# This file is the result of combining several RDB files, specifically # T0444.t2k.str2.rdb (weight 1.54425) # T0444.t2k.str4.rdb (weight 0.924988) # T0444.t2k.pb.rdb (weight 0.789901) # T0444.t2k.bys.rdb (weight 0.748322) # T0444.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 T0444.t2k.str2.rdb # ============================================ # TARGET T0444 # 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 T0444.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 162.639 # # ============================================ # Comments from T0444.t2k.str4.rdb # ============================================ # TARGET T0444 # 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 T0444.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 162.639 # # ============================================ # Comments from T0444.t2k.pb.rdb # ============================================ # TARGET T0444 # 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 T0444.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 162.639 # # ============================================ # Comments from T0444.t2k.bys.rdb # ============================================ # TARGET T0444 # 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 T0444.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 162.639 # # ============================================ # Comments from T0444.t2k.alpha.rdb # ============================================ # TARGET T0444 # 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 T0444.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 162.639 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3006 0.1148 0.5847 2 H 0.2820 0.1045 0.6135 3 H 0.2855 0.1437 0.5708 4 H 0.2650 0.1598 0.5752 5 H 0.2292 0.1721 0.5987 6 H 0.2096 0.1750 0.6154 7 H 0.1836 0.1567 0.6597 8 S 0.1729 0.1771 0.6500 9 S 0.1167 0.1998 0.6835 10 G 0.1311 0.1422 0.7267 11 V 0.2738 0.1005 0.6257 12 D 0.2778 0.0985 0.6236 13 L 0.1947 0.2619 0.5434 14 G 0.1616 0.1801 0.6583 15 T 0.1743 0.2431 0.5827 16 E 0.1373 0.3810 0.4817 17 N 0.1532 0.3759 0.4709 18 L 0.1685 0.4102 0.4213 19 Y 0.1799 0.4246 0.3954 20 F 0.2136 0.3989 0.3875 21 Q 0.2293 0.3665 0.4042 22 S 0.2017 0.3654 0.4329 23 M 0.2094 0.3140 0.4766 24 S 0.1962 0.2406 0.5633 25 D 0.1658 0.1738 0.6605 26 T 0.1159 0.2674 0.6167 27 N 0.1225 0.2252 0.6523 28 E 0.1123 0.3921 0.4956 29 S 0.1464 0.4017 0.4519 30 E 0.1789 0.4446 0.3765 31 I 0.1875 0.4500 0.3624 32 K 0.1836 0.3852 0.4312 33 S 0.1452 0.3281 0.5267 34 N 0.1112 0.2524 0.6364 35 E 0.1646 0.2625 0.5729 36 E 0.2227 0.2523 0.5250 37 P 0.2123 0.3773 0.4104 38 L 0.2187 0.3749 0.4064 39 L 0.1921 0.3374 0.4705 40 R 0.1757 0.2163 0.6080 41 K 0.2020 0.1549 0.6430 42 S 0.2135 0.1140 0.6725 43 S 0.1851 0.2009 0.6140 44 R 0.2331 0.1901 0.5768 45 R 0.4618 0.1176 0.4206 46 F 0.6255 0.0550 0.3194 47 V 0.6708 0.0406 0.2885 48 I 0.6435 0.0451 0.3114 49 F 0.4958 0.0395 0.4646 50 P 0.3578 0.0889 0.5533 51 I 0.2851 0.1116 0.6033 52 Q 0.2213 0.1166 0.6621 53 Y 0.1719 0.0898 0.7383 54 P 0.0175 0.6614 0.3210 55 D 0.0139 0.8136 0.1725 56 I 0.0094 0.8853 0.1053 57 W 0.0084 0.9200 0.0717 58 K 0.0083 0.9245 0.0672 59 M 0.0083 0.9237 0.0680 60 Y 0.0083 0.9222 0.0695 61 K 0.0083 0.9231 0.0686 62 Q 0.0084 0.9195 0.0721 63 A 0.0087 0.9055 0.0858 64 Q 0.0095 0.8695 0.1210 65 A 0.0154 0.7719 0.2127 66 S 0.0368 0.5193 0.4439 67 F 0.1280 0.2395 0.6325 68 W 0.2291 0.1104 0.6605 69 T 0.1847 0.0340 0.7813 70 A 0.0615 0.5409 0.3976 71 E 0.0732 0.5610 0.3658 72 E 0.2489 0.3069 0.4442 73 V 0.3795 0.0792 0.5414 74 D 0.2289 0.0486 0.7225 75 L 0.0863 0.4340 0.4797 76 S 0.0730 0.3811 0.5459 77 K 0.0639 0.3972 0.5390 78 D 0.1022 0.2506 0.6472 79 L 0.0756 0.4946 0.4298 80 P 0.0338 0.6847 0.2815 81 H 0.0426 0.6267 0.3307 82 W 0.0355 0.7205 0.2441 83 N 0.0391 0.6112 0.3497 84 K 0.0619 0.3600 0.5781 85 L 0.1589 0.1335 0.7076 86 K 0.1373 0.1110 0.7517 87 A 0.0167 0.6586 0.3247 88 D 0.0124 0.7915 0.1962 89 E 0.0120 0.8931 0.0949 90 K 0.0089 0.9114 0.0796 91 Y 0.0083 0.9191 0.0726 92 F 0.0084 0.9186 0.0729 93 I 0.0083 0.9198 0.0718 94 S 0.0083 0.9210 0.0707 95 H 0.0083 0.9228 0.0689 96 I 0.0084 0.9199 0.0718 97 L 0.0084 0.9198 0.0719 98 A 0.0084 0.9190 0.0726 99 F 0.0090 0.9145 0.0765 100 F 0.0116 0.8955 0.0930 101 A 0.0132 0.8502 0.1366 102 A 0.0235 0.7598 0.2168 103 S 0.0410 0.6750 0.2840 104 D 0.0415 0.5903 0.3681 105 G 0.0555 0.5629 0.3816 106 I 0.1192 0.5894 0.2914 107 V 0.1429 0.5699 0.2872 108 N 0.0982 0.5557 0.3462 109 E 0.0334 0.7177 0.2489 110 N 0.0438 0.6727 0.2836 111 L 0.0416 0.7484 0.2101 112 V 0.0293 0.8209 0.1498 113 E 0.0160 0.8645 0.1195 114 R 0.0218 0.8206 0.1576 115 F 0.0503 0.7195 0.2303 116 S 0.0617 0.6657 0.2726 117 Q 0.0317 0.6833 0.2850 118 E 0.0591 0.5178 0.4231 119 V 0.1689 0.3596 0.4716 120 Q 0.1859 0.2543 0.5598 121 V 0.1527 0.3263 0.5210 122 P 0.0390 0.6881 0.2729 123 E 0.0278 0.8054 0.1668 124 A 0.0179 0.8847 0.0973 125 R 0.0153 0.8993 0.0854 126 C 0.0151 0.9042 0.0807 127 F 0.0137 0.9065 0.0799 128 Y 0.0125 0.9043 0.0832 129 G 0.0109 0.9057 0.0834 130 F 0.0106 0.9079 0.0815 131 Q 0.0096 0.9126 0.0778 132 I 0.0102 0.9126 0.0772 133 L 0.0106 0.9048 0.0846 134 I 0.0111 0.8995 0.0894 135 E 0.0112 0.8967 0.0921 136 N 0.0141 0.8776 0.1083 137 V 0.0223 0.8477 0.1300 138 H 0.0216 0.8609 0.1174 139 S 0.0111 0.8889 0.1000 140 E 0.0095 0.8959 0.0945 141 M 0.0095 0.9095 0.0810 142 Y 0.0091 0.9169 0.0740 143 S 0.0086 0.9192 0.0722 144 L 0.0087 0.9204 0.0709 145 L 0.0099 0.9141 0.0760 146 I 0.0096 0.9087 0.0818 147 D 0.0123 0.8900 0.0977 148 T 0.0264 0.7933 0.1804 149 Y 0.0643 0.6428 0.2929 150 I 0.1162 0.4555 0.4284 151 R 0.1510 0.2776 0.5714 152 D 0.1770 0.0706 0.7524 153 P 0.0133 0.6485 0.3382 154 K 0.0144 0.7415 0.2441 155 K 0.0185 0.8374 0.1441 156 R 0.0130 0.8830 0.1040 157 E 0.0113 0.8957 0.0930 158 F 0.0121 0.8987 0.0892 159 L 0.0141 0.8822 0.1036 160 F 0.0136 0.8891 0.0973 161 N 0.0126 0.8854 0.1021 162 A 0.0210 0.8420 0.1371 163 I 0.0266 0.8133 0.1601 164 E 0.0359 0.7223 0.2418 165 T 0.0602 0.5625 0.3772 166 M 0.0944 0.4526 0.4530 167 P 0.0145 0.7894 0.1960 168 Y 0.0122 0.8529 0.1349 169 V 0.0111 0.9038 0.0852 170 K 0.0089 0.9103 0.0808 171 K 0.0088 0.9139 0.0774 172 K 0.0104 0.9026 0.0870 173 A 0.0098 0.9083 0.0818 174 D 0.0084 0.9177 0.0739 175 W 0.0085 0.9182 0.0733 176 A 0.0089 0.9136 0.0775 177 L 0.0089 0.9138 0.0772 178 R 0.0096 0.9053 0.0851 179 W 0.0154 0.8725 0.1121 180 I 0.0247 0.8201 0.1552 181 A 0.0259 0.7315 0.2426 182 D 0.0395 0.5619 0.3986 183 R 0.0519 0.5064 0.4417 184 K 0.0398 0.6142 0.3460 185 S 0.0242 0.7389 0.2369 186 T 0.0243 0.7698 0.2060 187 F 0.0183 0.8362 0.1455 188 G 0.0113 0.8949 0.0937 189 E 0.0099 0.9111 0.0790 190 R 0.0098 0.9176 0.0726 191 V 0.0094 0.9208 0.0699 192 V 0.0093 0.9211 0.0696 193 A 0.0088 0.9191 0.0720 194 F 0.0094 0.9187 0.0719 195 A 0.0117 0.9117 0.0767 196 A 0.0131 0.8979 0.0890 197 V 0.0294 0.8522 0.1184 198 E 0.0240 0.8228 0.1532 199 G 0.0599 0.7580 0.1820 200 V 0.0807 0.7267 0.1925 201 F 0.0978 0.6906 0.2116 202 F 0.1079 0.6368 0.2553 203 S 0.0743 0.6368 0.2889 204 G 0.0403 0.7129 0.2468 205 S 0.0183 0.8245 0.1572 206 F 0.0124 0.8847 0.1029 207 A 0.0113 0.9111 0.0776 208 A 0.0106 0.9165 0.0729 209 I 0.0106 0.9185 0.0709 210 F 0.0103 0.9172 0.0725 211 W 0.0113 0.9110 0.0778 212 L 0.0118 0.8981 0.0901 213 K 0.0118 0.8713 0.1169 214 K 0.0204 0.7590 0.2206 215 R 0.0540 0.2654 0.6806 216 G 0.0483 0.0980 0.8537 217 L 0.1663 0.0982 0.7355 218 M 0.2122 0.0492 0.7386 219 P 0.1362 0.2492 0.6146 220 G 0.0798 0.2369 0.6833 221 L 0.1560 0.4760 0.3680 222 T 0.1666 0.6058 0.2276 223 F 0.1599 0.6558 0.1843 224 S 0.1307 0.7091 0.1603 225 N 0.0907 0.7564 0.1529 226 E 0.0942 0.7634 0.1425 227 L 0.1176 0.6984 0.1839 228 I 0.1480 0.6008 0.2513 229 S 0.1597 0.4742 0.3661 230 R 0.0935 0.4806 0.4258 231 D 0.1140 0.3630 0.5231 232 E 0.0471 0.5544 0.3985 233 G 0.0605 0.5923 0.3472 234 L 0.0781 0.6693 0.2526 235 H 0.0674 0.7440 0.1886 236 C 0.0314 0.8500 0.1186 237 D 0.0107 0.9028 0.0865 238 F 0.0089 0.9171 0.0740 239 A 0.0083 0.9232 0.0686 240 C 0.0083 0.9240 0.0678 241 L 0.0083 0.9243 0.0675 242 M 0.0083 0.9215 0.0701 243 F 0.0084 0.9181 0.0735 244 Q 0.0086 0.9124 0.0790 245 Y 0.0097 0.8841 0.1062 246 L 0.0154 0.8125 0.1721 247 V 0.0297 0.6602 0.3101 248 N 0.0477 0.2936 0.6587 249 K 0.1504 0.0960 0.7537 250 P 0.1531 0.0728 0.7741 251 S 0.1308 0.1132 0.7560 252 E 0.0131 0.7389 0.2480 253 E 0.0100 0.8574 0.1326 254 R 0.0098 0.9156 0.0746 255 V 0.0084 0.9153 0.0763 256 R 0.0083 0.9200 0.0716 257 E 0.0083 0.9248 0.0669 258 I 0.0083 0.9245 0.0673 259 I 0.0083 0.9215 0.0702 260 V 0.0083 0.9223 0.0694 261 D 0.0083 0.9220 0.0697 262 A 0.0084 0.9195 0.0721 263 V 0.0083 0.9219 0.0698 264 K 0.0083 0.9212 0.0705 265 I 0.0083 0.9219 0.0698 266 E 0.0083 0.9211 0.0706 267 Q 0.0084 0.9165 0.0751 268 E 0.0084 0.9178 0.0738 269 F 0.0086 0.9097 0.0817 270 L 0.0089 0.9033 0.0879 271 T 0.0088 0.8964 0.0948 272 E 0.0100 0.8437 0.1462 273 A 0.0267 0.6878 0.2856 274 L 0.1170 0.4106 0.4724 275 P 0.0751 0.4786 0.4462 276 V 0.0784 0.2994 0.6222 277 G 0.0881 0.2234 0.6885 278 L 0.2027 0.2317 0.5656 279 I 0.2097 0.2002 0.5902 280 G 0.1515 0.1685 0.6800 281 M 0.2151 0.1925 0.5924 282 N 0.1736 0.1966 0.6298 283 C 0.0177 0.7570 0.2253 284 I 0.0095 0.8691 0.1215 285 L 0.0087 0.9165 0.0748 286 M 0.0084 0.9189 0.0727 287 K 0.0084 0.9181 0.0735 288 Q 0.0084 0.9184 0.0732 289 Y 0.0084 0.9181 0.0735 290 I 0.0086 0.9197 0.0717 291 E 0.0093 0.9172 0.0735 292 F 0.0096 0.9134 0.0770 293 V 0.0118 0.9030 0.0852 294 A 0.0115 0.8963 0.0922 295 D 0.0097 0.9113 0.0790 296 R 0.0097 0.8966 0.0937 297 L 0.0091 0.9135 0.0774 298 L 0.0086 0.9166 0.0748 299 V 0.0087 0.9092 0.0822 300 E 0.0138 0.8183 0.1679 301 L 0.0551 0.4199 0.5250 302 G 0.0447 0.0830 0.8724 303 F 0.1581 0.0704 0.7715 304 S 0.2014 0.1003 0.6983 305 K 0.2272 0.2695 0.5034 306 V 0.2772 0.2634 0.4594 307 F 0.2809 0.1496 0.5696 308 Q 0.2248 0.1682 0.6071 309 A 0.1422 0.3013 0.5565 310 E 0.1317 0.2464 0.6219 311 N 0.1901 0.1027 0.7072 312 P 0.0876 0.3570 0.5554 313 F 0.0784 0.5068 0.4149 314 D 0.0306 0.7428 0.2266 315 F 0.0297 0.7673 0.2030 316 M 0.0411 0.8098 0.1491 317 E 0.0205 0.8520 0.1276 318 N 0.0369 0.7945 0.1686 319 I 0.0907 0.6994 0.2099 320 S 0.0891 0.6798 0.2311 321 L 0.0862 0.6390 0.2748 322 E 0.0905 0.3001 0.6093 323 G 0.0784 0.1206 0.8011 324 K 0.2049 0.1443 0.6508 325 T 0.3201 0.1142 0.5657 326 N 0.2418 0.0772 0.6810