# This file is the result of combining several RDB files, specifically # 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) # 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.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 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0503 0.0305 0.9192 2 R 0.0747 0.0743 0.8509 3 A 0.0700 0.3480 0.5820 4 E 0.0609 0.4262 0.5130 5 D 0.1314 0.4682 0.4004 6 Y 0.3539 0.2575 0.3886 7 E 0.5605 0.2097 0.2299 8 V 0.6491 0.2100 0.1408 9 L 0.6807 0.1613 0.1580 10 Y 0.6514 0.1746 0.1740 11 T 0.6164 0.1873 0.1963 12 I 0.4425 0.1404 0.4171 13 G 0.2789 0.0543 0.6668 14 T 0.2487 0.0686 0.6827 15 G 0.2056 0.0636 0.7308 16 S 0.2208 0.0971 0.6820 17 Y 0.3685 0.0984 0.5331 18 G 0.5502 0.0706 0.3792 19 R 0.7910 0.0507 0.1583 20 C 0.8868 0.0189 0.0943 21 Q 0.8912 0.0152 0.0936 22 K 0.9151 0.0073 0.0776 23 I 0.9048 0.0105 0.0846 24 R 0.9051 0.0070 0.0879 25 R 0.8839 0.0068 0.1092 26 K 0.5964 0.0537 0.3499 27 S 0.3024 0.0720 0.6256 28 D 0.0545 0.0211 0.9245 29 G 0.0821 0.0281 0.8898 30 K 0.6194 0.0110 0.3695 31 I 0.9160 0.0036 0.0804 32 L 0.9127 0.0067 0.0806 33 V 0.9248 0.0038 0.0714 34 W 0.9134 0.0044 0.0822 35 K 0.8867 0.0078 0.1055 36 E 0.8610 0.0104 0.1287 37 L 0.7090 0.0203 0.2706 38 D 0.4305 0.0305 0.5390 39 Y 0.0655 0.4731 0.4614 40 G 0.0626 0.3912 0.5463 41 S 0.0644 0.3801 0.5555 42 M 0.1428 0.1633 0.6939 43 T 0.0919 0.1531 0.7550 44 E 0.0165 0.7880 0.1955 45 A 0.0110 0.8433 0.1457 46 E 0.0102 0.8535 0.1364 47 K 0.0099 0.9029 0.0872 48 Q 0.0105 0.9169 0.0727 49 M 0.0096 0.9181 0.0722 50 L 0.0072 0.9365 0.0563 51 V 0.0052 0.9466 0.0482 52 S 0.0053 0.9494 0.0453 53 E 0.0048 0.9554 0.0398 54 V 0.0047 0.9594 0.0359 55 N 0.0047 0.9593 0.0361 56 L 0.0047 0.9561 0.0392 57 L 0.0049 0.9456 0.0495 58 R 0.0055 0.9044 0.0901 59 E 0.0078 0.7836 0.2085 60 L 0.0445 0.4998 0.4557 61 K 0.0405 0.2122 0.7473 62 H 0.0785 0.0404 0.8811 63 P 0.0207 0.2711 0.7082 64 N 0.0658 0.2540 0.6802 65 I 0.2837 0.3987 0.3177 66 V 0.4034 0.3767 0.2199 67 R 0.5600 0.2993 0.1407 68 Y 0.5283 0.3566 0.1151 69 Y 0.4990 0.3533 0.1476 70 D 0.4525 0.3470 0.2005 71 R 0.4434 0.3160 0.2407 72 I 0.4559 0.2416 0.3025 73 I 0.5005 0.1984 0.3012 74 D 0.3025 0.1604 0.5371 75 R 0.1461 0.1474 0.7064 76 T 0.1075 0.0898 0.8027 77 N 0.0578 0.0842 0.8580 78 T 0.1086 0.0655 0.8259 79 T 0.7388 0.0139 0.2473 80 L 0.9129 0.0036 0.0835 81 Y 0.9298 0.0035 0.0667 82 I 0.9317 0.0033 0.0650 83 V 0.9229 0.0046 0.0725 84 M 0.8891 0.0080 0.1029 85 E 0.7942 0.0241 0.1817 86 Y 0.5901 0.0576 0.3523 87 C 0.2360 0.0582 0.7058 88 E 0.0976 0.0765 0.8259 89 G 0.0534 0.1088 0.8378 90 G 0.0536 0.2869 0.6595 91 D 0.1314 0.4236 0.4450 92 L 0.0268 0.8646 0.1086 93 A 0.0113 0.9211 0.0676 94 S 0.0123 0.9315 0.0562 95 V 0.0270 0.9193 0.0537 96 I 0.0445 0.8934 0.0622 97 T 0.0377 0.8543 0.1080 98 K 0.0389 0.7353 0.2258 99 G 0.0492 0.3408 0.6101 100 T 0.0638 0.1131 0.8231 101 K 0.0847 0.1362 0.7791 102 E 0.0784 0.1762 0.7454 103 R 0.0784 0.1703 0.7513 104 Q 0.1828 0.1327 0.6846 105 Y 0.2852 0.0834 0.6314 106 L 0.1503 0.0190 0.8307 107 D 0.0764 0.0179 0.9057 108 E 0.0048 0.9508 0.0444 109 E 0.0047 0.9602 0.0352 110 F 0.0047 0.9607 0.0347 111 V 0.0047 0.9612 0.0342 112 L 0.0046 0.9613 0.0341 113 R 0.0046 0.9614 0.0339 114 V 0.0046 0.9610 0.0344 115 M 0.0047 0.9609 0.0345 116 T 0.0046 0.9616 0.0338 117 Q 0.0046 0.9615 0.0339 118 L 0.0046 0.9612 0.0342 119 T 0.0046 0.9612 0.0342 120 L 0.0046 0.9605 0.0349 121 A 0.0046 0.9596 0.0358 122 L 0.0047 0.9601 0.0353 123 K 0.0047 0.9584 0.0369 124 E 0.0048 0.9532 0.0420 125 C 0.0056 0.9331 0.0613 126 H 0.0100 0.8519 0.1381 127 R 0.0149 0.7188 0.2662 128 R 0.0479 0.3765 0.5756 129 S 0.0481 0.0697 0.8822 130 D 0.0419 0.1172 0.8409 131 G 0.0544 0.0742 0.8714 132 G 0.1099 0.0483 0.8418 133 H 0.2651 0.0237 0.7112 134 T 0.6878 0.0194 0.2928 135 V 0.8058 0.0154 0.1788 136 L 0.8088 0.0245 0.1667 137 H 0.6865 0.0521 0.2614 138 R 0.3895 0.1132 0.4973 139 D 0.2355 0.1154 0.6491 140 L 0.1647 0.1113 0.7239 141 K 0.1076 0.0599 0.8325 142 P 0.0727 0.3865 0.5409 143 A 0.0923 0.4419 0.4658 144 N 0.1856 0.4154 0.3991 145 V 0.4429 0.1928 0.3643 146 F 0.6119 0.1107 0.2774 147 L 0.5750 0.0702 0.3547 148 D 0.1853 0.0578 0.7569 149 G 0.0243 0.1584 0.8173 150 K 0.0467 0.0804 0.8729 151 Q 0.0726 0.0466 0.8808 152 N 0.2473 0.0217 0.7311 153 V 0.7793 0.0082 0.2124 154 K 0.8509 0.0139 0.1351 155 L 0.8201 0.0286 0.1512 156 G 0.6356 0.0492 0.3152 157 D 0.4359 0.0876 0.4765 158 F 0.2302 0.1923 0.5775 159 G 0.1579 0.2078 0.6344 160 L 0.2167 0.3856 0.3977 161 A 0.2311 0.4495 0.3194 162 R 0.2738 0.4730 0.2533 163 I 0.3073 0.4594 0.2333 164 L 0.2987 0.3625 0.3387 165 N 0.1715 0.1887 0.6398 166 H 0.0704 0.1576 0.7720 167 D 0.0609 0.1205 0.8187 168 T 0.0763 0.1278 0.7959 169 S 0.1820 0.1228 0.6952 170 F 0.4233 0.1208 0.4559 171 A 0.5022 0.1079 0.3899 172 K 0.5683 0.0929 0.3388 173 A 0.5990 0.0718 0.3291 174 F 0.5750 0.0641 0.3609 175 V 0.4267 0.0685 0.5048 176 G 0.1835 0.0517 0.7647 177 T 0.1235 0.0783 0.7982 178 P 0.0767 0.3839 0.5394 179 Y 0.0586 0.4897 0.4518 180 Y 0.1000 0.4858 0.4143 181 M 0.1326 0.3332 0.5342 182 S 0.1241 0.2281 0.6478 183 P 0.0264 0.8118 0.1618 184 E 0.0262 0.8896 0.0842 185 Q 0.0242 0.8977 0.0781 186 M 0.0292 0.8636 0.1072 187 N 0.0220 0.6537 0.3243 188 R 0.0260 0.2781 0.6959 189 M 0.0718 0.0965 0.8317 190 S 0.0829 0.1118 0.8054 191 Y 0.0922 0.0866 0.8212 192 N 0.0690 0.0567 0.8743 193 E 0.0390 0.5109 0.4501 194 K 0.0476 0.6541 0.2983 195 S 0.0682 0.7097 0.2222 196 D 0.0661 0.7213 0.2126 197 I 0.0411 0.8597 0.0992 198 W 0.0210 0.8784 0.1006 199 S 0.0150 0.9154 0.0696 200 L 0.0111 0.9261 0.0629 201 G 0.0063 0.9494 0.0443 202 C 0.0050 0.9569 0.0380 203 L 0.0047 0.9597 0.0356 204 L 0.0053 0.9586 0.0361 205 Y 0.0051 0.9580 0.0370 206 E 0.0054 0.9532 0.0414 207 L 0.0067 0.9361 0.0572 208 C 0.0174 0.8624 0.1202 209 A 0.0382 0.6845 0.2773 210 L 0.0741 0.3441 0.5818 211 M 0.0799 0.0726 0.8475 212 P 0.0702 0.0317 0.8980 213 P 0.0698 0.1056 0.8246 214 F 0.0890 0.1661 0.7449 215 T 0.0769 0.1885 0.7346 216 A 0.0694 0.1946 0.7360 217 F 0.0739 0.1341 0.7920 218 S 0.0913 0.0927 0.8159 219 Q 0.0054 0.9295 0.0650 220 K 0.0048 0.9557 0.0395 221 E 0.0050 0.9562 0.0387 222 L 0.0052 0.9555 0.0392 223 A 0.0051 0.9515 0.0434 224 G 0.0050 0.9418 0.0531 225 K 0.0061 0.9365 0.0573 226 I 0.0144 0.9115 0.0741 227 R 0.0184 0.8516 0.1300 228 E 0.0335 0.5422 0.4243 229 G 0.0298 0.1394 0.8309 230 K 0.0758 0.1052 0.8190 231 F 0.1653 0.0910 0.7437 232 R 0.1941 0.0993 0.7067 233 R 0.2015 0.0938 0.7047 234 I 0.1278 0.0454 0.8268 235 P 0.0879 0.0907 0.8213 236 Y 0.0571 0.2146 0.7283 237 R 0.0825 0.2037 0.7138 238 Y 0.0878 0.0913 0.8209 239 S 0.0611 0.0516 0.8873 240 D 0.0052 0.8822 0.1126 241 E 0.0053 0.9083 0.0863 242 L 0.0049 0.9519 0.0432 243 N 0.0047 0.9585 0.0368 244 E 0.0047 0.9588 0.0365 245 I 0.0047 0.9571 0.0382 246 I 0.0047 0.9576 0.0376 247 T 0.0047 0.9543 0.0409 248 R 0.0051 0.9352 0.0597 249 M 0.0055 0.8780 0.1165 250 L 0.0198 0.7389 0.2413 251 N 0.0399 0.4117 0.5484 252 L 0.0738 0.2115 0.7147 253 K 0.0905 0.0427 0.8668 254 D 0.0114 0.4466 0.5420 255 Y 0.0145 0.4169 0.5686 256 H 0.0420 0.3626 0.5954 257 R 0.1040 0.0485 0.8476 258 P 0.1312 0.0391 0.8297 259 S 0.1154 0.0502 0.8344 260 V 0.0049 0.9423 0.0528 261 E 0.0047 0.9559 0.0394 262 E 0.0048 0.9538 0.0414 263 I 0.0054 0.9373 0.0573 264 L 0.0062 0.8294 0.1644 265 E 0.0130 0.5141 0.4730 266 N 0.0778 0.1277 0.7945 267 P 0.0120 0.5198 0.4682 268 L 0.0373 0.5356 0.4270 269 I 0.1108 0.5940 0.2952 270 L 0.2029 0.4370 0.3601 271 E 0.1550 0.2720 0.5730 272 H 0.0991 0.0939 0.8071 273 H 0.0741 0.0768 0.8491 274 H 0.0716 0.0950 0.8335 275 H 0.0938 0.0946 0.8117 276 H 0.0788 0.0590 0.8621 277 H 0.0496 0.0365 0.9139