# This file is the result of combining several RDB files, specifically # T0434.t04.str2.rdb (weight 1.54425) # T0434.t04.str4.rdb (weight 0.924988) # T0434.t04.pb.rdb (weight 0.789901) # T0434.t04.bys.rdb (weight 0.748322) # T0434.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 T0434.t04.str2.rdb # ============================================ # TARGET T0434 # 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 T0434.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 1387 # # ============================================ # Comments from T0434.t04.str4.rdb # ============================================ # TARGET T0434 # 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 T0434.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 1387 # # ============================================ # Comments from T0434.t04.pb.rdb # ============================================ # TARGET T0434 # 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 T0434.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 1387 # # ============================================ # Comments from T0434.t04.bys.rdb # ============================================ # TARGET T0434 # 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 T0434.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 1387 # # ============================================ # Comments from T0434.t04.alpha.rdb # ============================================ # TARGET T0434 # 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 T0434.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 1387 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2702 0.1125 0.6173 2 G 0.1931 0.0820 0.7249 3 S 0.1975 0.1728 0.6297 4 S 0.2071 0.1745 0.6184 5 H 0.2928 0.1437 0.5636 6 H 0.3734 0.1202 0.5064 7 H 0.3454 0.1246 0.5300 8 H 0.3712 0.1370 0.4917 9 H 0.3418 0.1219 0.5363 10 H 0.2911 0.1603 0.5485 11 S 0.2128 0.1595 0.6276 12 S 0.1291 0.1809 0.6900 13 G 0.1034 0.1126 0.7840 14 L 0.2671 0.0521 0.6808 15 V 0.3731 0.0386 0.5883 16 P 0.3468 0.0837 0.5695 17 R 0.2973 0.1157 0.5870 18 G 0.2146 0.0955 0.6899 19 S 0.2178 0.1263 0.6559 20 K 0.2281 0.1233 0.6486 21 M 0.2414 0.1608 0.5978 22 D 0.2089 0.1253 0.6659 23 M 0.2150 0.2169 0.5681 24 E 0.1506 0.3009 0.5484 25 D 0.1681 0.2599 0.5720 26 A 0.0960 0.4172 0.4867 27 D 0.1066 0.3324 0.5610 28 M 0.1514 0.3121 0.5364 29 T 0.1818 0.2690 0.5492 30 L 0.1532 0.4072 0.4395 31 W 0.1739 0.3595 0.4666 32 T 0.1782 0.3041 0.5177 33 E 0.1206 0.4514 0.4280 34 A 0.0764 0.5748 0.3488 35 E 0.0782 0.5526 0.3693 36 F 0.1000 0.5363 0.3637 37 E 0.0959 0.5638 0.3403 38 E 0.1145 0.5115 0.3739 39 K 0.1635 0.3642 0.4723 40 C 0.2002 0.2447 0.5551 41 T 0.2105 0.2560 0.5335 42 Y 0.2968 0.2048 0.4984 43 I 0.3093 0.1769 0.5139 44 V 0.3080 0.1920 0.5000 45 N 0.2980 0.1734 0.5286 46 D 0.2826 0.1442 0.5732 47 H 0.2556 0.0488 0.6956 48 P 0.1671 0.1665 0.6664 49 W 0.1251 0.2989 0.5760 50 D 0.1252 0.2243 0.6505 51 S 0.1814 0.1490 0.6696 52 G 0.1626 0.1309 0.7064 53 A 0.1858 0.1672 0.6470 54 D 0.1491 0.1594 0.6915 55 G 0.1236 0.1570 0.7194 56 G 0.1356 0.1324 0.7320 57 T 0.2400 0.1311 0.6289 58 S 0.2482 0.2193 0.5325 59 V 0.2579 0.3196 0.4225 60 Q 0.2635 0.3807 0.3557 61 A 0.2493 0.4363 0.3144 62 E 0.2474 0.3856 0.3670 63 A 0.2708 0.2347 0.4945 64 S 0.2438 0.1213 0.6348 65 L 0.2658 0.0374 0.6968 66 P 0.2463 0.0418 0.7120 67 R 0.2799 0.1556 0.5644 68 N 0.3871 0.0809 0.5320 69 L 0.6375 0.0166 0.3460 70 L 0.7188 0.0130 0.2683 71 F 0.7576 0.0075 0.2349 72 K 0.6822 0.0197 0.2980 73 Y 0.5979 0.0274 0.3747 74 A 0.3982 0.0525 0.5493 75 T 0.2886 0.1297 0.5817 76 N 0.2436 0.1544 0.6020 77 S 0.1798 0.2070 0.6132 78 E 0.1575 0.2558 0.5867 79 E 0.2486 0.2068 0.5446 80 V 0.4135 0.1243 0.4622 81 I 0.5753 0.0816 0.3431 82 G 0.6653 0.0481 0.2867 83 V 0.7284 0.0493 0.2223 84 M 0.7102 0.0505 0.2393 85 S 0.5915 0.0862 0.3223 86 K 0.4094 0.2134 0.3772 87 E 0.4312 0.1673 0.4015 88 Y 0.3864 0.1186 0.4949 89 I 0.2997 0.0596 0.6406 90 P 0.1815 0.0816 0.7369 91 K 0.0917 0.2063 0.7019 92 G 0.0480 0.1186 0.8334 93 T 0.3058 0.0364 0.6578 94 R 0.6000 0.0327 0.3673 95 F 0.6443 0.0376 0.3182 96 G 0.5978 0.0254 0.3767 97 P 0.5788 0.0841 0.3371 98 L 0.5364 0.0961 0.3675 99 I 0.4693 0.0816 0.4491 100 G 0.4198 0.0655 0.5147 101 E 0.6298 0.0444 0.3258 102 I 0.6647 0.0277 0.3076 103 Y 0.5521 0.0361 0.4118 104 T 0.2894 0.0449 0.6657 105 N 0.1492 0.2945 0.5563 106 D 0.0983 0.4275 0.4742 107 T 0.1679 0.3317 0.5004 108 V 0.2473 0.1703 0.5824 109 P 0.1635 0.2737 0.5629 110 K 0.1238 0.4062 0.4700 111 N 0.1414 0.2632 0.5954 112 A 0.1222 0.2832 0.5947 113 N 0.1283 0.1582 0.7134 114 R 0.2185 0.1281 0.6534 115 K 0.3273 0.1114 0.5614 116 Y 0.5248 0.0743 0.4010 117 F 0.6756 0.0384 0.2860 118 W 0.7542 0.0217 0.2241 119 R 0.7692 0.0176 0.2132 120 I 0.7355 0.0281 0.2364 121 Y 0.5785 0.0592 0.3623 122 S 0.3459 0.1360 0.5181 123 R 0.1447 0.1261 0.7292 124 G 0.0891 0.0986 0.8123 125 E 0.2286 0.0672 0.7043 126 L 0.3741 0.0532 0.5727 127 H 0.4967 0.0629 0.4404 128 H 0.7009 0.0213 0.2777 129 F 0.7437 0.0148 0.2415 130 I 0.7371 0.0167 0.2461 131 D 0.5251 0.0377 0.4372 132 G 0.3008 0.1439 0.5553 133 F 0.2135 0.1558 0.6307 134 N 0.1669 0.2034 0.6297 135 E 0.0996 0.3695 0.5309 136 E 0.1248 0.3346 0.5407 137 K 0.1418 0.2979 0.5604 138 S 0.1614 0.2651 0.5735 139 N 0.1830 0.2745 0.5426 140 W 0.1919 0.4083 0.3998 141 M 0.2529 0.4081 0.3389 142 R 0.3351 0.3581 0.3068 143 Y 0.4316 0.2162 0.3522 144 V 0.4732 0.1175 0.4093 145 N 0.3169 0.0670 0.6161 146 P 0.1205 0.3561 0.5234 147 A 0.1100 0.3258 0.5642 148 H 0.1549 0.1643 0.6808 149 S 0.1887 0.0662 0.7451 150 P 0.0711 0.3424 0.5865 151 R 0.0979 0.2587 0.6434 152 E 0.1806 0.3390 0.4804 153 Q 0.2777 0.3121 0.4102 154 N 0.4489 0.1726 0.3785 155 L 0.5608 0.1259 0.3133 156 A 0.6655 0.0965 0.2381 157 A 0.6957 0.0663 0.2380 158 C 0.6532 0.0624 0.2844 159 Q 0.5312 0.1137 0.3551 160 N 0.2513 0.1032 0.6455 161 G 0.1506 0.0682 0.7812 162 M 0.2930 0.0541 0.6529 163 N 0.5603 0.0265 0.4132 164 I 0.7815 0.0071 0.2114 165 Y 0.8084 0.0059 0.1857 166 F 0.8230 0.0042 0.1728 167 Y 0.8118 0.0072 0.1810 168 T 0.7763 0.0078 0.2159 169 I 0.6715 0.0236 0.3049 170 K 0.6183 0.0173 0.3644 171 P 0.5582 0.0320 0.4098 172 I 0.3548 0.0280 0.6172 173 P 0.1912 0.0244 0.7844 174 A 0.0872 0.2199 0.6929 175 N 0.0414 0.1339 0.8247 176 Q 0.3092 0.0533 0.6375 177 E 0.6464 0.0283 0.3253 178 L 0.7825 0.0146 0.2029 179 L 0.7841 0.0129 0.2030 180 V 0.7591 0.0238 0.2171 181 W 0.5661 0.0977 0.3362 182 Y 0.3926 0.1736 0.4338 183 C 0.2394 0.2170 0.5435 184 R 0.1267 0.4089 0.4644 185 D 0.1182 0.4701 0.4117 186 F 0.0746 0.6232 0.3023 187 A 0.0555 0.6764 0.2681 188 E 0.0511 0.6931 0.2558 189 R 0.0902 0.5575 0.3524 190 L 0.1301 0.3685 0.5014 191 H 0.1573 0.1841 0.6586 192 Y 0.2348 0.0604 0.7048 193 P 0.2108 0.0806 0.7086 194 Y 0.2413 0.0650 0.6937 195 P 0.1841 0.1309 0.6850 196 G 0.1497 0.1292 0.7211 197 E 0.2265 0.1709 0.6026 198 L 0.2178 0.2494 0.5328 199 T 0.2419 0.2025 0.5555 200 M 0.2569 0.2127 0.5304 201 M 0.2782 0.2060 0.5158 202 N 0.2758 0.1807 0.5435 203 L 0.2573 0.2022 0.5404 204 T 0.2279 0.1758 0.5963 205 Q 0.2056 0.1777 0.6167