# This file is the result of combining several RDB files, specifically # T0292.t06.dssp-ebghstl.rdb (weight 1.53986) # T0292.t06.stride-ebghtl.rdb (weight 1.24869) # T0292.t06.str2.rdb (weight 1.54758) # T0292.t06.alpha.rdb (weight 0.659012) # T0292.t04.dssp-ebghstl.rdb (weight 1.53986) # T0292.t04.stride-ebghtl.rdb (weight 1.24869) # T0292.t04.str2.rdb (weight 1.54758) # T0292.t04.alpha.rdb (weight 0.659012) # T0292.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0292.t2k.stride-ebghtl.rdb (weight 1.24869) # T0292.t2k.str2.rdb (weight 1.54758) # T0292.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 T0292.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0292 # 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 T0292.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 13116 # # ============================================ # Comments from T0292.t06.stride-ebghtl.rdb # ============================================ # TARGET T0292 # 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 T0292.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 13116 # # ============================================ # Comments from T0292.t06.str2.rdb # ============================================ # TARGET T0292 # 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 T0292.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 13116 # # ============================================ # Comments from T0292.t06.alpha.rdb # ============================================ # TARGET T0292 # 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 T0292.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 13116 # # ============================================ # Comments from T0292.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0292 # 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 T0292.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 36.1358 # # ============================================ # Comments from T0292.t04.stride-ebghtl.rdb # ============================================ # TARGET T0292 # 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 T0292.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 36.1358 # # ============================================ # Comments from T0292.t04.str2.rdb # ============================================ # TARGET T0292 # 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 T0292.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 36.1358 # # ============================================ # Comments from T0292.t04.alpha.rdb # ============================================ # TARGET T0292 # 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 T0292.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 36.1358 # # ============================================ # Comments from T0292.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0292 # 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 T0292.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 4523 # # ============================================ # Comments from T0292.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0292 # 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 T0292.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 4523 # # ============================================ # Comments from T0292.t2k.str2.rdb # ============================================ # TARGET T0292 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0292.t2k-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 4523 # # ============================================ # Comments from T0292.t2k.alpha.rdb # ============================================ # TARGET T0292 # 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 T0292.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 4523 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0644 0.0521 0.8835 2 R 0.0586 0.2029 0.7385 3 A 0.0438 0.5023 0.4539 4 E 0.0402 0.5562 0.4036 5 D 0.0527 0.5848 0.3625 6 Y 0.1507 0.4948 0.3544 7 E 0.2673 0.4576 0.2752 8 V 0.3717 0.4310 0.1973 9 L 0.4385 0.3644 0.1971 10 Y 0.3798 0.3495 0.2707 11 T 0.4527 0.2907 0.2566 12 I 0.3621 0.1967 0.4412 13 G 0.2798 0.0704 0.6498 14 T 0.2443 0.0609 0.6949 15 G 0.1708 0.0400 0.7893 16 S 0.2267 0.0624 0.7108 17 Y 0.4876 0.0508 0.4617 18 G 0.6357 0.0393 0.3251 19 R 0.8408 0.0225 0.1367 20 C 0.8983 0.0084 0.0933 21 Q 0.8941 0.0104 0.0954 22 K 0.9072 0.0065 0.0864 23 I 0.9027 0.0074 0.0899 24 R 0.8869 0.0100 0.1031 25 R 0.8381 0.0084 0.1535 26 K 0.3159 0.0868 0.5972 27 S 0.0894 0.0880 0.8226 28 D 0.0713 0.0317 0.8970 29 G 0.1026 0.0326 0.8648 30 K 0.6555 0.0085 0.3361 31 I 0.9063 0.0031 0.0906 32 L 0.9011 0.0062 0.0927 33 V 0.9160 0.0053 0.0787 34 W 0.9068 0.0082 0.0849 35 K 0.8945 0.0087 0.0968 36 E 0.8798 0.0098 0.1105 37 L 0.7890 0.0189 0.1921 38 D 0.5666 0.0356 0.3977 39 Y 0.1320 0.2764 0.5916 40 G 0.0526 0.3007 0.6467 41 S 0.0502 0.2745 0.6752 42 M 0.0711 0.1431 0.7858 43 T 0.0534 0.1028 0.8437 44 E 0.0090 0.8203 0.1707 45 A 0.0079 0.8603 0.1318 46 E 0.0068 0.9080 0.0852 47 K 0.0059 0.9331 0.0610 48 Q 0.0057 0.9412 0.0531 49 M 0.0049 0.9470 0.0481 50 L 0.0048 0.9531 0.0421 51 V 0.0047 0.9576 0.0377 52 S 0.0047 0.9560 0.0392 53 E 0.0047 0.9578 0.0375 54 V 0.0047 0.9594 0.0359 55 N 0.0047 0.9584 0.0369 56 L 0.0047 0.9568 0.0385 57 L 0.0049 0.9487 0.0464 58 R 0.0055 0.9079 0.0866 59 E 0.0078 0.7858 0.2065 60 L 0.0431 0.4662 0.4907 61 K 0.0473 0.1187 0.8340 62 H 0.0831 0.0413 0.8756 63 P 0.0234 0.1783 0.7984 64 N 0.0872 0.1778 0.7350 65 I 0.6304 0.1051 0.2645 66 V 0.7875 0.0526 0.1599 67 R 0.7875 0.0489 0.1636 68 Y 0.7528 0.0760 0.1711 69 Y 0.6434 0.1285 0.2282 70 D 0.6627 0.1007 0.2366 71 R 0.6725 0.1044 0.2231 72 I 0.7737 0.0499 0.1764 73 I 0.7489 0.0407 0.2104 74 D 0.4257 0.0521 0.5222 75 R 0.0925 0.1205 0.7870 76 T 0.0602 0.0968 0.8430 77 N 0.1021 0.0877 0.8102 78 T 0.1200 0.0675 0.8125 79 T 0.5426 0.0197 0.4377 80 L 0.7764 0.0047 0.2189 81 Y 0.8987 0.0045 0.0968 82 I 0.9249 0.0033 0.0717 83 V 0.9191 0.0046 0.0763 84 M 0.9066 0.0060 0.0875 85 E 0.8824 0.0075 0.1101 86 Y 0.7951 0.0123 0.1926 87 C 0.5082 0.0250 0.4669 88 E 0.1416 0.0741 0.7843 89 G 0.0575 0.0396 0.9029 90 G 0.0819 0.0592 0.8589 91 D 0.1933 0.1515 0.6552 92 L 0.0185 0.8891 0.0923 93 A 0.0094 0.9304 0.0601 94 S 0.0102 0.9364 0.0535 95 V 0.0116 0.9276 0.0608 96 I 0.0207 0.8889 0.0904 97 T 0.0202 0.8258 0.1540 98 K 0.0185 0.7115 0.2700 99 G 0.0316 0.5490 0.4194 100 T 0.0327 0.4660 0.5013 101 K 0.0391 0.4368 0.5241 102 E 0.0383 0.3577 0.6041 103 R 0.0512 0.1962 0.7526 104 Q 0.0754 0.1019 0.8227 105 Y 0.1154 0.0634 0.8211 106 L 0.1036 0.0309 0.8655 107 D 0.0564 0.0338 0.9098 108 E 0.0058 0.9381 0.0561 109 E 0.0048 0.9544 0.0409 110 F 0.0048 0.9564 0.0388 111 V 0.0047 0.9593 0.0360 112 L 0.0047 0.9604 0.0349 113 R 0.0047 0.9605 0.0348 114 V 0.0047 0.9602 0.0351 115 M 0.0047 0.9602 0.0351 116 T 0.0047 0.9600 0.0353 117 Q 0.0047 0.9602 0.0352 118 L 0.0047 0.9593 0.0360 119 T 0.0047 0.9578 0.0374 120 L 0.0047 0.9577 0.0376 121 A 0.0047 0.9575 0.0378 122 L 0.0047 0.9557 0.0396 123 K 0.0048 0.9491 0.0460 124 E 0.0049 0.9300 0.0652 125 C 0.0060 0.9116 0.0824 126 H 0.0092 0.8312 0.1596 127 R 0.0172 0.5957 0.3871 128 R 0.0306 0.3747 0.5947 129 S 0.0718 0.1888 0.7394 130 D 0.0522 0.1528 0.7950 131 G 0.0493 0.1521 0.7986 132 G 0.0736 0.0961 0.8303 133 H 0.1599 0.0786 0.7614 134 T 0.3871 0.0567 0.5562 135 V 0.6172 0.0517 0.3311 136 L 0.6739 0.0549 0.2712 137 H 0.5107 0.0951 0.3942 138 R 0.2470 0.1269 0.6261 139 D 0.2173 0.1080 0.6746 140 L 0.2142 0.0550 0.7308 141 K 0.1764 0.0254 0.7982 142 P 0.0975 0.3660 0.5365 143 A 0.1005 0.4206 0.4789 144 N 0.2181 0.4185 0.3634 145 V 0.6677 0.0869 0.2454 146 F 0.7895 0.0285 0.1820 147 L 0.7832 0.0137 0.2031 148 D 0.2605 0.0222 0.7173 149 G 0.0387 0.1121 0.8493 150 K 0.0659 0.0230 0.9111 151 Q 0.1664 0.0295 0.8041 152 N 0.5591 0.0083 0.4326 153 V 0.8797 0.0037 0.1167 154 K 0.8811 0.0054 0.1135 155 L 0.8195 0.0114 0.1691 156 G 0.5757 0.0371 0.3872 157 D 0.3662 0.0407 0.5931 158 F 0.1644 0.0855 0.7501 159 G 0.1830 0.1848 0.6322 160 L 0.2036 0.4187 0.3777 161 A 0.2273 0.4775 0.2953 162 R 0.3059 0.4732 0.2209 163 I 0.3606 0.3718 0.2675 164 L 0.3743 0.1788 0.4469 165 N 0.1929 0.0921 0.7149 166 H 0.0825 0.1112 0.8063 167 D 0.0636 0.1187 0.8177 168 T 0.0910 0.1371 0.7719 169 S 0.1781 0.1207 0.7012 170 F 0.3197 0.1196 0.5607 171 A 0.4000 0.0845 0.5156 172 K 0.4781 0.0586 0.4632 173 A 0.5437 0.0453 0.4110 174 F 0.5283 0.0558 0.4159 175 V 0.4018 0.0709 0.5274 176 G 0.2252 0.0472 0.7277 177 T 0.1392 0.0807 0.7801 178 P 0.0585 0.4622 0.4793 179 Y 0.0593 0.5250 0.4157 180 Y 0.0696 0.5419 0.3885 181 M 0.1030 0.3925 0.5044 182 S 0.0723 0.3948 0.5328 183 P 0.0286 0.8030 0.1683 184 E 0.0236 0.8626 0.1139 185 Q 0.0295 0.8464 0.1241 186 M 0.0407 0.7754 0.1839 187 N 0.0461 0.4629 0.4910 188 R 0.0428 0.1572 0.8001 189 M 0.0767 0.0612 0.8621 190 S 0.0789 0.0637 0.8573 191 Y 0.1077 0.0737 0.8186 192 N 0.0731 0.0647 0.8623 193 E 0.0589 0.2676 0.6735 194 K 0.0697 0.4056 0.5246 195 S 0.1416 0.3624 0.4960 196 D 0.1631 0.4445 0.3924 197 I 0.1134 0.7362 0.1504 198 W 0.0677 0.8231 0.1092 199 S 0.0454 0.8584 0.0962 200 L 0.0081 0.9290 0.0630 201 G 0.0052 0.9489 0.0458 202 C 0.0047 0.9601 0.0353 203 L 0.0047 0.9604 0.0349 204 L 0.0047 0.9601 0.0352 205 Y 0.0047 0.9586 0.0367 206 E 0.0051 0.9553 0.0395 207 L 0.0061 0.9404 0.0535 208 C 0.0125 0.8379 0.1497 209 A 0.0438 0.5490 0.4072 210 L 0.0370 0.1540 0.8090 211 M 0.0708 0.0406 0.8886 212 P 0.0942 0.0364 0.8694 213 P 0.0670 0.0732 0.8598 214 F 0.0762 0.0802 0.8436 215 T 0.0568 0.0981 0.8451 216 A 0.0546 0.0891 0.8563 217 F 0.0494 0.0993 0.8512 218 S 0.0764 0.0581 0.8655 219 Q 0.0092 0.8961 0.0946 220 K 0.0050 0.9426 0.0523 221 E 0.0049 0.9493 0.0458 222 L 0.0054 0.9511 0.0436 223 A 0.0047 0.9485 0.0468 224 G 0.0058 0.9458 0.0484 225 K 0.0084 0.9352 0.0564 226 I 0.0081 0.9280 0.0639 227 R 0.0128 0.8681 0.1192 228 E 0.0297 0.5422 0.4281 229 G 0.0579 0.1948 0.7473 230 K 0.0815 0.0725 0.8461 231 F 0.1244 0.0493 0.8263 232 R 0.0930 0.0507 0.8563 233 R 0.0886 0.0595 0.8519 234 I 0.0833 0.0665 0.8502 235 P 0.0761 0.1020 0.8219 236 Y 0.0369 0.2283 0.7349 237 R 0.0651 0.1642 0.7707 238 Y 0.0809 0.0475 0.8716 239 S 0.0539 0.0204 0.9257 240 D 0.0054 0.8561 0.1385 241 E 0.0050 0.8857 0.1094 242 L 0.0052 0.9469 0.0479 243 N 0.0047 0.9589 0.0363 244 E 0.0049 0.9574 0.0377 245 I 0.0050 0.9559 0.0391 246 I 0.0048 0.9548 0.0404 247 T 0.0051 0.9485 0.0464 248 R 0.0057 0.9363 0.0579 249 M 0.0067 0.9098 0.0835 250 L 0.0216 0.7584 0.2200 251 N 0.0363 0.5001 0.4636 252 L 0.0760 0.2043 0.7197 253 K 0.0871 0.0290 0.8839 254 D 0.0067 0.4298 0.5635 255 Y 0.0093 0.4369 0.5539 256 H 0.0204 0.4230 0.5566 257 R 0.0883 0.0790 0.8327 258 P 0.1077 0.0526 0.8398 259 S 0.0996 0.0298 0.8706 260 V 0.0070 0.9181 0.0749 261 E 0.0052 0.9463 0.0485 262 E 0.0052 0.9465 0.0483 263 I 0.0059 0.9421 0.0521 264 L 0.0077 0.8683 0.1240 265 E 0.0115 0.5745 0.4140 266 N 0.0755 0.1574 0.7671 267 P 0.0114 0.5146 0.4740 268 L 0.0185 0.5745 0.4070 269 I 0.0701 0.6423 0.2876 270 L 0.0885 0.4866 0.4249 271 E 0.0921 0.2755 0.6324 272 H 0.0981 0.1338 0.7681 273 H 0.0901 0.0815 0.8284 274 H 0.0805 0.0627 0.8568 275 H 0.0474 0.1436 0.8090 276 H 0.0480 0.1085 0.8435 277 H 0.0564 0.0363 0.9073