# This file is the result of combining several RDB files, specifically # T0440.t04.str2.rdb (weight 1.54425) # T0440.t04.str4.rdb (weight 0.924988) # T0440.t04.pb.rdb (weight 0.789901) # T0440.t04.bys.rdb (weight 0.748322) # T0440.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 T0440.t04.str2.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1433 # # ============================================ # Comments from T0440.t04.str4.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1433 # # ============================================ # Comments from T0440.t04.pb.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1433 # # ============================================ # Comments from T0440.t04.bys.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1433 # # ============================================ # Comments from T0440.t04.alpha.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1433 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3068 0.0556 0.6377 2 K 0.3563 0.0595 0.5842 3 R 0.4410 0.1068 0.4522 4 D 0.3906 0.1234 0.4859 5 G 0.3613 0.1253 0.5134 6 H 0.4578 0.0932 0.4490 7 T 0.4713 0.0838 0.4450 8 H 0.3792 0.0802 0.5406 9 T 0.3483 0.1021 0.5496 10 E 0.3073 0.1666 0.5262 11 F 0.3100 0.1455 0.5445 12 C 0.2127 0.0814 0.7059 13 P 0.0853 0.3285 0.5863 14 H 0.0748 0.2279 0.6973 15 G 0.1289 0.2173 0.6537 16 T 0.1301 0.1699 0.7001 17 H 0.1324 0.1485 0.7191 18 D 0.1239 0.1670 0.7091 19 D 0.1525 0.0772 0.7703 20 V 0.0124 0.7264 0.2612 21 E 0.0091 0.8719 0.1190 22 E 0.0083 0.9215 0.0702 23 M 0.0084 0.9228 0.0688 24 V 0.0083 0.9233 0.0684 25 L 0.0083 0.9247 0.0670 26 K 0.0083 0.9237 0.0680 27 A 0.0084 0.9190 0.0725 28 I 0.0088 0.9023 0.0888 29 E 0.0122 0.8162 0.1716 30 L 0.0545 0.2281 0.7174 31 D 0.0527 0.0678 0.8795 32 F 0.1792 0.0480 0.7727 33 D 0.2776 0.0964 0.6260 34 E 0.7234 0.0325 0.2441 35 Y 0.7460 0.0159 0.2382 36 S 0.7896 0.0082 0.2021 37 I 0.7678 0.0207 0.2115 38 V 0.6669 0.0308 0.3022 39 E 0.3502 0.1096 0.5402 40 H 0.2023 0.1210 0.6767 41 A 0.2050 0.1016 0.6934 42 P 0.1433 0.2314 0.6253 43 L 0.1656 0.2425 0.5918 44 S 0.1523 0.2018 0.6459 45 S 0.0844 0.5463 0.3693 46 E 0.0309 0.7473 0.2218 47 F 0.0337 0.7950 0.1713 48 M 0.0421 0.7759 0.1819 49 K 0.0375 0.7714 0.1910 50 N 0.0426 0.7266 0.2308 51 T 0.0444 0.6904 0.2652 52 A 0.0654 0.5394 0.3952 53 G 0.0536 0.4360 0.5104 54 D 0.0814 0.4191 0.4995 55 K 0.0760 0.4531 0.4709 56 E 0.1118 0.3619 0.5263 57 A 0.1771 0.3544 0.4685 58 V 0.2335 0.3788 0.3877 59 T 0.2449 0.4732 0.2819 60 T 0.2087 0.5145 0.2769 61 A 0.1765 0.5438 0.2797 62 S 0.1265 0.6008 0.2727 63 M 0.1203 0.6103 0.2694 64 A 0.1020 0.5838 0.3143 65 M 0.0725 0.5958 0.3317 66 S 0.0594 0.5334 0.4072 67 D 0.0790 0.3701 0.5509 68 L 0.1699 0.2084 0.6217 69 P 0.1173 0.3209 0.5618 70 Y 0.2027 0.3017 0.4956 71 Y 0.3369 0.1901 0.4730 72 F 0.4238 0.1590 0.4172 73 K 0.4431 0.1381 0.4188 74 K 0.4518 0.1500 0.3982 75 M 0.3483 0.2586 0.3931 76 N 0.3691 0.3108 0.3201 77 H 0.4818 0.2423 0.2758 78 I 0.4708 0.2403 0.2889 79 K 0.3789 0.2903 0.3308 80 K 0.2772 0.4035 0.3193 81 K 0.2345 0.3645 0.4010 82 Y 0.2099 0.2903 0.4999 83 A 0.1547 0.2760 0.5693 84 S 0.1406 0.2495 0.6100 85 D 0.2700 0.1451 0.5849 86 L 0.5918 0.0434 0.3648 87 L 0.7158 0.0308 0.2534 88 I 0.7882 0.0161 0.1957 89 H 0.7348 0.0230 0.2422 90 I 0.6381 0.0397 0.3222 91 G 0.4976 0.0402 0.4622 92 F 0.5867 0.0319 0.3814 93 E 0.6130 0.0394 0.3476 94 V 0.5641 0.0570 0.3789 95 D 0.3596 0.0848 0.5556 96 Y 0.2519 0.2400 0.5082 97 L 0.1989 0.2583 0.5428 98 I 0.1222 0.3436 0.5342 99 G 0.0841 0.3191 0.5968 100 Y 0.0893 0.5000 0.4107 101 E 0.0385 0.7329 0.2286 102 D 0.0276 0.8035 0.1689 103 F 0.0244 0.8253 0.1503 104 T 0.0127 0.8759 0.1113 105 R 0.0091 0.9015 0.0894 106 D 0.0087 0.9109 0.0804 107 F 0.0095 0.8981 0.0924 108 L 0.0106 0.8652 0.1242 109 N 0.0118 0.7856 0.2025 110 E 0.0215 0.6423 0.3362 111 Y 0.0687 0.3618 0.5695 112 G 0.0904 0.2514 0.6582 113 P 0.0517 0.5087 0.4396 114 Q 0.0807 0.4360 0.4833 115 T 0.1115 0.3615 0.5269 116 D 0.0928 0.3856 0.5216 117 D 0.1773 0.3576 0.4651 118 G 0.3603 0.2874 0.3523 119 V 0.4804 0.2485 0.2711 120 L 0.4920 0.2283 0.2797 121 S 0.5032 0.1772 0.3196 122 L 0.3963 0.2448 0.3589 123 H 0.3332 0.2473 0.4195 124 F 0.2770 0.2688 0.4543 125 L 0.2337 0.2588 0.5075 126 E 0.1962 0.1927 0.6111 127 G 0.1523 0.1391 0.7086 128 Q 0.1482 0.2230 0.6288 129 G 0.1408 0.1825 0.6767 130 G 0.1823 0.1523 0.6653 131 F 0.2211 0.1603 0.6186 132 R 0.2482 0.1274 0.6244 133 S 0.2278 0.1659 0.6063 134 I 0.2055 0.2701 0.5244 135 D 0.2220 0.2516 0.5264 136 F 0.2291 0.2746 0.4962 137 S 0.1997 0.1812 0.6191 138 A 0.1337 0.3652 0.5010 139 E 0.0638 0.5764 0.3597 140 D 0.0564 0.6347 0.3088 141 Y 0.0447 0.6864 0.2689 142 N 0.0358 0.7451 0.2191 143 E 0.0217 0.7847 0.1937 144 G 0.0285 0.7759 0.1956 145 I 0.0434 0.7691 0.1875 146 V 0.0522 0.7545 0.1933 147 Q 0.0569 0.6911 0.2520 148 F 0.0798 0.4946 0.4255 149 Y 0.0967 0.3228 0.5805 150 G 0.0852 0.2387 0.6761 151 G 0.1078 0.2210 0.6712 152 F 0.0272 0.6641 0.3086 153 E 0.0108 0.8521 0.1370 154 Q 0.0092 0.9151 0.0757 155 A 0.0089 0.9181 0.0729 156 Q 0.0084 0.9185 0.0731 157 L 0.0083 0.9204 0.0713 158 A 0.0085 0.9136 0.0779 159 Y 0.0097 0.8904 0.1000 160 L 0.0104 0.8740 0.1156 161 E 0.0116 0.8285 0.1599 162 G 0.0186 0.7600 0.2214 163 V 0.0322 0.7832 0.1845 164 K 0.0329 0.8133 0.1538 165 Q 0.0499 0.7899 0.1602 166 S 0.0746 0.7316 0.1938 167 I 0.1201 0.6469 0.2330 168 E 0.1429 0.5685 0.2885 169 A 0.1318 0.4780 0.3903 170 D 0.0889 0.4200 0.4912 171 L 0.0836 0.3041 0.6123 172 G 0.0842 0.2124 0.7035 173 L 0.1796 0.1844 0.6360 174 F 0.2556 0.1089 0.6355 175 K 0.2069 0.0787 0.7144 176 P 0.0815 0.5411 0.3774 177 R 0.0926 0.5517 0.3557 178 R 0.1377 0.5248 0.3375 179 M 0.1287 0.5350 0.3364 180 G 0.1405 0.4925 0.3670 181 H 0.1193 0.5520 0.3287 182 I 0.0292 0.7658 0.2050 183 S 0.0172 0.8558 0.1270 184 L 0.0151 0.8836 0.1013 185 C 0.0152 0.8798 0.1050 186 Q 0.0138 0.8837 0.1025 187 K 0.0204 0.8218 0.1578 188 F 0.0517 0.6235 0.3248 189 Q 0.0597 0.4224 0.5179 190 Q 0.0830 0.3508 0.5662 191 F 0.1466 0.2653 0.5881 192 F 0.1797 0.2442 0.5761 193 G 0.1440 0.3612 0.4948 194 E 0.1117 0.4848 0.4035 195 D 0.1174 0.3526 0.5300 196 T 0.1464 0.2510 0.6026 197 S 0.0381 0.5828 0.3791 198 D 0.0289 0.6636 0.3076 199 F 0.0404 0.6898 0.2698 200 S 0.0347 0.7708 0.1945 201 E 0.0106 0.8535 0.1360 202 E 0.0108 0.8694 0.1198 203 V 0.0112 0.8858 0.1030 204 M 0.0089 0.9103 0.0808 205 E 0.0084 0.9194 0.0722 206 K 0.0085 0.9169 0.0747 207 F 0.0084 0.9199 0.0718 208 R 0.0083 0.9235 0.0682 209 V 0.0083 0.9244 0.0673 210 I 0.0083 0.9237 0.0681 211 L 0.0083 0.9224 0.0693 212 A 0.0083 0.9241 0.0677 213 L 0.0083 0.9233 0.0684 214 V 0.0085 0.9154 0.0762 215 K 0.0089 0.8802 0.1109 216 K 0.0127 0.7567 0.2306 217 R 0.0563 0.2207 0.7230 218 D 0.0609 0.0699 0.8692 219 Y 0.2451 0.0316 0.7233 220 E 0.6273 0.0321 0.3406 221 L 0.7675 0.0093 0.2233 222 D 0.7682 0.0108 0.2210 223 F 0.7471 0.0154 0.2374 224 N 0.5622 0.0531 0.3847 225 T 0.3169 0.1392 0.5438 226 A 0.1811 0.1841 0.6348 227 G 0.1300 0.2092 0.6608 228 L 0.1744 0.2347 0.5909 229 F 0.2305 0.1728 0.5968 230 K 0.2593 0.1268 0.6139 231 P 0.1897 0.2229 0.5874 232 L 0.1642 0.3044 0.5313 233 C 0.1497 0.1999 0.6504 234 G 0.1145 0.1324 0.7531 235 E 0.1896 0.0955 0.7149 236 T 0.2070 0.1210 0.6720 237 Y 0.2277 0.0537 0.7186 238 P 0.1637 0.0776 0.7587 239 P 0.0561 0.5633 0.3806 240 K 0.0130 0.8143 0.1726 241 K 0.0111 0.8831 0.1058 242 I 0.0092 0.9160 0.0748 243 V 0.0083 0.9208 0.0708 244 T 0.0083 0.9235 0.0682 245 L 0.0083 0.9211 0.0705 246 A 0.0086 0.9142 0.0772 247 S 0.0092 0.8892 0.1015 248 E 0.0148 0.7942 0.1910 249 L 0.0612 0.2911 0.6477 250 Q 0.0531 0.0741 0.8728 251 I 0.2104 0.0179 0.7716 252 P 0.4004 0.0366 0.5630 253 F 0.7728 0.0142 0.2131 254 V 0.7748 0.0119 0.2133 255 Y 0.7044 0.0267 0.2688 256 G 0.5036 0.0485 0.4479 257 S 0.2736 0.1053 0.6211 258 D 0.1855 0.1973 0.6172 259 S 0.1217 0.3065 0.5718 260 H 0.1418 0.2226 0.6356 261 G 0.1529 0.1904 0.6567 262 V 0.1110 0.4207 0.4683 263 Q 0.1063 0.4563 0.4374 264 D 0.1281 0.4449 0.4270 265 I 0.1134 0.4268 0.4597 266 G 0.0999 0.3268 0.5733 267 R 0.1107 0.3570 0.5322 268 G 0.1090 0.2637 0.6273 269 Y 0.1406 0.3856 0.4738 270 S 0.1216 0.4975 0.3808 271 T 0.1436 0.5307 0.3257 272 Y 0.1639 0.4827 0.3535 273 C 0.1895 0.3864 0.4241 274 Q 0.1342 0.3918 0.4740 275 K 0.1406 0.3324 0.5271