# This file is the result of combining several RDB files, specifically # T0422.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0422.t2k.stride-ebghtl.rdb (weight 1.24869) # T0422.t2k.str2.rdb (weight 1.54758) # T0422.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 T0422.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0422 # 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 T0422.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 5596 # # ============================================ # Comments from T0422.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0422 # 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 T0422.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 5596 # # ============================================ # Comments from T0422.t2k.str2.rdb # ============================================ # TARGET T0422 # 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 T0422.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 5596 # # ============================================ # Comments from T0422.t2k.alpha.rdb # ============================================ # TARGET T0422 # 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 T0422.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 5596 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1297 0.0572 0.8131 2 H 0.2167 0.0647 0.7186 3 H 0.2087 0.0842 0.7071 4 H 0.1341 0.1321 0.7338 5 H 0.1011 0.2382 0.6608 6 H 0.1371 0.2673 0.5956 7 H 0.2802 0.2867 0.4331 8 S 0.2947 0.3598 0.3455 9 S 0.2619 0.3932 0.3449 10 G 0.2909 0.4871 0.2220 11 V 0.2995 0.5563 0.1442 12 D 0.2889 0.5771 0.1340 13 L 0.2921 0.5424 0.1655 14 G 0.2854 0.4767 0.2379 15 T 0.2611 0.3964 0.3425 16 E 0.2131 0.2255 0.5614 17 N 0.1568 0.1214 0.7217 18 L 0.3115 0.0823 0.6061 19 Y 0.6621 0.0356 0.3023 20 F 0.8178 0.0169 0.1652 21 Q 0.8587 0.0123 0.1290 22 S 0.8284 0.0135 0.1581 23 M 0.7110 0.0155 0.2735 24 V 0.4226 0.0171 0.5603 25 P 0.2005 0.0228 0.7767 26 P 0.1192 0.0560 0.8248 27 I 0.1210 0.0615 0.8175 28 P 0.1391 0.1058 0.7551 29 K 0.2984 0.1079 0.5936 30 Q 0.5846 0.1064 0.3089 31 D 0.7049 0.1130 0.1820 32 G 0.7349 0.1227 0.1425 33 G 0.6960 0.1515 0.1525 34 E 0.6218 0.1902 0.1880 35 Q 0.4961 0.2347 0.2692 36 N 0.3519 0.2818 0.3663 37 G 0.2408 0.3213 0.4379 38 G 0.2043 0.3234 0.4723 39 M 0.1519 0.3867 0.4614 40 Q 0.1017 0.5652 0.3332 41 C 0.1084 0.6142 0.2775 42 K 0.1461 0.6317 0.2221 43 P 0.1771 0.6272 0.1956 44 Y 0.2017 0.6046 0.1937 45 G 0.1714 0.6857 0.1428 46 A 0.1760 0.6866 0.1373 47 G 0.1854 0.6935 0.1211 48 P 0.1693 0.7062 0.1244 49 T 0.1734 0.6750 0.1516 50 E 0.1562 0.6607 0.1831 51 P 0.1047 0.6548 0.2405 52 A 0.0902 0.6015 0.3084 53 H 0.1081 0.5109 0.3809 54 P 0.1286 0.4443 0.4271 55 V 0.1702 0.3914 0.4383 56 D 0.2032 0.3166 0.4801 57 E 0.2131 0.2627 0.5242 58 R 0.1856 0.2411 0.5732 59 L 0.1532 0.2135 0.6333 60 K 0.1463 0.1651 0.6887 61 N 0.1883 0.1408 0.6709 62 L 0.2288 0.1191 0.6521 63 E 0.1970 0.1458 0.6572 64 P 0.1282 0.2653 0.6065 65 K 0.1103 0.2859 0.6037 66 M 0.0959 0.2913 0.6128 67 I 0.0905 0.2576 0.6519 68 E 0.0573 0.4111 0.5316 69 L 0.0573 0.4955 0.4472 70 I 0.0609 0.5412 0.3978 71 M 0.0696 0.5064 0.4240 72 N 0.0918 0.4385 0.4697 73 E 0.0781 0.4695 0.4524 74 I 0.0889 0.4528 0.4583 75 M 0.0699 0.4757 0.4544 76 D 0.0693 0.4583 0.4724 77 H 0.0758 0.3876 0.5366 78 G 0.0883 0.2021 0.7095 79 P 0.0870 0.1340 0.7791 80 P 0.1159 0.1118 0.7722 81 V 0.1869 0.0714 0.7418 82 N 0.1418 0.0605 0.7977 83 W 0.0382 0.6125 0.3493 84 E 0.0247 0.6365 0.3388 85 D 0.0335 0.6627 0.3038 86 I 0.1481 0.3532 0.4987 87 A 0.1787 0.1971 0.6243 88 G 0.0958 0.1318 0.7725 89 V 0.0194 0.6648 0.3157 90 E 0.0068 0.9077 0.0856 91 F 0.0061 0.9276 0.0662 92 A 0.0058 0.9406 0.0536 93 K 0.0049 0.9535 0.0416 94 A 0.0049 0.9531 0.0420 95 T 0.0048 0.9514 0.0438 96 I 0.0048 0.9521 0.0431 97 K 0.0050 0.9552 0.0398 98 E 0.0051 0.9489 0.0460 99 I 0.0050 0.9431 0.0520 100 V 0.0067 0.9241 0.0692 101 V 0.0073 0.8597 0.1330 102 W 0.0121 0.7518 0.2361 103 P 0.0199 0.5816 0.3985 104 M 0.0252 0.5510 0.4238 105 L 0.0403 0.3705 0.5892 106 R 0.0525 0.3498 0.5977 107 P 0.0169 0.7049 0.2783 108 D 0.0173 0.7339 0.2489 109 I 0.0270 0.7301 0.2429 110 F 0.0419 0.6675 0.2906 111 T 0.0438 0.5647 0.3915 112 G 0.0537 0.3103 0.6360 113 L 0.0491 0.1345 0.8164 114 R 0.0866 0.0867 0.8267 115 G 0.1243 0.0598 0.8159 116 P 0.1080 0.0419 0.8501 117 P 0.1136 0.0338 0.8525 118 K 0.1324 0.0631 0.8045 119 G 0.4846 0.0215 0.4939 120 I 0.8375 0.0055 0.1571 121 L 0.9102 0.0052 0.0846 122 L 0.8958 0.0052 0.0989 123 F 0.7198 0.0209 0.2593 124 G 0.3848 0.0100 0.6052 125 P 0.1213 0.0316 0.8471 126 P 0.0275 0.0884 0.8841 127 G 0.0245 0.0674 0.9081 128 T 0.0550 0.0641 0.8809 129 G 0.0362 0.1327 0.8311 130 K 0.0160 0.8635 0.1205 131 T 0.0051 0.9477 0.0472 132 L 0.0048 0.9589 0.0363 133 I 0.0047 0.9597 0.0356 134 G 0.0047 0.9599 0.0355 135 K 0.0047 0.9601 0.0352 136 C 0.0047 0.9601 0.0352 137 I 0.0047 0.9582 0.0371 138 A 0.0049 0.9540 0.0411 139 S 0.0061 0.9269 0.0671 140 Q 0.0078 0.8619 0.1303 141 S 0.0491 0.4595 0.4913 142 G 0.0391 0.0246 0.9363 143 A 0.0680 0.0092 0.9228 144 T 0.2082 0.0136 0.7783 145 F 0.7982 0.0082 0.1936 146 F 0.8899 0.0079 0.1022 147 S 0.9159 0.0039 0.0802 148 I 0.8485 0.0066 0.1449 149 S 0.5187 0.0101 0.4712 150 A 0.0662 0.5254 0.4084 151 S 0.0173 0.7381 0.2446 152 S 0.0180 0.8108 0.1713 153 L 0.0368 0.7800 0.1833 154 T 0.0640 0.6756 0.2604 155 S 0.0512 0.5866 0.3622 156 K 0.0523 0.4962 0.4515 157 W 0.1051 0.3688 0.5261 158 V 0.0718 0.3454 0.5828 159 G 0.0601 0.3252 0.6147 160 E 0.0641 0.3965 0.5393 161 G 0.0396 0.5253 0.4351 162 E 0.0056 0.9347 0.0596 163 K 0.0052 0.9464 0.0484 164 M 0.0049 0.9508 0.0443 165 V 0.0048 0.9554 0.0398 166 R 0.0047 0.9581 0.0371 167 A 0.0047 0.9578 0.0375 168 L 0.0048 0.9543 0.0408 169 F 0.0049 0.9505 0.0446 170 A 0.0050 0.9456 0.0494 171 V 0.0056 0.9290 0.0655 172 A 0.0073 0.9086 0.0841 173 R 0.0071 0.8712 0.1217 174 C 0.0115 0.7380 0.2505 175 Q 0.0466 0.3660 0.5874 176 Q 0.0524 0.0483 0.8993 177 P 0.0632 0.0422 0.8946 178 A 0.6569 0.0146 0.3285 179 V 0.9074 0.0054 0.0872 180 I 0.9272 0.0050 0.0678 181 F 0.9170 0.0087 0.0743 182 I 0.8453 0.0435 0.1112 183 D 0.4749 0.1449 0.3802 184 E 0.2196 0.3395 0.4409 185 I 0.1019 0.6371 0.2610 186 D 0.1014 0.7011 0.1975 187 S 0.0799 0.7014 0.2188 188 L 0.0650 0.6479 0.2871 189 L 0.0766 0.5493 0.3741 190 S 0.0557 0.4653 0.4790 191 Q 0.0663 0.3870 0.5468 192 R 0.0785 0.2490 0.6725 193 G 0.0571 0.1716 0.7714 194 D 0.0517 0.1518 0.7965 195 G 0.0479 0.1341 0.8180 196 E 0.0474 0.1453 0.8073 197 H 0.0479 0.2751 0.6771 198 E 0.0260 0.5836 0.3904 199 S 0.0166 0.8072 0.1762 200 S 0.0093 0.8932 0.0975 201 R 0.0069 0.9291 0.0640 202 R 0.0066 0.9416 0.0518 203 I 0.0054 0.9515 0.0431 204 K 0.0049 0.9570 0.0381 205 T 0.0047 0.9586 0.0367 206 E 0.0047 0.9583 0.0371 207 F 0.0047 0.9567 0.0386 208 L 0.0051 0.9509 0.0440 209 V 0.0054 0.9326 0.0620 210 Q 0.0078 0.8818 0.1103 211 L 0.0370 0.7224 0.2406 212 D 0.0373 0.4371 0.5256 213 G 0.0480 0.2571 0.6949 214 A 0.0848 0.1913 0.7239 215 T 0.1335 0.1633 0.7032 216 T 0.1140 0.1901 0.6959 217 S 0.0797 0.1699 0.7504 218 S 0.0604 0.2143 0.7253 219 E 0.0659 0.1362 0.7979 220 D 0.0818 0.0767 0.8415 221 R 0.2248 0.0367 0.7385 222 I 0.7249 0.0045 0.2705 223 L 0.9070 0.0033 0.0898 224 V 0.9291 0.0031 0.0678 225 V 0.9181 0.0041 0.0779 226 G 0.8592 0.0104 0.1304 227 A 0.5323 0.0342 0.4335 228 T 0.2196 0.0437 0.7366 229 N 0.0987 0.0272 0.8741 230 R 0.0835 0.0539 0.8626 231 P 0.0263 0.5384 0.4353 232 Q 0.0193 0.5504 0.4304 233 E 0.0596 0.4868 0.4536 234 I 0.0987 0.2700 0.6312 235 D 0.0656 0.1735 0.7609 236 E 0.0067 0.8444 0.1489 237 A 0.0058 0.8783 0.1159 238 A 0.0085 0.8623 0.1292 239 R 0.0163 0.8077 0.1760 240 R 0.0335 0.5944 0.3722 241 R 0.0597 0.4139 0.5265 242 L 0.1536 0.1416 0.7048 243 V 0.1724 0.1207 0.7070 244 K 0.5255 0.0514 0.4231 245 R 0.7838 0.0185 0.1977 246 L 0.8570 0.0059 0.1371 247 Y 0.8312 0.0048 0.1640 248 I 0.4416 0.0113 0.5471 249 P 0.1234 0.0232 0.8534 250 L 0.0870 0.0161 0.8969 251 P 0.0806 0.0202 0.8992 252 E 0.0616 0.0136 0.9248 253 A 0.0056 0.9029 0.0915 254 S 0.0049 0.9393 0.0558 255 A 0.0049 0.9494 0.0457 256 R 0.0047 0.9565 0.0388 257 K 0.0047 0.9582 0.0371 258 Q 0.0047 0.9571 0.0382 259 I 0.0047 0.9563 0.0391 260 V 0.0047 0.9562 0.0391 261 I 0.0048 0.9497 0.0455 262 N 0.0053 0.9314 0.0633 263 L 0.0068 0.8978 0.0954 264 M 0.0161 0.7752 0.2088 265 S 0.0170 0.6136 0.3695 266 K 0.0249 0.4120 0.5631 267 E 0.0674 0.2296 0.7030 268 Q 0.0761 0.1311 0.7929 269 C 0.0887 0.1210 0.7903 270 C 0.0753 0.1119 0.8128 271 L 0.0570 0.2218 0.7212 272 S 0.0396 0.2675 0.6928 273 E 0.0465 0.4729 0.4806 274 E 0.0364 0.5897 0.3739 275 E 0.0554 0.6337 0.3109 276 I 0.0076 0.9193 0.0731 277 E 0.0074 0.9391 0.0535 278 Q 0.0058 0.9465 0.0477 279 I 0.0055 0.9443 0.0502 280 V 0.0057 0.9279 0.0665 281 Q 0.0065 0.8560 0.1375 282 Q 0.0169 0.7262 0.2570 283 S 0.0676 0.1905 0.7419 284 D 0.0168 0.1617 0.8214 285 A 0.0211 0.1182 0.8606 286 F 0.0690 0.0999 0.8310 287 S 0.0712 0.1676 0.7611 288 G 0.0069 0.8826 0.1105 289 A 0.0051 0.9384 0.0565 290 D 0.0050 0.9497 0.0452 291 M 0.0047 0.9571 0.0382 292 T 0.0047 0.9591 0.0363 293 Q 0.0047 0.9575 0.0378 294 L 0.0047 0.9568 0.0385 295 C 0.0048 0.9547 0.0405 296 R 0.0050 0.9469 0.0481 297 E 0.0049 0.9456 0.0495 298 A 0.0049 0.9432 0.0518 299 S 0.0051 0.9256 0.0693 300 L 0.0050 0.9289 0.0660 301 G 0.0052 0.9262 0.0686 302 P 0.0051 0.9301 0.0648 303 I 0.0054 0.9158 0.0788 304 R 0.0070 0.8823 0.1107 305 S 0.0203 0.7306 0.2491 306 L 0.0273 0.5561 0.4166 307 Q 0.0366 0.4514 0.5120 308 T 0.0298 0.5026 0.4677 309 A 0.0504 0.4834 0.4662 310 D 0.0705 0.4235 0.5060 311 I 0.0642 0.4559 0.4799 312 A 0.0137 0.8518 0.1345 313 T 0.0112 0.8782 0.1106 314 I 0.0103 0.8887 0.1010 315 T 0.0068 0.9168 0.0764 316 P 0.0064 0.9235 0.0701 317 D 0.0061 0.9198 0.0741 318 Q 0.0073 0.9076 0.0851 319 V 0.0080 0.9129 0.0791 320 R 0.0089 0.9168 0.0743 321 P 0.0072 0.9141 0.0787 322 I 0.0102 0.8950 0.0948 323 A 0.0150 0.8452 0.1398 324 Y 0.0228 0.7756 0.2016 325 I 0.0317 0.6338 0.3345 326 D 0.0191 0.7568 0.2241 327 F 0.0120 0.8715 0.1165 328 E 0.0133 0.8818 0.1049 329 N 0.0155 0.8941 0.0904 330 A 0.0144 0.8880 0.0975 331 F 0.0177 0.8602 0.1221 332 R 0.0226 0.7917 0.1857 333 T 0.0364 0.6672 0.2964 334 V 0.0531 0.4102 0.5367 335 R 0.0605 0.1705 0.7691 336 P 0.0143 0.5334 0.4523 337 S 0.0221 0.5310 0.4469 338 V 0.0351 0.5145 0.4504 339 S 0.0575 0.4451 0.4973 340 P 0.0092 0.8557 0.1350 341 K 0.0092 0.8838 0.1070 342 D 0.0061 0.9207 0.0732 343 L 0.0051 0.9438 0.0511 344 E 0.0051 0.9473 0.0476 345 L 0.0049 0.9483 0.0468 346 Y 0.0055 0.9450 0.0495 347 E 0.0057 0.9390 0.0553 348 N 0.0070 0.9198 0.0732 349 W 0.0095 0.8847 0.1058 350 N 0.0175 0.7855 0.1970 351 K 0.0193 0.6766 0.3041 352 T 0.0308 0.5259 0.4434 353 F 0.0620 0.3071 0.6310 354 G 0.0527 0.1464 0.8009 355 C 0.0646 0.1175 0.8179 356 G 0.0561 0.0772 0.8666 357 K 0.0489 0.0912 0.8598