# This file is the result of combining several RDB files, specifically # T0413.t04.str2.rdb (weight 1.54425) # T0413.t04.str4.rdb (weight 0.924988) # T0413.t04.pb.rdb (weight 0.789901) # T0413.t04.bys.rdb (weight 0.748322) # T0413.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 T0413.t04.str2.rdb # ============================================ # TARGET T0413 # 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 T0413.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 2041 # # ============================================ # Comments from T0413.t04.str4.rdb # ============================================ # TARGET T0413 # 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 T0413.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 2041 # # ============================================ # Comments from T0413.t04.pb.rdb # ============================================ # TARGET T0413 # 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 T0413.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 2041 # # ============================================ # Comments from T0413.t04.bys.rdb # ============================================ # TARGET T0413 # 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 T0413.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 2041 # # ============================================ # Comments from T0413.t04.alpha.rdb # ============================================ # TARGET T0413 # 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 T0413.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 2041 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2136 0.1212 0.6653 2 N 0.1088 0.3076 0.5835 3 A 0.1174 0.2253 0.6573 4 M 0.2148 0.0964 0.6889 5 K 0.2495 0.0399 0.7106 6 P 0.2768 0.1174 0.6059 7 A 0.3282 0.1688 0.5029 8 D 0.4270 0.1341 0.4389 9 L 0.3737 0.1964 0.4298 10 T 0.3104 0.1820 0.5076 11 N 0.2172 0.1954 0.5874 12 A 0.1178 0.4055 0.4767 13 D 0.0887 0.4772 0.4341 14 R 0.0874 0.5991 0.3136 15 I 0.0970 0.6344 0.2685 16 A 0.0984 0.6647 0.2369 17 L 0.0913 0.6831 0.2256 18 E 0.0943 0.6091 0.2966 19 L 0.1111 0.4536 0.4352 20 G 0.0871 0.3405 0.5725 21 H 0.1364 0.3090 0.5546 22 A 0.1680 0.2257 0.6063 23 G 0.1617 0.1275 0.7108 24 R 0.2272 0.0887 0.6841 25 N 0.2823 0.0482 0.6695 26 A 0.3543 0.0684 0.5773 27 I 0.5108 0.0289 0.4603 28 P 0.6015 0.0276 0.3709 29 Y 0.6501 0.0260 0.3239 30 L 0.6228 0.0225 0.3547 31 D 0.4449 0.0446 0.5106 32 D 0.3418 0.1304 0.5278 33 D 0.2671 0.1842 0.5487 34 R 0.1667 0.2500 0.5832 35 N 0.1634 0.1816 0.6550 36 A 0.1213 0.1816 0.6970 37 D 0.1327 0.1094 0.7579 38 R 0.3421 0.0337 0.6242 39 P 0.5401 0.0300 0.4299 40 F 0.7108 0.0189 0.2702 41 T 0.7406 0.0140 0.2454 42 L 0.7771 0.0088 0.2141 43 N 0.7804 0.0103 0.2093 44 T 0.7910 0.0084 0.2006 45 Y 0.7361 0.0148 0.2491 46 R 0.5668 0.0166 0.4166 47 P 0.3329 0.0393 0.6279 48 Y 0.1480 0.1774 0.6746 49 G 0.0813 0.1257 0.7930 50 Y 0.1783 0.0859 0.7358 51 T 0.1975 0.0372 0.7653 52 P 0.1349 0.2233 0.6418 53 D 0.1518 0.1355 0.7127 54 R 0.3082 0.0269 0.6649 55 P 0.4639 0.0185 0.5176 56 V 0.7993 0.0066 0.1941 57 V 0.8107 0.0046 0.1847 58 V 0.8121 0.0045 0.1834 59 V 0.7957 0.0067 0.1975 60 Q 0.6948 0.0231 0.2821 61 H 0.4473 0.0500 0.5027 62 G 0.2565 0.0790 0.6644 63 V 0.2289 0.1151 0.6560 64 L 0.1908 0.1692 0.6399 65 R 0.1689 0.2008 0.6303 66 N 0.1577 0.1607 0.6816 67 G 0.1247 0.2574 0.6179 68 A 0.1095 0.3570 0.5335 69 D 0.1310 0.3499 0.5191 70 Y 0.1001 0.4694 0.4305 71 R 0.0917 0.5082 0.4001 72 D 0.0819 0.5255 0.3926 73 F 0.0687 0.5330 0.3983 74 W 0.0759 0.5487 0.3755 75 I 0.0645 0.6330 0.3025 76 P 0.0257 0.8126 0.1617 77 A 0.0174 0.8582 0.1244 78 A 0.0173 0.8501 0.1326 79 D 0.0221 0.7853 0.1926 80 R 0.0494 0.5372 0.4134 81 H 0.0899 0.1741 0.7360 82 K 0.1074 0.0572 0.8353 83 L 0.4383 0.0094 0.5523 84 L 0.6999 0.0109 0.2892 85 I 0.8002 0.0047 0.1951 86 V 0.7835 0.0088 0.2077 87 A 0.6863 0.0078 0.3058 88 P 0.4524 0.0382 0.5093 89 T 0.2819 0.0692 0.6489 90 F 0.2064 0.1093 0.6843 91 S 0.1468 0.1587 0.6944 92 D 0.1295 0.1781 0.6924 93 E 0.1980 0.1619 0.6401 94 I 0.2351 0.1473 0.6177 95 W 0.2243 0.0978 0.6778 96 P 0.1493 0.2214 0.6294 97 G 0.1133 0.1555 0.7312 98 V 0.1824 0.2215 0.5961 99 E 0.1705 0.2941 0.5354 100 S 0.1683 0.3039 0.5278 101 Y 0.1406 0.2998 0.5596 102 N 0.1411 0.2617 0.5972 103 N 0.1230 0.1961 0.6808 104 G 0.1186 0.1493 0.7321 105 R 0.2161 0.2211 0.5628 106 A 0.2855 0.2892 0.4253 107 F 0.3446 0.2598 0.3955 108 T 0.3077 0.2783 0.4140 109 A 0.2318 0.3594 0.4089 110 A 0.1825 0.2560 0.5615 111 G 0.1712 0.1583 0.6705 112 N 0.1998 0.0608 0.7394 113 P 0.1292 0.2919 0.5788 114 R 0.1500 0.2723 0.5777 115 H 0.1709 0.1887 0.6404 116 V 0.1394 0.2535 0.6071 117 D 0.1076 0.1872 0.7052 118 G 0.0827 0.2111 0.7061 119 W 0.1556 0.2871 0.5573 120 T 0.1772 0.3639 0.4589 121 Y 0.0137 0.7941 0.1922 122 A 0.0092 0.8777 0.1130 123 L 0.0084 0.9193 0.0723 124 V 0.0083 0.9215 0.0702 125 A 0.0083 0.9232 0.0685 126 R 0.0083 0.9211 0.0706 127 V 0.0083 0.9236 0.0681 128 L 0.0083 0.9229 0.0688 129 A 0.0083 0.9223 0.0694 130 N 0.0085 0.9168 0.0748 131 I 0.0085 0.9153 0.0762 132 R 0.0091 0.8857 0.1052 133 A 0.0116 0.7900 0.1984 134 A 0.0380 0.4961 0.4659 135 E 0.0770 0.2539 0.6691 136 I 0.1469 0.1852 0.6678 137 A 0.2520 0.1109 0.6371 138 D 0.2195 0.0417 0.7388 139 C 0.0655 0.4652 0.4693 140 E 0.1241 0.3849 0.4910 141 Q 0.4138 0.1393 0.4469 142 V 0.7012 0.0271 0.2717 143 Y 0.7406 0.0238 0.2356 144 L 0.7507 0.0255 0.2238 145 F 0.5655 0.0637 0.3709 146 G 0.3324 0.0959 0.5717 147 H 0.1869 0.2295 0.5836 148 S 0.1199 0.3490 0.5311 149 A 0.0405 0.6050 0.3546 150 G 0.0270 0.7681 0.2049 151 G 0.0116 0.8988 0.0896 152 Q 0.0094 0.9191 0.0715 153 F 0.0087 0.9229 0.0684 154 V 0.0086 0.9235 0.0679 155 H 0.0085 0.9232 0.0682 156 R 0.0086 0.9209 0.0705 157 L 0.0092 0.9085 0.0823 158 M 0.0120 0.8661 0.1219 159 S 0.0224 0.7399 0.2377 160 S 0.0530 0.4362 0.5108 161 Q 0.1501 0.1380 0.7119 162 P 0.0590 0.3528 0.5882 163 H 0.0798 0.2220 0.6983 164 A 0.2071 0.1761 0.6167 165 P 0.2506 0.1676 0.5817 166 F 0.3575 0.2102 0.4322 167 H 0.4715 0.1773 0.3512 168 A 0.6914 0.0572 0.2513 169 V 0.7180 0.0332 0.2487 170 T 0.7451 0.0260 0.2289 171 A 0.7041 0.0339 0.2620 172 A 0.5221 0.0747 0.4032 173 N 0.3509 0.0673 0.5818 174 P 0.1987 0.1685 0.6329 175 G 0.1626 0.1368 0.7006 176 W 0.1956 0.2092 0.5952 177 Y 0.2162 0.1623 0.6215 178 T 0.2167 0.1187 0.6647 179 L 0.2108 0.1219 0.6673 180 P 0.1535 0.2849 0.5616 181 T 0.1377 0.3912 0.4711 182 F 0.1391 0.4137 0.4472 183 E 0.1406 0.4000 0.4594 184 H 0.1748 0.3171 0.5082 185 R 0.2229 0.1993 0.5779 186 F 0.2266 0.0909 0.6825 187 P 0.1509 0.2929 0.5563 188 E 0.1137 0.3752 0.5111 189 G 0.0997 0.2913 0.6091 190 L 0.1456 0.2963 0.5581 191 D 0.1321 0.2009 0.6670 192 G 0.1032 0.1731 0.7236 193 V 0.1588 0.1335 0.7077 194 G 0.1526 0.1529 0.6945 195 L 0.1679 0.1977 0.6344 196 T 0.1758 0.1872 0.6371 197 E 0.1426 0.3158 0.5416 198 D 0.0906 0.4774 0.4320 199 H 0.0502 0.6109 0.3389 200 L 0.0448 0.6918 0.2634 201 A 0.0460 0.7381 0.2159 202 R 0.0334 0.6837 0.2829 203 L 0.0619 0.4911 0.4470 204 L 0.1522 0.2697 0.5781 205 A 0.1776 0.1466 0.6758 206 Y 0.2844 0.0541 0.6615 207 P 0.3614 0.0770 0.5616 208 M 0.7469 0.0271 0.2260 209 T 0.7793 0.0191 0.2016 210 I 0.7839 0.0174 0.1987 211 L 0.7211 0.0312 0.2477 212 A 0.4794 0.0565 0.4641 213 G 0.2455 0.0719 0.6826 214 D 0.1806 0.1866 0.6328 215 Q 0.1524 0.2703 0.5773 216 D 0.1885 0.2261 0.5854 217 I 0.1622 0.2847 0.5531 218 A 0.2236 0.1854 0.5910 219 T 0.2899 0.0686 0.6415 220 D 0.2049 0.0583 0.7368 221 D 0.1646 0.1947 0.6408 222 P 0.0518 0.4649 0.4833 223 N 0.0687 0.3106 0.6207 224 L 0.1209 0.2249 0.6542 225 P 0.0546 0.4980 0.4474 226 S 0.0680 0.5439 0.3881 227 E 0.0612 0.6290 0.3097 228 P 0.0146 0.8399 0.1455 229 A 0.0096 0.8971 0.0933 230 A 0.0096 0.8962 0.0941 231 L 0.0162 0.8390 0.1448 232 R 0.0223 0.7243 0.2534 233 Q 0.0697 0.3681 0.5621 234 G 0.0945 0.1654 0.7401 235 P 0.1163 0.2672 0.6165 236 H 0.1671 0.2318 0.6011 237 R 0.1751 0.2385 0.5864 238 Y 0.1902 0.2779 0.5320 239 A 0.1942 0.2680 0.5378 240 R 0.1838 0.3194 0.4969 241 A 0.2017 0.2872 0.5111 242 R 0.2494 0.2697 0.4810 243 H 0.2634 0.2440 0.4926 244 Y 0.2208 0.2648 0.5143 245 Y 0.1680 0.2900 0.5420 246 E 0.1289 0.3129 0.5582 247 A 0.1501 0.2860 0.5638 248 G 0.1455 0.3277 0.5268 249 Q 0.1578 0.4834 0.3588 250 R 0.1394 0.6173 0.2433 251 A 0.0925 0.7435 0.1640 252 A 0.0581 0.7989 0.1431 253 A 0.0384 0.8090 0.1525 254 Q 0.0547 0.6909 0.2543 255 R 0.0837 0.2755 0.6408 256 G 0.0689 0.0906 0.8405 257 L 0.2009 0.0287 0.7704 258 P 0.2445 0.0660 0.6895 259 F 0.3049 0.1148 0.5803 260 G 0.3819 0.0498 0.5682 261 W 0.5956 0.0127 0.3917 262 Q 0.7160 0.0112 0.2728 263 L 0.7943 0.0051 0.2006 264 Q 0.7692 0.0095 0.2214 265 V 0.7365 0.0081 0.2553 266 V 0.5268 0.0167 0.4565 267 P 0.2226 0.0754 0.7020 268 G 0.1128 0.0800 0.8072 269 I 0.1884 0.1068 0.7048 270 G 0.1912 0.1048 0.7040 271 H 0.2178 0.1312 0.6510 272 D 0.2212 0.1681 0.6107 273 G 0.2342 0.2039 0.5619 274 Q 0.2152 0.2704 0.5144 275 A 0.1868 0.3289 0.4843 276 M 0.1131 0.4955 0.3914 277 S 0.0652 0.6438 0.2911 278 Q 0.0494 0.7212 0.2294 279 V 0.0574 0.7486 0.1940 280 C 0.0558 0.7781 0.1661 281 A 0.0393 0.8101 0.1507 282 S 0.0584 0.7708 0.1709 283 L 0.0891 0.7303 0.1806 284 W 0.1425 0.6311 0.2264 285 F 0.1542 0.5310 0.3148 286 D 0.1255 0.4869 0.3876 287 G 0.0934 0.4669 0.4397 288 R 0.1333 0.3185 0.5482 289 M 0.1617 0.1768 0.6615 290 P 0.0411 0.5407 0.4183 291 D 0.0415 0.4922 0.4664 292 A 0.0699 0.5801 0.3500 293 A 0.0786 0.6264 0.2951 294 E 0.0830 0.6535 0.2635 295 L 0.0796 0.6627 0.2578 296 A 0.0702 0.6612 0.2687 297 R 0.0825 0.6217 0.2957 298 L 0.0877 0.5399 0.3724 299 A 0.1204 0.3479 0.5317 300 G 0.1182 0.2602 0.6216 301 S 0.1460 0.2695 0.5845 302 Q 0.1617 0.2754 0.5628 303 S 0.1931 0.2140 0.5929 304 A 0.1942 0.2026 0.6032