# This file is the result of combining several RDB files, specifically # T0149.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0149.t2k.stride-ebghtl.rdb (weight 1.24869) # T0149.t2k.str.rdb (weight 1.53983) # T0149.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 T0149.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0149 # 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 T0149.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 106 # # ============================================ # Comments from T0149.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0149 # 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 T0149.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 106 # # ============================================ # Comments from T0149.t2k.str.rdb # ============================================ # TARGET T0149 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0149.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 106 # # ============================================ # Comments from T0149.t2k.alpha.rdb # ============================================ # TARGET T0149 # 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 T0149.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 106 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0556 0.0333 0.9111 2 N 0.1188 0.0337 0.8475 3 P 0.2206 0.0379 0.7415 4 I 0.2395 0.0158 0.7447 5 A 0.4526 0.0106 0.5368 6 V 0.8881 0.0053 0.1066 7 T 0.9133 0.0050 0.0817 8 L 0.9229 0.0044 0.0726 9 L 0.8732 0.0105 0.1163 10 T 0.6836 0.0276 0.2888 11 G 0.3177 0.0231 0.6592 12 F 0.1820 0.0590 0.7590 13 L 0.0618 0.1087 0.8295 14 G 0.0465 0.0976 0.8559 15 A 0.0359 0.1406 0.8235 16 G 0.0303 0.1616 0.8080 17 K 0.0127 0.8047 0.1826 18 T 0.0055 0.9130 0.0815 19 T 0.0048 0.9537 0.0415 20 L 0.0053 0.9547 0.0400 21 L 0.0047 0.9567 0.0386 22 R 0.0050 0.9557 0.0392 23 H 0.0050 0.9529 0.0421 24 I 0.0058 0.9415 0.0527 25 L 0.0078 0.9121 0.0801 26 N 0.0139 0.7905 0.1956 27 E 0.0427 0.5139 0.4434 28 Q 0.0466 0.1684 0.7850 29 H 0.0283 0.1067 0.8650 30 G 0.0209 0.0684 0.9107 31 Y 0.1651 0.0245 0.8105 32 K 0.5947 0.0072 0.3981 33 I 0.8692 0.0039 0.1269 34 A 0.9150 0.0040 0.0810 35 V 0.9281 0.0036 0.0683 36 I 0.9202 0.0038 0.0760 37 E 0.8632 0.0122 0.1247 38 N 0.6803 0.0220 0.2977 39 E 0.4260 0.0456 0.5284 40 F 0.2425 0.0843 0.6732 41 G 0.1908 0.0795 0.7297 42 E 0.2828 0.1099 0.6073 43 V 0.3675 0.1034 0.5291 44 S 0.2365 0.1248 0.6388 45 V 0.1515 0.2452 0.6033 46 D 0.1033 0.3615 0.5352 47 D 0.0150 0.8269 0.1582 48 Q 0.0171 0.8680 0.1148 49 L 0.0326 0.8545 0.1130 50 I 0.0670 0.7740 0.1589 51 G 0.0819 0.6659 0.2522 52 D 0.0743 0.4822 0.4435 53 R 0.0607 0.2602 0.6792 54 A 0.0664 0.0652 0.8684 55 T 0.2618 0.0436 0.6947 56 Q 0.5467 0.0360 0.4173 57 I 0.7947 0.0233 0.1821 58 K 0.8208 0.0253 0.1539 59 T 0.8212 0.0236 0.1552 60 L 0.6449 0.0385 0.3166 61 T 0.3468 0.0759 0.5773 62 N 0.1324 0.0730 0.7947 63 G 0.1327 0.0615 0.8057 64 C 0.2834 0.0648 0.6518 65 I 0.3691 0.1457 0.4852 66 C 0.3248 0.1647 0.5105 67 C 0.1921 0.2082 0.5996 68 S 0.1088 0.1820 0.7091 69 R 0.0554 0.3449 0.5997 70 S 0.0232 0.5709 0.4060 71 N 0.0110 0.7559 0.2331 72 E 0.0112 0.8105 0.1783 73 L 0.0069 0.8925 0.1006 74 E 0.0050 0.9373 0.0577 75 D 0.0048 0.9443 0.0509 76 A 0.0045 0.9483 0.0472 77 L 0.0044 0.9526 0.0430 78 L 0.0045 0.9520 0.0435 79 D 0.0045 0.9445 0.0509 80 L 0.0048 0.9301 0.0651 81 L 0.0064 0.9037 0.0898 82 D 0.0073 0.8506 0.1421 83 N 0.0092 0.7885 0.2023 84 L 0.0154 0.7246 0.2601 85 D 0.0133 0.6981 0.2886 86 K 0.0221 0.5294 0.4485 87 G 0.0298 0.3978 0.5724 88 N 0.0405 0.2435 0.7159 89 I 0.0657 0.1304 0.8038 90 Q 0.0939 0.0537 0.8524 91 F 0.1576 0.0120 0.8303 92 D 0.2416 0.0434 0.7150 93 R 0.9142 0.0043 0.0814 94 L 0.9324 0.0036 0.0641 95 V 0.9300 0.0037 0.0663 96 I 0.9118 0.0056 0.0826 97 E 0.7238 0.0142 0.2620 98 C 0.3437 0.0312 0.6252 99 T 0.1596 0.0708 0.7696 100 G 0.1134 0.1118 0.7748 101 M 0.0876 0.1816 0.7307 102 A 0.0843 0.1691 0.7466 103 D 0.0859 0.1275 0.7865 104 P 0.0389 0.3731 0.5880 105 G 0.0301 0.6773 0.2926 106 P 0.0381 0.7746 0.1873 107 I 0.0221 0.8935 0.0844 108 I 0.0244 0.9042 0.0714 109 Q 0.0291 0.8888 0.0822 110 T 0.0323 0.8501 0.1176 111 F 0.0892 0.7312 0.1796 112 F 0.1211 0.6207 0.2582 113 S 0.1028 0.4677 0.4295 114 H 0.0898 0.3176 0.5926 115 E 0.0357 0.4634 0.5009 116 V 0.0489 0.4090 0.5421 117 L 0.0898 0.3065 0.6037 118 C 0.0862 0.3130 0.6008 119 Q 0.0912 0.3342 0.5746 120 R 0.1702 0.3087 0.5212 121 Y 0.3905 0.1270 0.4825 122 L 0.4853 0.0764 0.4383 123 L 0.4329 0.1041 0.4630 124 D 0.2841 0.0917 0.6241 125 G 0.5349 0.0368 0.4283 126 V 0.8613 0.0067 0.1319 127 I 0.9127 0.0052 0.0822 128 A 0.9157 0.0055 0.0788 129 L 0.9186 0.0055 0.0760 130 V 0.8530 0.0141 0.1328 131 D 0.6340 0.0107 0.3553 132 A 0.0693 0.4130 0.5177 133 V 0.0286 0.4929 0.4785 134 H 0.0344 0.5976 0.3680 135 A 0.0389 0.5054 0.4557 136 D 0.0411 0.4638 0.4951 137 E 0.0320 0.3738 0.5942 138 Q 0.0414 0.2718 0.6867 139 M 0.0484 0.3026 0.6490 140 N 0.0416 0.3662 0.5922 141 Q 0.0395 0.5513 0.4092 142 F 0.0187 0.7311 0.2501 143 T 0.0127 0.7929 0.1944 144 I 0.0167 0.7928 0.1906 145 A 0.0269 0.7909 0.1822 146 Q 0.0119 0.8848 0.1033 147 S 0.0131 0.8691 0.1177 148 Q 0.0163 0.8484 0.1352 149 V 0.0542 0.7806 0.1652 150 G 0.0436 0.7223 0.2341 151 Y 0.0882 0.4389 0.4730 152 A 0.2095 0.1189 0.6716 153 D 0.1396 0.0950 0.7654 154 R 0.8816 0.0094 0.1090 155 I 0.9286 0.0039 0.0675 156 L 0.9284 0.0054 0.0662 157 L 0.8767 0.0171 0.1061 158 T 0.5847 0.0200 0.3953 159 K 0.1387 0.1738 0.6875 160 T 0.0902 0.2885 0.6213 161 D 0.0796 0.3410 0.5794 162 V 0.0730 0.2283 0.6987 163 A 0.0805 0.1542 0.7653 164 G 0.0591 0.1312 0.8097 165 E 0.0233 0.4480 0.5286 166 A 0.0202 0.6020 0.3778 167 E 0.0125 0.7500 0.2376 168 K 0.0128 0.8433 0.1439 169 L 0.0064 0.9019 0.0916 170 H 0.0061 0.9374 0.0565 171 E 0.0058 0.9456 0.0485 172 R 0.0049 0.9472 0.0479 173 L 0.0056 0.9410 0.0534 174 A 0.0070 0.9212 0.0718 175 R 0.0121 0.8413 0.1466 176 I 0.0423 0.6346 0.3232 177 N 0.0696 0.0883 0.8421 178 A 0.0147 0.1595 0.8258 179 R 0.0260 0.1034 0.8707 180 A 0.1633 0.0406 0.7961 181 P 0.5508 0.0276 0.4216 182 V 0.8288 0.0141 0.1571 183 Y 0.8411 0.0148 0.1441 184 T 0.7748 0.0179 0.2073 185 V 0.4813 0.0344 0.4844 186 T 0.1785 0.0734 0.7481 187 H 0.0640 0.1632 0.7728 188 G 0.0616 0.1377 0.8006 189 D 0.1498 0.1057 0.7445 190 I 0.2476 0.0285 0.7239 191 D 0.1143 0.0275 0.8582 192 L 0.0133 0.7906 0.1961 193 G 0.0089 0.8449 0.1462 194 L 0.0143 0.8491 0.1366 195 L 0.0520 0.7304 0.2177 196 F 0.0802 0.5524 0.3673 197 N 0.1044 0.2980 0.5976 198 T 0.0787 0.2679 0.6534 199 N 0.0885 0.2165 0.6950 200 G 0.1448 0.2453 0.6099 201 F 0.1984 0.2086 0.5930 202 M 0.1831 0.1876 0.6293 203 L 0.0916 0.2372 0.6712 204 E 0.0676 0.2446 0.6878 205 E 0.0552 0.2874 0.6574 206 N 0.0796 0.2888 0.6317 207 V 0.1196 0.3142 0.5663 208 V 0.1332 0.2970 0.5698 209 S 0.1072 0.3630 0.5298 210 T 0.0752 0.3814 0.5434 211 K 0.0766 0.3244 0.5990 212 P 0.0829 0.2780 0.6391 213 R 0.0804 0.2578 0.6618 214 F 0.1015 0.2363 0.6623 215 H 0.1108 0.1815 0.7077 216 F 0.1177 0.1700 0.7123 217 I 0.0942 0.3411 0.5646 218 A 0.0996 0.3820 0.5184 219 D 0.1136 0.3906 0.4958 220 K 0.0942 0.3755 0.5304 221 Q 0.1005 0.2810 0.6184 222 N 0.0757 0.2017 0.7225 223 D 0.1066 0.0776 0.8158 224 I 0.3106 0.0433 0.6461 225 S 0.3814 0.0601 0.5585 226 S 0.6183 0.0341 0.3476 227 I 0.7815 0.0183 0.2002 228 V 0.8561 0.0108 0.1331 229 V 0.8510 0.0112 0.1378 230 E 0.7509 0.0153 0.2337 231 L 0.4708 0.0281 0.5011 232 D 0.1778 0.0594 0.7628 233 Y 0.1405 0.0372 0.8224 234 P 0.1743 0.0332 0.7925 235 V 0.2162 0.0220 0.7618 236 D 0.1076 0.0179 0.8745 237 I 0.0050 0.8954 0.0997 238 S 0.0046 0.9308 0.0646 239 E 0.0046 0.9426 0.0528 240 V 0.0045 0.9500 0.0456 241 S 0.0045 0.9505 0.0450 242 R 0.0046 0.9439 0.0515 243 V 0.0046 0.9360 0.0593 244 M 0.0048 0.9182 0.0770 245 E 0.0054 0.8628 0.1319 246 N 0.0074 0.7801 0.2125 247 L 0.0154 0.7346 0.2500 248 L 0.0214 0.6866 0.2920 249 L 0.0221 0.6695 0.3084 250 E 0.0321 0.5742 0.3936 251 S 0.0510 0.3967 0.5523 252 A 0.0633 0.2092 0.7275 253 D 0.0551 0.1732 0.7717 254 K 0.1033 0.1892 0.7075 255 L 0.4917 0.0786 0.4296 256 L 0.7411 0.0380 0.2209 257 R 0.8341 0.0209 0.1450 258 Y 0.8521 0.0154 0.1326 259 K 0.7643 0.0324 0.2033 260 G 0.7620 0.0219 0.2161 261 M 0.8641 0.0143 0.1215 262 L 0.8816 0.0141 0.1043 263 W 0.8419 0.0123 0.1459 264 I 0.6407 0.0255 0.3338 265 D 0.1589 0.0782 0.7630 266 G 0.0541 0.0708 0.8751 267 E 0.1239 0.0589 0.8172 268 P 0.1938 0.0855 0.7207 269 N 0.3906 0.0739 0.5355 270 R 0.7238 0.0349 0.2413 271 L 0.8541 0.0208 0.1251 272 L 0.8828 0.0212 0.0960 273 F 0.8660 0.0258 0.1081 274 Q 0.7910 0.0395 0.1695 275 G 0.6733 0.0554 0.2713 276 V 0.5517 0.0821 0.3662 277 Q 0.4017 0.1004 0.4980 278 R 0.3757 0.1277 0.4966 279 L 0.5083 0.1133 0.3784 280 Y 0.5495 0.0746 0.3760 281 S 0.3896 0.0734 0.5370 282 A 0.2596 0.1007 0.6397 283 D 0.1504 0.0935 0.7561 284 W 0.0951 0.1762 0.7287 285 D 0.0809 0.1980 0.7211 286 R 0.0836 0.2127 0.7037 287 P 0.1000 0.2383 0.6616 288 W 0.1221 0.1878 0.6901 289 G 0.1022 0.1446 0.7532 290 D 0.0555 0.2061 0.7384 291 E 0.0503 0.1410 0.8087 292 K 0.1057 0.0934 0.8010 293 P 0.2130 0.0552 0.7318 294 H 0.2180 0.0473 0.7346 295 S 0.3278 0.0366 0.6356 296 T 0.7659 0.0108 0.2233 297 M 0.9033 0.0042 0.0925 298 V 0.9179 0.0042 0.0779 299 F 0.9166 0.0040 0.0794 300 I 0.8258 0.0156 0.1586 301 G 0.4693 0.0280 0.5028 302 I 0.1396 0.0915 0.7689 303 Q 0.1130 0.0528 0.8342 304 L 0.0958 0.0400 0.8642 305 P 0.0754 0.0191 0.9055 306 E 0.0052 0.8948 0.0999 307 E 0.0046 0.9403 0.0551 308 E 0.0046 0.9499 0.0454 309 I 0.0045 0.9537 0.0418 310 R 0.0046 0.9504 0.0450 311 A 0.0048 0.9331 0.0621 312 A 0.0054 0.9086 0.0860 313 F 0.0078 0.8919 0.1003 314 A 0.0058 0.8471 0.1471 315 G 0.0075 0.7159 0.2767 316 L 0.0247 0.5022 0.4732 317 R 0.0375 0.3105 0.6519 318 K 0.0241 0.0667 0.9092