# This file is the result of combining several RDB files, specifically # T0506.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0506.t2k.stride-ebghtl.rdb (weight 1.24869) # T0506.t2k.str2.rdb (weight 1.54758) # T0506.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 T0506.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0506 # 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 T0506.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 157 # # ============================================ # Comments from T0506.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0506 # 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 T0506.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 157 # # ============================================ # Comments from T0506.t2k.str2.rdb # ============================================ # TARGET T0506 # 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 T0506.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 157 # # ============================================ # Comments from T0506.t2k.alpha.rdb # ============================================ # TARGET T0506 # 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 T0506.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 157 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1182 0.0856 0.7962 2 L 0.1976 0.0892 0.7133 3 D 0.1417 0.1073 0.7510 4 V 0.1047 0.0979 0.7974 5 A 0.0859 0.1727 0.7414 6 P 0.0861 0.1529 0.7610 7 P 0.1204 0.1408 0.7389 8 V 0.1171 0.0797 0.8032 9 I 0.1212 0.1046 0.7742 10 T 0.1356 0.1098 0.7546 11 P 0.1064 0.1477 0.7459 12 R 0.0758 0.1765 0.7477 13 G 0.0855 0.1978 0.7168 14 T 0.1244 0.1921 0.6835 15 K 0.1247 0.1707 0.7046 16 I 0.1084 0.1788 0.7128 17 E 0.1109 0.1483 0.7408 18 P 0.0818 0.1914 0.7268 19 S 0.0851 0.2044 0.7105 20 A 0.0809 0.1383 0.7808 21 G 0.0717 0.1095 0.8188 22 A 0.0640 0.0874 0.8487 23 P 0.0618 0.0840 0.8542 24 F 0.0209 0.4995 0.4796 25 E 0.0232 0.6182 0.3585 26 A 0.0069 0.8592 0.1338 27 V 0.0050 0.9272 0.0678 28 R 0.0049 0.9443 0.0508 29 V 0.0047 0.9561 0.0392 30 A 0.0047 0.9584 0.0369 31 R 0.0047 0.9594 0.0359 32 D 0.0047 0.9570 0.0383 33 V 0.0048 0.9514 0.0438 34 L 0.0050 0.9369 0.0582 35 H 0.0053 0.8665 0.1282 36 T 0.0091 0.7634 0.2274 37 S 0.0256 0.6231 0.3513 38 R 0.0406 0.4255 0.5339 39 T 0.1180 0.5093 0.3727 40 A 0.2278 0.4957 0.2766 41 A 0.3725 0.4035 0.2240 42 L 0.4537 0.3317 0.2146 43 A 0.4264 0.2751 0.2985 44 T 0.4092 0.1797 0.4111 45 L 0.3471 0.0729 0.5800 46 D 0.2800 0.0363 0.6838 47 P 0.1180 0.1744 0.7076 48 V 0.0583 0.2087 0.7330 49 S 0.0488 0.1261 0.8252 50 G 0.0591 0.0623 0.8786 51 Y 0.1626 0.0257 0.8117 52 P 0.3024 0.0406 0.6570 53 Y 0.3900 0.0527 0.5573 54 T 0.5008 0.0324 0.4669 55 T 0.6360 0.0185 0.3455 56 A 0.7696 0.0219 0.2085 57 T 0.7893 0.0141 0.1966 58 N 0.7573 0.0178 0.2249 59 I 0.6971 0.0289 0.2740 60 G 0.6239 0.0257 0.3504 61 I 0.6064 0.0213 0.3723 62 E 0.1366 0.0194 0.8440 63 P 0.0161 0.1193 0.8647 64 D 0.0477 0.0218 0.9306 65 G 0.0491 0.0269 0.9240 66 T 0.1723 0.0106 0.8171 67 P 0.6934 0.0074 0.2992 68 F 0.8528 0.0128 0.1344 69 F 0.8876 0.0151 0.0973 70 F 0.8560 0.0214 0.1225 71 A 0.6432 0.0672 0.2896 72 A 0.2878 0.1053 0.6069 73 G 0.0598 0.4988 0.4415 74 L 0.0284 0.6187 0.3530 75 T 0.0235 0.7538 0.2227 76 L 0.0158 0.8150 0.1692 77 H 0.0258 0.7848 0.1894 78 A 0.0216 0.8683 0.1101 79 R 0.0198 0.8802 0.1000 80 N 0.0198 0.8452 0.1349 81 M 0.0176 0.8008 0.1816 82 E 0.0273 0.5843 0.3884 83 T 0.0398 0.3927 0.5675 84 D 0.0742 0.0565 0.8693 85 A 0.0333 0.1158 0.8509 86 R 0.1804 0.1103 0.7094 87 I 0.6278 0.0270 0.3451 88 S 0.8316 0.0161 0.1524 89 V 0.9111 0.0063 0.0825 90 T 0.9039 0.0047 0.0913 91 L 0.8340 0.0093 0.1566 92 A 0.6313 0.0128 0.3559 93 P 0.3454 0.0173 0.6373 94 F 0.1274 0.0615 0.8111 95 G 0.0738 0.0720 0.8542 96 K 0.0543 0.0894 0.8564 97 G 0.0507 0.0754 0.8739 98 D 0.0921 0.0581 0.8498 99 A 0.0510 0.2804 0.6686 100 L 0.0442 0.3150 0.6408 101 T 0.0869 0.2559 0.6573 102 L 0.1782 0.0592 0.7626 103 P 0.2975 0.0453 0.6572 104 R 0.7244 0.0206 0.2550 105 L 0.8795 0.0066 0.1138 106 T 0.8981 0.0062 0.0958 107 L 0.9151 0.0051 0.0798 108 V 0.8666 0.0148 0.1185 109 G 0.8441 0.0087 0.1472 110 R 0.8686 0.0083 0.1231 111 A 0.8320 0.0107 0.1573 112 D 0.7936 0.0100 0.1964 113 R 0.6821 0.0098 0.3081 114 I 0.1866 0.0148 0.7986 115 G 0.0759 0.0209 0.9032 116 P 0.0161 0.4281 0.5558 117 D 0.0105 0.5010 0.4885 118 E 0.0164 0.5704 0.4132 119 V 0.0169 0.7018 0.2813 120 P 0.0078 0.8713 0.1209 121 L 0.0064 0.9260 0.0676 122 A 0.0064 0.9380 0.0557 123 I 0.0054 0.9506 0.0440 124 A 0.0048 0.9539 0.0413 125 R 0.0048 0.9543 0.0409 126 Y 0.0049 0.9490 0.0461 127 I 0.0050 0.9377 0.0573 128 A 0.0058 0.8861 0.1081 129 R 0.0136 0.7593 0.2271 130 Y 0.0588 0.2135 0.7277 131 P 0.0207 0.3697 0.6096 132 K 0.0209 0.4098 0.5693 133 A 0.0436 0.5545 0.4019 134 K 0.0443 0.5752 0.3805 135 L 0.0763 0.5164 0.4073 136 Y 0.1178 0.4376 0.4446 137 L 0.1582 0.2030 0.6388 138 S 0.1555 0.1364 0.7081 139 L 0.1013 0.1610 0.7377 140 P 0.0682 0.1189 0.8129 141 D 0.1347 0.0942 0.7710 142 T 0.5522 0.0271 0.4207 143 R 0.7627 0.0310 0.2064 144 L 0.9038 0.0043 0.0918 145 Y 0.8999 0.0059 0.0942 146 R 0.9185 0.0035 0.0780 147 L 0.8948 0.0039 0.1012 148 R 0.8422 0.0049 0.1528 149 T 0.7901 0.0106 0.1993 150 E 0.7304 0.0363 0.2333 151 G 0.8624 0.0101 0.1275 152 V 0.8775 0.0080 0.1145 153 Q 0.9046 0.0065 0.0889 154 I 0.8911 0.0090 0.0999 155 N 0.7263 0.0278 0.2459 156 G 0.4117 0.0518 0.5365 157 G 0.1690 0.0823 0.7486 158 P 0.2000 0.0898 0.7102 159 A 0.2461 0.0849 0.6690 160 R 0.3906 0.0759 0.5335 161 N 0.5523 0.0674 0.3803 162 A 0.6365 0.0604 0.3031 163 S 0.7456 0.0383 0.2161 164 N 0.5465 0.0260 0.4274 165 I 0.2383 0.0280 0.7337 166 T 0.0164 0.7977 0.1858 167 P 0.0102 0.8280 0.1618 168 A 0.0103 0.8648 0.1249 169 D 0.0170 0.8189 0.1641 170 L 0.0265 0.7015 0.2720 171 R 0.0320 0.5262 0.4417 172 T 0.0560 0.2795 0.6645 173 D 0.0651 0.1264 0.8085 174 L 0.0424 0.3624 0.5952 175 S 0.0355 0.3868 0.5777 176 G 0.0423 0.3984 0.5594 177 A 0.0293 0.6020 0.3686 178 E 0.0233 0.6072 0.3695 179 E 0.0169 0.7661 0.2171 180 L 0.0104 0.8277 0.1619 181 M 0.0095 0.8443 0.1462 182 A 0.0081 0.8480 0.1439 183 A 0.0099 0.8267 0.1634 184 A 0.0063 0.8844 0.1093 185 E 0.0060 0.9119 0.0821 186 S 0.0052 0.9259 0.0689 187 E 0.0048 0.9354 0.0598 188 A 0.0049 0.9329 0.0622 189 T 0.0051 0.9064 0.0885 190 R 0.0061 0.7965 0.1974 191 L 0.0155 0.6635 0.3210 192 N 0.0192 0.4432 0.5376 193 A 0.0130 0.6195 0.3675 194 I 0.0331 0.5270 0.4400 195 K 0.0263 0.6630 0.3107 196 G 0.0070 0.9030 0.0901 197 E 0.0054 0.9415 0.0531 198 A 0.0048 0.9527 0.0425 199 S 0.0047 0.9560 0.0393 200 R 0.0047 0.9569 0.0384 201 L 0.0047 0.9563 0.0389 202 A 0.0048 0.9514 0.0438 203 V 0.0050 0.9343 0.0607 204 L 0.0062 0.8742 0.1195 205 A 0.0108 0.7409 0.2483 206 G 0.0370 0.4843 0.4787 207 A 0.0504 0.2406 0.7090 208 K 0.0612 0.1083 0.8306 209 T 0.0852 0.1199 0.7949 210 G 0.0882 0.1163 0.7955 211 R 0.3058 0.0916 0.6026 212 W 0.6865 0.0289 0.2846 213 K 0.8272 0.0152 0.1575 214 I 0.8728 0.0085 0.1187 215 T 0.8277 0.0224 0.1499 216 S 0.7909 0.0121 0.1970 217 I 0.7407 0.0209 0.2385 218 D 0.2815 0.0212 0.6973 219 P 0.0471 0.1844 0.7685 220 D 0.0570 0.0777 0.8653 221 G 0.1628 0.1085 0.7287 222 I 0.4128 0.0314 0.5558 223 D 0.7781 0.0194 0.2026 224 L 0.8521 0.0207 0.1272 225 A 0.8156 0.0281 0.1563 226 S 0.5964 0.0493 0.3544 227 A 0.1967 0.0555 0.7478 228 S 0.1301 0.0518 0.8181 229 D 0.2413 0.0882 0.6705 230 L 0.5097 0.0612 0.4291 231 A 0.6479 0.0453 0.3068 232 R 0.7357 0.0335 0.2308 233 L 0.7109 0.0283 0.2608 234 W 0.6450 0.0345 0.3205 235 F 0.5212 0.0339 0.4449 236 A 0.3925 0.0479 0.5595 237 E 0.2336 0.0508 0.7157 238 R 0.1540 0.0579 0.7881 239 V 0.1220 0.0609 0.8171 240 E 0.0710 0.0908 0.8382 241 T 0.0720 0.0555 0.8726 242 L 0.0126 0.7483 0.2390 243 K 0.0060 0.8782 0.1158 244 Q 0.0067 0.9125 0.0809 245 F 0.0054 0.9308 0.0638 246 E 0.0047 0.9519 0.0434 247 K 0.0047 0.9532 0.0421 248 A 0.0048 0.9548 0.0404 249 L 0.0048 0.9483 0.0470 250 A 0.0048 0.9391 0.0561 251 Q 0.0051 0.8959 0.0989 252 L 0.0068 0.7620 0.2311 253 L 0.0297 0.4954 0.4748 254 K 0.0162 0.1685 0.8153