# This file is the result of combining several RDB files, specifically # T0487.t04.str2.rdb (weight 1.54425) # T0487.t04.str4.rdb (weight 0.924988) # T0487.t04.pb.rdb (weight 0.789901) # T0487.t04.bys.rdb (weight 0.748322) # T0487.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 T0487.t04.str2.rdb # ============================================ # TARGET T0487 # 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 T0487.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 6.70837 # # ============================================ # Comments from T0487.t04.str4.rdb # ============================================ # TARGET T0487 # 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 T0487.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 6.70837 # # ============================================ # Comments from T0487.t04.pb.rdb # ============================================ # TARGET T0487 # 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 T0487.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 6.70837 # # ============================================ # Comments from T0487.t04.bys.rdb # ============================================ # TARGET T0487 # 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 T0487.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 6.70837 # # ============================================ # Comments from T0487.t04.alpha.rdb # ============================================ # TARGET T0487 # 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 T0487.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 6.70837 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 N 0.2360 0.1226 0.6414 2 R 0.3105 0.1539 0.5355 3 F 0.4453 0.1396 0.4151 4 A 0.5616 0.0954 0.3430 5 L 0.5813 0.0614 0.3573 6 R 0.6024 0.0384 0.3592 7 P 0.4711 0.0585 0.4704 8 L 0.3271 0.0666 0.6063 9 N 0.1935 0.0146 0.7919 10 P 0.0199 0.6549 0.3252 11 E 0.0179 0.7084 0.2737 12 E 0.0446 0.5112 0.4442 13 L 0.1929 0.2069 0.6002 14 R 0.2341 0.0941 0.6718 15 P 0.2251 0.2525 0.5224 16 W 0.3075 0.2500 0.4424 17 R 0.5501 0.1347 0.3152 18 L 0.6732 0.0638 0.2631 19 E 0.7384 0.0270 0.2346 20 V 0.7636 0.0138 0.2226 21 V 0.6696 0.0201 0.3103 22 L 0.5410 0.0349 0.4240 23 D 0.3246 0.0258 0.6496 24 P 0.2425 0.0637 0.6938 25 P 0.1991 0.0431 0.7577 26 P 0.1212 0.1720 0.7068 27 G 0.0618 0.1472 0.7910 28 R 0.1197 0.2029 0.6774 29 E 0.1194 0.2971 0.5835 30 E 0.1395 0.3268 0.5337 31 V 0.1039 0.5695 0.3267 32 Y 0.0665 0.7056 0.2279 33 P 0.0164 0.8685 0.1151 34 L 0.0097 0.9010 0.0893 35 L 0.0087 0.9143 0.0770 36 A 0.0084 0.9188 0.0728 37 Q 0.0084 0.9215 0.0701 38 V 0.0084 0.9189 0.0727 39 A 0.0087 0.9110 0.0803 40 R 0.0097 0.8891 0.1012 41 R 0.0194 0.7484 0.2322 42 A 0.0742 0.2774 0.6483 43 G 0.0713 0.1023 0.8264 44 G 0.2664 0.0718 0.6618 45 V 0.6047 0.0460 0.3493 46 T 0.7699 0.0158 0.2143 47 V 0.7616 0.0235 0.2149 48 R 0.6904 0.0260 0.2836 49 M 0.4158 0.0852 0.4991 50 G 0.2270 0.0985 0.6745 51 D 0.1875 0.1372 0.6753 52 G 0.1936 0.1363 0.6701 53 L 0.3529 0.1221 0.5250 54 A 0.4194 0.0921 0.4885 55 S 0.4149 0.0589 0.5262 56 W 0.3527 0.0833 0.5640 57 S 0.3130 0.0389 0.6481 58 P 0.2177 0.0355 0.7468 59 P 0.1479 0.2847 0.5674 60 E 0.2328 0.2847 0.4825 61 V 0.4690 0.1459 0.3851 62 L 0.5622 0.0910 0.3469 63 V 0.5420 0.0785 0.3796 64 L 0.3506 0.1385 0.5109 65 E 0.1886 0.2499 0.5615 66 G 0.1239 0.1937 0.6824 67 T 0.2065 0.2427 0.5508 68 L 0.2221 0.3621 0.4158 69 A 0.2207 0.4143 0.3650 70 R 0.2346 0.3639 0.4015 71 M 0.2449 0.2736 0.4815 72 G 0.2104 0.1904 0.5992 73 Q 0.2803 0.1455 0.5742 74 T 0.3080 0.0950 0.5970 75 Y 0.1880 0.3258 0.4863 76 A 0.2111 0.3358 0.4531 77 Y 0.3899 0.1959 0.4143 78 R 0.5684 0.0963 0.3353 79 L 0.5917 0.0831 0.3252 80 Y 0.5181 0.0607 0.4213 81 P 0.3529 0.1663 0.4808 82 K 0.2067 0.1640 0.6293 83 G 0.1688 0.1027 0.7286 84 R 0.2678 0.0846 0.6477 85 R 0.3942 0.0413 0.5645 86 P 0.3941 0.0765 0.5294 87 L 0.3274 0.0704 0.6022 88 D 0.2290 0.0277 0.7433 89 P 0.0895 0.2938 0.6167 90 K 0.0959 0.2364 0.6677 91 D 0.1689 0.0780 0.7531 92 P 0.0245 0.4646 0.5110 93 G 0.0232 0.5922 0.3846 94 E 0.0176 0.8224 0.1600 95 R 0.0112 0.8934 0.0954 96 S 0.0089 0.9161 0.0750 97 V 0.0084 0.9214 0.0701 98 L 0.0083 0.9209 0.0708 99 S 0.0083 0.9232 0.0685 100 A 0.0083 0.9223 0.0694 101 L 0.0083 0.9227 0.0690 102 A 0.0083 0.9170 0.0747 103 R 0.0083 0.9200 0.0717 104 R 0.0084 0.9106 0.0811 105 L 0.0087 0.8944 0.0969 106 L 0.0088 0.8997 0.0915 107 Q 0.0089 0.9026 0.0885 108 E 0.0093 0.8922 0.0986 109 R 0.0177 0.8175 0.1648 110 L 0.0369 0.7327 0.2305 111 R 0.0596 0.6526 0.2878 112 R 0.1325 0.4394 0.4280 113 L 0.1850 0.2514 0.5636 114 E 0.1552 0.1720 0.6729 115 G 0.2004 0.0981 0.7015 116 V 0.5143 0.0466 0.4391 117 W 0.6422 0.0411 0.3167 118 V 0.6216 0.0624 0.3160 119 E 0.4727 0.1002 0.4272 120 G 0.3911 0.0948 0.5141 121 L 0.4348 0.1798 0.3854 122 A 0.5092 0.1909 0.2999 123 V 0.5493 0.1837 0.2669 124 Y 0.4965 0.2021 0.3014 125 R 0.4276 0.2430 0.3294 126 R 0.3407 0.2839 0.3754 127 E 0.2574 0.3301 0.4125 128 H 0.2830 0.2606 0.4563 129 A 0.2312 0.2271 0.5417 130 R 0.2039 0.1284 0.6677 131 G 0.1953 0.0613 0.7433 132 P 0.1956 0.1572 0.6472 133 G 0.3325 0.1137 0.5538 134 W 0.6074 0.0740 0.3186 135 R 0.6988 0.0497 0.2515 136 V 0.6708 0.0559 0.2732 137 L 0.4955 0.0791 0.4254 138 G 0.2972 0.0633 0.6394 139 G 0.2809 0.0648 0.6542 140 A 0.5384 0.0532 0.4084 141 V 0.7223 0.0212 0.2565 142 L 0.7332 0.0228 0.2440 143 D 0.7452 0.0177 0.2370 144 L 0.7795 0.0159 0.2047 145 W 0.7710 0.0130 0.2160 146 V 0.7321 0.0126 0.2553 147 S 0.4330 0.0356 0.5314 148 D 0.1841 0.2094 0.6065 149 S 0.1066 0.1674 0.7260 150 G 0.1463 0.0839 0.7698 151 A 0.5417 0.0310 0.4273 152 F 0.7270 0.0178 0.2551 153 L 0.7627 0.0149 0.2224 154 L 0.7915 0.0109 0.1976 155 E 0.7756 0.0108 0.2135 156 V 0.7231 0.0195 0.2574 157 D 0.4235 0.0202 0.5563 158 P 0.0945 0.4857 0.4198 159 A 0.0706 0.4335 0.4959 160 Y 0.2304 0.3599 0.4097 161 R 0.4284 0.2531 0.3185 162 I 0.4574 0.2259 0.3167 163 L 0.3261 0.1652 0.5087 164 C 0.2087 0.1076 0.6837 165 E 0.1006 0.3556 0.5438 166 M 0.1561 0.3060 0.5379 167 S 0.2041 0.2501 0.5458 168 L 0.0273 0.7534 0.2193 169 E 0.0140 0.8614 0.1246 170 A 0.0142 0.9098 0.0761 171 W 0.0121 0.9066 0.0813 172 L 0.0143 0.8754 0.1103 173 A 0.0205 0.7924 0.1872 174 Q 0.0533 0.4818 0.4650 175 G 0.0921 0.1922 0.7157 176 H 0.1444 0.1077 0.7480 177 P 0.1411 0.1761 0.6828 178 L 0.2171 0.0835 0.6994 179 P 0.2082 0.1147 0.6770 180 K 0.2818 0.1480 0.5702 181 R 0.4321 0.0722 0.4957 182 V 0.5506 0.0749 0.3744 183 R 0.5518 0.1006 0.3476 184 N 0.5116 0.0928 0.3956 185 A 0.3428 0.1912 0.4660 186 Y 0.2815 0.1559 0.5626 187 D 0.1865 0.1325 0.6810 188 R 0.1460 0.1905 0.6634 189 R 0.2174 0.1854 0.5972 190 T 0.3965 0.1279 0.4756 191 W 0.4276 0.2293 0.3431 192 E 0.4186 0.3267 0.2547 193 L 0.4106 0.2932 0.2962 194 L 0.3984 0.2737 0.3279 195 R 0.3649 0.2304 0.4047 196 L 0.2592 0.2067 0.5341 197 G 0.2166 0.1219 0.6615 198 E 0.1758 0.1940 0.6301 199 E 0.2205 0.1504 0.6291 200 D 0.2113 0.0367 0.7520 201 P 0.0577 0.4592 0.4831 202 K 0.0824 0.3623 0.5553 203 E 0.2178 0.2116 0.5706 204 L 0.3721 0.0412 0.5867 205 P 0.3282 0.0493 0.6225 206 L 0.2527 0.0417 0.7056 207 P 0.1455 0.1599 0.6947 208 G 0.0951 0.1551 0.7499 209 G 0.1050 0.1142 0.7809 210 L 0.2828 0.0860 0.6312 211 S 0.3397 0.1752 0.4850 212 L 0.1855 0.4734 0.3411 213 L 0.1814 0.5418 0.2769 214 D 0.1767 0.5673 0.2559 215 Y 0.1469 0.5912 0.2619 216 H 0.1717 0.5155 0.3128 217 A 0.1089 0.5775 0.3136 218 S 0.0960 0.4746 0.4294 219 K 0.1004 0.2642 0.6354 220 G 0.0970 0.1556 0.7474 221 R 0.1801 0.1610 0.6589 222 L 0.2656 0.1336 0.6008 223 Q 0.2377 0.1483 0.6139 224 G 0.2014 0.1153 0.6833 225 R 0.2733 0.1264 0.6003 226 E 0.2473 0.1119 0.6408 227 G 0.2197 0.0681 0.7122 228 G 0.4545 0.0234 0.5221 229 R 0.6939 0.0160 0.2901 230 V 0.8027 0.0058 0.1915 231 A 0.8025 0.0063 0.1912 232 W 0.7967 0.0057 0.1976 233 V 0.7749 0.0096 0.2154 234 A 0.6408 0.0237 0.3355 235 D 0.3794 0.0150 0.6056 236 P 0.1186 0.2680 0.6134 237 K 0.1174 0.2153 0.6673 238 D 0.2026 0.1038 0.6936 239 P 0.0666 0.3316 0.6018 240 R 0.1054 0.2468 0.6477 241 K 0.2138 0.0871 0.6991 242 P 0.2049 0.0927 0.7024 243 I 0.2329 0.1019 0.6652 244 P 0.1999 0.3213 0.4788 245 H 0.1891 0.3991 0.4118 246 L 0.1303 0.5354 0.3343 247 T 0.1097 0.5285 0.3618 248 G 0.0876 0.5364 0.3760 249 L 0.1257 0.4992 0.3750 250 L 0.2212 0.3238 0.4549 251 V 0.2758 0.2412 0.4830 252 P 0.2255 0.2715 0.5030 253 V 0.2964 0.3006 0.4030 254 L 0.4228 0.1991 0.3780 255 T 0.3315 0.2179 0.4507 256 L 0.1383 0.5322 0.3295 257 E 0.0723 0.6656 0.2622 258 D 0.0671 0.6907 0.2422 259 L 0.0443 0.7107 0.2450 260 H 0.0475 0.6702 0.2822 261 E 0.0454 0.6855 0.2691 262 E 0.0567 0.6285 0.3148 263 E 0.0759 0.3956 0.5285 264 G 0.0568 0.2134 0.7298 265 S 0.1501 0.2297 0.6202 266 L 0.1824 0.3590 0.4586 267 A 0.2058 0.3462 0.4479 268 L 0.2497 0.2563 0.4940 269 S 0.2395 0.1414 0.6191 270 L 0.2368 0.1002 0.6630 271 P 0.1626 0.2310 0.6064 272 W 0.0690 0.5866 0.3443 273 E 0.0554 0.7233 0.2213 274 E 0.0668 0.7465 0.1867 275 R 0.0514 0.7829 0.1657 276 R 0.0408 0.8160 0.1433 277 R 0.0511 0.8063 0.1426 278 R 0.0580 0.7850 0.1570 279 T 0.0211 0.8591 0.1198 280 R 0.0109 0.8942 0.0949 281 E 0.0122 0.9076 0.0802 282 I 0.0109 0.9073 0.0817 283 A 0.0091 0.9112 0.0796 284 S 0.0087 0.9112 0.0801 285 W 0.0101 0.8938 0.0961 286 I 0.0146 0.8493 0.1361 287 G 0.0137 0.8223 0.1640 288 R 0.0259 0.7628 0.2113 289 R 0.0709 0.5836 0.3455 290 L 0.1161 0.4287 0.4552 291 G 0.1262 0.3664 0.5073 292 L 0.1944 0.2443 0.5613 293 G 0.2092 0.1171 0.6738 294 T 0.2297 0.0563 0.7140 295 P 0.1833 0.1236 0.6931