# This file is the result of combining several RDB files, specifically # T0373.t06.dssp-ebghstl.rdb (weight 1.53986) # T0373.t06.stride-ebghtl.rdb (weight 1.24869) # T0373.t06.str2.rdb (weight 1.54758) # T0373.t06.alpha.rdb (weight 0.659012) # T0373.t04.dssp-ebghstl.rdb (weight 1.53986) # T0373.t04.stride-ebghtl.rdb (weight 1.24869) # T0373.t04.str2.rdb (weight 1.54758) # T0373.t04.alpha.rdb (weight 0.659012) # T0373.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0373.t2k.stride-ebghtl.rdb (weight 1.24869) # T0373.t2k.str2.rdb (weight 1.54758) # T0373.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 T0373.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0373 # Using neural net t06-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 T0373.t06-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 191.992 # # ============================================ # Comments from T0373.t06.stride-ebghtl.rdb # ============================================ # TARGET T0373 # Using neural net t06-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 T0373.t06-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 191.992 # # ============================================ # Comments from T0373.t06.str2.rdb # ============================================ # TARGET T0373 # Using neural net t06-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 T0373.t06-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 191.992 # # ============================================ # Comments from T0373.t06.alpha.rdb # ============================================ # TARGET T0373 # Using neural net t06-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 T0373.t06-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 191.992 # # ============================================ # Comments from T0373.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0373 # Using neural net t06-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 T0373.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 151.605 # # ============================================ # Comments from T0373.t04.stride-ebghtl.rdb # ============================================ # TARGET T0373 # 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 T0373.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 151.605 # # ============================================ # Comments from T0373.t04.str2.rdb # ============================================ # TARGET T0373 # 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 T0373.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 151.605 # # ============================================ # Comments from T0373.t04.alpha.rdb # ============================================ # TARGET T0373 # 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 T0373.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 151.605 # # ============================================ # Comments from T0373.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0373 # 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 T0373.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 1092 # # ============================================ # Comments from T0373.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0373 # 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 T0373.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 1092 # # ============================================ # Comments from T0373.t2k.str2.rdb # ============================================ # TARGET T0373 # 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 T0373.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 1092 # # ============================================ # Comments from T0373.t2k.alpha.rdb # ============================================ # TARGET T0373 # 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 T0373.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 1092 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0619 0.0454 0.8927 2 P 0.0691 0.0487 0.8822 3 T 0.0649 0.1418 0.7934 4 N 0.0400 0.2496 0.7105 5 Q 0.0129 0.6970 0.2901 6 D 0.0078 0.8163 0.1759 7 L 0.0059 0.8990 0.0951 8 Q 0.0054 0.9309 0.0638 9 L 0.0048 0.9481 0.0471 10 A 0.0047 0.9575 0.0378 11 A 0.0047 0.9591 0.0362 12 H 0.0047 0.9586 0.0367 13 L 0.0047 0.9592 0.0361 14 R 0.0047 0.9592 0.0362 15 S 0.0047 0.9579 0.0374 16 Q 0.0047 0.9579 0.0373 17 V 0.0047 0.9588 0.0365 18 T 0.0048 0.9564 0.0388 19 T 0.0048 0.9541 0.0411 20 L 0.0048 0.9506 0.0446 21 T 0.0050 0.9444 0.0507 22 R 0.0053 0.9344 0.0602 23 R 0.0052 0.9308 0.0641 24 L 0.0060 0.9241 0.0699 25 R 0.0053 0.9307 0.0640 26 R 0.0052 0.9334 0.0615 27 E 0.0051 0.9325 0.0624 28 A 0.0063 0.9150 0.0787 29 Q 0.0063 0.8810 0.1127 30 A 0.0084 0.7767 0.2149 31 D 0.0464 0.3340 0.6195 32 P 0.0419 0.0534 0.9047 33 V 0.0755 0.0257 0.8988 34 Q 0.0584 0.0177 0.9239 35 F 0.0085 0.8776 0.1138 36 S 0.0051 0.9231 0.0718 37 Q 0.0051 0.9476 0.0473 38 L 0.0051 0.9578 0.0371 39 V 0.0062 0.9571 0.0367 40 V 0.0059 0.9577 0.0364 41 L 0.0078 0.9556 0.0367 42 G 0.0059 0.9564 0.0377 43 A 0.0054 0.9530 0.0417 44 I 0.0059 0.9359 0.0582 45 D 0.0076 0.8871 0.1053 46 R 0.0106 0.7728 0.2166 47 L 0.0450 0.5072 0.4478 48 G 0.0378 0.1426 0.8196 49 G 0.0396 0.0955 0.8649 50 D 0.0539 0.0645 0.8815 51 V 0.1068 0.0203 0.8729 52 T 0.0914 0.0137 0.8949 53 P 0.0064 0.9249 0.0686 54 S 0.0047 0.9473 0.0480 55 E 0.0048 0.9531 0.0421 56 L 0.0047 0.9564 0.0389 57 A 0.0048 0.9512 0.0440 58 A 0.0050 0.9371 0.0579 59 A 0.0059 0.8963 0.0978 60 E 0.0402 0.5486 0.4112 61 R 0.0296 0.1359 0.8345 62 M 0.0717 0.0568 0.8715 63 R 0.0702 0.0348 0.8950 64 S 0.0352 0.5231 0.4417 65 S 0.0133 0.6688 0.3178 66 N 0.0164 0.8203 0.1632 67 L 0.0059 0.9312 0.0629 68 A 0.0047 0.9557 0.0396 69 A 0.0047 0.9584 0.0369 70 L 0.0047 0.9591 0.0362 71 L 0.0047 0.9584 0.0369 72 R 0.0048 0.9586 0.0366 73 E 0.0048 0.9582 0.0370 74 L 0.0050 0.9553 0.0397 75 E 0.0056 0.9358 0.0585 76 R 0.0062 0.8593 0.1345 77 G 0.0443 0.2570 0.6987 78 G 0.0342 0.0301 0.9357 79 L 0.1674 0.0300 0.8026 80 I 0.7125 0.0136 0.2739 81 V 0.7640 0.0192 0.2168 82 R 0.7387 0.0182 0.2431 83 H 0.6086 0.0121 0.3793 84 A 0.3653 0.0150 0.6197 85 D 0.1677 0.0138 0.8185 86 P 0.0154 0.3026 0.6820 87 Q 0.0206 0.2050 0.7743 88 D 0.1036 0.2295 0.6669 89 G 0.1054 0.1165 0.7782 90 R 0.4309 0.0486 0.5206 91 R 0.7505 0.0144 0.2351 92 T 0.8365 0.0112 0.1523 93 R 0.8868 0.0067 0.1065 94 V 0.8795 0.0065 0.1139 95 S 0.8444 0.0052 0.1504 96 L 0.5709 0.0082 0.4209 97 S 0.1197 0.0127 0.8676 98 S 0.0060 0.8353 0.1588 99 E 0.0081 0.9043 0.0876 100 G 0.0062 0.9270 0.0668 101 R 0.0050 0.9512 0.0438 102 R 0.0047 0.9505 0.0447 103 N 0.0050 0.9430 0.0521 104 L 0.0053 0.9330 0.0617 105 Y 0.0063 0.9038 0.0898 106 G 0.0077 0.8357 0.1567 107 N 0.0106 0.7680 0.2214 108 R 0.0089 0.8044 0.1867 109 A 0.0067 0.8331 0.1601 110 K 0.0080 0.8530 0.1390 111 R 0.0074 0.8829 0.1097 112 E 0.0060 0.9064 0.0875 113 E 0.0054 0.9375 0.0571 114 W 0.0049 0.9422 0.0529 115 L 0.0051 0.9474 0.0475 116 V 0.0051 0.9437 0.0511 117 R 0.0053 0.9334 0.0613 118 A 0.0065 0.9049 0.0887 119 M 0.0104 0.7819 0.2076 120 H 0.0169 0.5058 0.4773 121 A 0.0287 0.2791 0.6921 122 C 0.0412 0.1238 0.8350 123 L 0.0575 0.0187 0.9237 124 D 0.0463 0.0169 0.9367 125 E 0.0053 0.9112 0.0835 126 S 0.0051 0.9370 0.0579 127 E 0.0049 0.9477 0.0473 128 R 0.0047 0.9587 0.0366 129 A 0.0047 0.9546 0.0407 130 L 0.0048 0.9529 0.0423 131 L 0.0048 0.9516 0.0436 132 A 0.0048 0.9534 0.0418 133 A 0.0048 0.9458 0.0494 134 A 0.0049 0.9409 0.0542 135 G 0.0048 0.9496 0.0457 136 P 0.0047 0.9498 0.0455 137 L 0.0047 0.9519 0.0434 138 L 0.0047 0.9489 0.0464 139 T 0.0048 0.9437 0.0515 140 R 0.0051 0.9055 0.0894 141 L 0.0068 0.8346 0.1586 142 A 0.0173 0.7113 0.2715 143 Q 0.0185 0.5235 0.4580 144 F 0.0232 0.4954 0.4814 145 E 0.0301 0.3712 0.5987 146 E 0.0400 0.2497 0.7103 147 P 0.0468 0.2228 0.7303 148 M 0.0482 0.2913 0.6605 149 P 0.0500 0.3321 0.6180 150 T 0.0457 0.5267 0.4276 151 N 0.0529 0.6006 0.3465 152 Q 0.0724 0.6730 0.2546 153 D 0.1248 0.6865 0.1887 154 L 0.1430 0.6802 0.1768 155 Q 0.1666 0.6056 0.2277 156 L 0.1563 0.5047 0.3389 157 A 0.0991 0.3281 0.5729 158 A 0.0699 0.1699 0.7601 159 H 0.0612 0.1555 0.7833 160 L 0.0376 0.3073 0.6552 161 R 0.0490 0.3637 0.5873 162 S 0.0411 0.5245 0.4343 163 Q 0.0307 0.7610 0.2084 164 V 0.0338 0.8212 0.1450 165 T 0.0313 0.8564 0.1123 166 T 0.0284 0.8587 0.1129 167 L 0.0222 0.8536 0.1242 168 T 0.0158 0.8651 0.1191 169 R 0.0103 0.8982 0.0914 170 R 0.0076 0.9136 0.0788 171 L 0.0074 0.9264 0.0661 172 R 0.0077 0.9315 0.0608 173 R 0.0078 0.9289 0.0633 174 E 0.0069 0.9130 0.0801 175 A 0.0089 0.8562 0.1350 176 Q 0.0166 0.7354 0.2480 177 A 0.0422 0.5147 0.4432 178 D 0.0454 0.2148 0.7398 179 P 0.0399 0.3283 0.6318 180 V 0.0272 0.6599 0.3129 181 Q 0.0205 0.7449 0.2345 182 F 0.0246 0.7929 0.1826 183 S 0.0180 0.8061 0.1759 184 Q 0.0157 0.8448 0.1394 185 L 0.0138 0.8516 0.1346 186 V 0.0179 0.8596 0.1225 187 V 0.0116 0.8800 0.1083 188 L 0.0139 0.8648 0.1213 189 G 0.0113 0.8177 0.1710 190 A 0.0142 0.8050 0.1808 191 I 0.0091 0.8663 0.1246 192 D 0.0084 0.8485 0.1431 193 R 0.0125 0.8010 0.1865 194 L 0.0207 0.7247 0.2546 195 G 0.0259 0.5694 0.4047 196 G 0.0287 0.4348 0.5365 197 D 0.0454 0.2881 0.6665 198 V 0.0724 0.2290 0.6987 199 T 0.0553 0.1371 0.8076 200 P 0.0340 0.5962 0.3699 201 S 0.0419 0.6466 0.3115 202 E 0.0150 0.8586 0.1264 203 L 0.0265 0.8592 0.1143 204 A 0.0341 0.8476 0.1184 205 A 0.0441 0.8399 0.1159 206 A 0.0548 0.7934 0.1518 207 E 0.0731 0.7030 0.2239 208 R 0.1394 0.4295 0.4311 209 M 0.1221 0.3251 0.5527 210 R 0.0823 0.2270 0.6907 211 S 0.0706 0.1519 0.7774 212 S 0.0511 0.1563 0.7926 213 N 0.1183 0.1492 0.7325 214 L 0.4215 0.1605 0.4181 215 A 0.6398 0.1479 0.2123 216 A 0.7605 0.1270 0.1126 217 L 0.7557 0.1418 0.1025 218 L 0.6725 0.2305 0.0970 219 R 0.6988 0.2092 0.0920 220 E 0.7257 0.1745 0.0998 221 L 0.6223 0.2082 0.1695 222 E 0.3565 0.2856 0.3579 223 R 0.1130 0.2849 0.6021 224 G 0.0662 0.1623 0.7714 225 G 0.0949 0.1470 0.7581 226 L 0.1595 0.2079 0.6326 227 I 0.2160 0.2044 0.5796 228 V 0.1954 0.1684 0.6362 229 R 0.1641 0.1255 0.7104 230 H 0.1268 0.0838 0.7895 231 A 0.1308 0.0608 0.8084 232 D 0.1256 0.0532 0.8212 233 P 0.0733 0.2676 0.6591 234 Q 0.0336 0.5049 0.4615 235 D 0.0411 0.5195 0.4394 236 G 0.0621 0.3553 0.5826 237 R 0.1411 0.2369 0.6221 238 R 0.2397 0.1338 0.6265 239 T 0.2917 0.1408 0.5676 240 R 0.3371 0.1378 0.5251 241 V 0.2690 0.2286 0.5024 242 S 0.2133 0.2832 0.5035 243 L 0.1729 0.2589 0.5682 244 S 0.1828 0.1528 0.6644 245 S 0.1158 0.1543 0.7299 246 E 0.0404 0.5976 0.3620 247 G 0.0372 0.6509 0.3119 248 R 0.0749 0.6252 0.2998 249 R 0.1313 0.5583 0.3104 250 N 0.1014 0.4570 0.4415 251 L 0.0583 0.4108 0.5309 252 Y 0.0721 0.1967 0.7312 253 G 0.1013 0.0904 0.8082 254 N 0.0823 0.0795 0.8383 255 R 0.0408 0.1771 0.7821 256 A 0.0405 0.1271 0.8324 257 K 0.0615 0.1149 0.8237 258 R 0.1267 0.0717 0.8017 259 E 0.2828 0.0711 0.6460 260 E 0.2973 0.0549 0.6478 261 W 0.3319 0.0866 0.5814 262 L 0.3262 0.1293 0.5445 263 V 0.3995 0.1010 0.4995 264 R 0.2416 0.0712 0.6872 265 A 0.1467 0.1454 0.7079 266 M 0.1090 0.1485 0.7425 267 H 0.0971 0.2140 0.6889 268 A 0.0850 0.1537 0.7614 269 C 0.0981 0.1281 0.7738 270 L 0.0782 0.1058 0.8160 271 D 0.0404 0.1743 0.7853 272 E 0.0262 0.3375 0.6363 273 S 0.0345 0.3720 0.5935 274 E 0.0448 0.4591 0.4961 275 R 0.0609 0.4014 0.5377 276 A 0.0659 0.3829 0.5512 277 L 0.0491 0.3014 0.6495 278 L 0.0283 0.4817 0.4900 279 A 0.0100 0.6778 0.3122 280 A 0.0118 0.6090 0.3792 281 A 0.0341 0.5113 0.4546 282 G 0.0382 0.4312 0.5306 283 P 0.0171 0.6518 0.3311 284 L 0.0200 0.7581 0.2219 285 L 0.0274 0.8076 0.1651 286 T 0.0397 0.8059 0.1544 287 R 0.0396 0.7967 0.1637 288 L 0.0352 0.8021 0.1627 289 A 0.0473 0.7371 0.2156 290 Q 0.0500 0.6683 0.2816 291 F 0.0725 0.5269 0.4006 292 E 0.0838 0.3221 0.5941 293 E 0.0565 0.1173 0.8262 294 P 0.0338 0.0536 0.9126