# This file is the result of combining several RDB files, specifically # T0248.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0248.t2k.stride-ebghtl.rdb (weight 1.24869) # T0248.t2k.str2.rdb (weight 1.54758) # T0248.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 T0248.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0248 # 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 T0248.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 5 # # ============================================ # Comments from T0248.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0248 # 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 T0248.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 5 # # ============================================ # Comments from T0248.t2k.str2.rdb # ============================================ # TARGET T0248 # 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 T0248.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 5 # # ============================================ # Comments from T0248.t2k.alpha.rdb # ============================================ # TARGET T0248 # 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 T0248.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 5 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0448 0.1087 0.8465 2 I 0.0842 0.1702 0.7456 3 N 0.0796 0.2225 0.6978 4 K 0.0666 0.2462 0.6872 5 P 0.0154 0.7516 0.2330 6 N 0.0102 0.8300 0.1598 7 Q 0.0103 0.8688 0.1209 8 F 0.0075 0.9169 0.0757 9 V 0.0066 0.9280 0.0654 10 N 0.0065 0.8996 0.0940 11 H 0.0074 0.8646 0.1281 12 L 0.0158 0.8494 0.1348 13 S 0.0154 0.7954 0.1891 14 A 0.0192 0.7089 0.2719 15 L 0.0349 0.6428 0.3223 16 K 0.0501 0.4832 0.4667 17 K 0.0649 0.4006 0.5345 18 H 0.1127 0.3569 0.5304 19 F 0.1214 0.4201 0.4585 20 A 0.0873 0.4247 0.4880 21 S 0.0842 0.4005 0.5153 22 Y 0.0073 0.9116 0.0811 23 K 0.0052 0.9389 0.0559 24 E 0.0050 0.9419 0.0531 25 L 0.0048 0.9454 0.0498 26 R 0.0050 0.9403 0.0546 27 E 0.0053 0.9120 0.0827 28 A 0.0074 0.8687 0.1239 29 F 0.0171 0.8135 0.1694 30 N 0.0122 0.7652 0.2226 31 D 0.0166 0.6662 0.3171 32 Y 0.0324 0.5764 0.3912 33 H 0.0558 0.4997 0.4445 34 K 0.0552 0.4336 0.5112 35 H 0.0623 0.3181 0.6196 36 N 0.0424 0.3211 0.6365 37 G 0.0301 0.3633 0.6066 38 D 0.0446 0.4139 0.5415 39 E 0.0439 0.6430 0.3131 40 L 0.0500 0.7247 0.2252 41 T 0.0484 0.7823 0.1693 42 T 0.0411 0.8677 0.0912 43 F 0.0436 0.8608 0.0955 44 F 0.0274 0.8933 0.0793 45 L 0.0098 0.9241 0.0661 46 H 0.0071 0.9298 0.0631 47 Q 0.0055 0.9364 0.0582 48 F 0.0054 0.9456 0.0490 49 D 0.0052 0.9419 0.0528 50 K 0.0052 0.9336 0.0613 51 V 0.0057 0.9405 0.0538 52 M 0.0058 0.9365 0.0577 53 E 0.0077 0.9056 0.0867 54 L 0.0098 0.8565 0.1337 55 V 0.0260 0.7487 0.2253 56 K 0.0223 0.6579 0.3198 57 Q 0.0249 0.6150 0.3601 58 K 0.0334 0.6985 0.2681 59 D 0.0361 0.7221 0.2418 60 F 0.0104 0.8756 0.1139 61 K 0.0075 0.9234 0.0692 62 T 0.0061 0.9283 0.0656 63 A 0.0049 0.9372 0.0579 64 Q 0.0052 0.9442 0.0506 65 S 0.0054 0.9306 0.0640 66 R 0.0064 0.9197 0.0739 67 C 0.0083 0.9135 0.0781 68 E 0.0059 0.9123 0.0818 69 E 0.0068 0.8895 0.1037 70 E 0.0082 0.8412 0.1506 71 L 0.0167 0.7053 0.2780 72 A 0.0192 0.5322 0.4486 73 A 0.0482 0.2342 0.7176 74 P 0.0261 0.2659 0.7080 75 Y 0.0678 0.2592 0.6730 76 L 0.1104 0.1316 0.7580 77 P 0.0675 0.1580 0.7745 78 K 0.0121 0.7837 0.2042 79 P 0.0082 0.8743 0.1175 80 L 0.0062 0.9102 0.0836 81 V 0.0051 0.9291 0.0659 82 S 0.0053 0.9275 0.0672 83 F 0.0049 0.9365 0.0586 84 F 0.0051 0.9383 0.0566 85 Q 0.0049 0.9314 0.0636 86 S 0.0051 0.9183 0.0765 87 L 0.0050 0.9300 0.0651 88 L 0.0058 0.9323 0.0619 89 Q 0.0078 0.9144 0.0779 90 L 0.0095 0.8920 0.0985 91 V 0.0179 0.8510 0.1310 92 N 0.0178 0.7800 0.2022 93 H 0.0117 0.8523 0.1360 94 D 0.0132 0.8583 0.1284 95 L 0.0172 0.8417 0.1411 96 L 0.0201 0.8096 0.1704 97 E 0.0185 0.7679 0.2135 98 Q 0.0317 0.6757 0.2926 99 Q 0.0224 0.7437 0.2339 100 N 0.0233 0.7519 0.2248 101 A 0.0206 0.8018 0.1777 102 A 0.0182 0.7972 0.1847 103 L 0.0147 0.7660 0.2193 104 A 0.0158 0.6412 0.3430 105 S 0.0207 0.4293 0.5500 106 L 0.0628 0.2108 0.7264 107 P 0.0652 0.1538 0.7811 108 A 0.0066 0.8659 0.1275 109 A 0.0054 0.9255 0.0692 110 K 0.0055 0.9379 0.0565 111 I 0.0063 0.9433 0.0504 112 I 0.0072 0.9473 0.0455 113 E 0.0072 0.9489 0.0438 114 L 0.0060 0.9425 0.0514 115 V 0.0063 0.9311 0.0625 116 L 0.0082 0.8824 0.1094 117 Q 0.0156 0.6416 0.3428 118 D 0.0267 0.2564 0.7169 119 Y 0.0647 0.1102 0.8251 120 P 0.0472 0.2495 0.7033 121 N 0.0338 0.4104 0.5557 122 K 0.0578 0.4710 0.4711 123 L 0.1215 0.5501 0.3284 124 N 0.1802 0.5944 0.2253 125 M 0.1989 0.6608 0.1404 126 I 0.1713 0.7231 0.1056 127 H 0.1450 0.7481 0.1070 128 Y 0.1555 0.7213 0.1232 129 L 0.1767 0.6820 0.1413 130 L 0.1424 0.6529 0.2048 131 P 0.0968 0.5875 0.3157 132 K 0.0769 0.5466 0.3765 133 T 0.0785 0.5305 0.3910 134 K 0.0506 0.5121 0.4372 135 A 0.0320 0.3846 0.5834 136 F 0.0686 0.2115 0.7199 137 V 0.1666 0.0551 0.7783 138 K 0.1241 0.0399 0.8360 139 P 0.0238 0.6583 0.3179 140 H 0.0166 0.6899 0.2935 141 L 0.0173 0.8075 0.1752 142 L 0.0516 0.7963 0.1521 143 Q 0.0714 0.7647 0.1639 144 R 0.1113 0.7032 0.1855 145 L 0.1499 0.6734 0.1766 146 Q 0.1844 0.6061 0.2095 147 F 0.3426 0.5103 0.1470 148 V 0.4284 0.4333 0.1383 149 L 0.4703 0.3277 0.2020 150 T 0.3065 0.2315 0.4620 151 D 0.1038 0.3396 0.5566 152 S 0.0400 0.6064 0.3537 153 E 0.0530 0.6257 0.3213 154 L 0.0413 0.6677 0.2910 155 L 0.0340 0.6328 0.3332 156 E 0.0384 0.6020 0.3596 157 L 0.0198 0.6479 0.3323 158 K 0.0319 0.5835 0.3847 159 R 0.0298 0.7188 0.2514 160 F 0.0406 0.8018 0.1576 161 S 0.0383 0.8423 0.1194 162 F 0.0197 0.9126 0.0677 163 F 0.0158 0.9277 0.0565 164 Q 0.0087 0.9330 0.0582 165 A 0.0067 0.9221 0.0712 166 L 0.0086 0.8790 0.1124 167 N 0.0101 0.7329 0.2570 168 Q 0.0181 0.5536 0.4283 169 I 0.0725 0.1582 0.7692 170 P 0.0645 0.1332 0.8023 171 G 0.0564 0.2868 0.6568 172 F 0.0755 0.3015 0.6230 173 Q 0.0872 0.2484 0.6644 174 G 0.1105 0.1149 0.7746 175 E 0.2246 0.1033 0.6721 176 Q 0.4650 0.0913 0.4437 177 V 0.6201 0.1052 0.2747 178 E 0.7204 0.0761 0.2035 179 Y 0.7417 0.0740 0.1843 180 F 0.6971 0.0822 0.2207 181 N 0.5503 0.1066 0.3431 182 S 0.2541 0.1888 0.5571 183 K 0.2074 0.2658 0.5268 184 L 0.2920 0.2359 0.4721 185 K 0.3345 0.1034 0.5621 186 Q 0.5882 0.0319 0.3800 187 K 0.8578 0.0113 0.1310 188 F 0.8972 0.0059 0.0969 189 T 0.9176 0.0041 0.0784 190 L 0.8967 0.0048 0.0985 191 T 0.8534 0.0061 0.1406 192 L 0.6230 0.0555 0.3215 193 G 0.2894 0.0871 0.6235 194 E 0.3630 0.1030 0.5341 195 F 0.5502 0.0812 0.3686 196 E 0.6092 0.0808 0.3100 197 I 0.5855 0.0916 0.3229 198 A 0.4593 0.1281 0.4126 199 Q 0.3081 0.1589 0.5330 200 Q 0.1337 0.1502 0.7161 201 P 0.0365 0.2693 0.6943 202 D 0.0337 0.2787 0.6876 203 A 0.0368 0.4772 0.4860 204 K 0.0136 0.7148 0.2716 205 A 0.0065 0.9023 0.0912 206 Y 0.0061 0.9146 0.0793 207 F 0.0048 0.9459 0.0493 208 E 0.0048 0.9551 0.0401 209 Q 0.0049 0.9552 0.0399 210 L 0.0048 0.9540 0.0412 211 I 0.0048 0.9543 0.0410 212 T 0.0048 0.9455 0.0496 213 Q 0.0051 0.9266 0.0684 214 I 0.0089 0.9153 0.0758 215 Q 0.0094 0.8952 0.0955 216 Q 0.0112 0.8517 0.1372 217 L 0.0206 0.7725 0.2069 218 F 0.0500 0.6366 0.3134 219 L 0.0630 0.4407 0.4963 220 K 0.0486 0.3153 0.6362 221 E 0.0561 0.1966 0.7473 222 P 0.0405 0.2950 0.6645 223 V 0.0405 0.4300 0.5295 224 N 0.0216 0.6298 0.3486 225 A 0.0112 0.8704 0.1184 226 E 0.0074 0.8982 0.0944 227 F 0.0075 0.9149 0.0776 228 A 0.0051 0.9425 0.0524 229 N 0.0051 0.9476 0.0473 230 E 0.0050 0.9460 0.0490 231 I 0.0048 0.9533 0.0419 232 I 0.0049 0.9503 0.0448 233 D 0.0049 0.9507 0.0444 234 A 0.0052 0.9412 0.0536 235 F 0.0054 0.9345 0.0601 236 L 0.0072 0.8894 0.1034 237 V 0.0090 0.8367 0.1543 238 S 0.0177 0.7059 0.2765 239 Y 0.0517 0.5603 0.3880 240 F 0.0831 0.1416 0.7753 241 P 0.0343 0.1596 0.8061 242 L 0.0371 0.1476 0.8153 243 H 0.0654 0.0653 0.8693 244 P 0.0327 0.1125 0.8547 245 P 0.0495 0.0702 0.8803 246 V 0.1628 0.0491 0.7881 247 P 0.2303 0.0470 0.7227 248 L 0.0206 0.8068 0.1726 249 A 0.0063 0.8629 0.1309 250 Q 0.0062 0.9181 0.0758 251 L 0.0053 0.9354 0.0593 252 A 0.0051 0.9464 0.0484 253 A 0.0050 0.9495 0.0454 254 K 0.0049 0.9473 0.0477 255 I 0.0048 0.9503 0.0449 256 Y 0.0048 0.9543 0.0409 257 E 0.0049 0.9540 0.0412 258 Y 0.0050 0.9485 0.0465 259 V 0.0054 0.9483 0.0462 260 S 0.0058 0.9469 0.0473 261 Q 0.0066 0.9275 0.0659 262 I 0.0084 0.9044 0.0872 263 V 0.0195 0.8104 0.1701 264 L 0.0228 0.6319 0.3453 265 N 0.0395 0.3052 0.6553 266 E 0.0526 0.2297 0.7176 267 A 0.1291 0.1662 0.7047 268 V 0.1051 0.2286 0.6663 269 N 0.0985 0.2044 0.6970 270 L 0.0966 0.1611 0.7423 271 K 0.0821 0.1201 0.7979 272 D 0.0776 0.0712 0.8512 273 E 0.0189 0.4496 0.5315 274 L 0.0501 0.5151 0.4348 275 I 0.1105 0.6726 0.2169 276 K 0.1923 0.6527 0.1550 277 L 0.2924 0.6141 0.0935 278 I 0.2999 0.6215 0.0786 279 V 0.1781 0.7146 0.1073 280 H 0.0855 0.7710 0.1435 281 T 0.0544 0.8204 0.1251 282 L 0.0379 0.8576 0.1045 283 Y 0.0443 0.8489 0.1067 284 E 0.0252 0.8358 0.1390 285 Q 0.0187 0.8026 0.1787 286 L 0.0333 0.7286 0.2381 287 D 0.0316 0.5405 0.4279 288 R 0.0435 0.4721 0.4844 289 P 0.0505 0.4087 0.5407 290 V 0.0606 0.3052 0.6342 291 G 0.0633 0.1997 0.7370 292 D 0.0923 0.1688 0.7389 293 E 0.0827 0.1529 0.7644 294 N 0.0487 0.0363 0.9150