# This file is the result of combining several RDB files, specifically # T0434.t06.str2.rdb (weight 1.54425) # T0434.t06.str4.rdb (weight 0.924988) # T0434.t06.pb.rdb (weight 0.789901) # T0434.t06.bys.rdb (weight 0.748322) # T0434.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 T0434.t06.str2.rdb # ============================================ # TARGET T0434 # 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 T0434.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 1436 # # ============================================ # Comments from T0434.t06.str4.rdb # ============================================ # TARGET T0434 # 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 T0434.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 1436 # # ============================================ # Comments from T0434.t06.pb.rdb # ============================================ # TARGET T0434 # 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 T0434.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 1436 # # ============================================ # Comments from T0434.t06.bys.rdb # ============================================ # TARGET T0434 # 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 T0434.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 1436 # # ============================================ # Comments from T0434.t06.alpha.rdb # ============================================ # TARGET T0434 # 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 T0434.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 1436 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2188 0.1027 0.6786 2 G 0.1748 0.0878 0.7375 3 S 0.2220 0.1489 0.6292 4 S 0.2631 0.1834 0.5536 5 H 0.3072 0.2008 0.4919 6 H 0.2641 0.2267 0.5092 7 H 0.2625 0.1973 0.5402 8 H 0.2583 0.1749 0.5669 9 H 0.2421 0.1382 0.6197 10 H 0.1523 0.2265 0.6212 11 S 0.1237 0.2432 0.6331 12 S 0.1355 0.1796 0.6849 13 G 0.1321 0.1249 0.7430 14 L 0.2888 0.0662 0.6450 15 V 0.3634 0.0398 0.5967 16 P 0.3311 0.0621 0.6069 17 R 0.2664 0.1009 0.6327 18 G 0.2040 0.1219 0.6741 19 S 0.2037 0.1596 0.6367 20 K 0.2159 0.1515 0.6326 21 M 0.2546 0.1114 0.6340 22 D 0.2051 0.0943 0.7006 23 M 0.1502 0.2682 0.5815 24 E 0.1087 0.3315 0.5597 25 D 0.1309 0.2637 0.6054 26 A 0.1132 0.3633 0.5236 27 D 0.1151 0.3716 0.5133 28 M 0.1498 0.3611 0.4891 29 T 0.1799 0.3359 0.4841 30 L 0.1700 0.3668 0.4633 31 W 0.1988 0.3072 0.4940 32 T 0.1809 0.3210 0.4982 33 E 0.0629 0.6087 0.3284 34 A 0.0529 0.6344 0.3128 35 E 0.0834 0.5325 0.3842 36 F 0.1249 0.4200 0.4551 37 E 0.0898 0.4730 0.4372 38 E 0.1047 0.4172 0.4781 39 K 0.1619 0.3451 0.4930 40 C 0.2768 0.2486 0.4746 41 T 0.3695 0.2052 0.4253 42 Y 0.4437 0.1366 0.4196 43 I 0.3698 0.1018 0.5284 44 V 0.2349 0.1336 0.6315 45 N 0.1074 0.2884 0.6042 46 D 0.1240 0.1961 0.6799 47 H 0.2246 0.0607 0.7147 48 P 0.1757 0.1489 0.6753 49 W 0.1910 0.1555 0.6535 50 D 0.1841 0.1222 0.6936 51 S 0.1301 0.2448 0.6251 52 G 0.1338 0.2011 0.6651 53 A 0.1945 0.1649 0.6406 54 D 0.1357 0.1825 0.6818 55 G 0.1053 0.1382 0.7565 56 G 0.1698 0.0936 0.7366 57 T 0.3712 0.0740 0.5548 58 S 0.4196 0.1164 0.4640 59 V 0.3971 0.1956 0.4073 60 Q 0.3484 0.2505 0.4011 61 A 0.2388 0.3809 0.3803 62 E 0.1918 0.4112 0.3970 63 A 0.2112 0.2941 0.4948 64 S 0.1970 0.2081 0.5950 65 L 0.2216 0.0915 0.6869 66 P 0.1751 0.1205 0.7044 67 R 0.1130 0.2614 0.6256 68 N 0.1719 0.1354 0.6926 69 L 0.3972 0.0331 0.5697 70 L 0.6178 0.0244 0.3578 71 F 0.7304 0.0119 0.2577 72 K 0.7557 0.0129 0.2314 73 Y 0.7166 0.0128 0.2706 74 A 0.6610 0.0268 0.3122 75 T 0.5566 0.0409 0.4025 76 N 0.3126 0.0532 0.6342 77 S 0.1497 0.2313 0.6191 78 E 0.1452 0.2545 0.6002 79 E 0.2344 0.2066 0.5590 80 V 0.3643 0.1360 0.4997 81 I 0.5133 0.0993 0.3874 82 G 0.6311 0.0763 0.2925 83 V 0.7037 0.0669 0.2294 84 M 0.7043 0.0670 0.2287 85 S 0.5972 0.0881 0.3146 86 K 0.4069 0.2057 0.3874 87 E 0.4229 0.1733 0.4038 88 Y 0.3171 0.1650 0.5180 89 I 0.2836 0.0546 0.6618 90 P 0.1731 0.1210 0.7059 91 K 0.0754 0.2124 0.7122 92 G 0.0408 0.1183 0.8409 93 T 0.2706 0.0376 0.6918 94 R 0.5819 0.0343 0.3839 95 F 0.6058 0.0362 0.3580 96 G 0.5749 0.0302 0.3949 97 P 0.5072 0.0902 0.4026 98 L 0.4646 0.1196 0.4158 99 I 0.3742 0.1169 0.5089 100 G 0.3587 0.0644 0.5769 101 E 0.5853 0.0476 0.3671 102 I 0.6525 0.0318 0.3157 103 Y 0.5670 0.0378 0.3951 104 T 0.3678 0.0339 0.5983 105 N 0.1302 0.2866 0.5832 106 D 0.1096 0.3693 0.5211 107 T 0.1975 0.2856 0.5169 108 V 0.2697 0.1357 0.5946 109 P 0.1998 0.2547 0.5454 110 K 0.1788 0.3391 0.4822 111 N 0.1689 0.2691 0.5621 112 A 0.1243 0.3067 0.5691 113 N 0.1334 0.1851 0.6815 114 R 0.1830 0.2105 0.6065 115 K 0.2488 0.2089 0.5423 116 Y 0.4710 0.1302 0.3988 117 F 0.6286 0.0822 0.2892 118 W 0.7195 0.0571 0.2235 119 R 0.7618 0.0337 0.2045 120 I 0.7457 0.0363 0.2180 121 Y 0.6514 0.0519 0.2967 122 S 0.4932 0.1243 0.3825 123 R 0.2121 0.1171 0.6709 124 G 0.1145 0.1056 0.7799 125 E 0.2477 0.0865 0.6658 126 L 0.4019 0.0659 0.5322 127 H 0.5030 0.0591 0.4378 128 H 0.7191 0.0283 0.2526 129 F 0.7298 0.0187 0.2516 130 I 0.7321 0.0180 0.2499 131 D 0.5259 0.0271 0.4470 132 G 0.2718 0.1774 0.5507 133 F 0.1678 0.2036 0.6287 134 N 0.1504 0.1892 0.6605 135 E 0.0752 0.4089 0.5159 136 E 0.0882 0.4064 0.5054 137 K 0.1167 0.3095 0.5738 138 S 0.1282 0.2855 0.5863 139 N 0.1455 0.3120 0.5425 140 W 0.1028 0.6019 0.2953 141 M 0.1346 0.6216 0.2439 142 R 0.1701 0.6097 0.2202 143 Y 0.2611 0.4322 0.3067 144 V 0.3183 0.2622 0.4195 145 N 0.2521 0.1224 0.6255 146 P 0.1033 0.2998 0.5968 147 A 0.1095 0.2528 0.6377 148 H 0.1393 0.1550 0.7057 149 S 0.1794 0.0916 0.7290 150 P 0.0709 0.3914 0.5377 151 R 0.0862 0.3009 0.6129 152 E 0.2065 0.3167 0.4768 153 Q 0.3750 0.2143 0.4108 154 N 0.5203 0.1374 0.3423 155 L 0.6372 0.0917 0.2710 156 A 0.7076 0.0570 0.2354 157 A 0.7443 0.0409 0.2147 158 C 0.7011 0.0481 0.2509 159 Q 0.6142 0.0705 0.3153 160 N 0.2433 0.0861 0.6706 161 G 0.1452 0.0597 0.7951 162 M 0.3574 0.0557 0.5869 163 N 0.6434 0.0232 0.3334 164 I 0.7789 0.0074 0.2138 165 Y 0.8111 0.0068 0.1821 166 F 0.8167 0.0056 0.1777 167 Y 0.8040 0.0095 0.1865 168 T 0.7853 0.0117 0.2031 169 I 0.6891 0.0309 0.2800 170 K 0.6499 0.0274 0.3227 171 P 0.4833 0.0566 0.4601 172 I 0.3514 0.0274 0.6212 173 P 0.1908 0.0213 0.7878 174 A 0.0746 0.2557 0.6697 175 N 0.0423 0.1247 0.8330 176 Q 0.3190 0.0352 0.6458 177 E 0.6629 0.0197 0.3175 178 L 0.7569 0.0176 0.2255 179 L 0.7960 0.0108 0.1933 180 V 0.7630 0.0151 0.2219 181 W 0.6484 0.0532 0.2984 182 Y 0.5095 0.0908 0.3997 183 C 0.3213 0.1419 0.5368 184 R 0.2030 0.2838 0.5133 185 D 0.1617 0.3277 0.5106 186 F 0.1088 0.5034 0.3878 187 A 0.0770 0.5828 0.3402 188 E 0.0887 0.5635 0.3478 189 R 0.1207 0.4202 0.4590 190 L 0.1572 0.2681 0.5746 191 H 0.1848 0.1428 0.6723 192 Y 0.2626 0.0601 0.6774 193 P 0.2142 0.0698 0.7161 194 Y 0.2365 0.0598 0.7037 195 P 0.1505 0.1372 0.7123 196 G 0.1199 0.1338 0.7463 197 E 0.2314 0.1441 0.6245 198 L 0.2422 0.2372 0.5206 199 T 0.2661 0.2377 0.4963 200 M 0.2932 0.2121 0.4947 201 M 0.2374 0.1931 0.5695 202 N 0.2089 0.1516 0.6396 203 L 0.2110 0.1657 0.6233 204 T 0.2236 0.1402 0.6362 205 Q 0.1985 0.1677 0.6338