# This file is the result of combining several RDB files, specifically # T0199.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0199.t2k.stride-ebghtl.rdb (weight 1.24869) # T0199.t2k.str2.rdb (weight 1.54758) # T0199.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 T0199.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0199 # 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 T0199.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 100 # # ============================================ # Comments from T0199.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0199 # 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 T0199.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 100 # # ============================================ # Comments from T0199.t2k.str2.rdb # ============================================ # TARGET T0199 # 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 T0199.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 100 # # ============================================ # Comments from T0199.t2k.alpha.rdb # ============================================ # TARGET T0199 # 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 T0199.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 100 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0398 0.2002 0.7600 2 R 0.0677 0.4761 0.4562 3 R 0.0472 0.6117 0.3411 4 L 0.0384 0.6370 0.3247 5 N 0.0394 0.6253 0.3353 6 R 0.0372 0.6287 0.3341 7 K 0.0312 0.6428 0.3260 8 N 0.0298 0.6523 0.3180 9 N 0.0207 0.7585 0.2208 10 E 0.0140 0.8306 0.1554 11 A 0.0109 0.8354 0.1536 12 L 0.0094 0.8175 0.1731 13 K 0.0124 0.6843 0.3034 14 K 0.0183 0.5667 0.4149 15 L 0.0407 0.5149 0.4445 16 N 0.0197 0.5768 0.4035 17 D 0.0057 0.8787 0.1156 18 R 0.0055 0.9135 0.0809 19 Q 0.0047 0.9400 0.0552 20 R 0.0048 0.9522 0.0430 21 K 0.0048 0.9552 0.0401 22 V 0.0047 0.9572 0.0381 23 L 0.0047 0.9590 0.0363 24 Y 0.0047 0.9591 0.0362 25 C 0.0047 0.9590 0.0363 26 I 0.0047 0.9587 0.0366 27 V 0.0047 0.9567 0.0386 28 R 0.0048 0.9564 0.0389 29 E 0.0052 0.9508 0.0440 30 Y 0.0053 0.9448 0.0499 31 I 0.0061 0.9271 0.0668 32 E 0.0101 0.8383 0.1515 33 N 0.0415 0.4526 0.5059 34 K 0.0301 0.0660 0.9039 35 K 0.0744 0.0286 0.8969 36 P 0.1729 0.0435 0.7836 37 V 0.2242 0.1088 0.6670 38 S 0.1951 0.1223 0.6826 39 S 0.1018 0.5774 0.3207 40 Q 0.0466 0.8247 0.1287 41 R 0.0442 0.8504 0.1054 42 V 0.0493 0.8581 0.0926 43 L 0.0403 0.8627 0.0970 44 E 0.0374 0.8407 0.1219 45 V 0.0351 0.7516 0.2133 46 S 0.0510 0.4513 0.4977 47 N 0.0426 0.1258 0.8316 48 I 0.0828 0.1382 0.7790 49 E 0.1006 0.0812 0.8182 50 F 0.1503 0.0892 0.7606 51 S 0.1018 0.0658 0.8324 52 S 0.0214 0.8043 0.1743 53 A 0.0173 0.8700 0.1127 54 T 0.0170 0.9026 0.0805 55 I 0.0165 0.9145 0.0690 56 R 0.0141 0.9186 0.0673 57 N 0.0233 0.9174 0.0592 58 D 0.0072 0.9415 0.0513 59 M 0.0093 0.9399 0.0508 60 K 0.0095 0.9384 0.0521 61 K 0.0068 0.9404 0.0528 62 L 0.0061 0.9398 0.0541 63 E 0.0091 0.9162 0.0747 64 Y 0.0114 0.8745 0.1142 65 L 0.0376 0.4036 0.5588 66 G 0.0331 0.1060 0.8609 67 Y 0.1112 0.1699 0.7189 68 I 0.3360 0.1703 0.4936 69 Y 0.2560 0.1257 0.6182 70 Q 0.1671 0.0844 0.7485 71 P 0.2002 0.0947 0.7051 72 H 0.2634 0.0757 0.6608 73 T 0.2312 0.0710 0.6978 74 S 0.2350 0.0824 0.6826 75 A 0.1840 0.1247 0.6913 76 G 0.2084 0.0756 0.7160 77 R 0.2788 0.0510 0.6702 78 I 0.2898 0.0393 0.6709 79 P 0.1778 0.0518 0.7705 80 T 0.0792 0.1119 0.8089 81 D 0.0090 0.8633 0.1277 82 K 0.0138 0.8615 0.1247 83 G 0.0096 0.9011 0.0893 84 L 0.0088 0.9314 0.0598 85 R 0.0180 0.9249 0.0571 86 F 0.0222 0.9104 0.0673 87 Y 0.0340 0.8772 0.0888 88 Y 0.0304 0.8801 0.0895 89 E 0.0220 0.8418 0.1362 90 E 0.0228 0.7469 0.2303 91 M 0.0520 0.5477 0.4003 92 L 0.0988 0.2508 0.6504 93 K 0.1019 0.0839 0.8142 94 I 0.0841 0.1035 0.8124 95 S 0.0621 0.1242 0.8138 96 K 0.0696 0.0965 0.8339 97 E 0.0722 0.0638 0.8640 98 T 0.0520 0.0719 0.8761 99 S 0.0063 0.8940 0.0997 100 E 0.0053 0.9195 0.0752 101 A 0.0053 0.9343 0.0605 102 D 0.0051 0.9450 0.0499 103 L 0.0060 0.9432 0.0508 104 A 0.0051 0.9463 0.0485 105 V 0.0056 0.9423 0.0521 106 E 0.0057 0.9406 0.0537 107 T 0.0070 0.9055 0.0875 108 F 0.0113 0.8309 0.1578 109 K 0.0225 0.7236 0.2539 110 S 0.0263 0.5320 0.4417 111 M 0.0278 0.3514 0.6208 112 P 0.0307 0.2851 0.6842 113 L 0.0600 0.2072 0.7328 114 A 0.0771 0.1438 0.7790 115 D 0.0913 0.1289 0.7798 116 P 0.0056 0.9326 0.0618 117 E 0.0048 0.9533 0.0419 118 K 0.0048 0.9572 0.0380 119 V 0.0048 0.9584 0.0369 120 L 0.0047 0.9582 0.0370 121 F 0.0047 0.9574 0.0379 122 L 0.0047 0.9559 0.0394 123 A 0.0047 0.9564 0.0389 124 G 0.0047 0.9575 0.0378 125 N 0.0048 0.9546 0.0405 126 L 0.0049 0.9461 0.0491 127 L 0.0050 0.9431 0.0518 128 A 0.0058 0.9240 0.0702 129 R 0.0076 0.8458 0.1465 130 L 0.0128 0.7398 0.2474 131 T 0.0533 0.4755 0.4713 132 E 0.0293 0.1034 0.8673 133 G 0.0914 0.0577 0.8509 134 Y 0.2862 0.0428 0.6710 135 V 0.7740 0.0415 0.1845 136 L 0.8889 0.0206 0.0905 137 I 0.8663 0.0241 0.1096 138 E 0.7639 0.0200 0.2161 139 R 0.3514 0.0170 0.6316 140 P 0.1651 0.0512 0.7837 141 N 0.1254 0.0490 0.8256 142 T 0.1021 0.1651 0.7328 143 R 0.0753 0.1959 0.7288 144 D 0.1115 0.2743 0.6142 145 L 0.2416 0.1637 0.5947 146 K 0.5628 0.0734 0.3638 147 I 0.7576 0.0202 0.2221 148 L 0.7765 0.0318 0.1918 149 R 0.8224 0.0107 0.1669 150 V 0.8025 0.0058 0.1917 151 M 0.8697 0.0038 0.1266 152 L 0.9124 0.0031 0.0845 153 I 0.8860 0.0055 0.1085 154 P 0.8307 0.0047 0.1645 155 V 0.5153 0.0253 0.4594 156 S 0.1415 0.0257 0.8328 157 E 0.0169 0.1140 0.8692 158 D 0.0519 0.0707 0.8774 159 Y 0.6983 0.0115 0.2902 160 L 0.9011 0.0034 0.0955 161 I 0.9290 0.0036 0.0674 162 F 0.9334 0.0032 0.0635 163 S 0.9311 0.0032 0.0657 164 I 0.9235 0.0033 0.0732 165 L 0.8921 0.0042 0.1037 166 T 0.6246 0.0078 0.3675 167 E 0.1769 0.0759 0.7472 168 F 0.0539 0.0302 0.9159 169 G 0.0876 0.0330 0.8794 170 V 0.4615 0.0189 0.5196 171 S 0.8652 0.0040 0.1307 172 K 0.8413 0.0156 0.1431 173 V 0.8669 0.0057 0.1274 174 T 0.8519 0.0066 0.1415 175 P 0.8846 0.0052 0.1102 176 I 0.8695 0.0053 0.1252 177 K 0.8060 0.0073 0.1867 178 T 0.4810 0.0147 0.5042 179 Q 0.1806 0.0618 0.7577 180 E 0.0611 0.1509 0.7881 181 R 0.0859 0.1114 0.8027 182 L 0.1331 0.0340 0.8329 183 N 0.0822 0.0240 0.8939 184 W 0.0064 0.8668 0.1268 185 E 0.0056 0.8904 0.1040 186 E 0.0062 0.9138 0.0800 187 I 0.0069 0.9170 0.0761 188 E 0.0071 0.9038 0.0891 189 R 0.0078 0.8767 0.1155 190 Q 0.0125 0.8490 0.1385 191 L 0.0223 0.8179 0.1598 192 N 0.0202 0.7993 0.1805 193 F 0.0132 0.8322 0.1546 194 L 0.0186 0.7907 0.1907 195 L 0.0389 0.6434 0.3177 196 R 0.0448 0.2409 0.7143 197 G 0.0303 0.0591 0.9106 198 R 0.1302 0.0169 0.8529 199 T 0.1440 0.0201 0.8359 200 V 0.0119 0.8511 0.1370 201 G 0.0071 0.8902 0.1026 202 E 0.0066 0.9173 0.0761 203 V 0.0071 0.9139 0.0790 204 L 0.0088 0.8926 0.0986 205 M 0.0106 0.8523 0.1371 206 G 0.0133 0.8440 0.1427 207 K 0.0182 0.8292 0.1527 208 I 0.0136 0.8214 0.1650 209 E 0.0121 0.7994 0.1884 210 S 0.0133 0.7658 0.2209 211 L 0.0230 0.6658 0.3112 212 K 0.0173 0.7523 0.2304 213 G 0.0116 0.8561 0.1323 214 S 0.0119 0.8976 0.0905 215 G 0.0088 0.9348 0.0564 216 F 0.0086 0.9443 0.0471 217 L 0.0082 0.9462 0.0456 218 R 0.0076 0.9447 0.0477 219 L 0.0090 0.9366 0.0543 220 I 0.0106 0.9168 0.0726 221 E 0.0146 0.8543 0.1311 222 S 0.0251 0.7546 0.2203 223 L 0.0551 0.6034 0.3414 224 I 0.0523 0.4821 0.4655 225 G 0.0513 0.3804 0.5683 226 E 0.0546 0.3202 0.6252 227 T 0.0763 0.2860 0.6377 228 V 0.0817 0.3840 0.5344 229 E 0.1349 0.4012 0.4640 230 R 0.2927 0.2991 0.4081 231 Y 0.5971 0.1651 0.2378 232 L 0.6391 0.1828 0.1780 233 D 0.6144 0.1956 0.1901 234 A 0.2894 0.2848 0.4258 235 G 0.1870 0.2253 0.5876 236 L 0.2334 0.3963 0.3703 237 E 0.2124 0.4697 0.3180 238 N 0.1674 0.4594 0.3732 239 L 0.1339 0.3647 0.5014 240 L 0.0749 0.2651 0.6601 241 K 0.0604 0.1854 0.7542 242 D 0.0353 0.4439 0.5208 243 E 0.0273 0.4546 0.5181 244 T 0.0368 0.4950 0.4682 245 L 0.0487 0.2721 0.6792 246 T 0.0800 0.1588 0.7613 247 L 0.0053 0.9033 0.0914 248 E 0.0049 0.9216 0.0735 249 D 0.0059 0.9124 0.0817 250 I 0.0055 0.9394 0.0551 251 R 0.0049 0.9527 0.0423 252 N 0.0050 0.9496 0.0454 253 L 0.0050 0.9472 0.0479 254 L 0.0048 0.9479 0.0473 255 E 0.0048 0.9273 0.0679 256 E 0.0049 0.9167 0.0784 257 V 0.0067 0.8902 0.1032 258 K 0.0078 0.8325 0.1597 259 D 0.0127 0.7143 0.2731 260 Q 0.0219 0.6901 0.2879 261 K 0.0289 0.7180 0.2531 262 F 0.0340 0.7816 0.1845 263 L 0.0354 0.8453 0.1193 264 E 0.0480 0.8255 0.1264 265 S 0.0537 0.7874 0.1589 266 L 0.0640 0.7071 0.2289 267 V 0.0955 0.4275 0.4770 268 G 0.0586 0.2122 0.7293 269 E 0.0463 0.0864 0.8673 270 G 0.0910 0.0587 0.8504 271 I 0.6334 0.0109 0.3556 272 T 0.8768 0.0047 0.1185 273 V 0.9082 0.0037 0.0880 274 R 0.8876 0.0049 0.1075 275 I 0.7155 0.0193 0.2652 276 G 0.2814 0.0549 0.6638 277 R 0.1416 0.1245 0.7339 278 E 0.0970 0.1984 0.7046 279 I 0.0951 0.1901 0.7148 280 G 0.0755 0.1590 0.7655 281 R 0.0835 0.2065 0.7100 282 K 0.0993 0.2480 0.6526 283 K 0.1094 0.2475 0.6431 284 L 0.1108 0.2706 0.6186 285 E 0.0675 0.2999 0.6326 286 K 0.1212 0.1375 0.7413 287 F 0.3571 0.0187 0.6243 288 A 0.6693 0.0091 0.3216 289 V 0.9010 0.0039 0.0951 290 F 0.9020 0.0057 0.0923 291 S 0.8839 0.0050 0.1111 292 G 0.7908 0.0079 0.2013 293 K 0.6558 0.0172 0.3270 294 Y 0.6511 0.0301 0.3188 295 F 0.6981 0.0290 0.2728 296 K 0.4650 0.0432 0.4918 297 G 0.0731 0.0334 0.8936 298 E 0.0671 0.0508 0.8821 299 S 0.5279 0.0122 0.4599 300 P 0.7671 0.0058 0.2270 301 I 0.7840 0.0226 0.1934 302 G 0.8409 0.0094 0.1497 303 S 0.9047 0.0036 0.0917 304 V 0.9137 0.0050 0.0812 305 Y 0.9220 0.0035 0.0745 306 L 0.9039 0.0053 0.0908 307 F 0.7822 0.0169 0.2009 308 T 0.4286 0.0172 0.5542 309 S 0.1865 0.0962 0.7173 310 K 0.1412 0.1431 0.7158 311 V 0.1354 0.1521 0.7125 312 T 0.0939 0.0828 0.8233 313 K 0.0799 0.1275 0.7926 314 Y 0.0234 0.6710 0.3056 315 D 0.0081 0.8506 0.1413 316 R 0.0101 0.8721 0.1178 317 N 0.0078 0.9219 0.0703 318 H 0.0053 0.9520 0.0427 319 R 0.0047 0.9578 0.0375 320 V 0.0047 0.9591 0.0362 321 F 0.0047 0.9605 0.0348 322 E 0.0047 0.9607 0.0346 323 Y 0.0047 0.9606 0.0347 324 I 0.0047 0.9596 0.0357 325 L 0.0047 0.9596 0.0357 326 N 0.0049 0.9565 0.0386 327 R 0.0049 0.9535 0.0416 328 L 0.0048 0.9501 0.0451 329 S 0.0049 0.9515 0.0437 330 E 0.0053 0.9366 0.0581 331 Y 0.0062 0.9130 0.0808 332 F 0.0118 0.8612 0.1270 333 T 0.0126 0.7654 0.2220 334 S 0.0201 0.7084 0.2716 335 T 0.0248 0.6403 0.3349 336 S 0.0534 0.4706 0.4760 337 R 0.0416 0.2734 0.6851 338 R 0.0313 0.0571 0.9116