# This file is the result of combining several RDB files, specifically # T0444.t04.str2.rdb (weight 1.54425) # T0444.t04.str4.rdb (weight 0.924988) # T0444.t04.pb.rdb (weight 0.789901) # T0444.t04.bys.rdb (weight 0.748322) # T0444.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 T0444.t04.str2.rdb # ============================================ # TARGET T0444 # 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 T0444.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 707 # # ============================================ # Comments from T0444.t04.str4.rdb # ============================================ # TARGET T0444 # 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 T0444.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 707 # # ============================================ # Comments from T0444.t04.pb.rdb # ============================================ # TARGET T0444 # 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 T0444.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 707 # # ============================================ # Comments from T0444.t04.bys.rdb # ============================================ # TARGET T0444 # 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 T0444.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 707 # # ============================================ # Comments from T0444.t04.alpha.rdb # ============================================ # TARGET T0444 # 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 T0444.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 707 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3088 0.2129 0.4783 2 H 0.3254 0.1738 0.5008 3 H 0.3113 0.1825 0.5063 4 H 0.2774 0.1849 0.5377 5 H 0.2565 0.1605 0.5829 6 H 0.2348 0.1549 0.6103 7 H 0.2203 0.1746 0.6050 8 S 0.1983 0.2103 0.5914 9 S 0.1865 0.2072 0.6063 10 G 0.2382 0.1700 0.5918 11 V 0.3701 0.1547 0.4751 12 D 0.3146 0.1301 0.5552 13 L 0.1697 0.2463 0.5840 14 G 0.1411 0.1994 0.6595 15 T 0.2121 0.2243 0.5636 16 E 0.2167 0.2916 0.4916 17 N 0.2190 0.2850 0.4960 18 L 0.2781 0.2944 0.4275 19 Y 0.4013 0.2808 0.3179 20 F 0.3748 0.3095 0.3157 21 Q 0.3439 0.2902 0.3659 22 S 0.2799 0.2436 0.4765 23 M 0.1449 0.3474 0.5077 24 S 0.1378 0.3191 0.5431 25 D 0.1309 0.3029 0.5662 26 T 0.1615 0.2257 0.6128 27 N 0.1537 0.2183 0.6281 28 E 0.1408 0.3383 0.5208 29 S 0.1648 0.3496 0.4856 30 E 0.1875 0.3627 0.4497 31 I 0.2582 0.3067 0.4351 32 K 0.2163 0.2949 0.4887 33 S 0.1624 0.2908 0.5468 34 N 0.1377 0.2026 0.6597 35 E 0.1555 0.2073 0.6372 36 E 0.2660 0.1391 0.5949 37 P 0.2395 0.2812 0.4793 38 L 0.2328 0.3844 0.3828 39 L 0.2819 0.3037 0.4143 40 R 0.2286 0.2580 0.5135 41 K 0.1846 0.2410 0.5744 42 S 0.2013 0.1611 0.6376 43 S 0.1988 0.2132 0.5880 44 R 0.2527 0.2346 0.5127 45 R 0.3902 0.1638 0.4460 46 F 0.5659 0.0830 0.3511 47 V 0.6600 0.0465 0.2935 48 I 0.6284 0.0397 0.3319 49 F 0.5145 0.0280 0.4574 50 P 0.3666 0.0552 0.5782 51 I 0.3112 0.1025 0.5863 52 Q 0.2111 0.1031 0.6859 53 Y 0.1935 0.0895 0.7170 54 P 0.0287 0.6647 0.3066 55 D 0.0232 0.7849 0.1919 56 I 0.0110 0.8835 0.1054 57 W 0.0088 0.9127 0.0785 58 K 0.0086 0.9212 0.0703 59 M 0.0085 0.9215 0.0699 60 Y 0.0085 0.9208 0.0707 61 K 0.0086 0.9197 0.0717 62 Q 0.0088 0.9153 0.0759 63 A 0.0112 0.8997 0.0891 64 Q 0.0147 0.8472 0.1381 65 A 0.0249 0.7270 0.2481 66 S 0.0640 0.4390 0.4971 67 F 0.1732 0.2214 0.6054 68 W 0.2511 0.1260 0.6229 69 T 0.2117 0.0431 0.7452 70 A 0.0783 0.4572 0.4645 71 E 0.0704 0.4655 0.4641 72 E 0.1987 0.2802 0.5211 73 V 0.3643 0.0800 0.5557 74 D 0.2522 0.0602 0.6876 75 L 0.1146 0.4202 0.4652 76 S 0.0898 0.4281 0.4822 77 K 0.0800 0.4005 0.5195 78 D 0.1266 0.2353 0.6381 79 L 0.1316 0.3519 0.5165 80 P 0.0802 0.4926 0.4273 81 H 0.0713 0.5945 0.3342 82 W 0.0501 0.6236 0.3262 83 N 0.0493 0.5380 0.4128 84 K 0.0935 0.3125 0.5940 85 L 0.1831 0.1398 0.6771 86 K 0.1447 0.0743 0.7810 87 A 0.0174 0.6583 0.3243 88 D 0.0184 0.7351 0.2466 89 E 0.0161 0.8574 0.1265 90 K 0.0136 0.8969 0.0895 91 Y 0.0122 0.9065 0.0813 92 F 0.0114 0.9138 0.0748 93 I 0.0089 0.9137 0.0775 94 S 0.0084 0.9208 0.0709 95 H 0.0087 0.9184 0.0729 96 I 0.0090 0.9160 0.0750 97 L 0.0093 0.9138 0.0769 98 A 0.0099 0.9099 0.0803 99 F 0.0165 0.8853 0.0983 100 F 0.0296 0.8450 0.1254 101 A 0.0468 0.7698 0.1834 102 A 0.0617 0.6594 0.2789 103 S 0.0781 0.5209 0.4010 104 D 0.0829 0.4139 0.5033 105 G 0.1032 0.4175 0.4792 106 I 0.1455 0.4947 0.3598 107 V 0.1762 0.4908 0.3330 108 N 0.1407 0.5196 0.3397 109 E 0.0585 0.6735 0.2679 110 N 0.0572 0.6809 0.2618 111 L 0.0441 0.7427 0.2131 112 V 0.0296 0.8202 0.1502 113 E 0.0200 0.8612 0.1187 114 R 0.0292 0.8197 0.1511 115 F 0.0467 0.7323 0.2209 116 S 0.0561 0.6737 0.2702 117 Q 0.0457 0.6460 0.3083 118 E 0.1018 0.4143 0.4839 119 V 0.1995 0.2107 0.5898 120 Q 0.1830 0.1319 0.6851 121 V 0.1804 0.1195 0.7002 122 P 0.0571 0.5506 0.3923 123 E 0.0374 0.7238 0.2388 124 A 0.0468 0.7975 0.1557 125 R 0.0491 0.8286 0.1223 126 C 0.0610 0.8334 0.1056 127 F 0.0450 0.8534 0.1016 128 Y 0.0353 0.8659 0.0988 129 G 0.0232 0.8804 0.0964 130 F 0.0152 0.9014 0.0834 131 Q 0.0117 0.9118 0.0765 132 I 0.0123 0.9082 0.0795 133 L 0.0112 0.9040 0.0848 134 I 0.0112 0.8985 0.0904 135 E 0.0126 0.8867 0.1007 136 N 0.0206 0.8337 0.1457 137 V 0.0326 0.7816 0.1858 138 H 0.0336 0.7827 0.1837 139 S 0.0108 0.8907 0.0985 140 E 0.0090 0.9061 0.0849 141 M 0.0094 0.9155 0.0751 142 Y 0.0086 0.9182 0.0732 143 S 0.0086 0.9203 0.0711 144 L 0.0089 0.9178 0.0733 145 L 0.0097 0.9116 0.0787 146 I 0.0127 0.8920 0.0953 147 D 0.0155 0.8656 0.1189 148 T 0.0336 0.7630 0.2034 149 Y 0.0911 0.5526 0.3563 150 I 0.1373 0.3874 0.4753 151 R 0.1638 0.1986 0.6375 152 D 0.1778 0.0432 0.7790 153 P 0.0137 0.6625 0.3238 154 K 0.0128 0.7721 0.2150 155 K 0.0184 0.8411 0.1405 156 R 0.0145 0.8722 0.1133 157 E 0.0131 0.8833 0.1037 158 F 0.0161 0.8863 0.0976 159 L 0.0210 0.8735 0.1055 160 F 0.0201 0.8659 0.1141 161 N 0.0267 0.8289 0.1444 162 A 0.0278 0.8019 0.1703 163 I 0.0437 0.7651 0.1912 164 E 0.0382 0.7150 0.2469 165 T 0.0566 0.5538 0.3896 166 M 0.1012 0.4363 0.4625 167 P 0.0165 0.7796 0.2039 168 Y 0.0172 0.8396 0.1432 169 V 0.0132 0.8865 0.1003 170 K 0.0107 0.9044 0.0850 171 K 0.0101 0.8984 0.0915 172 K 0.0133 0.8808 0.1060 173 A 0.0116 0.8862 0.1022 174 D 0.0094 0.8925 0.0981 175 W 0.0113 0.8836 0.1050 176 A 0.0154 0.8723 0.1124 177 L 0.0225 0.8610 0.1165 178 R 0.0347 0.8301 0.1352 179 W 0.0551 0.7422 0.2027 180 I 0.1079 0.5702 0.3219 181 A 0.0901 0.4801 0.4297 182 D 0.0758 0.3678 0.5564 183 R 0.0968 0.3128 0.5904 184 K 0.0761 0.4821 0.4418 185 S 0.0368 0.6797 0.2835 186 T 0.0287 0.7691 0.2022 187 F 0.0223 0.8341 0.1436 188 G 0.0129 0.8918 0.0953 189 E 0.0097 0.9136 0.0767 190 R 0.0119 0.9144 0.0737 191 V 0.0134 0.9151 0.0715 192 V 0.0160 0.9101 0.0739 193 A 0.0140 0.9101 0.0759 194 F 0.0225 0.8931 0.0844 195 A 0.0382 0.8539 0.1079 196 A 0.0461 0.8197 0.1342 197 V 0.0611 0.7560 0.1829 198 E 0.0574 0.6940 0.2485 199 G 0.0919 0.6297 0.2784 200 V 0.1245 0.6366 0.2389 201 F 0.1740 0.6236 0.2025 202 F 0.1804 0.6045 0.2151 203 S 0.0957 0.6643 0.2400 204 G 0.0497 0.7444 0.2059 205 S 0.0244 0.8297 0.1459 206 F 0.0139 0.8838 0.1022 207 A 0.0141 0.9035 0.0824 208 A 0.0115 0.9141 0.0744 209 I 0.0104 0.9163 0.0733 210 F 0.0097 0.9188 0.0715 211 W 0.0104 0.9118 0.0778 212 L 0.0111 0.8990 0.0899 213 K 0.0120 0.8643 0.1237 214 K 0.0163 0.7445 0.2392 215 R 0.0622 0.3168 0.6210 216 G 0.0500 0.1122 0.8377 217 L 0.1366 0.1203 0.7432 218 M 0.1778 0.0742 0.7480 219 P 0.1155 0.2733 0.6112 220 G 0.0835 0.2649 0.6516 221 L 0.1354 0.3862 0.4784 222 T 0.1500 0.5390 0.3110 223 F 0.1383 0.6360 0.2257 224 S 0.1164 0.6838 0.1998 225 N 0.1158 0.7055 0.1787 226 E 0.1176 0.7104 0.1720 227 L 0.1633 0.6388 0.1979 228 I 0.2318 0.4952 0.2729 229 S 0.1871 0.4068 0.4061 230 R 0.1403 0.3962 0.4635 231 D 0.1278 0.3339 0.5383 232 E 0.0602 0.5042 0.4355 233 G 0.0790 0.5303 0.3907 234 L 0.0935 0.5989 0.3076 235 H 0.0940 0.6502 0.2558 236 C 0.0353 0.8251 0.1395 237 D 0.0138 0.8976 0.0885 238 F 0.0119 0.9110 0.0770 239 A 0.0095 0.9209 0.0696 240 C 0.0090 0.9233 0.0678 241 L 0.0089 0.9234 0.0677 242 M 0.0085 0.9230 0.0685 243 F 0.0089 0.9183 0.0728 244 Q 0.0093 0.9114 0.0792 245 Y 0.0155 0.8785 0.1061 246 L 0.0284 0.7965 0.1751 247 V 0.0416 0.6328 0.3256 248 N 0.0627 0.2995 0.6378 249 K 0.1654 0.0834 0.7512 250 P 0.1480 0.0650 0.7870 251 S 0.1415 0.0987 0.7597 252 E 0.0126 0.7183 0.2691 253 E 0.0096 0.8576 0.1328 254 R 0.0091 0.9106 0.0803 255 V 0.0084 0.9200 0.0716 256 R 0.0083 0.9234 0.0683 257 E 0.0083 0.9242 0.0675 258 I 0.0083 0.9245 0.0673 259 I 0.0083 0.9222 0.0695 260 V 0.0083 0.9228 0.0689 261 D 0.0084 0.9221 0.0696 262 A 0.0083 0.9218 0.0699 263 V 0.0083 0.9227 0.0690 264 K 0.0083 0.9247 0.0670 265 I 0.0084 0.9214 0.0702 266 E 0.0083 0.9223 0.0693 267 Q 0.0083 0.9211 0.0706 268 E 0.0084 0.9189 0.0727 269 F 0.0090 0.9087 0.0822 270 L 0.0094 0.8865 0.1041 271 T 0.0092 0.8892 0.1016 272 E 0.0122 0.8459 0.1419 273 A 0.0349 0.6472 0.3179 274 L 0.1105 0.3773 0.5122 275 P 0.0701 0.4134 0.5165 276 V 0.0936 0.2884 0.6180 277 G 0.1020 0.2122 0.6857 278 L 0.1959 0.2605 0.5436 279 I 0.2045 0.2441 0.5513 280 G 0.1945 0.1510 0.6544 281 M 0.2641 0.1262 0.6097 282 N 0.2141 0.0906 0.6953 283 C 0.0146 0.7329 0.2525 284 I 0.0093 0.8678 0.1229 285 L 0.0084 0.9191 0.0725 286 M 0.0084 0.9199 0.0717 287 K 0.0083 0.9223 0.0694 288 Q 0.0083 0.9227 0.0690 289 Y 0.0083 0.9232 0.0685 290 I 0.0088 0.9217 0.0695 291 E 0.0084 0.9225 0.0690 292 F 0.0097 0.9194 0.0709 293 V 0.0107 0.9096 0.0796 294 A 0.0096 0.9065 0.0839 295 D 0.0095 0.9080 0.0825 296 R 0.0084 0.9165 0.0751 297 L 0.0085 0.9171 0.0745 298 L 0.0088 0.9085 0.0827 299 V 0.0094 0.9036 0.0869 300 E 0.0155 0.7999 0.1846 301 L 0.0599 0.3542 0.5859 302 G 0.0498 0.1042 0.8460 303 F 0.1487 0.0933 0.7580 304 S 0.1771 0.1535 0.6694 305 K 0.2058 0.2641 0.5301 306 V 0.2274 0.2358 0.5369 307 F 0.2578 0.1621 0.5801 308 Q 0.2251 0.1630 0.6119 309 A 0.1417 0.2633 0.5950 310 E 0.1189 0.2218 0.6594 311 N 0.1751 0.1180 0.7068 312 P 0.0887 0.3890 0.5224 313 F 0.1056 0.5307 0.3637 314 D 0.0786 0.6583 0.2631 315 F 0.0442 0.8093 0.1465 316 M 0.0504 0.8064 0.1432 317 E 0.0462 0.7810 0.1727 318 N 0.0959 0.6175 0.2866 319 I 0.2137 0.4208 0.3655 320 S 0.2239 0.2598 0.5164 321 L 0.0937 0.4774 0.4290 322 E 0.0926 0.2579 0.6496 323 G 0.0938 0.1693 0.7368 324 K 0.2174 0.1481 0.6346 325 T 0.3226 0.1200 0.5574 326 N 0.2496 0.0896 0.6607