# This file is the result of combining several RDB files, specifically # T0550.t04.dssp-ebghstl.rdb (weight 1.53986) # T0550.t04.stride-ebghtl.rdb (weight 1.24869) # T0550.t04.str2.rdb (weight 1.54758) # T0550.t04.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 T0550.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0550 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0550.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 604 # # ============================================ # Comments from T0550.t04.stride-ebghtl.rdb # ============================================ # TARGET T0550 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0550.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 604 # # ============================================ # Comments from T0550.t04.str2.rdb # ============================================ # TARGET T0550 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0550.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 604 # # ============================================ # Comments from T0550.t04.alpha.rdb # ============================================ # TARGET T0550 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0550.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 604 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0320 0.4038 0.5642 2 K 0.0163 0.8321 0.1516 3 N 0.0118 0.8959 0.0922 4 I 0.0051 0.9538 0.0412 5 Y 0.0047 0.9593 0.0360 6 I 0.0047 0.9610 0.0343 7 Y 0.0046 0.9613 0.0341 8 L 0.0047 0.9611 0.0342 9 S 0.0046 0.9614 0.0340 10 L 0.0046 0.9615 0.0339 11 L 0.0046 0.9614 0.0340 12 A 0.0046 0.9613 0.0340 13 V 0.0046 0.9612 0.0341 14 I 0.0046 0.9611 0.0342 15 V 0.0047 0.9590 0.0363 16 L 0.0051 0.9472 0.0476 17 G 0.0073 0.9135 0.0792 18 T 0.0198 0.8338 0.1464 19 A 0.0447 0.5921 0.3633 20 C 0.0745 0.3286 0.5968 21 N 0.0598 0.1808 0.7594 22 N 0.0396 0.1727 0.7878 23 E 0.0441 0.2292 0.7267 24 W 0.0554 0.3096 0.6350 25 E 0.0696 0.3364 0.5940 26 D 0.0697 0.3666 0.5637 27 E 0.0803 0.4667 0.4531 28 Q 0.1356 0.4138 0.4506 29 Y 0.1762 0.3356 0.4882 30 E 0.1400 0.3273 0.5327 31 Q 0.1646 0.2363 0.5992 32 Y 0.4096 0.1211 0.4693 33 V 0.6203 0.0482 0.3314 34 S 0.6508 0.0315 0.3177 35 F 0.5228 0.0320 0.4452 36 K 0.3743 0.0443 0.5814 37 A 0.3078 0.0302 0.6620 38 P 0.3341 0.0565 0.6094 39 I 0.4233 0.0613 0.5153 40 A 0.3907 0.0661 0.5432 41 S 0.2421 0.0623 0.6956 42 G 0.1340 0.0722 0.7938 43 S 0.1563 0.0897 0.7540 44 D 0.1195 0.0778 0.8027 45 G 0.1700 0.0465 0.7835 46 V 0.5003 0.0231 0.4766 47 T 0.7341 0.0130 0.2529 48 T 0.8614 0.0051 0.1336 49 I 0.9025 0.0035 0.0939 50 Y 0.9144 0.0034 0.0822 51 V 0.9091 0.0039 0.0870 52 R 0.8956 0.0047 0.0998 53 Y 0.8479 0.0098 0.1422 54 K 0.5776 0.0344 0.3881 55 D 0.2594 0.0675 0.6730 56 N 0.0960 0.0418 0.8622 57 G 0.1697 0.0334 0.7968 58 K 0.6190 0.0157 0.3653 59 V 0.8723 0.0038 0.1239 60 T 0.8975 0.0086 0.0938 61 Y 0.9184 0.0037 0.0779 62 Q 0.9182 0.0031 0.0786 63 L 0.9106 0.0037 0.0857 64 P 0.9117 0.0033 0.0850 65 I 0.9053 0.0037 0.0909 66 I 0.8673 0.0054 0.1272 67 V 0.6979 0.0112 0.2909 68 S 0.3521 0.0377 0.6102 69 G 0.1539 0.0325 0.8136 70 S 0.3167 0.0393 0.6440 71 T 0.4445 0.0283 0.5272 72 V 0.3879 0.0629 0.5492 73 N 0.2891 0.0761 0.6347 74 S 0.2058 0.1103 0.6839 75 Q 0.2402 0.0884 0.6713 76 D 0.3667 0.0380 0.5953 77 R 0.6414 0.0098 0.3488 78 D 0.8141 0.0040 0.1819 79 I 0.8991 0.0037 0.0972 80 H 0.9127 0.0037 0.0836 81 I 0.9184 0.0033 0.0782 82 A 0.8593 0.0042 0.1365 83 V 0.6619 0.0103 0.3278 84 D 0.1378 0.0090 0.8532 85 K 0.0069 0.7858 0.2073 86 D 0.0052 0.8951 0.0997 87 T 0.0058 0.9241 0.0701 88 L 0.0070 0.9352 0.0578 89 K 0.0074 0.9330 0.0596 90 T 0.0077 0.9057 0.0866 91 L 0.0152 0.8386 0.1462 92 N 0.0414 0.6295 0.3291 93 I 0.0185 0.7324 0.2491 94 E 0.0286 0.6720 0.2994 95 R 0.0349 0.5410 0.4240 96 F 0.1044 0.3429 0.5527 97 S 0.0946 0.1905 0.7149 98 L 0.1057 0.1273 0.7671 99 Y 0.0973 0.0796 0.8231 100 R 0.0890 0.0677 0.8433 101 P 0.0449 0.4102 0.5449 102 E 0.0752 0.4457 0.4791 103 L 0.3162 0.3598 0.3240 104 W 0.4931 0.2635 0.2434 105 Y 0.5529 0.2327 0.2144 106 T 0.5447 0.2107 0.2446 107 E 0.5468 0.1742 0.2790 108 M 0.3581 0.0967 0.5452 109 E 0.1973 0.1155 0.6872 110 E 0.0561 0.3409 0.6031 111 D 0.0506 0.2401 0.7093 112 K 0.2632 0.1571 0.5797 113 Y 0.6112 0.0233 0.3655 114 E 0.6733 0.0188 0.3079 115 F 0.4179 0.0124 0.5697 116 P 0.1957 0.0510 0.7532 117 E 0.1186 0.0775 0.8039 118 T 0.4403 0.0331 0.5266 119 V 0.7833 0.0073 0.2093 120 H 0.8554 0.0057 0.1389 121 I 0.6894 0.0070 0.3036 122 P 0.3287 0.0115 0.6599 123 A 0.0549 0.0798 0.8654 124 G 0.0396 0.0573 0.9031 125 S 0.3265 0.0397 0.6338 126 C 0.6422 0.0187 0.3391 127 V 0.6898 0.0276 0.2825 128 E 0.7243 0.0187 0.2570 129 L 0.8116 0.0068 0.1816 130 L 0.8730 0.0040 0.1229 131 N 0.9032 0.0034 0.0934 132 I 0.9014 0.0036 0.0949 133 D 0.8823 0.0036 0.1142 134 F 0.7911 0.0070 0.2019 135 N 0.4883 0.0070 0.5047 136 L 0.0792 0.5244 0.3964 137 Q 0.0305 0.5205 0.4489 138 D 0.0473 0.5489 0.4038 139 I 0.1480 0.2311 0.6209 140 D 0.1271 0.1716 0.7013 141 M 0.0811 0.4331 0.4859 142 L 0.1127 0.2322 0.6550 143 E 0.1984 0.1581 0.6435 144 K 0.5227 0.0453 0.4320 145 W 0.8091 0.0090 0.1819 146 V 0.8621 0.0036 0.1343 147 L 0.8467 0.0062 0.1471 148 P 0.8259 0.0042 0.1699 149 L 0.8454 0.0042 0.1504 150 T 0.8935 0.0040 0.1025 151 I 0.8756 0.0042 0.1202 152 V 0.7356 0.0136 0.2508 153 D 0.5476 0.0188 0.4336 154 D 0.1672 0.0709 0.7619 155 G 0.1025 0.0619 0.8357 156 S 0.2223 0.0624 0.7152 157 Y 0.4192 0.0363 0.5445 158 A 0.6349 0.0303 0.3348 159 Y 0.6976 0.0368 0.2656 160 Q 0.5945 0.0368 0.3687 161 S 0.4510 0.0699 0.4790 162 H 0.1887 0.0455 0.7658 163 P 0.0646 0.1563 0.7791 164 R 0.1038 0.1811 0.7151 165 K 0.2462 0.2442 0.5096 166 N 0.4077 0.2574 0.3349 167 Y 0.5317 0.3254 0.1430 168 A 0.5864 0.3017 0.1119 169 K 0.5689 0.3226 0.1085 170 A 0.5417 0.3422 0.1160 171 L 0.4794 0.3641 0.1565 172 L 0.3644 0.3777 0.2579 173 K 0.2685 0.2927 0.4387 174 V 0.3047 0.1831 0.5123 175 V 0.3012 0.0558 0.6430 176 P 0.2524 0.0725 0.6751 177 F 0.1926 0.1141 0.6932 178 N 0.1825 0.1535 0.6639 179 N 0.1340 0.2587 0.6074 180 Y 0.1471 0.2630 0.5900 181 S 0.1376 0.1857 0.6766 182 G 0.0992 0.1175 0.7833 183 S 0.1611 0.1088 0.7300 184 Y 0.2311 0.1148 0.6542 185 T 0.1987 0.1016 0.6997 186 A 0.1588 0.1480 0.6932 187 S 0.2628 0.1206 0.6166 188 S 0.4772 0.0794 0.4433 189 M 0.6595 0.0342 0.3063 190 K 0.7627 0.0240 0.2133 191 V 0.8154 0.0203 0.1643 192 Y 0.7752 0.0277 0.1971 193 T 0.7398 0.0291 0.2312 194 Y 0.6252 0.0454 0.3294 195 I 0.4180 0.0536 0.5284 196 N 0.1421 0.0525 0.8054 197 G 0.0854 0.0444 0.8702 198 K 0.1589 0.0253 0.8158 199 P 0.1690 0.0678 0.7632 200 D 0.1574 0.1151 0.7275 201 T 0.3172 0.1193 0.5635 202 N 0.4711 0.0645 0.4645 203 A 0.6450 0.0469 0.3080 204 R 0.7722 0.0289 0.1989 205 T 0.8082 0.0272 0.1646 206 T 0.7600 0.0318 0.2081 207 D 0.7376 0.0261 0.2363 208 K 0.7516 0.0300 0.2184 209 R 0.6777 0.0300 0.2923 210 T 0.4436 0.0881 0.4683 211 G 0.2649 0.0776 0.6575 212 Y 0.3836 0.0660 0.5504 213 V 0.5438 0.0422 0.4140 214 V 0.4558 0.0470 0.4972 215 D 0.3280 0.0539 0.6180 216 N 0.1742 0.0934 0.7325 217 N 0.2190 0.0721 0.7089 218 S 0.6202 0.0486 0.3313 219 I 0.8310 0.0278 0.1411 220 F 0.8468 0.0304 0.1228 221 F 0.7981 0.0426 0.1594 222 Y 0.6761 0.0773 0.2466 223 A 0.4032 0.1274 0.4694 224 G 0.2175 0.1135 0.6690 225 L 0.3431 0.1228 0.5341 226 I 0.4040 0.1144 0.4816 227 N 0.2552 0.1195 0.6253 228 E 0.1099 0.2751 0.6151 229 D 0.1110 0.2431 0.6458 230 M 0.0970 0.3204 0.5826 231 D 0.0838 0.2886 0.6275 232 K 0.0415 0.6743 0.2842 233 D 0.0630 0.7150 0.2220 234 M 0.1084 0.6698 0.2217 235 R 0.1294 0.5449 0.3257 236 K 0.1120 0.5036 0.3844 237 K 0.0800 0.3205 0.5995 238 Y 0.1553 0.0913 0.7533 239 K 0.4271 0.0197 0.5532 240 I 0.8121 0.0056 0.1823 241 N 0.8949 0.0040 0.1010 242 V 0.9147 0.0033 0.0820 243 H 0.9146 0.0039 0.0815 244 F 0.8780 0.0052 0.1168 245 K 0.5459 0.0208 0.4333 246 E 0.1558 0.0675 0.7767 247 D 0.0697 0.0326 0.8977 248 G 0.1164 0.0396 0.8440 249 T 0.5870 0.0201 0.3929 250 L 0.8231 0.0070 0.1699 251 D 0.7725 0.0106 0.2170 252 M 0.7108 0.0174 0.2719 253 K 0.5559 0.0262 0.4180 254 Q 0.3673 0.0727 0.5601 255 D 0.2131 0.0617 0.7253 256 D 0.1131 0.0302 0.8567 257 P 0.0266 0.1758 0.7976 258 S 0.0474 0.1490 0.8037 259 N 0.1125 0.1298 0.7577 260 E 0.1942 0.0715 0.7343 261 M 0.4255 0.0657 0.5088 262 E 0.5228 0.0738 0.4034 263 F 0.7167 0.0405 0.2428 264 E 0.7482 0.0381 0.2137 265 L 0.6726 0.0381 0.2894 266 I 0.4450 0.0446 0.5104 267 G 0.1689 0.0545 0.7767 268 T 0.1437 0.0267 0.8296 269 P 0.1801 0.0788 0.7411 270 T 0.5435 0.0569 0.3996 271 Y 0.7940 0.0273 0.1787 272 S 0.8331 0.0299 0.1370 273 S 0.8723 0.0214 0.1063 274 T 0.8855 0.0174 0.0971 275 S 0.8964 0.0134 0.0902 276 V 0.8845 0.0181 0.0974 277 M 0.7925 0.0341 0.1735 278 D 0.4382 0.0745 0.4872 279 A 0.2132 0.1080 0.6788 280 T 0.3834 0.0850 0.5316 281 R 0.5126 0.0883 0.3991 282 P 0.6343 0.0818 0.2839 283 Y 0.6318 0.1154 0.2528 284 L 0.6578 0.1176 0.2246 285 E 0.3060 0.0963 0.5978 286 R 0.3589 0.0681 0.5730 287 R 0.7909 0.0381 0.1710 288 Y 0.8943 0.0202 0.0855 289 V 0.8658 0.0273 0.1069 290 Q 0.8644 0.0221 0.1135 291 I 0.8144 0.0280 0.1577 292 M 0.7161 0.0420 0.2419 293 F 0.5941 0.0603 0.3456 294 E 0.5267 0.0646 0.4086 295 Y 0.4640 0.0470 0.4890 296 D 0.2899 0.0419 0.6682 297 F 0.1818 0.0958 0.7224 298 Q 0.1321 0.1282 0.7397 299 D 0.1718 0.1307 0.6975 300 F 0.3209 0.0965 0.5826 301 T 0.4319 0.0781 0.4899 302 Y 0.4027 0.0865 0.5109 303 G 0.2306 0.0681 0.7013 304 G 0.1282 0.0864 0.7854 305 S 0.1360 0.0978 0.7662 306 G 0.1957 0.0963 0.7080 307 T 0.2794 0.0841 0.6365 308 E 0.3840 0.0820 0.5340 309 V 0.4819 0.0663 0.4518 310 I 0.4099 0.0413 0.5488 311 P 0.2953 0.0682 0.6365 312 I 0.2668 0.1180 0.6152 313 K 0.2387 0.1509 0.6104 314 Y 0.3530 0.1156 0.5313 315 R 0.4769 0.0983 0.4248 316 V 0.5067 0.1236 0.3697 317 A 0.3317 0.1754 0.4929 318 G 0.3434 0.1299 0.5267 319 S 0.5280 0.1742 0.2978 320 M 0.5414 0.2783 0.1803 321 T 0.4477 0.3791 0.1732 322 L 0.4145 0.4480 0.1374 323 L 0.4643 0.4099 0.1258 324 R 0.4530 0.4051 0.1419 325 N 0.3686 0.4045 0.2268 326 I 0.2228 0.3667 0.4106 327 N 0.1276 0.2204 0.6521 328 T 0.1693 0.1422 0.6886 329 Q 0.2025 0.0510 0.7466 330 I 0.1353 0.0131 0.8516 331 P 0.0693 0.0124 0.9183 332 D 0.0052 0.9318 0.0630 333 E 0.0050 0.9515 0.0436 334 D 0.0051 0.9486 0.0463 335 Q 0.0061 0.9349 0.0590 336 Q 0.0085 0.8574 0.1341 337 I 0.0122 0.6711 0.3167 338 E 0.0187 0.3302 0.6511 339 W 0.0340 0.0858 0.8802