# This file is the result of combining several RDB files, specifically # T0395.t2k.str2.rdb (weight 1.54425) # T0395.t2k.str4.rdb (weight 0.924988) # T0395.t2k.pb.rdb (weight 0.789901) # T0395.t2k.bys.rdb (weight 0.748322) # T0395.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 T0395.t2k.str2.rdb # ============================================ # TARGET T0395 # 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 T0395.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 268 # # ============================================ # Comments from T0395.t2k.str4.rdb # ============================================ # TARGET T0395 # 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 T0395.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 268 # # ============================================ # Comments from T0395.t2k.pb.rdb # ============================================ # TARGET T0395 # 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 T0395.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 268 # # ============================================ # Comments from T0395.t2k.bys.rdb # ============================================ # TARGET T0395 # 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 T0395.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 268 # # ============================================ # Comments from T0395.t2k.alpha.rdb # ============================================ # TARGET T0395 # 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 T0395.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 268 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2725 0.1517 0.5758 2 R 0.2532 0.1551 0.5917 3 L 0.1884 0.2145 0.5971 4 G 0.1669 0.1658 0.6673 5 D 0.1774 0.2275 0.5952 6 A 0.1180 0.5416 0.3405 7 A 0.1524 0.6099 0.2378 8 E 0.2747 0.5274 0.1978 9 L 0.3209 0.4749 0.2043 10 C 0.3042 0.4396 0.2562 11 Y 0.1894 0.4981 0.3125 12 N 0.1433 0.3989 0.4578 13 L 0.1517 0.2752 0.5731 14 T 0.1457 0.2275 0.6268 15 S 0.0890 0.3561 0.5549 16 S 0.0902 0.4248 0.4850 17 Y 0.1131 0.5292 0.3577 18 L 0.1013 0.6249 0.2738 19 Q 0.1111 0.6113 0.2776 20 I 0.1506 0.5225 0.3270 21 A 0.1462 0.4725 0.3813 22 A 0.1012 0.4992 0.3996 23 E 0.0887 0.4727 0.4387 24 S 0.0763 0.5001 0.4236 25 D 0.0580 0.6223 0.3197 26 S 0.0364 0.7774 0.1863 27 I 0.0211 0.8602 0.1187 28 I 0.0128 0.8957 0.0915 29 A 0.0106 0.8943 0.0951 30 Q 0.0117 0.8810 0.1074 31 T 0.0136 0.8855 0.1009 32 Q 0.0097 0.9059 0.0845 33 R 0.0089 0.9103 0.0808 34 A 0.0105 0.8998 0.0897 35 I 0.0104 0.9006 0.0890 36 N 0.0119 0.8789 0.1092 37 T 0.0161 0.8493 0.1346 38 T 0.0193 0.8350 0.1458 39 K 0.0163 0.8362 0.1475 40 S 0.0188 0.8229 0.1583 41 I 0.0304 0.8050 0.1646 42 L 0.0346 0.8110 0.1544 43 I 0.0300 0.8237 0.1463 44 N 0.0350 0.7919 0.1731 45 E 0.0559 0.7324 0.2117 46 T 0.1043 0.5999 0.2958 47 F 0.1227 0.4861 0.3912 48 P 0.0624 0.6615 0.2761 49 K 0.0816 0.5762 0.3421 50 W 0.1574 0.4103 0.4323 51 S 0.2258 0.2052 0.5690 52 P 0.1490 0.2934 0.5576 53 L 0.1255 0.2399 0.6346 54 N 0.1188 0.1474 0.7338 55 G 0.1216 0.1248 0.7536 56 E 0.3961 0.0555 0.5484 57 I 0.6859 0.0154 0.2987 58 S 0.7725 0.0119 0.2156 59 F 0.7977 0.0102 0.1921 60 S 0.7577 0.0169 0.2255 61 Y 0.5931 0.0526 0.3542 62 N 0.3105 0.0835 0.6060 63 G 0.1246 0.1200 0.7554 64 G 0.1343 0.1240 0.7416 65 K 0.0995 0.3611 0.5394 66 D 0.0856 0.5118 0.4026 67 C 0.0611 0.7308 0.2080 68 Q 0.0526 0.8243 0.1231 69 V 0.0308 0.8803 0.0890 70 L 0.0120 0.9169 0.0711 71 L 0.0092 0.9221 0.0688 72 L 0.0083 0.9243 0.0674 73 L 0.0083 0.9232 0.0685 74 Y 0.0084 0.9169 0.0747 75 L 0.0086 0.9029 0.0885 76 S 0.0105 0.8514 0.1380 77 C 0.0255 0.7060 0.2685 78 L 0.0563 0.4731 0.4707 79 W 0.0781 0.3951 0.5268 80 E 0.1005 0.2259 0.6736 81 Y 0.2926 0.0718 0.6356 82 Y 0.4723 0.0350 0.4926 83 I 0.6959 0.0180 0.2862 84 V 0.7667 0.0134 0.2200 85 K 0.7513 0.0108 0.2379 86 L 0.6416 0.0464 0.3120 87 S 0.3573 0.0604 0.5822 88 Q 0.1658 0.1927 0.6415 89 S 0.1375 0.2085 0.6540 90 Q 0.1618 0.2002 0.6380 91 F 0.1967 0.1733 0.6300 92 D 0.1590 0.1172 0.7238 93 G 0.0658 0.4435 0.4907 94 K 0.1136 0.3965 0.4899 95 F 0.2157 0.3372 0.4471 96 H 0.2537 0.2822 0.4641 97 R 0.2805 0.2357 0.4837 98 F 0.2582 0.1220 0.6198 99 P 0.1308 0.3875 0.4816 100 L 0.0957 0.4765 0.4277 101 T 0.1588 0.3973 0.4439 102 K 0.2167 0.2558 0.5275 103 L 0.2874 0.1342 0.5784 104 P 0.2427 0.1960 0.5613 105 T 0.3211 0.1726 0.5064 106 V 0.4199 0.0726 0.5075 107 F 0.4752 0.0586 0.4662 108 I 0.4762 0.0616 0.4622 109 D 0.3447 0.0617 0.5936 110 H 0.2477 0.2054 0.5469 111 D 0.1910 0.2690 0.5400 112 D 0.2007 0.2264 0.5729 113 T 0.1893 0.2486 0.5621 114 F 0.1926 0.2199 0.5875 115 K 0.1112 0.4279 0.4609 116 T 0.0967 0.4507 0.4526 117 L 0.0374 0.7238 0.2388 118 E 0.0184 0.8349 0.1467 119 N 0.0144 0.8710 0.1146 120 F 0.0142 0.8900 0.0958 121 I 0.0116 0.9039 0.0846 122 E 0.0095 0.9106 0.0800 123 E 0.0107 0.8986 0.0907 124 T 0.0200 0.8593 0.1207 125 S 0.0262 0.8211 0.1527 126 L 0.0346 0.7512 0.2142 127 R 0.0679 0.5674 0.3646 128 Y 0.1185 0.3595 0.5220 129 S 0.1413 0.2070 0.6517 130 L 0.1736 0.2622 0.5643 131 S 0.2425 0.2057 0.5519 132 L 0.3536 0.1724 0.4740 133 Y 0.3655 0.1280 0.5065 134 E 0.3347 0.1699 0.4953 135 S 0.2413 0.2370 0.5217 136 D 0.1656 0.2181 0.6163 137 R 0.1404 0.2335 0.6261 138 D 0.1175 0.3409 0.5416 139 K 0.1200 0.4234 0.4566 140 C 0.1660 0.4324 0.4016 141 E 0.1888 0.4369 0.3743 142 T 0.1505 0.5065 0.3430 143 M 0.0921 0.6687 0.2392 144 A 0.0384 0.8055 0.1562 145 E 0.0279 0.8401 0.1320 146 A 0.0304 0.8041 0.1655 147 F 0.0337 0.8131 0.1531 148 E 0.0256 0.8423 0.1321 149 T 0.0143 0.8939 0.0918 150 F 0.0112 0.8638 0.1250 151 L 0.0098 0.8900 0.1002 152 Q 0.0115 0.8144 0.1741 153 V 0.0352 0.6346 0.3302 154 F 0.1395 0.3120 0.5485 155 P 0.0430 0.4002 0.5568 156 E 0.0696 0.2049 0.7255 157 T 0.2722 0.0704 0.6574 158 K 0.4879 0.0419 0.4702 159 A 0.7746 0.0082 0.2172 160 I 0.7872 0.0068 0.2060 161 V 0.7781 0.0061 0.2158 162 I 0.7449 0.0173 0.2378 163 G 0.6548 0.0188 0.3264 164 I 0.5578 0.0357 0.4065 165 R 0.4475 0.0439 0.5085 166 H 0.3201 0.1357 0.5442 167 T 0.2256 0.1545 0.6199 168 D 0.2222 0.0858 0.6920 169 P 0.1499 0.2554 0.5947 170 F 0.1462 0.2918 0.5620 171 G 0.1472 0.3204 0.5324 172 E 0.1402 0.4160 0.4437 173 H 0.1834 0.2947 0.5219 174 L 0.2343 0.1634 0.6023 175 K 0.3144 0.0629 0.6227 176 P 0.3067 0.0888 0.6045 177 I 0.3774 0.1165 0.5061 178 Q 0.4148 0.0926 0.4926 179 K 0.3550 0.1579 0.4872 180 T 0.2848 0.1148 0.6004 181 D 0.2172 0.0639 0.7189 182 A 0.0439 0.3949 0.5612 183 N 0.0623 0.2643 0.6734 184 W 0.1669 0.1368 0.6963 185 P 0.1211 0.3119 0.5670 186 D 0.1729 0.3258 0.5013 187 F 0.3482 0.2854 0.3664 188 Y 0.5367 0.1463 0.3170 189 R 0.6118 0.1061 0.2821 190 L 0.5879 0.1139 0.2982 191 Q 0.4816 0.0910 0.4274 192 P 0.2778 0.2383 0.4839 193 L 0.2430 0.2835 0.4734 194 L 0.3079 0.2634 0.4287 195 H 0.3069 0.2162 0.4768 196 W 0.2573 0.2536 0.4891 197 N 0.1810 0.1964 0.6227 198 L 0.0170 0.7329 0.2501 199 A 0.0105 0.8478 0.1417 200 N 0.0089 0.9087 0.0824 201 I 0.0089 0.9027 0.0885 202 W 0.0083 0.9218 0.0699 203 S 0.0085 0.9232 0.0684 204 F 0.0085 0.9205 0.0709 205 L 0.0088 0.9156 0.0756 206 L 0.0099 0.8813 0.1088 207 Y 0.0159 0.7936 0.1906 208 S 0.0454 0.3231 0.6315 209 N 0.0422 0.0912 0.8667 210 E 0.1707 0.0474 0.7819 211 P 0.2265 0.1066 0.6668 212 I 0.3179 0.1875 0.4946 213 C 0.2731 0.2227 0.5042 214 E 0.1015 0.6128 0.2857 215 L 0.0909 0.6328 0.2763 216 Y 0.0975 0.6074 0.2951 217 R 0.1242 0.4802 0.3957 218 Y 0.1059 0.1876 0.7066 219 G 0.0880 0.0852 0.8268 220 F 0.2760 0.0708 0.6532 221 T 0.3781 0.0720 0.5499 222 S 0.3788 0.0836 0.5375 223 L 0.2847 0.1693 0.5460 224 G 0.2153 0.1248 0.6599 225 N 0.2451 0.1073 0.6476 226 V 0.2141 0.1939 0.5920 227 E 0.1952 0.2424 0.5624 228 E 0.1821 0.2002 0.6178 229 T 0.2049 0.1562 0.6389 230 L 0.2375 0.0896 0.6729 231 P 0.2127 0.1086 0.6787 232 N 0.2094 0.0505 0.7401 233 P 0.0574 0.4813 0.4612 234 H 0.0804 0.4521 0.4675 235 L 0.2072 0.3305 0.4623 236 R 0.2674 0.1517 0.5809 237 K 0.2002 0.2083 0.5915 238 D 0.1498 0.1648 0.6853 239 K 0.1136 0.2647 0.6217 240 N 0.1422 0.1934 0.6643 241 S 0.1982 0.1620 0.6398 242 T 0.2331 0.0717 0.6952 243 P 0.2188 0.1949 0.5862 244 L 0.2349 0.2464 0.5187 245 K 0.3370 0.2029 0.4601 246 L 0.3523 0.1917 0.4560 247 N 0.3259 0.1914 0.4827 248 F 0.2954 0.2892 0.4154 249 E 0.2577 0.3818 0.3605 250 W 0.2444 0.4389 0.3167 251 E 0.2052 0.4924 0.3024 252 I 0.1753 0.5474 0.2773 253 E 0.1397 0.5672 0.2932 254 N 0.1319 0.4824 0.3857 255 R 0.1468 0.3879 0.4653 256 Y 0.1854 0.3031 0.5115 257 K 0.2163 0.2306 0.5531 258 H 0.2469 0.1855 0.5675 259 N 0.2007 0.1736 0.6257 260 E 0.1636 0.3247 0.5118 261 V 0.1701 0.3256 0.5044 262 T 0.2172 0.2534 0.5295 263 K 0.1988 0.2767 0.5245 264 A 0.2117 0.2096 0.5787 265 E 0.2537 0.0885 0.6579 266 P 0.2396 0.1009 0.6595 267 I 0.2916 0.0570 0.6513 268 P 0.2406 0.1733 0.5861 269 I 0.2311 0.2639 0.5050 270 A 0.1907 0.2590 0.5504 271 D 0.1305 0.3276 0.5419 272 E 0.0572 0.5686 0.3742 273 D 0.0964 0.5094 0.3942 274 L 0.1639 0.4751 0.3610 275 V 0.2233 0.4481 0.3286 276 K 0.2359 0.4625 0.3016 277 I 0.1651 0.5643 0.2706 278 E 0.1281 0.5579 0.3139 279 N 0.1360 0.4280 0.4360 280 L 0.1644 0.3419 0.4937 281 H 0.1501 0.3123 0.5376 282 E 0.0771 0.4710 0.4519 283 D 0.0946 0.3422 0.5632 284 Y 0.1731 0.2016 0.6252 285 Y 0.2230 0.0832 0.6939 286 P 0.1576 0.2490 0.5933 287 G 0.2061 0.2165 0.5774 288 W 0.4228 0.1924 0.3848 289 Y 0.5578 0.1308 0.3114 290 L 0.5451 0.1154 0.3395 291 V 0.3920 0.1468 0.4611 292 D 0.2354 0.1832 0.5814 293 D 0.1013 0.4858 0.4129 294 K 0.0752 0.5782 0.3466 295 L 0.0921 0.6537 0.2542 296 E 0.0861 0.6892 0.2248 297 R 0.1303 0.5281 0.3416 298 A 0.1156 0.3942 0.4903 299 G 0.1104 0.2712 0.6184 300 R 0.1896 0.2391 0.5713 301 I 0.2157 0.2527 0.5316 302 K 0.2311 0.2767 0.4923 303 K 0.2313 0.2353 0.5334 304 K 0.1731 0.2727 0.5542