# This file is the result of combining several RDB files, specifically # T0195.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0195.t2k.stride-ebghtl.rdb (weight 1.24869) # T0195.t2k.str2.rdb (weight 1.54758) # T0195.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 T0195.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0195 # 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 T0195.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 117 # # ============================================ # Comments from T0195.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0195 # 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 T0195.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 117 # # ============================================ # Comments from T0195.t2k.str2.rdb # ============================================ # TARGET T0195 # 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 T0195.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 117 # # ============================================ # Comments from T0195.t2k.alpha.rdb # ============================================ # TARGET T0195 # 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 T0195.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 117 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1146 0.0511 0.8343 2 K 0.3732 0.0641 0.5627 3 V 0.5816 0.0850 0.3334 4 V 0.6290 0.0924 0.2786 5 K 0.5841 0.0932 0.3227 6 E 0.5886 0.1112 0.3002 7 F 0.4969 0.0812 0.4219 8 S 0.4437 0.0909 0.4654 9 V 0.4026 0.0803 0.5171 10 C 0.3252 0.0696 0.6053 11 G 0.2379 0.0593 0.7027 12 G 0.3455 0.0505 0.6039 13 R 0.6491 0.0270 0.3239 14 L 0.8334 0.0101 0.1566 15 I 0.8736 0.0097 0.1167 16 K 0.8940 0.0072 0.0989 17 L 0.8731 0.0100 0.1169 18 S 0.8644 0.0098 0.1258 19 H 0.7242 0.0251 0.2507 20 N 0.5459 0.0467 0.4074 21 S 0.2648 0.1254 0.6098 22 N 0.0845 0.3529 0.5625 23 S 0.0881 0.3591 0.5527 24 T 0.0738 0.2218 0.7044 25 K 0.0769 0.0590 0.8642 26 T 0.2031 0.0355 0.7613 27 S 0.2952 0.0202 0.6846 28 M 0.5236 0.0094 0.4670 29 N 0.7273 0.0039 0.2688 30 V 0.8836 0.0037 0.1127 31 N 0.9153 0.0034 0.0814 32 I 0.9169 0.0032 0.0799 33 Y 0.8792 0.0041 0.1166 34 L 0.6466 0.0064 0.3470 35 P 0.2846 0.0192 0.6962 36 K 0.0723 0.3149 0.6127 37 H 0.0625 0.3770 0.5605 38 Y 0.0690 0.3639 0.5670 39 Y 0.0880 0.2260 0.6860 40 A 0.0580 0.2099 0.7321 41 Q 0.0606 0.1948 0.7446 42 D 0.0614 0.1971 0.7415 43 F 0.0688 0.2388 0.6925 44 P 0.0621 0.2778 0.6601 45 R 0.0513 0.2891 0.6596 46 N 0.0588 0.2139 0.7273 47 K 0.0829 0.1052 0.8119 48 R 0.1047 0.0580 0.8373 49 I 0.1651 0.0130 0.8219 50 P 0.3633 0.0076 0.6291 51 T 0.9123 0.0044 0.0833 52 V 0.9284 0.0051 0.0665 53 F 0.9253 0.0059 0.0688 54 Y 0.9134 0.0088 0.0778 55 L 0.8136 0.0162 0.1702 56 S 0.4096 0.0297 0.5607 57 G 0.1663 0.0408 0.7928 58 L 0.1513 0.0574 0.7912 59 T 0.1076 0.0694 0.8230 60 C 0.0793 0.0604 0.8603 61 T 0.0656 0.0547 0.8797 62 P 0.0173 0.6257 0.3570 63 D 0.0129 0.6951 0.2921 64 N 0.0249 0.7371 0.2381 65 A 0.0295 0.7926 0.1778 66 S 0.0370 0.7763 0.1867 67 E 0.0416 0.7529 0.2056 68 K 0.0351 0.7160 0.2489 69 A 0.0330 0.5967 0.3704 70 F 0.0255 0.5862 0.3883 71 W 0.0117 0.8196 0.1687 72 Q 0.0088 0.8989 0.0923 73 F 0.0084 0.9314 0.0602 74 Q 0.0071 0.9426 0.0503 75 A 0.0059 0.9425 0.0517 76 D 0.0058 0.9203 0.0739 77 K 0.0091 0.8197 0.1712 78 Y 0.0523 0.2782 0.6695 79 G 0.0470 0.0181 0.9349 80 F 0.4235 0.0070 0.5696 81 A 0.8782 0.0042 0.1176 82 I 0.9191 0.0031 0.0779 83 V 0.8982 0.0055 0.0963 84 F 0.7350 0.0053 0.2597 85 P 0.3420 0.0295 0.6285 86 D 0.1550 0.0275 0.8176 87 T 0.0998 0.0463 0.8540 88 S 0.0720 0.0448 0.8832 89 P 0.0631 0.1437 0.7931 90 R 0.0621 0.1338 0.8042 91 G 0.0714 0.1292 0.7994 92 D 0.0815 0.1559 0.7625 93 E 0.1129 0.1480 0.7391 94 V 0.1310 0.1254 0.7436 95 A 0.0790 0.1579 0.7631 96 N 0.0752 0.1386 0.7862 97 D 0.0948 0.0776 0.8276 98 P 0.1155 0.1302 0.7543 99 E 0.0900 0.1939 0.7161 100 G 0.0705 0.3039 0.6256 101 S 0.0804 0.3656 0.5540 102 W 0.1262 0.3413 0.5325 103 D 0.1462 0.2543 0.5995 104 F 0.1192 0.2291 0.6517 105 G 0.1171 0.1137 0.7693 106 Q 0.1058 0.1239 0.7703 107 G 0.1234 0.1088 0.7679 108 A 0.2325 0.1012 0.6663 109 G 0.3263 0.0838 0.5900 110 F 0.4859 0.0869 0.4272 111 Y 0.5583 0.0724 0.3694 112 L 0.4671 0.1058 0.4272 113 N 0.3094 0.1385 0.5521 114 A 0.1480 0.2944 0.5576 115 T 0.1325 0.2570 0.6105 116 Q 0.1357 0.2323 0.6320 117 E 0.1307 0.1668 0.7025 118 P 0.1217 0.3024 0.5759 119 Y 0.1232 0.3398 0.5371 120 A 0.1189 0.3369 0.5442 121 Q 0.0758 0.3120 0.6122 122 H 0.0861 0.1999 0.7139 123 Y 0.1063 0.2150 0.6787 124 Q 0.1441 0.2363 0.6197 125 M 0.0883 0.6180 0.2938 126 Y 0.0589 0.7585 0.1825 127 D 0.0557 0.8098 0.1345 128 Y 0.0631 0.8183 0.1186 129 I 0.0493 0.8300 0.1207 130 H 0.0275 0.8638 0.1087 131 K 0.0113 0.8693 0.1195 132 E 0.0108 0.8588 0.1305 133 L 0.0077 0.8696 0.1228 134 P 0.0049 0.9429 0.0522 135 Q 0.0048 0.9497 0.0455 136 T 0.0048 0.9505 0.0446 137 L 0.0052 0.9409 0.0539 138 D 0.0059 0.9042 0.0899 139 S 0.0074 0.8010 0.1916 140 H 0.0168 0.6202 0.3630 141 F 0.0909 0.3174 0.5917 142 N 0.0633 0.3153 0.6214 143 K 0.0813 0.2901 0.6286 144 N 0.0977 0.2092 0.6931 145 G 0.0591 0.2004 0.7405 146 D 0.0559 0.1703 0.7738 147 V 0.0708 0.1758 0.7534 148 K 0.0594 0.2225 0.7181 149 L 0.1243 0.2156 0.6601 150 D 0.2396 0.1007 0.6596 151 F 0.1926 0.0694 0.7380 152 L 0.0366 0.4098 0.5536 153 D 0.0661 0.3058 0.6281 154 N 0.2386 0.2761 0.4853 155 V 0.6045 0.0423 0.3532 156 A 0.8080 0.0256 0.1664 157 I 0.8689 0.0221 0.1090 158 T 0.7887 0.0482 0.1631 159 G 0.5819 0.0722 0.3459 160 H 0.3128 0.1406 0.5466 161 S 0.1637 0.1829 0.6534 162 M 0.0555 0.4755 0.4689 163 G 0.0283 0.5997 0.3720 164 G 0.0073 0.8992 0.0935 165 Y 0.0051 0.9507 0.0442 166 G 0.0047 0.9582 0.0371 167 A 0.0047 0.9599 0.0354 168 I 0.0047 0.9598 0.0355 169 C 0.0048 0.9586 0.0365 170 G 0.0053 0.9521 0.0427 171 Y 0.0062 0.9337 0.0601 172 L 0.0094 0.8623 0.1283 173 K 0.0210 0.6657 0.3133 174 G 0.0422 0.2926 0.6651 175 Y 0.0428 0.1034 0.8537 176 S 0.0662 0.0980 0.8359 177 G 0.0483 0.2159 0.7357 178 K 0.0748 0.2495 0.6757 179 R 0.2081 0.2570 0.5348 180 Y 0.4808 0.1346 0.3847 181 K 0.5607 0.1308 0.3084 182 S 0.7528 0.0967 0.1505 183 C 0.7592 0.1035 0.1374 184 S 0.6907 0.1291 0.1801 185 A 0.5895 0.1391 0.2713 186 F 0.4117 0.1287 0.4597 187 A 0.2538 0.0924 0.6538 188 P 0.2021 0.1318 0.6661 189 I 0.2349 0.1298 0.6353 190 V 0.2017 0.1030 0.6953 191 N 0.1512 0.0722 0.7766 192 P 0.0347 0.4687 0.4967 193 S 0.0321 0.4591 0.5088 194 N 0.0475 0.4277 0.5248 195 V 0.0748 0.1509 0.7743 196 P 0.0390 0.3463 0.6147 197 W 0.0264 0.4516 0.5220 198 G 0.0269 0.5636 0.4095 199 Q 0.0211 0.7802 0.1987 200 K 0.0192 0.8412 0.1396 201 A 0.0221 0.8416 0.1363 202 F 0.0233 0.8321 0.1447 203 K 0.0255 0.8114 0.1632 204 G 0.0332 0.7635 0.2033 205 Y 0.0438 0.6669 0.2893 206 L 0.0697 0.4090 0.5213 207 G 0.0517 0.1919 0.7565 208 E 0.0515 0.2378 0.7107 209 E 0.0488 0.2765 0.6747 210 K 0.0383 0.4209 0.5408 211 A 0.0338 0.4995 0.4667 212 Q 0.0405 0.5279 0.4316 213 W 0.0251 0.6181 0.3568 214 E 0.0300 0.5990 0.3709 215 A 0.0375 0.5984 0.3641 216 Y 0.0470 0.4987 0.4543 217 D 0.0548 0.4078 0.5375 218 P 0.0057 0.9207 0.0735 219 C 0.0061 0.9350 0.0588 220 L 0.0059 0.9412 0.0529 221 L 0.0064 0.9411 0.0525 222 I 0.0073 0.9232 0.0696 223 K 0.0087 0.8412 0.1501 224 N 0.0154 0.6803 0.3043 225 I 0.0427 0.3915 0.5658 226 R 0.0376 0.2724 0.6900 227 H 0.0431 0.1632 0.7937 228 V 0.0562 0.1759 0.7679 229 G 0.0737 0.1446 0.7817 230 D 0.1051 0.0751 0.8198 231 D 0.1648 0.0402 0.7950 232 R 0.4301 0.0466 0.5234 233 I 0.8141 0.0288 0.1571 234 L 0.8796 0.0201 0.1003 235 I 0.8736 0.0225 0.1039 236 H 0.8253 0.0277 0.1469 237 V 0.4134 0.0455 0.5411 238 G 0.1518 0.0727 0.7756 239 D 0.0954 0.1909 0.7137 240 S 0.0516 0.3043 0.6440 241 D 0.0683 0.3306 0.6011 242 P 0.0143 0.5772 0.4086 243 F 0.0205 0.5756 0.4038 244 L 0.0280 0.5999 0.3721 245 E 0.0204 0.6206 0.3590 246 E 0.0185 0.5383 0.4432 247 H 0.0319 0.4341 0.5340 248 L 0.0538 0.2514 0.6948 249 K 0.0542 0.1123 0.8335 250 P 0.0101 0.8027 0.1871 251 E 0.0062 0.8919 0.1019 252 L 0.0064 0.9199 0.0738 253 L 0.0049 0.9458 0.0492 254 L 0.0053 0.9533 0.0414 255 E 0.0047 0.9560 0.0393 256 A 0.0047 0.9567 0.0386 257 V 0.0048 0.9554 0.0398 258 K 0.0052 0.9418 0.0530 259 A 0.0074 0.8844 0.1081 260 T 0.0457 0.3292 0.6252 261 S 0.0478 0.0262 0.9260 262 W 0.0674 0.0210 0.9116 263 Q 0.0745 0.0777 0.8478 264 D 0.0869 0.1163 0.7968 265 Y 0.3483 0.0530 0.5987 266 V 0.7295 0.0092 0.2613 267 E 0.8528 0.0054 0.1419 268 I 0.8701 0.0041 0.1257 269 K 0.8297 0.0051 0.1652 270 K 0.7106 0.0097 0.2796 271 V 0.3426 0.0140 0.6435 272 H 0.0944 0.0521 0.8535 273 G 0.0655 0.0355 0.8990 274 F 0.0897 0.0897 0.8206 275 D 0.1670 0.0786 0.7544 276 H 0.2892 0.1524 0.5584 277 S 0.3944 0.2309 0.3747 278 Y 0.3987 0.3968 0.2045 279 Y 0.4571 0.3995 0.1433 280 F 0.4082 0.4819 0.1099 281 V 0.3696 0.5159 0.1145 282 S 0.3045 0.5517 0.1438 283 T 0.1948 0.5431 0.2621 284 F 0.1098 0.5374 0.3527 285 V 0.0199 0.8148 0.1653 286 P 0.0064 0.9203 0.0734 287 E 0.0053 0.9287 0.0661 288 H 0.0051 0.9420 0.0529 289 A 0.0047 0.9575 0.0378 290 E 0.0047 0.9588 0.0365 291 F 0.0048 0.9556 0.0396 292 H 0.0048 0.9544 0.0408 293 A 0.0050 0.9454 0.0496 294 R 0.0057 0.9006 0.0936 295 N 0.0089 0.7908 0.2002 296 L 0.0539 0.5081 0.4380 297 G 0.0490 0.2373 0.7136 298 L 0.0613 0.1807 0.7580 299 I 0.0463 0.0399 0.9139