# This file is the result of combining several RDB files, specifically # T0315.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0315.t2k.stride-ebghtl.rdb (weight 1.24869) # T0315.t2k.str2.rdb (weight 1.54758) # T0315.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 T0315.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0315 # 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 T0315.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 700 # # ============================================ # Comments from T0315.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0315 # 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 T0315.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 700 # # ============================================ # Comments from T0315.t2k.str2.rdb # ============================================ # TARGET T0315 # 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 T0315.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 199.191 # # ============================================ # Comments from T0315.t2k.alpha.rdb # ============================================ # TARGET T0315 # 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 T0315.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 700 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2412 0.0733 0.6854 2 L 0.5202 0.0434 0.4363 3 I 0.6204 0.0357 0.3439 4 D 0.4873 0.0411 0.4716 5 T 0.3790 0.0903 0.5307 6 H 0.3715 0.0857 0.5429 7 V 0.3786 0.0960 0.5254 8 H 0.3819 0.0789 0.5392 9 L 0.2195 0.1143 0.6662 10 N 0.0912 0.0722 0.8366 11 D 0.0514 0.3611 0.5875 12 E 0.0359 0.4737 0.4904 13 Q 0.0326 0.4684 0.4990 14 Y 0.0570 0.3239 0.6192 15 D 0.0348 0.4255 0.5397 16 D 0.0136 0.5046 0.4818 17 D 0.0358 0.4614 0.5028 18 L 0.0073 0.8720 0.1208 19 S 0.0053 0.9293 0.0654 20 E 0.0049 0.9467 0.0484 21 V 0.0048 0.9537 0.0415 22 I 0.0049 0.9546 0.0405 23 T 0.0049 0.9555 0.0396 24 R 0.0048 0.9554 0.0398 25 A 0.0048 0.9548 0.0404 26 R 0.0050 0.9445 0.0505 27 E 0.0064 0.8926 0.1010 28 A 0.0424 0.3240 0.6336 29 G 0.0415 0.0207 0.9378 30 V 0.1358 0.0089 0.8552 31 D 0.4731 0.0246 0.5023 32 R 0.9009 0.0055 0.0936 33 M 0.9251 0.0041 0.0708 34 F 0.9209 0.0040 0.0751 35 V 0.8690 0.0062 0.1249 36 V 0.6704 0.0285 0.3011 37 G 0.3685 0.0270 0.6045 38 F 0.2123 0.0327 0.7550 39 N 0.1203 0.0166 0.8631 40 K 0.0092 0.6592 0.3316 41 S 0.0062 0.7205 0.2734 42 T 0.0100 0.7796 0.2103 43 I 0.0096 0.8783 0.1121 44 E 0.0067 0.9326 0.0607 45 R 0.0097 0.9341 0.0563 46 A 0.0116 0.9416 0.0468 47 M 0.0069 0.9522 0.0409 48 K 0.0054 0.9513 0.0433 49 L 0.0051 0.9434 0.0515 50 I 0.0065 0.9264 0.0671 51 D 0.0064 0.8419 0.1517 52 E 0.0139 0.6441 0.3420 53 Y 0.0709 0.1319 0.7972 54 D 0.0178 0.1484 0.8338 55 F 0.0391 0.1095 0.8514 56 L 0.5477 0.0488 0.4035 57 Y 0.7701 0.0293 0.2006 58 G 0.8456 0.0229 0.1315 59 I 0.8512 0.0236 0.1252 60 I 0.7084 0.0436 0.2480 61 G 0.5263 0.0295 0.4442 62 W 0.4261 0.0287 0.5451 63 H 0.2447 0.0233 0.7320 64 P 0.0807 0.2835 0.6358 65 V 0.0451 0.3822 0.5728 66 D 0.0556 0.4081 0.5363 67 A 0.0524 0.4348 0.5128 68 I 0.0350 0.4061 0.5589 69 D 0.0342 0.3940 0.5717 70 F 0.0430 0.3404 0.6166 71 T 0.0455 0.2731 0.6815 72 E 0.0112 0.8142 0.1745 73 E 0.0087 0.8591 0.1322 74 H 0.0071 0.9035 0.0894 75 L 0.0050 0.9447 0.0502 76 E 0.0050 0.9481 0.0469 77 W 0.0050 0.9491 0.0459 78 I 0.0048 0.9512 0.0440 79 E 0.0049 0.9513 0.0438 80 S 0.0053 0.9346 0.0600 81 L 0.0063 0.8859 0.1078 82 A 0.0103 0.7106 0.2792 83 Q 0.0165 0.4221 0.5614 84 H 0.0682 0.0702 0.8616 85 P 0.0354 0.0815 0.8830 86 K 0.2003 0.0611 0.7386 87 V 0.8291 0.0043 0.1666 88 I 0.8738 0.0205 0.1057 89 G 0.9152 0.0041 0.0807 90 I 0.8895 0.0096 0.1009 91 G 0.8068 0.0124 0.1808 92 E 0.6736 0.0282 0.2983 93 M 0.4712 0.0632 0.4656 94 G 0.3628 0.0672 0.5700 95 L 0.3523 0.0954 0.5522 96 D 0.2754 0.1115 0.6131 97 Y 0.1974 0.1749 0.6276 98 H 0.1502 0.1153 0.7345 99 W 0.0674 0.1141 0.8185 100 D 0.0568 0.0859 0.8573 101 K 0.0392 0.1545 0.8063 102 S 0.0464 0.1336 0.8200 103 P 0.0430 0.2536 0.7034 104 A 0.0076 0.9055 0.0868 105 D 0.0052 0.9510 0.0438 106 V 0.0050 0.9532 0.0419 107 Q 0.0047 0.9582 0.0371 108 K 0.0047 0.9603 0.0350 109 E 0.0047 0.9601 0.0352 110 V 0.0047 0.9592 0.0361 111 F 0.0047 0.9598 0.0356 112 R 0.0047 0.9605 0.0348 113 K 0.0047 0.9611 0.0342 114 Q 0.0047 0.9592 0.0361 115 I 0.0048 0.9596 0.0356 116 A 0.0047 0.9593 0.0360 117 L 0.0047 0.9597 0.0356 118 A 0.0049 0.9550 0.0401 119 K 0.0054 0.9412 0.0534 120 R 0.0071 0.8774 0.1156 121 L 0.0496 0.5018 0.4485 122 K 0.0406 0.0296 0.9298 123 L 0.0594 0.0096 0.9310 124 P 0.1668 0.0077 0.8255 125 I 0.8721 0.0071 0.1208 126 I 0.9242 0.0043 0.0715 127 I 0.9121 0.0064 0.0815 128 H 0.7851 0.0165 0.1984 129 N 0.2806 0.0620 0.6574 130 R 0.0974 0.2056 0.6970 131 E 0.0538 0.3143 0.6320 132 A 0.0378 0.4824 0.4798 133 T 0.0215 0.6017 0.3769 134 Q 0.0120 0.8744 0.1136 135 D 0.0071 0.9291 0.0638 136 C 0.0054 0.9506 0.0441 137 I 0.0047 0.9586 0.0367 138 D 0.0047 0.9588 0.0365 139 I 0.0047 0.9574 0.0379 140 L 0.0048 0.9507 0.0445 141 L 0.0051 0.9341 0.0608 142 E 0.0070 0.8840 0.1089 143 E 0.0334 0.6718 0.2948 144 H 0.0539 0.2538 0.6924 145 A 0.0524 0.2458 0.7018 146 E 0.0381 0.3129 0.6490 147 E 0.0602 0.2216 0.7182 148 V 0.1753 0.0734 0.7514 149 G 0.2261 0.0394 0.7345 150 G 0.7322 0.0152 0.2527 151 I 0.9006 0.0066 0.0929 152 M 0.9084 0.0071 0.0845 153 H 0.8866 0.0072 0.1063 154 S 0.7043 0.0203 0.2754 155 F 0.4322 0.0285 0.5393 156 S 0.1931 0.0309 0.7760 157 G 0.0777 0.0277 0.8946 158 S 0.0686 0.0384 0.8930 159 P 0.0062 0.9392 0.0546 160 E 0.0056 0.9523 0.0420 161 I 0.0050 0.9565 0.0385 162 A 0.0048 0.9568 0.0384 163 D 0.0052 0.9554 0.0394 164 I 0.0048 0.9529 0.0423 165 V 0.0049 0.9478 0.0472 166 T 0.0055 0.9423 0.0521 167 N 0.0057 0.9218 0.0724 168 K 0.0083 0.8533 0.1385 169 L 0.0485 0.2577 0.6937 170 N 0.0355 0.0245 0.9400 171 F 0.2174 0.0167 0.7659 172 Y 0.7866 0.0088 0.2046 173 I 0.8750 0.0079 0.1171 174 S 0.8616 0.0094 0.1290 175 L 0.7860 0.0155 0.1985 176 G 0.4537 0.0361 0.5101 177 G 0.2825 0.0498 0.6677 178 P 0.3587 0.0692 0.5721 179 V 0.4281 0.1009 0.4710 180 T 0.3586 0.1132 0.5282 181 F 0.1596 0.1659 0.6745 182 K 0.0356 0.3110 0.6534 183 N 0.0389 0.2556 0.7055 184 A 0.0291 0.5017 0.4692 185 K 0.0228 0.6345 0.3427 186 Q 0.0182 0.6494 0.3325 187 P 0.0076 0.8807 0.1117 188 K 0.0067 0.9309 0.0624 189 E 0.0117 0.9304 0.0579 190 V 0.0078 0.9277 0.0644 191 A 0.0136 0.8747 0.1117 192 K 0.0180 0.7369 0.2451 193 H 0.0277 0.4880 0.4843 194 V 0.0749 0.0909 0.8342 195 S 0.0891 0.0724 0.8385 196 M 0.0352 0.4375 0.5274 197 E 0.0414 0.4478 0.5108 198 R 0.3339 0.3016 0.3645 199 L 0.7399 0.0680 0.1921 200 L 0.8338 0.0392 0.1270 201 V 0.8151 0.0480 0.1370 202 E 0.6862 0.0590 0.2548 203 T 0.4170 0.0535 0.5295 204 D 0.1784 0.0554 0.7661 205 A 0.0913 0.1146 0.7941 206 P 0.0362 0.2770 0.6867 207 Y 0.0584 0.2469 0.6947 208 L 0.1106 0.1347 0.7547 209 S 0.0965 0.0605 0.8430 210 P 0.1226 0.0474 0.8301 211 H 0.1471 0.0422 0.8107 212 P 0.1544 0.0716 0.7741 213 Y 0.1487 0.0800 0.7713 214 R 0.1361 0.1029 0.7610 215 G 0.1003 0.0727 0.8270 216 K 0.1494 0.0477 0.8028 217 R 0.1829 0.0657 0.7514 218 N 0.1248 0.0714 0.8038 219 E 0.0950 0.0810 0.8240 220 P 0.0693 0.2993 0.6313 221 A 0.0392 0.5057 0.4551 222 R 0.0573 0.5537 0.3890 223 V 0.0146 0.8858 0.0996 224 T 0.0048 0.9513 0.0439 225 L 0.0048 0.9579 0.0373 226 V 0.0047 0.9600 0.0353 227 A 0.0047 0.9599 0.0354 228 E 0.0047 0.9607 0.0347 229 Q 0.0047 0.9602 0.0351 230 I 0.0047 0.9577 0.0375 231 A 0.0048 0.9570 0.0382 232 E 0.0052 0.9422 0.0527 233 L 0.0101 0.8966 0.0933 234 K 0.0418 0.5437 0.4145 235 G 0.0342 0.0357 0.9301 236 L 0.0549 0.0124 0.9327 237 S 0.0588 0.0117 0.9295 238 Y 0.0050 0.9350 0.0600 239 E 0.0047 0.9532 0.0421 240 E 0.0047 0.9565 0.0387 241 V 0.0047 0.9589 0.0364 242 C 0.0047 0.9590 0.0363 243 E 0.0047 0.9558 0.0395 244 Q 0.0048 0.9491 0.0461 245 T 0.0053 0.9416 0.0531 246 T 0.0049 0.9344 0.0608 247 K 0.0059 0.9180 0.0761 248 N 0.0055 0.9239 0.0707 249 A 0.0048 0.9414 0.0538 250 E 0.0049 0.9397 0.0553 251 K 0.0062 0.9185 0.0753 252 L 0.0128 0.8664 0.1208 253 F 0.0564 0.5772 0.3664 254 N 0.0471 0.1056 0.8473 255 L 0.0706 0.0539 0.8756 256 N 0.0697 0.0468 0.8836 257 S 0.0418 0.0696 0.8886