# This file is the result of combining several RDB files, specifically # T0262.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0262.t2k.stride-ebghtl.rdb (weight 1.24869) # T0262.t2k.str2.rdb (weight 1.54758) # T0262.t2k.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 T0262.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0262 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0262.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 58 # # ============================================ # Comments from T0262.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0262 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0262.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 58 # # ============================================ # Comments from T0262.t2k.str2.rdb # ============================================ # TARGET T0262 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0262.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 58 # # ============================================ # Comments from T0262.t2k.alpha.rdb # ============================================ # TARGET T0262 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0262.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 58 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0703 0.0274 0.9024 2 P 0.0881 0.0333 0.8786 3 S 0.1247 0.0840 0.7912 4 S 0.0867 0.4287 0.4846 5 S 0.1120 0.5389 0.3491 6 Q 0.1869 0.6170 0.1961 7 Y 0.1893 0.6251 0.1855 8 R 0.2086 0.5848 0.2066 9 R 0.2203 0.5499 0.2298 10 Y 0.1891 0.4251 0.3858 11 Q 0.1505 0.2456 0.6039 12 D 0.0831 0.0488 0.8681 13 P 0.0316 0.1190 0.8494 14 H 0.0537 0.0632 0.8831 15 H 0.1012 0.0438 0.8550 16 P 0.0490 0.1117 0.8393 17 S 0.1099 0.0961 0.7941 18 I 0.1386 0.0553 0.8061 19 P 0.1707 0.0424 0.7868 20 T 0.2082 0.0468 0.7450 21 P 0.1660 0.0641 0.7699 22 T 0.1785 0.0618 0.7597 23 T 0.2484 0.0440 0.7077 24 L 0.1386 0.0257 0.8357 25 F 0.0801 0.0229 0.8970 26 S 0.0993 0.0210 0.8797 27 Q 0.1125 0.0220 0.8654 28 P 0.0890 0.0272 0.8838 29 S 0.1982 0.0510 0.7508 30 L 0.4600 0.0652 0.4747 31 E 0.4966 0.0519 0.4514 32 I 0.3599 0.0821 0.5580 33 L 0.1746 0.0704 0.7550 34 G 0.0952 0.0456 0.8592 35 G 0.0647 0.0556 0.8797 36 G 0.0627 0.2385 0.6989 37 V 0.0494 0.4693 0.4812 38 A 0.0239 0.6466 0.3295 39 E 0.0422 0.5870 0.3708 40 E 0.0498 0.5656 0.3846 41 L 0.0771 0.3691 0.5538 42 P 0.0436 0.5981 0.3583 43 E 0.0748 0.6554 0.2698 44 L 0.1286 0.6983 0.1731 45 A 0.2286 0.5767 0.1947 46 L 0.2931 0.4539 0.2530 47 C 0.3000 0.3150 0.3850 48 C 0.1690 0.2372 0.5938 49 D 0.0912 0.1155 0.7933 50 G 0.0855 0.1217 0.7928 51 T 0.1924 0.1098 0.6978 52 V 0.2332 0.1079 0.6589 53 V 0.1758 0.0988 0.7254 54 E 0.1244 0.1129 0.7627 55 G 0.1155 0.0952 0.7892 56 R 0.1340 0.0849 0.7811 57 S 0.1197 0.0948 0.7855 58 N 0.1172 0.0985 0.7844 59 C 0.0940 0.1136 0.7925 60 R 0.0880 0.0933 0.8187 61 C 0.1265 0.1147 0.7589 62 K 0.1559 0.1980 0.6461 63 A 0.1941 0.2412 0.5647 64 R 0.2853 0.2469 0.4678 65 A 0.4079 0.2032 0.3889 66 V 0.3762 0.1598 0.4640 67 L 0.2042 0.0651 0.7306 68 P 0.0785 0.0875 0.8340 69 G 0.0306 0.2047 0.7648 70 G 0.0466 0.2119 0.7414 71 M 0.1254 0.3072 0.5674 72 R 0.2586 0.3957 0.3457 73 V 0.2325 0.5700 0.1976 74 R 0.1790 0.6551 0.1658 75 L 0.0597 0.8161 0.1242 76 S 0.0321 0.8796 0.0883 77 K 0.0148 0.9295 0.0558 78 T 0.0070 0.9476 0.0454 79 L 0.0062 0.9504 0.0434 80 A 0.0051 0.9540 0.0409 81 G 0.0049 0.9474 0.0477 82 I 0.0050 0.9408 0.0542 83 L 0.0066 0.8937 0.0997 84 R 0.0100 0.7260 0.2640 85 H 0.0349 0.4919 0.4732 86 H 0.0386 0.2151 0.7463 87 P 0.0113 0.6802 0.3085 88 G 0.0113 0.7077 0.2810 89 R 0.0192 0.7592 0.2217 90 Y 0.0596 0.3392 0.6012 91 G 0.0745 0.0538 0.8717 92 V 0.2646 0.0170 0.7183 93 R 0.4790 0.0106 0.5104 94 L 0.5617 0.0140 0.4243 95 T 0.1169 0.0236 0.8595 96 R 0.0185 0.1287 0.8528 97 E 0.0564 0.0337 0.9099 98 G 0.1079 0.0490 0.8431 99 W 0.4221 0.0259 0.5521 100 A 0.6674 0.0157 0.3169 101 R 0.4706 0.0278 0.5015 102 V 0.0080 0.9208 0.0711 103 S 0.0048 0.9483 0.0469 104 E 0.0049 0.9539 0.0412 105 V 0.0048 0.9514 0.0438 106 V 0.0056 0.9303 0.0641 107 E 0.0070 0.8779 0.1152 108 G 0.0071 0.8549 0.1380 109 L 0.0192 0.7924 0.1884 110 R 0.0169 0.7002 0.2829 111 K 0.0181 0.6746 0.3073 112 A 0.0295 0.4309 0.5396 113 G 0.0359 0.1701 0.7940 114 W 0.0733 0.1398 0.7870 115 S 0.0664 0.2072 0.7265 116 W 0.1242 0.1583 0.7175 117 V 0.1951 0.0535 0.7514 118 E 0.1378 0.0468 0.8154 119 E 0.0060 0.9352 0.0588 120 W 0.0048 0.9487 0.0465 121 H 0.0050 0.9521 0.0429 122 I 0.0057 0.9535 0.0408 123 V 0.0082 0.9492 0.0426 124 G 0.0090 0.9419 0.0491 125 V 0.0091 0.9306 0.0603 126 A 0.0198 0.8857 0.0944 127 L 0.0248 0.7523 0.2229 128 H 0.0415 0.4065 0.5520 129 D 0.0642 0.0619 0.8739 130 P 0.0233 0.1632 0.8135 131 K 0.0586 0.1631 0.7783 132 G 0.0938 0.1628 0.7434 133 R 0.3984 0.0681 0.5335 134 Y 0.7993 0.0163 0.1844 135 E 0.8624 0.0089 0.1287 136 L 0.8040 0.0139 0.1822 137 R 0.5368 0.0354 0.4278 138 N 0.1415 0.0713 0.7872 139 G 0.1348 0.0750 0.7902 140 E 0.6179 0.0352 0.3470 141 I 0.7612 0.0297 0.2091 142 R 0.8013 0.0308 0.1679 143 A 0.7443 0.0569 0.1988 144 R 0.6073 0.0727 0.3199 145 Y 0.4980 0.0684 0.4336 146 G 0.3714 0.0573 0.5713 147 H 0.3810 0.0402 0.5788 148 S 0.3842 0.0499 0.5659 149 I 0.3971 0.0598 0.5431 150 P 0.3936 0.0571 0.5493 151 V 0.2774 0.0548 0.6678 152 N 0.3049 0.0489 0.6462 153 V 0.2209 0.0889 0.6903 154 E 0.2034 0.0834 0.7132 155 P 0.1752 0.0876 0.7372 156 L 0.1184 0.0628 0.8188 157 P 0.0692 0.1556 0.7752 158 G 0.0683 0.1331 0.7986 159 E 0.0962 0.0574 0.8464 160 P 0.0877 0.0309 0.8815 161 P 0.0910 0.0496 0.8594 162 P 0.1981 0.1007 0.7012 163 I 0.6978 0.0910 0.2112 164 L 0.8077 0.0640 0.1283 165 Y 0.7976 0.0514 0.1510 166 H 0.5878 0.0717 0.3405 167 G 0.2147 0.0700 0.7154 168 T 0.1156 0.0921 0.7923 169 T 0.0544 0.2872 0.6584 170 E 0.0183 0.7090 0.2727 171 E 0.0160 0.7344 0.2496 172 A 0.0167 0.7223 0.2610 173 L 0.0126 0.8446 0.1427 174 P 0.0056 0.9293 0.0651 175 L 0.0054 0.9435 0.0512 176 I 0.0051 0.9474 0.0475 177 M 0.0054 0.9412 0.0534 178 E 0.0060 0.9013 0.0927 179 R 0.0404 0.5450 0.4145 180 G 0.0377 0.1250 0.8373 181 I 0.0921 0.0759 0.8320 182 M 0.1237 0.0780 0.7983 183 R 0.1108 0.2611 0.6282 184 G 0.0901 0.2716 0.6383 185 R 0.1587 0.1925 0.6488 186 R 0.3010 0.0646 0.6344 187 L 0.4268 0.0474 0.5258 188 K 0.8026 0.0196 0.1778 189 V 0.8212 0.0172 0.1616 190 H 0.8213 0.0149 0.1638 191 L 0.7390 0.0214 0.2396 192 T 0.4669 0.0261 0.5070 193 S 0.2181 0.0644 0.7175 194 S 0.1431 0.0496 0.8073 195 L 0.0640 0.3087 0.6273 196 E 0.0489 0.3396 0.6115 197 D 0.0950 0.2958 0.6092 198 A 0.2584 0.1933 0.5484 199 V 0.5450 0.1281 0.3268 200 S 0.7106 0.0970 0.1924 201 T 0.6842 0.0898 0.2260 202 G 0.5828 0.0946 0.3226 203 R 0.5286 0.0811 0.3903 204 R 0.4761 0.0741 0.4498 205 H 0.3086 0.0675 0.6239 206 G 0.0966 0.0869 0.8165 207 N 0.0655 0.0469 0.8877 208 L 0.1444 0.0124 0.8433 209 V 0.3222 0.0066 0.6712 210 A 0.8858 0.0035 0.1107 211 V 0.9233 0.0034 0.0732 212 L 0.9265 0.0035 0.0700 213 L 0.9236 0.0034 0.0730 214 V 0.8095 0.0089 0.1816 215 D 0.4977 0.0056 0.4967 216 V 0.0186 0.7186 0.2628 217 E 0.0064 0.8728 0.1208 218 C 0.0061 0.9089 0.0850 219 L 0.0071 0.9192 0.0737 220 R 0.0105 0.9124 0.0771 221 R 0.0135 0.8142 0.1724 222 R 0.0468 0.2500 0.7032 223 G 0.0422 0.0246 0.9332 224 L 0.1138 0.0109 0.8753 225 K 0.5285 0.0102 0.4612 226 V 0.8442 0.0072 0.1485 227 E 0.8875 0.0068 0.1057 228 R 0.8787 0.0055 0.1158 229 M 0.6014 0.0195 0.3791 230 S 0.1087 0.0950 0.7963 231 K 0.0456 0.0440 0.9104 232 T 0.1496 0.0324 0.8180 233 V 0.8139 0.0050 0.1811 234 Y 0.9128 0.0033 0.0838 235 T 0.8774 0.0071 0.1154 236 V 0.5262 0.0154 0.4584 237 D 0.1503 0.0657 0.7840 238 W 0.0781 0.0385 0.8834 239 V 0.1339 0.0152 0.8509 240 P 0.0753 0.0198 0.9049 241 P 0.0080 0.8145 0.1776 242 E 0.0071 0.8614 0.1315 243 C 0.0101 0.8854 0.1044 244 I 0.0239 0.8813 0.0947 245 A 0.0305 0.8700 0.0994 246 E 0.0382 0.8531 0.1088 247 V 0.0545 0.8208 0.1247 248 R 0.0777 0.7521 0.1702 249 R 0.0988 0.5547 0.3465 250 E 0.0773 0.4113 0.5114 251 S 0.1059 0.1881 0.7060 252 L 0.0418 0.1375 0.8207 253 G 0.0377 0.0616 0.9007 254 R 0.1224 0.0321 0.8455 255 S 0.1523 0.0282 0.8195 256 L 0.0439 0.0449 0.9113