# This file is the result of combining several RDB files, specifically # T0200.t04.dssp-ebghstl.rdb (weight 1.53986) # T0200.t04.stride-ebghtl.rdb (weight 1.24869) # T0200.t04.str2.rdb (weight 1.54758) # T0200.t04.alpha.rdb (weight 0.659012) # 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 T0200.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0200 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0200.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 230 # # ============================================ # Comments from T0200.t04.stride-ebghtl.rdb # ============================================ # TARGET T0200 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0200.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 230 # # ============================================ # Comments from T0200.t04.str2.rdb # ============================================ # TARGET T0200 # Using neural net t04-2621-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 T0200.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 230 # # ============================================ # Comments from T0200.t04.alpha.rdb # ============================================ # TARGET T0200 # Using neural net t04-2621-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 T0200.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 230 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2767 0.0066 0.7167 2 R 0.8231 0.0055 0.1715 3 V 0.9018 0.0033 0.0949 4 L 0.8981 0.0063 0.0956 5 F 0.8886 0.0065 0.1049 6 I 0.6779 0.0305 0.2915 7 G 0.3467 0.0375 0.6158 8 D 0.3184 0.0667 0.6148 9 V 0.2762 0.1101 0.6137 10 F 0.1855 0.0976 0.7169 11 G 0.0943 0.0778 0.8279 12 Q 0.0682 0.1130 0.8188 13 P 0.0465 0.3323 0.6212 14 G 0.0367 0.4191 0.5441 15 R 0.0187 0.8273 0.1540 16 R 0.0098 0.9193 0.0709 17 V 0.0086 0.9346 0.0568 18 L 0.0083 0.9237 0.0680 19 Q 0.0082 0.9083 0.0835 20 N 0.0102 0.8079 0.1818 21 H 0.0136 0.7173 0.2691 22 L 0.0526 0.4128 0.5346 23 P 0.0158 0.6565 0.3277 24 T 0.0216 0.6473 0.3311 25 I 0.0467 0.6121 0.3412 26 R 0.0829 0.3184 0.5987 27 P 0.0337 0.3841 0.5821 28 Q 0.0579 0.2243 0.7178 29 F 0.1566 0.0345 0.8090 30 D 0.2414 0.0396 0.7189 31 F 0.8713 0.0053 0.1234 32 V 0.9270 0.0034 0.0696 33 I 0.9314 0.0032 0.0654 34 V 0.8963 0.0070 0.0967 35 N 0.6832 0.0066 0.3103 36 M 0.3170 0.0970 0.5859 37 E 0.1110 0.1297 0.7593 38 N 0.1164 0.1617 0.7219 39 S 0.0450 0.2779 0.6771 40 A 0.0790 0.2382 0.6828 41 G 0.0851 0.1662 0.7487 42 G 0.0787 0.0981 0.8232 43 F 0.0881 0.0831 0.8288 44 G 0.0749 0.0947 0.8304 45 M 0.0883 0.0652 0.8465 46 H 0.0538 0.0800 0.8663 47 R 0.0087 0.9021 0.0892 48 D 0.0048 0.9499 0.0453 49 A 0.0048 0.9537 0.0415 50 A 0.0047 0.9577 0.0376 51 R 0.0047 0.9581 0.0372 52 G 0.0047 0.9584 0.0369 53 A 0.0047 0.9571 0.0382 54 L 0.0049 0.9476 0.0475 55 E 0.0057 0.9033 0.0911 56 A 0.0430 0.4695 0.4874 57 G 0.0525 0.0205 0.9270 58 A 0.0974 0.0123 0.8903 59 G 0.2769 0.0550 0.6681 60 C 0.8622 0.0160 0.1218 61 L 0.9054 0.0075 0.0870 62 T 0.8918 0.0098 0.0984 63 L 0.6423 0.0393 0.3185 64 G 0.2517 0.0534 0.6949 65 N 0.1539 0.1555 0.6906 66 H 0.1687 0.2999 0.5314 67 A 0.2016 0.3676 0.4309 68 W 0.1647 0.2647 0.5705 69 H 0.1380 0.1622 0.6998 70 H 0.0658 0.1920 0.7421 71 K 0.0344 0.3427 0.6229 72 D 0.0614 0.3518 0.5867 73 I 0.0647 0.5706 0.3647 74 Y 0.0419 0.6824 0.2757 75 P 0.0208 0.7650 0.2141 76 M 0.0238 0.7784 0.1978 77 L 0.0462 0.7008 0.2530 78 S 0.0321 0.5560 0.4119 79 E 0.0241 0.4908 0.4850 80 D 0.0563 0.2936 0.6500 81 T 0.0437 0.1869 0.7694 82 Y 0.0874 0.0467 0.8659 83 P 0.1208 0.1136 0.7655 84 I 0.4646 0.0862 0.4492 85 V 0.4850 0.0438 0.4712 86 R 0.2979 0.0481 0.6540 87 P 0.2182 0.2129 0.5690 88 L 0.1686 0.2507 0.5807 89 N 0.1703 0.1786 0.6511 90 Y 0.1769 0.0892 0.7339 91 A 0.1566 0.0527 0.7907 92 D 0.0892 0.0295 0.8813 93 P 0.0273 0.1031 0.8696 94 G 0.0403 0.0694 0.8903 95 T 0.0793 0.0404 0.8803 96 P 0.0694 0.0653 0.8652 97 G 0.0795 0.0503 0.8702 98 V 0.1280 0.0342 0.8378 99 G 0.2190 0.0178 0.7631 100 W 0.5869 0.0095 0.4036 101 R 0.8507 0.0054 0.1440 102 T 0.9209 0.0033 0.0758 103 F 0.9121 0.0046 0.0832 104 D 0.8850 0.0041 0.1109 105 V 0.6477 0.0270 0.3253 106 N 0.0467 0.0195 0.9338 107 G 0.0477 0.0317 0.9207 108 E 0.7558 0.0073 0.2369 109 K 0.9204 0.0029 0.0767 110 L 0.9166 0.0058 0.0776 111 T 0.9318 0.0034 0.0649 112 V 0.9319 0.0031 0.0650 113 V 0.9165 0.0052 0.0784 114 N 0.7884 0.0044 0.2072 115 L 0.4017 0.0183 0.5800 116 L 0.0750 0.0500 0.8750 117 G 0.0459 0.0387 0.9154 118 R 0.3685 0.0264 0.6051 119 V 0.6869 0.0250 0.2881 120 F 0.6528 0.0468 0.3004 121 M 0.4190 0.0895 0.4915 122 E 0.2128 0.1115 0.6757 123 A 0.0750 0.3867 0.5383 124 V 0.0675 0.3795 0.5530 125 D 0.0500 0.3763 0.5737 126 N 0.0657 0.2580 0.6763 127 P 0.0186 0.7127 0.2687 128 F 0.0117 0.8495 0.1388 129 R 0.0139 0.8838 0.1023 130 T 0.0103 0.9054 0.0843 131 M 0.0062 0.9461 0.0477 132 D 0.0052 0.9560 0.0388 133 A 0.0048 0.9586 0.0367 134 L 0.0048 0.9568 0.0385 135 L 0.0051 0.9452 0.0496 136 E 0.0061 0.8947 0.0992 137 R 0.0146 0.7685 0.2169 138 D 0.0462 0.3843 0.5694 139 D 0.0517 0.0593 0.8890 140 L 0.0950 0.0110 0.8940 141 G 0.1399 0.0384 0.8217 142 T 0.8785 0.0046 0.1169 143 V 0.9329 0.0033 0.0639 144 F 0.9339 0.0032 0.0630 145 V 0.9199 0.0040 0.0762 146 D 0.8545 0.0047 0.1408 147 F 0.5275 0.0300 0.4425 148 H 0.1935 0.0632 0.7433 149 A 0.1086 0.1048 0.7866 150 E 0.0690 0.0878 0.8432 151 A 0.0897 0.0414 0.8689 152 T 0.0590 0.0848 0.8561 153 S 0.0063 0.8704 0.1233 154 E 0.0051 0.9327 0.0622 155 K 0.0051 0.9467 0.0482 156 E 0.0055 0.9507 0.0438 157 A 0.0076 0.9379 0.0545 158 M 0.0073 0.9123 0.0805 159 G 0.0097 0.8802 0.1101 160 W 0.0118 0.8454 0.1428 161 H 0.0166 0.7777 0.2057 162 L 0.0736 0.4243 0.5021 163 A 0.0505 0.3436 0.6059 164 G 0.0512 0.2440 0.7049 165 R 0.1571 0.1074 0.7355 166 V 0.4961 0.0157 0.4882 167 A 0.6379 0.0264 0.3357 168 A 0.9285 0.0034 0.0681 169 V 0.9326 0.0031 0.0643 170 I 0.9170 0.0059 0.0771 171 G 0.7885 0.0078 0.2038 172 T 0.2426 0.0228 0.7346 173 H 0.1571 0.0419 0.8010 174 T 0.1101 0.0981 0.7918 175 H 0.1448 0.0835 0.7718 176 V 0.1407 0.0361 0.8232 177 P 0.1918 0.0345 0.7738 178 T 0.1576 0.0390 0.8033 179 A 0.1228 0.1303 0.7469 180 D 0.1459 0.1012 0.7530 181 T 0.4370 0.0831 0.4799 182 R 0.7918 0.0288 0.1795 183 I 0.8540 0.0216 0.1244 184 L 0.5366 0.0335 0.4299 185 K 0.1302 0.0445 0.8254 186 G 0.0407 0.0226 0.9366 187 G 0.1079 0.0316 0.8605 188 T 0.5019 0.0086 0.4894 189 A 0.8619 0.0038 0.1344 190 Y 0.8636 0.0090 0.1274 191 Q 0.8506 0.0091 0.1403 192 T 0.6802 0.0234 0.2964 193 D 0.4611 0.0373 0.5016 194 A 0.2372 0.0833 0.6795 195 G 0.1854 0.0816 0.7330 196 F 0.2247 0.0584 0.7169 197 T 0.2762 0.0489 0.6749 198 G 0.1923 0.0286 0.7791 199 P 0.1834 0.0686 0.7480 200 H 0.1964 0.1587 0.6449 201 D 0.2282 0.1989 0.5729 202 S 0.2838 0.2422 0.4739 203 I 0.4255 0.2416 0.3329 204 I 0.3375 0.2433 0.4192 205 G 0.2006 0.1850 0.6144 206 S 0.2040 0.2021 0.5939 207 A 0.2305 0.2312 0.5384 208 I 0.2053 0.2849 0.5098 209 E 0.1622 0.2941 0.5437 210 G 0.2153 0.2798 0.5048 211 P 0.2762 0.3867 0.3371 212 L 0.3567 0.4242 0.2192 213 Q 0.3937 0.3875 0.2189 214 R 0.4509 0.3436 0.2055 215 F 0.5145 0.2747 0.2108 216 L 0.5564 0.1842 0.2594 217 T 0.4718 0.1394 0.3889 218 E 0.3034 0.0961 0.6005 219 R 0.2043 0.0300 0.7657 220 P 0.1368 0.0720 0.7912 221 H 0.2458 0.0815 0.6727 222 R 0.5730 0.0558 0.3712 223 Y 0.6794 0.0235 0.2971 224 G 0.7786 0.0154 0.2060 225 V 0.7549 0.0221 0.2230 226 A 0.5928 0.0393 0.3679 227 E 0.3960 0.0829 0.5211 228 G 0.3170 0.0542 0.6288 229 R 0.4235 0.0507 0.5258 230 A 0.6309 0.0297 0.3394 231 E 0.7430 0.0213 0.2356 232 L 0.7692 0.0191 0.2117 233 N 0.6513 0.0327 0.3160 234 G 0.6709 0.0259 0.3032 235 V 0.8079 0.0141 0.1781 236 A 0.8743 0.0100 0.1157 237 L 0.8701 0.0120 0.1179 238 H 0.8117 0.0122 0.1761 239 F 0.6225 0.0394 0.3381 240 E 0.2074 0.0612 0.7314 241 G 0.0511 0.0456 0.9033 242 G 0.0879 0.0493 0.8629 243 K 0.4418 0.0757 0.4825 244 A 0.6538 0.0791 0.2671 245 T 0.6890 0.0866 0.2244 246 A 0.6925 0.0980 0.2095 247 A 0.6537 0.1138 0.2324 248 E 0.6197 0.1279 0.2524 249 R 0.6160 0.1432 0.2408 250 Y 0.6009 0.1187 0.2804 251 R 0.5566 0.1227 0.3207 252 F 0.4834 0.1053 0.4113 253 I 0.3119 0.1092 0.5789 254 E 0.1910 0.0754 0.7336 255 D 0.0812 0.0411 0.8777