.6728 52 G 0.2080 0.1401 0.6519 53 L 0.3973 0.1183 0.4844 54 A 0.4637 0.0985 0.4378 55 S 0.4157 0.0803 0.5040 56 W 0.2919 0.1138 0.5943 57 S 0.2790 0.0350 0.6860 58 P 0.2163 0.0557 0.7280 59 P 0.1231 0.3135 0.5634 60 E 0.2636 0.3166 0.4199 61 V 0.5210 0.1482 0.3308 62 L 0.5899 0.0991 0.3111 63 V 0.5959 0.0746 0.3295 64 L 0.3992 0.1337 0.4671 65 E 0.1587 0.2717 0.5697 66 G 0.1180 0.2439 0.6381 67 T 0.1925 0.3481 0.4594 68 L 0.1949 0.4792 0.3259 69 A 0.1854 0.5050 0.3096 70 R 0.1994 0.4336 0.3671 71 M 0.1994 0.3127 0.4879 72 G 0.1826 0.2159 0.6016 73 Q 0.2546 0.1660 0.5793 74 T 0.2448 0.1267 0.6285 75 Y 0.1728 0.3220 0.5053 76 A 0.2209 0.3358 0.4433 77 Y 0.3236 0.3215 0.3549 78 R 0.4358 0.2161 0.3480 79 L 0.5018 0.1274 0.3708 80 Y 0.4194 0.0875 0.4930 81 P 0.2837 0.1889 0.5274 82 K 0.1602 0.2070 0.6327 83 G 0.1495 0.1133 0.7372 84 R 0.2615 0.0738 0.6648 85 R 0.3564 0.0458 0.5979 86 P 0.3283 0.0659 0.6058 87 L 0.3047 0.0678 0.6275 88 D 0.2307 0.0314 0.7379 89 P 0.1285 0.2363 0.6353 90 K 0.1234 0.2073 0.6692 91 D 0.1726 0.0799 0.7475 92 P 0.0267 0.6693 0.3040 93 G 0.0234 0.6939 0.2827 94 E 0.0204 0.8308 0.1488 95 R 0.0121 0.8991 0.0888 96 S 0.0092 0.9136 0.0772 97 V 0.0090 0.9173 0.0737 98 L 0.0084 0.9204 0.0713 99 S 0.0083 0.9231 0.0686 100 A 0.0083 0.9227 0.0690 101 L 0.0083 0.9229 0.0688 102 A 0.0084 0.9183 0.0733 103 R 0.0084 0.9185 0.0732 104 R 0.0084 0.9198 0.0718 105 L 0.0086 0.9153 0.0761 106 L 0.0091 0.9053 0.0856 107 Q 0.0091 0.9009 0.0900 108 E 0.0095 0.8937 0.0967 109 R 0.0143 0.8328 0.1529 110 L 0.0333 0.7546 0.2121 111 R 0.0544 0.6777 0.2679 112 R 0.0970 0.4692 0.4339 113 L 0.1421 0.2538 0.6041 114 E 0.1281 0.1666 0.7053 115 G 0.2378 0.0852 0.6770 116 V 0.5589 0.0430 0.3981 117 W 0.6588 0.0416 0.2996 118 V 0.6131 0.0601 0.3269 119 E 0.4642 0.1056 0.4303 120 G 0.3648 0.1143 0.5209 121 L 0.4128 0.2000 0.3872 122 A 0.4848 0.2221 0.2932 123 V 0.4891 0.2391 0.2718 124 Y 0.4700 0.2240 0.3060 125 R 0.4216 0.2322 0.3462 126 R 0.3928 0.2219 0.3853 127 E 0.3010 0.2992 0.3998 128 H 0.2783 0.2585 0.4632 129 A 0.2448 0.2213 0.5340 130 R 0.2303 0.1309 0.6388 131 G 0.2491 0.0500 0.7009 132 P 0.2274 0.1135 0.6592 133 G 0.3096 0.1174 0.5730 134 W 0.5377 0.0724 0.3899 135 R 0.6769 0.0581 0.2650 136 V 0.6597 0.0384 0.3019 137 L 0.4780 0.0727 0.4492 138 G 0.2718 0.0596 0.6685 139 G 0.2992 0.0411 0.6597 140 A 0.5638 0.0415 0.3948 141 V 0.7273 0.0196 0.2531 142 L 0.7386 0.0214 0.2400 143 D 0.7321 0.0235 0.2445 144 L 0.7759 0.0168 0.2073 145 W 0.7558 0.0158 0.2284 146 V 0.7383 0.0124 0.2493 147 S 0.5117 0.0241 0.4642 148 D 0.2049 0.2368 0.5583 149 S 0.0960 0.1916 0.7123 150 G 0.1333 0.0856 0.7810 151 A 0.5125 0.0256 0.4618 152 F 0.7391 0.0128 0.2481 153 L 0.7786 0.0153 0.2061 154 L 0.7837 0.0137 0.2027 155 E 0.7871 0.0116 0.2013 156 V 0.7538 0.0171 0.2291 157 D 0.3964 0.0159 0.5877 158 P 0.0640 0.5062 0.4298 159 A 0.0641 0.4812 0.4547 160 Y 0.2464 0.4282 0.3255 161 R 0.3890 0.2981 0.3129 162 I 0.4284 0.2310 0.3406 163 L 0.3981 0.1634 0.4385 164 C 0.2766 0.0924 0.6311 165 E 0.0726 0.3917 0.5356 166 M 0.0946 0.4016 0.5038 167 S 0.0987 0.4173 0.4840 168 L 0.0136 0.8238 0.1627 169 E 0.0099 0.8812 0.1089 170 A 0.0100 0.9184 0.0716 171 W 0.0103 0.9125 0.0772 172 L 0.0130 0.8847 0.1023 173 A 0.0147 0.7080 0.2772 174 Q 0.0395 0.4071 0.5535 175 G 0.0749 0.1598 0.7653 176 H 0.1425 0.1072 0.7503 177 P 0.1365 0.1435 0.7200 178 L 0.2316 0.0665 0.7019 179 P 0.2013 0.1300 0.6687 180 K 0.2654 0.2269 0.5077 181 R 0.3948 0.2319 0.3733 182 V 0.3865 0.2690 0.3445 183 R 0.4075 0.2717 0.3209 184 N 0.3505 0.2357 0.4137 185 A 0.2416 0.3118 0.4466 186 Y 0.2203 0.2209 0.5588 187 D 0.1788 0.1747 0.6466 188 R 0.1805 0.1854 0.6341 189 R 0.2570 0.1676 0.5754 190 T 0.3871 0.1396 0.4733 191 W 0.4606 0.1902 0.3492 192 E 0.5108 0.2011 0.2881 193 L 0.5115 0.2090 0.2795 194 L 0.4302 0.2503 0.3195 195 R 0.3822 0.2002 0.4176 196 L 0.3523 0.1568 0.4909 197 G 0.2354 0.1180 0.6465 198 E 0.1577 0.2224 0.6199 199 E 0.1874 0.1565 0.6561 200 D 0.1947 0.0488 0.7564 201 P 0.0512 0.4960 0.4528 202 K 0.0570 0.4399 0.5031 203 E 0.1594 0.3146 0.5260 204 L 0.3285 0.0414 0.6302 205 P 0.3512 0.0476 0.6012 206 L 0.2601 0.0407 0.6991 207 P 0.1332 0.2208 0.6459 208 G 0.0848 0.2004 0.7148 209 G 0.1105 0.1173 0.7722 210 L 0.2784 0.0639 0.6577 211 S 0.3023 0.0775 0.6202 212 L 0.1718 0.4866 0.3416 213 L 0.1254 0.6530 0.2216 214 D 0.1333 0.6964 0.1703 215 Y 0.1404 0.6411 0.2185 216 H 0.1435 0.5560 0.3005 217 A 0.0991 0.5760 0.3249 218 S 0.1091 0.4114 0.4795 219 K 0.0977 0.2580 0.6443 220 G 0.0948 0.1816 0.7236 221 R 0.2065 0.1684 0.6251 222 L 0.2618 0.1517 0.5865 223 Q 0.2287 0.1762 0.5950 224 G 0.2078 0.1534 0.6388 225 R 0.2866 0.1187 0.5947 226 E 0.1962 0.1186 0.6852 227 G 0.1652 0.0822 0.7526 228 G 0.3644 0.0261 0.6095 229 R 0.6321 0.0151 0.3527 230 V 0.7681 0.0060 0.2258 231 A 0.7904 0.0075 0.2021 232 W 0.7733 0.0071 0.2196 233 V 0.7263 0.0114 0.2623 234 A 0.6397 0.0226 0.3377 235 D 0.3769 0.0161 0.6069 236 P 0.1214 0.2514 0.6273 237 K 0.1124 0.2287 0.6588 238 D 0.1990 0.0770 0.7240 239 P 0.0746 0.3333 0.5921 240 R 0.1146 0.2430 0.6424 241 K 0.2292 0.0715 0.6993 242 P 0.2317 0.0927 0.6755 243 I 0.2631 0.0972 0.6397 244 P 0.1909 0.2930 0.5161 245 H 0.1662 0.4075 0.4263 246 L 0.1294 0.5237 0.3469 247 T 0.1020 0.4855 0.4125 248 G 0.0718 0.5167 0.4115 249 L 0.1185 0.4890 0.3925 250 L 0.1780 0.3712 0.4508 251 V 0.2205 0.2586 0.5209 252 P 0.2094 0.3793 0.4114 253 V 0.2729 0.3928 0.3342 254 L 0.4221 0.2690 0.3089 255 T 0.3364 0.2297 0.4339 256 L 0.0771 0.6243 0.2986 257 E 0.0339 0.7619 0.2042 258 D 0.0277 0.7781 0.1941 259 L 0.0268 0.8067 0.1665 260 H 0.0253 0.7879 0.1868 261 E 0.0231 0.7991 0.1778 262 E 0.0330 0.7179 0.2491 263 E 0.0549 0.4008 0.5443 264 G 0.0453 0.2069 0.7478 265 S 0.1381 0.2601 0.6019 266 L 0.1626 0.3599 0.4775 267 A 0.1862 0.3454 0.4684 268 L 0.2166 0.2403 0.5431 269 S 0.2211 0.1358 0.6432 270 L 0.2211 0.0803 0.6986 271 P 0.1441 0.2298 0.6261 272 W 0.0580 0.6191 0.3229 273 E 0.0412 0.7639 0.1949 274 E 0.0583 0.7672 0.1745 275 R 0.0500 0.7932 0.1567 276 R 0.0345 0.8359 0.1296 277 R 0.0422 0.8237 0.1341 278 R 0.0368 0.8301 0.1331 279 T 0.0178 0.8785 0.1037 280 R 0.0096 0.8993 0.0911 281 E 0.0093 0.9120 0.0787 282 I 0.0104 0.9093 0.0803 283 A 0.0089 0.9106 0.0805 284 S 0.0087 0.9077 0.0835 285 W 0.0097 0.8879 0.1024 286 I 0.0137 0.8531 0.1332 287 G 0.0124 0.8472 0.1404 288 R 0.0185 0.8426 0.1388 289 R 0.0446 0.7125 0.2429 290 L 0.0802 0.5413 0.3784 291 G 0.1032 0.3949 0.5019 292 L 0.1790 0.2371 0.5839 293 G 0.2041 0.1066 0.6893 294 T 0.2345 0.0522 0.7133 295 P 0.1831 0.1104 0.7065