# This file is the result of combining several RDB files, specifically # T0269.t04.dssp-ebghstl.rdb (weight 1.53986) # T0269.t04.stride-ebghtl.rdb (weight 1.24869) # T0269.t04.str2.rdb (weight 1.54758) # T0269.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 T0269.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0269 # 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 T0269.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 790.717 # # ============================================ # Comments from T0269.t04.stride-ebghtl.rdb # ============================================ # TARGET T0269 # 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 T0269.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 790.717 # # ============================================ # Comments from T0269.t04.str2.rdb # ============================================ # TARGET T0269 # 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 T0269.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 790.717 # # ============================================ # Comments from T0269.t04.alpha.rdb # ============================================ # TARGET T0269 # 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 T0269.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 790.717 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0645 0.0141 0.9214 2 P 0.0687 0.0537 0.8776 3 G 0.0780 0.0856 0.8364 4 S 0.0956 0.0893 0.8152 5 I 0.1362 0.0754 0.7884 6 P 0.1403 0.1036 0.7561 7 L 0.1857 0.1622 0.6522 8 I 0.1081 0.1690 0.7228 9 G 0.0573 0.0894 0.8533 10 E 0.1644 0.0469 0.7887 11 R 0.2909 0.0330 0.6761 12 F 0.1821 0.0157 0.8022 13 P 0.1409 0.0455 0.8136 14 E 0.4477 0.0423 0.5100 15 M 0.7377 0.0121 0.2502 16 E 0.8531 0.0069 0.1400 17 V 0.8673 0.0046 0.1281 18 T 0.7848 0.0052 0.2100 19 T 0.3863 0.0283 0.5855 20 D 0.0959 0.0814 0.8227 21 H 0.0666 0.0315 0.9019 22 G 0.1012 0.0311 0.8678 23 V 0.3823 0.0165 0.6012 24 I 0.7147 0.0078 0.2775 25 K 0.6237 0.0134 0.3629 26 L 0.2676 0.1820 0.5503 27 P 0.0881 0.4156 0.4963 28 D 0.0393 0.5532 0.4074 29 H 0.0899 0.3961 0.5139 30 Y 0.2242 0.2734 0.5023 31 V 0.2390 0.3605 0.4005 32 S 0.1631 0.2973 0.5395 33 Q 0.0500 0.0528 0.8972 34 G 0.0562 0.0254 0.9184 35 K 0.3189 0.0075 0.6736 36 W 0.8402 0.0031 0.1566 37 F 0.9229 0.0039 0.0733 38 V 0.9340 0.0032 0.0629 39 L 0.9322 0.0032 0.0646 40 F 0.9070 0.0043 0.0887 41 S 0.6079 0.0100 0.3821 42 H 0.1923 0.0153 0.7924 43 P 0.0853 0.0828 0.8319 44 A 0.0439 0.2123 0.7438 45 D 0.0583 0.2023 0.7394 46 F 0.0953 0.1521 0.7527 47 T 0.1067 0.0700 0.8233 48 P 0.0933 0.1419 0.7648 49 V 0.1140 0.1946 0.6914 50 C 0.1123 0.2804 0.6073 51 T 0.0396 0.6317 0.3288 52 T 0.0240 0.7195 0.2565 53 E 0.0273 0.7479 0.2248 54 F 0.0098 0.8810 0.1091 55 V 0.0061 0.9277 0.0662 56 S 0.0067 0.9319 0.0615 57 F 0.0053 0.9371 0.0576 58 A 0.0053 0.9386 0.0561 59 R 0.0051 0.9289 0.0660 60 R 0.0062 0.9031 0.0907 61 Y 0.0066 0.9346 0.0587 62 E 0.0048 0.9457 0.0496 63 D 0.0047 0.9534 0.0419 64 F 0.0048 0.9526 0.0426 65 Q 0.0048 0.9429 0.0523 66 R 0.0052 0.8788 0.1160 67 L 0.0401 0.3197 0.6402 68 G 0.0438 0.0124 0.9438 69 V 0.1266 0.0066 0.8668 70 D 0.8442 0.0055 0.1503 71 L 0.9200 0.0030 0.0770 72 I 0.8991 0.0127 0.0883 73 G 0.9225 0.0036 0.0738 74 L 0.8718 0.0060 0.1221 75 S 0.7254 0.0070 0.2676 76 V 0.3040 0.0740 0.6220 77 D 0.0930 0.0867 0.8203 78 S 0.0501 0.2165 0.7334 79 V 0.0299 0.4828 0.4873 80 F 0.0470 0.4955 0.4575 81 S 0.0534 0.4375 0.5092 82 H 0.0338 0.6485 0.3177 83 I 0.0094 0.8876 0.1030 84 K 0.0099 0.9062 0.0839 85 W 0.0071 0.9282 0.0646 86 K 0.0053 0.9546 0.0401 87 E 0.0047 0.9591 0.0362 88 W 0.0048 0.9579 0.0373 89 I 0.0049 0.9552 0.0399 90 E 0.0052 0.9483 0.0465 91 R 0.0073 0.8927 0.0999 92 H 0.0126 0.7447 0.2427 93 I 0.0568 0.4060 0.5372 94 G 0.0478 0.1007 0.8515 95 V 0.1058 0.0525 0.8417 96 R 0.1350 0.0447 0.8203 97 I 0.2576 0.0107 0.7318 98 P 0.1893 0.0107 0.7999 99 F 0.4086 0.0126 0.5788 100 P 0.4831 0.0206 0.4963 101 I 0.7080 0.0293 0.2627 102 I 0.7716 0.0155 0.2130 103 A 0.6940 0.0194 0.2866 104 D 0.1299 0.0243 0.8458 105 P 0.0133 0.1377 0.8490 106 Q 0.0459 0.0720 0.8821 107 G 0.0520 0.2460 0.7020 108 T 0.0583 0.6328 0.3090 109 V 0.1093 0.7950 0.0957 110 A 0.0440 0.8740 0.0820 111 R 0.0298 0.9051 0.0651 112 R 0.0316 0.8688 0.0997 113 L 0.0563 0.4704 0.4733 114 G 0.0522 0.0565 0.8913 115 L 0.1276 0.0479 0.8245 116 L 0.2849 0.0617 0.6534 117 H 0.1462 0.0709 0.7829 118 A 0.0501 0.3959 0.5540 119 E 0.0346 0.4470 0.5185 120 S 0.0558 0.3575 0.5867 121 A 0.0861 0.1647 0.7491 122 T 0.1741 0.1229 0.7030 123 H 0.2391 0.0707 0.6902 124 T 0.2761 0.0437 0.6802 125 V 0.3584 0.0164 0.6252 126 R 0.3695 0.0183 0.6122 127 G 0.7914 0.0065 0.2021 128 V 0.9113 0.0033 0.0855 129 F 0.9290 0.0034 0.0676 130 I 0.9290 0.0034 0.0675 131 V 0.8977 0.0057 0.0966 132 D 0.3865 0.0091 0.6044 133 A 0.0181 0.1040 0.8779 134 R 0.0454 0.0194 0.9352 135 G 0.0594 0.0250 0.9156 136 V 0.4522 0.0098 0.5380 137 I 0.9179 0.0030 0.0790 138 R 0.8957 0.0122 0.0921 139 T 0.9220 0.0039 0.0741 140 M 0.9175 0.0053 0.0772 141 L 0.8978 0.0057 0.0965 142 Y 0.7209 0.0187 0.2604 143 Y 0.3478 0.0198 0.6324 144 P 0.2236 0.0644 0.7120 145 M 0.1241 0.1068 0.7691 146 E 0.1091 0.1492 0.7416 147 L 0.0425 0.3693 0.5882 148 G 0.0344 0.2892 0.6763 149 R 0.0791 0.2771 0.6439 150 L 0.0514 0.5096 0.4390 151 V 0.0048 0.9538 0.0414 152 D 0.0047 0.9598 0.0355 153 E 0.0047 0.9604 0.0349 154 I 0.0047 0.9606 0.0347 155 L 0.0047 0.9609 0.0345 156 R 0.0046 0.9610 0.0343 157 I 0.0047 0.9591 0.0363 158 V 0.0047 0.9587 0.0366 159 K 0.0048 0.9548 0.0404 160 A 0.0053 0.9376 0.0571 161 L 0.0153 0.8680 0.1167 162 K 0.0116 0.7061 0.2823 163 L 0.0223 0.5445 0.4332 164 G 0.0497 0.2406 0.7097 165 D 0.0362 0.2828 0.6811 166 S 0.0504 0.2685 0.6810 167 L 0.1025 0.1306 0.7669 168 K 0.1460 0.1238 0.7301 169 R 0.4512 0.0420 0.5068 170 A 0.5134 0.0208 0.4659 171 V 0.4315 0.0255 0.5430 172 P 0.2476 0.0307 0.7217 173 A 0.1793 0.0457 0.7750 174 D 0.2018 0.0273 0.7709 175 W 0.0909 0.0300 0.8791 176 P 0.0629 0.0580 0.8791 177 N 0.0310 0.0912 0.8778 178 N 0.0380 0.0760 0.8860 179 E 0.2312 0.0756 0.6932 180 I 0.5637 0.0698 0.3665 181 I 0.4112 0.0878 0.5009 182 G 0.2355 0.0672 0.6973 183 E 0.1454 0.0787 0.7759 184 G 0.1644 0.0615 0.7741 185 L 0.4620 0.0258 0.5122 186 I 0.6643 0.0117 0.3240 187 V 0.4073 0.0092 0.5834 188 P 0.1602 0.0107 0.8291 189 P 0.0785 0.0158 0.9057 190 P 0.0771 0.0247 0.8982 191 T 0.1079 0.0163 0.8758 192 T 0.0687 0.0167 0.9145 193 E 0.0049 0.9407 0.0543 194 D 0.0047 0.9584 0.0369 195 Q 0.0047 0.9575 0.0378 196 A 0.0050 0.9550 0.0400 197 R 0.0052 0.9502 0.0445 198 A 0.0058 0.8966 0.0976 199 R 0.0084 0.8055 0.1861 200 M 0.0309 0.4933 0.4758 201 E 0.0230 0.4548 0.5222 202 S 0.0370 0.2018 0.7612 203 G 0.0341 0.0787 0.8872 204 Q 0.2021 0.0624 0.7355 205 Y 0.5226 0.0358 0.4415 206 R 0.6454 0.0450 0.3096 207 C 0.6450 0.0554 0.2996 208 L 0.5928 0.0668 0.3404 209 D 0.4651 0.0736 0.4613 210 W 0.3671 0.1972 0.4357 211 W 0.4193 0.2011 0.3796 212 F 0.5115 0.1460 0.3425 213 C 0.5287 0.0840 0.3873 214 W 0.3984 0.0632 0.5385 215 D 0.1724 0.0485 0.7791 216 T 0.1098 0.0359 0.8542 217 P 0.0771 0.0768 0.8461 218 A 0.0580 0.1298 0.8122 219 S 0.0562 0.1729 0.7709 220 R 0.0299 0.4012 0.5690 221 D 0.0305 0.4771 0.4924 222 D 0.0518 0.5586 0.3897 223 V 0.0376 0.7683 0.1941 224 E 0.0237 0.8644 0.1119 225 E 0.0231 0.8605 0.1164 226 A 0.0222 0.8473 0.1305 227 R 0.0244 0.8448 0.1308 228 R 0.0360 0.7960 0.1681 229 Y 0.0355 0.7066 0.2579 230 L 0.0300 0.4921 0.4779 231 R 0.0242 0.4793 0.4965 232 R 0.0389 0.5050 0.4561 233 A 0.0515 0.4291 0.5194 234 A 0.0423 0.3905 0.5671 235 E 0.0747 0.3009 0.6244 236 K 0.1106 0.2319 0.6576 237 P 0.0793 0.2914 0.6294 238 A 0.1140 0.4890 0.3970 239 K 0.2271 0.5096 0.2633 240 L 0.2207 0.5479 0.2314 241 L 0.1999 0.4694 0.3308 242 Y 0.2339 0.4298 0.3363 243 E 0.2900 0.4912 0.2188 244 E 0.2635 0.4449 0.2917 245 A 0.3524 0.3590 0.2886 246 R 0.4274 0.2996 0.2730 247 T 0.5250 0.2335 0.2416 248 H 0.4862 0.1759 0.3379 249 L 0.4665 0.1251 0.4084 250 H 0.2952 0.0659 0.6390