# This file is the result of combining several RDB files, specifically # T0165.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0165.t2k.stride-ebghtl.rdb (weight 1.24869) # T0165.t2k.str.rdb (weight 1.53983) # T0165.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 T0165.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0165 # 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 T0165.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 175 # # ============================================ # Comments from T0165.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0165 # 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 T0165.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 175 # # ============================================ # Comments from T0165.t2k.str.rdb # ============================================ # TARGET T0165 # 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 T0165.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 175 # # ============================================ # Comments from T0165.t2k.alpha.rdb # ============================================ # TARGET T0165 # 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 T0165.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 175 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0636 0.0288 0.9075 2 Q 0.1139 0.0823 0.8039 3 L 0.0969 0.1785 0.7247 4 F 0.0695 0.2104 0.7201 5 D 0.0675 0.1358 0.7967 6 L 0.0833 0.1012 0.8155 7 P 0.0712 0.1137 0.8151 8 L 0.0185 0.7503 0.2312 9 D 0.0118 0.8499 0.1383 10 Q 0.0162 0.8532 0.1306 11 L 0.0258 0.8337 0.1405 12 Q 0.0411 0.7736 0.1854 13 T 0.0651 0.7134 0.2215 14 Y 0.1209 0.5545 0.3245 15 K 0.1534 0.3292 0.5175 16 P 0.0890 0.1492 0.7617 17 E 0.0826 0.0750 0.8424 18 K 0.0859 0.0508 0.8633 19 T 0.0926 0.0495 0.8579 20 A 0.0865 0.0398 0.8737 21 P 0.0686 0.1199 0.8115 22 K 0.0352 0.3333 0.6315 23 D 0.0465 0.4179 0.5356 24 F 0.0308 0.6175 0.3517 25 S 0.0260 0.6703 0.3037 26 E 0.0212 0.7108 0.2680 27 F 0.0316 0.6696 0.2988 28 W 0.0352 0.6391 0.3257 29 K 0.0303 0.5740 0.3956 30 L 0.0268 0.5226 0.4506 31 S 0.0373 0.5625 0.4002 32 L 0.0180 0.8089 0.1731 33 E 0.0137 0.8305 0.1558 34 E 0.0160 0.8164 0.1677 35 L 0.0185 0.7903 0.1912 36 A 0.0246 0.7308 0.2445 37 K 0.0286 0.6473 0.3241 38 V 0.0574 0.4722 0.4704 39 Q 0.0749 0.3700 0.5551 40 A 0.0696 0.4162 0.5142 41 E 0.1129 0.4040 0.4831 42 P 0.1701 0.3960 0.4338 43 D 0.2095 0.3808 0.4097 44 L 0.2111 0.3217 0.4671 45 Q 0.1678 0.2482 0.5840 46 P 0.1224 0.2293 0.6482 47 V 0.0905 0.2195 0.6899 48 D 0.0741 0.1438 0.7821 49 Y 0.0895 0.0960 0.8145 50 P 0.0964 0.0942 0.8094 51 A 0.1055 0.1005 0.7940 52 D 0.1002 0.1117 0.7881 53 G 0.1991 0.0682 0.7326 54 V 0.3162 0.0247 0.6590 55 K 0.4403 0.0129 0.5468 56 V 0.5821 0.0099 0.4080 57 Y 0.7882 0.0104 0.2013 58 R 0.8945 0.0038 0.1018 59 L 0.8977 0.0047 0.0976 60 T 0.9130 0.0038 0.0832 61 Y 0.8682 0.0054 0.1264 62 K 0.8020 0.0129 0.1851 63 S 0.3563 0.0163 0.6275 64 F 0.0536 0.1026 0.8438 65 G 0.0478 0.0330 0.9192 66 N 0.0624 0.0405 0.8971 67 A 0.4442 0.0118 0.5440 68 R 0.8312 0.0050 0.1637 69 I 0.8654 0.0060 0.1287 70 T 0.8696 0.0076 0.1228 71 G 0.8987 0.0065 0.0948 72 W 0.9133 0.0055 0.0812 73 Y 0.9109 0.0055 0.0836 74 A 0.8633 0.0100 0.1267 75 V 0.6903 0.0096 0.3001 76 P 0.3322 0.0227 0.6450 77 D 0.1123 0.0441 0.8436 78 K 0.0581 0.0716 0.8703 79 E 0.0465 0.0685 0.8850 80 G 0.0712 0.0446 0.8841 81 P 0.1227 0.0321 0.8452 82 H 0.1748 0.0114 0.8138 83 P 0.3666 0.0067 0.6267 84 A 0.8963 0.0044 0.0993 85 I 0.9322 0.0034 0.0643 86 V 0.9322 0.0035 0.0643 87 K 0.9241 0.0037 0.0723 88 Y 0.8306 0.0066 0.1628 89 H 0.4543 0.0231 0.5226 90 G 0.1610 0.0298 0.8091 91 Y 0.1028 0.0593 0.8378 92 N 0.0672 0.1433 0.7895 93 A 0.0532 0.1646 0.7822 94 S 0.0563 0.1567 0.7870 95 Y 0.0421 0.2230 0.7349 96 D 0.0334 0.2929 0.6737 97 G 0.0398 0.3671 0.5931 98 E 0.0365 0.5258 0.4377 99 I 0.0223 0.7093 0.2684 100 H 0.0105 0.8708 0.1187 101 E 0.0062 0.9208 0.0730 102 M 0.0049 0.9485 0.0466 103 V 0.0055 0.9525 0.0420 104 N 0.0049 0.9555 0.0396 105 W 0.0048 0.9536 0.0416 106 A 0.0046 0.9414 0.0540 107 L 0.0059 0.8747 0.1194 108 H 0.0410 0.2947 0.6643 109 G 0.0414 0.0183 0.9403 110 Y 0.2062 0.0100 0.7838 111 A 0.8411 0.0054 0.1536 112 T 0.9267 0.0035 0.0698 113 F 0.9255 0.0039 0.0706 114 G 0.9082 0.0042 0.0876 115 M 0.7770 0.0072 0.2158 116 L 0.3246 0.0145 0.6609 117 V 0.1066 0.0748 0.8186 118 R 0.0772 0.0976 0.8252 119 G 0.0841 0.0937 0.8221 120 Q 0.1003 0.0729 0.8267 121 Q 0.1237 0.0834 0.7930 122 S 0.0984 0.0941 0.8075 123 S 0.1096 0.1001 0.7903 124 E 0.0934 0.1486 0.7580 125 D 0.0980 0.1814 0.7206 126 T 0.1586 0.2241 0.6172 127 S 0.2135 0.2920 0.4945 128 I 0.2072 0.2950 0.4978 129 S 0.1858 0.2821 0.5321 130 P 0.1559 0.2576 0.5865 131 H 0.1335 0.2306 0.6359 132 G 0.1066 0.3274 0.5660 133 H 0.0872 0.3912 0.5216 134 A 0.0940 0.4746 0.4314 135 L 0.0825 0.6104 0.3071 136 G 0.1144 0.6389 0.2467 137 W 0.1510 0.6400 0.2090 138 M 0.1483 0.6562 0.1955 139 T 0.1413 0.6161 0.2427 140 K 0.1019 0.5144 0.3837 141 G 0.1059 0.3460 0.5482 142 I 0.1374 0.2504 0.6122 143 L 0.1337 0.2054 0.6609 144 D 0.0888 0.1286 0.7826 145 K 0.0349 0.2944 0.6707 146 D 0.0459 0.2546 0.6995 147 T 0.0973 0.3164 0.5863 148 Y 0.1516 0.3452 0.5031 149 Y 0.1665 0.3557 0.4777 150 Y 0.1178 0.4295 0.4527 151 R 0.0551 0.5560 0.3890 152 G 0.0451 0.6239 0.3311 153 V 0.0359 0.7845 0.1796 154 Y 0.0108 0.9215 0.0677 155 L 0.0070 0.9455 0.0476 156 D 0.0058 0.9485 0.0457 157 A 0.0044 0.9589 0.0367 158 V 0.0044 0.9608 0.0348 159 R 0.0044 0.9602 0.0355 160 A 0.0044 0.9591 0.0365 161 L 0.0044 0.9587 0.0370 162 E 0.0044 0.9561 0.0395 163 V 0.0044 0.9442 0.0513 164 I 0.0053 0.9302 0.0645 165 S 0.0062 0.8632 0.1306 166 S 0.0110 0.6444 0.3446 167 F 0.0567 0.2975 0.6458 168 D 0.0414 0.1688 0.7898 169 E 0.0552 0.1595 0.7853 170 V 0.1283 0.0610 0.8107 171 D 0.1171 0.0323 0.8506 172 E 0.0268 0.4122 0.5610 173 T 0.0280 0.3362 0.6358 174 R 0.1714 0.3041 0.5245 175 I 0.6952 0.0238 0.2810 176 G 0.8511 0.0180 0.1309 177 V 0.9027 0.0138 0.0835 178 T 0.7995 0.0404 0.1601 179 G 0.4919 0.0678 0.4404 180 G 0.2156 0.1762 0.6081 181 S 0.1209 0.2863 0.5928 182 Q 0.0164 0.7946 0.1890 183 G 0.0076 0.9105 0.0819 184 G 0.0046 0.9502 0.0452 185 G 0.0044 0.9589 0.0367 186 L 0.0044 0.9597 0.0359 187 T 0.0044 0.9593 0.0364 188 I 0.0045 0.9561 0.0394 189 A 0.0052 0.9436 0.0512 190 A 0.0078 0.9051 0.0871 191 A 0.0166 0.7755 0.2079 192 A 0.0271 0.5465 0.4265 193 L 0.0525 0.1769 0.7707 194 S 0.0524 0.1633 0.7843 195 D 0.0374 0.2558 0.7068 196 I 0.1823 0.2842 0.5335 197 P 0.5358 0.1079 0.3564 198 K 0.6850 0.0728 0.2422 199 A 0.8384 0.0374 0.1242 200 A 0.8653 0.0343 0.1005 201 V 0.8592 0.0360 0.1048 202 A 0.7714 0.0509 0.1777 203 D 0.5727 0.0756 0.3517 204 Y 0.3018 0.0776 0.6206 205 P 0.2146 0.1025 0.6828 206 Y 0.2055 0.1491 0.6454 207 L 0.1375 0.1974 0.6651 208 S 0.1260 0.2021 0.6720 209 N 0.0689 0.4500 0.4811 210 F 0.0792 0.5225 0.3983 211 E 0.0711 0.5678 0.3611 212 R 0.0799 0.5388 0.3813 213 A 0.1006 0.4949 0.4044 214 I 0.0948 0.4212 0.4840 215 D 0.0843 0.3679 0.5478 216 V 0.0705 0.3661 0.5634 217 A 0.0650 0.3776 0.5574 218 L 0.0458 0.5449 0.4093 219 E 0.0349 0.6275 0.3376 220 Q 0.0437 0.6218 0.3345 221 P 0.0460 0.6273 0.3268 222 Y 0.0494 0.6522 0.2984 223 L 0.0655 0.6286 0.3060 224 E 0.0743 0.6130 0.3126 225 I 0.0799 0.6368 0.2833 226 N 0.0803 0.6470 0.2727 227 S 0.0880 0.6282 0.2838 228 F 0.1013 0.5465 0.3522 229 F 0.1336 0.3982 0.4682 230 R 0.1341 0.2661 0.5998 231 R 0.0899 0.3199 0.5902 232 N 0.0845 0.2965 0.6190 233 G 0.0714 0.3365 0.5921 234 S 0.0614 0.3513 0.5873 235 P 0.0591 0.3328 0.6081 236 E 0.0577 0.3283 0.6139 237 T 0.0619 0.3149 0.6232 238 E 0.0390 0.5610 0.4000 239 V 0.0230 0.7619 0.2152 240 Q 0.0189 0.7839 0.1971 241 A 0.0190 0.7958 0.1852 242 M 0.0105 0.8514 0.1381 243 K 0.0095 0.8609 0.1295 244 T 0.0095 0.8453 0.1452 245 L 0.0149 0.7840 0.2012 246 S 0.0157 0.6960 0.2883 247 Y 0.0219 0.5346 0.4435 248 F 0.0495 0.2604 0.6902 249 D 0.0802 0.0922 0.8276 250 I 0.0111 0.7808 0.2082 251 M 0.0076 0.8468 0.1456 252 N 0.0108 0.8237 0.1655 253 L 0.0168 0.7558 0.2274 254 A 0.0258 0.7089 0.2653 255 D 0.0148 0.5658 0.4195 256 R 0.0277 0.3850 0.5873 257 V 0.1128 0.0895 0.7976 258 K 0.0729 0.0631 0.8640 259 V 0.1025 0.0204 0.8771 260 P 0.2168 0.0188 0.7644 261 V 0.8653 0.0080 0.1267 262 L 0.9224 0.0047 0.0729 263 M 0.9179 0.0048 0.0772 264 S 0.8867 0.0083 0.1051 265 I 0.6169 0.0229 0.3602 266 G 0.2366 0.0403 0.7231 267 L 0.1055 0.1201 0.7744 268 I 0.0857 0.1223 0.7920 269 D 0.1091 0.0756 0.8153 270 K 0.0478 0.1672 0.7850 271 V 0.0962 0.1385 0.7653 272 T 0.1225 0.0554 0.8221 273 P 0.0887 0.0483 0.8630 274 P 0.0140 0.7867 0.1992 275 S 0.0070 0.8468 0.1462 276 T 0.0067 0.8929 0.1003 277 V 0.0047 0.9331 0.0622 278 F 0.0044 0.9514 0.0442 279 A 0.0049 0.9529 0.0422 280 A 0.0052 0.9528 0.0420 281 Y 0.0050 0.9504 0.0446 282 N 0.0051 0.9463 0.0486 283 H 0.0054 0.9314 0.0632 284 L 0.0094 0.9081 0.0826 285 E 0.0098 0.8337 0.1565 286 T 0.0212 0.6398 0.3390 287 K 0.0455 0.1987 0.7558 288 K 0.0330 0.0277 0.9393 289 E 0.1882 0.0134 0.7984 290 L 0.6806 0.0057 0.3137 291 K 0.8289 0.0074 0.1637 292 V 0.8620 0.0075 0.1306 293 Y 0.7615 0.0105 0.2280 294 R 0.6318 0.0227 0.3455 295 Y 0.3881 0.0435 0.5685 296 F 0.2127 0.0403 0.7470 297 G 0.0950 0.1078 0.7972 298 H 0.0869 0.1089 0.8042 299 E 0.1127 0.1401 0.7472 300 Y 0.1254 0.1585 0.7162 301 I 0.1339 0.1594 0.7067 302 P 0.1071 0.1623 0.7306 303 A 0.1145 0.1615 0.7240 304 F 0.1058 0.1535 0.7407 305 Q 0.0551 0.3168 0.6281 306 T 0.0331 0.3708 0.5961 307 E 0.0345 0.3874 0.5781 308 K 0.0629 0.3514 0.5857 309 L 0.0188 0.8108 0.1704 310 A 0.0082 0.9111 0.0807 311 F 0.0095 0.9181 0.0724 312 F 0.0087 0.9183 0.0730 313 K 0.0128 0.8992 0.0880 314 Q 0.0148 0.8539 0.1313 315 H 0.0228 0.7418 0.2354 316 L 0.0576 0.5062 0.4362 317 K 0.0566 0.2987 0.6447 318 G 0.0363 0.0477 0.9161