# This file is the result of combining several RDB files, specifically # T0289.t04.dssp-ebghstl.rdb (weight 1.53986) # T0289.t04.stride-ebghtl.rdb (weight 1.24869) # T0289.t04.str2.rdb (weight 1.54758) # T0289.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 T0289.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 717 # # ============================================ # Comments from T0289.t04.stride-ebghtl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 717 # # ============================================ # Comments from T0289.t04.str2.rdb # ============================================ # TARGET T0289 # 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 T0289.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 717 # # ============================================ # Comments from T0289.t04.alpha.rdb # ============================================ # TARGET T0289 # 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 T0289.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 717 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0912 0.0428 0.8659 2 T 0.2515 0.0276 0.7209 3 S 0.4386 0.0360 0.5254 4 C 0.3975 0.0461 0.5565 5 V 0.3901 0.0569 0.5530 6 A 0.2244 0.0785 0.6971 7 E 0.1114 0.0947 0.7939 8 E 0.0961 0.0686 0.8353 9 P 0.1058 0.0806 0.8136 10 I 0.1809 0.0203 0.7988 11 K 0.2976 0.0101 0.6923 12 K 0.7756 0.0046 0.2199 13 I 0.9270 0.0033 0.0696 14 A 0.9330 0.0032 0.0638 15 I 0.9296 0.0032 0.0671 16 F 0.8931 0.0057 0.1013 17 G 0.7261 0.0180 0.2559 18 G 0.4332 0.0276 0.5393 19 T 0.3114 0.0499 0.6388 20 H 0.1724 0.0635 0.7642 21 G 0.0591 0.1621 0.7787 22 N 0.0515 0.1888 0.7597 23 E 0.0714 0.4466 0.4820 24 L 0.0543 0.6691 0.2766 25 T 0.0240 0.7718 0.2042 26 G 0.0057 0.9442 0.0501 27 V 0.0047 0.9597 0.0356 28 F 0.0046 0.9614 0.0340 29 L 0.0046 0.9612 0.0342 30 V 0.0046 0.9613 0.0341 31 T 0.0046 0.9611 0.0343 32 H 0.0046 0.9600 0.0354 33 W 0.0047 0.9568 0.0386 34 L 0.0048 0.9460 0.0491 35 K 0.0057 0.8708 0.1234 36 N 0.0280 0.6342 0.3379 37 G 0.0253 0.3978 0.5769 38 A 0.0319 0.4291 0.5390 39 E 0.0322 0.6047 0.3631 40 V 0.0597 0.5491 0.3912 41 H 0.0991 0.4322 0.4688 42 R 0.1107 0.3396 0.5497 43 A 0.0590 0.2179 0.7230 44 G 0.1034 0.0613 0.8354 45 L 0.4225 0.0093 0.5682 46 E 0.8438 0.0041 0.1521 47 V 0.9267 0.0032 0.0701 48 K 0.9208 0.0040 0.0752 49 P 0.9285 0.0031 0.0685 50 F 0.8674 0.0172 0.1154 51 I 0.7834 0.0073 0.2093 52 T 0.3748 0.0223 0.6029 53 N 0.1676 0.0250 0.8074 54 P 0.0220 0.7052 0.2728 55 R 0.0100 0.8454 0.1446 56 A 0.0114 0.9090 0.0796 57 V 0.0268 0.8982 0.0750 58 E 0.0254 0.8794 0.0952 59 K 0.0305 0.7725 0.1970 60 C 0.0841 0.5254 0.3905 61 T 0.1633 0.3071 0.5297 62 R 0.2553 0.2159 0.5287 63 Y 0.2649 0.1663 0.5689 64 I 0.1723 0.1005 0.7272 65 D 0.1367 0.0523 0.8110 66 C 0.2134 0.0620 0.7247 67 D 0.3536 0.0557 0.5907 68 L 0.1721 0.3282 0.4997 69 N 0.1941 0.3709 0.4349 70 R 0.2440 0.3595 0.3965 71 V 0.2436 0.1592 0.5972 72 F 0.1677 0.0535 0.7787 73 D 0.1060 0.0472 0.8468 74 L 0.0537 0.3215 0.6247 75 E 0.0263 0.3812 0.5925 76 N 0.0879 0.3851 0.5270 77 L 0.0530 0.4060 0.5410 78 S 0.0437 0.3563 0.6000 79 K 0.0411 0.3286 0.6303 80 E 0.0725 0.2021 0.7254 81 M 0.1064 0.1482 0.7455 82 S 0.0476 0.1637 0.7887 83 E 0.0302 0.2167 0.7531 84 D 0.0416 0.1695 0.7889 85 L 0.0569 0.1277 0.8154 86 P 0.0270 0.4149 0.5581 87 Y 0.0177 0.8372 0.1451 88 E 0.0099 0.9153 0.0747 89 V 0.0080 0.9407 0.0513 90 R 0.0069 0.9479 0.0452 91 R 0.0064 0.9478 0.0458 92 A 0.0047 0.9579 0.0374 93 Q 0.0047 0.9598 0.0355 94 E 0.0047 0.9588 0.0364 95 I 0.0049 0.9513 0.0438 96 N 0.0053 0.9430 0.0517 97 H 0.0068 0.8819 0.1113 98 L 0.0138 0.7626 0.2236 99 F 0.0558 0.4863 0.4579 100 G 0.0428 0.1146 0.8426 101 P 0.0370 0.2428 0.7202 102 K 0.0298 0.2939 0.6762 103 N 0.0429 0.2337 0.7234 104 S 0.0548 0.1772 0.7680 105 D 0.0510 0.1805 0.7685 106 D 0.0803 0.1244 0.7953 107 A 0.2202 0.0501 0.7296 108 Y 0.4514 0.0098 0.5388 109 D 0.6503 0.0101 0.3396 110 V 0.9263 0.0034 0.0704 111 V 0.9327 0.0032 0.0641 112 F 0.9266 0.0040 0.0694 113 D 0.8912 0.0036 0.1052 114 L 0.4995 0.0385 0.4620 115 H 0.2356 0.0599 0.7044 116 N 0.1340 0.1015 0.7644 117 T 0.1280 0.1040 0.7680 118 T 0.1002 0.1596 0.7402 119 S 0.0604 0.2603 0.6793 120 N 0.0887 0.2691 0.6423 121 M 0.1479 0.2119 0.6402 122 G 0.1508 0.0985 0.7508 123 C 0.2715 0.0888 0.6397 124 T 0.4280 0.1050 0.4670 125 L 0.4391 0.1193 0.4416 126 I 0.3824 0.1296 0.4880 127 L 0.2901 0.1914 0.5185 128 E 0.1923 0.2470 0.5607 129 D 0.1133 0.2941 0.5926 130 S 0.0782 0.3170 0.6048 131 R 0.0686 0.2710 0.6604 132 N 0.0651 0.2011 0.7338 133 D 0.0138 0.7073 0.2789 134 F 0.0124 0.7985 0.1892 135 L 0.0120 0.8547 0.1333 136 I 0.0120 0.8835 0.1045 137 Q 0.0130 0.8641 0.1229 138 M 0.0085 0.8787 0.1128 139 F 0.0080 0.8795 0.1125 140 H 0.0066 0.8975 0.0959 141 Y 0.0069 0.8940 0.0991 142 I 0.0192 0.8670 0.1139 143 K 0.0111 0.8772 0.1117 144 T 0.0151 0.8192 0.1656 145 C 0.0282 0.7227 0.2491 146 M 0.0505 0.4846 0.4649 147 A 0.0546 0.2294 0.7159 148 P 0.0550 0.1225 0.8225 149 L 0.1006 0.0359 0.8635 150 P 0.1538 0.0594 0.7868 151 C 0.5761 0.0522 0.3717 152 S 0.7670 0.0354 0.1976 153 V 0.7715 0.0443 0.1842 154 Y 0.6189 0.0550 0.3261 155 L 0.4354 0.0728 0.4918 156 I 0.2662 0.0913 0.6425 157 E 0.1586 0.0755 0.7659 158 H 0.0867 0.0636 0.8496 159 P 0.0378 0.1824 0.7798 160 S 0.0504 0.1867 0.7629 161 L 0.1034 0.3094 0.5872 162 K 0.1037 0.4005 0.4958 163 Y 0.1279 0.5144 0.3576 164 A 0.1217 0.5758 0.3025 165 T 0.1205 0.6188 0.2607 166 T 0.0891 0.6924 0.2185 167 R 0.0569 0.7259 0.2172 168 S 0.0595 0.6522 0.2883 169 I 0.0575 0.3957 0.5469 170 A 0.0714 0.1264 0.8023 171 K 0.1100 0.0581 0.8319 172 Y 0.1822 0.0182 0.7997 173 P 0.4912 0.0242 0.4846 174 V 0.8541 0.0142 0.1316 175 G 0.9035 0.0095 0.0870 176 I 0.9078 0.0082 0.0840 177 E 0.8688 0.0090 0.1222 178 V 0.5934 0.0237 0.3828 179 G 0.2437 0.0157 0.7406 180 P 0.1518 0.0492 0.7990 181 Q 0.1089 0.0438 0.8474 182 P 0.0675 0.0939 0.8387 183 H 0.0601 0.1153 0.8246 184 G 0.0788 0.1104 0.8109 185 V 0.1612 0.1272 0.7117 186 L 0.1549 0.0747 0.7704 187 R 0.0728 0.0749 0.8524 188 A 0.0052 0.9158 0.0790 189 D 0.0049 0.9295 0.0656 190 I 0.0053 0.9450 0.0497 191 L 0.0050 0.9571 0.0379 192 D 0.0046 0.9589 0.0364 193 Q 0.0046 0.9570 0.0383 194 M 0.0047 0.9588 0.0366 195 R 0.0047 0.9605 0.0348 196 R 0.0047 0.9584 0.0369 197 M 0.0047 0.9536 0.0417 198 L 0.0047 0.9596 0.0357 199 K 0.0047 0.9607 0.0346 200 H 0.0047 0.9576 0.0378 201 A 0.0048 0.9568 0.0385 202 L 0.0047 0.9554 0.0399 203 D 0.0048 0.9457 0.0495 204 F 0.0050 0.9349 0.0601 205 I 0.0083 0.9004 0.0914 206 Q 0.0072 0.8161 0.1768 207 R 0.0159 0.7989 0.1853 208 F 0.0602 0.6096 0.3301 209 N 0.0532 0.4610 0.4857 210 E 0.0356 0.2627 0.7017 211 G 0.0337 0.1004 0.8659 212 K 0.1117 0.0551 0.8333 213 E 0.2311 0.0286 0.7403 214 F 0.1182 0.0172 0.8647 215 P 0.0802 0.0155 0.9043 216 P 0.0822 0.0722 0.8456 217 C 0.1254 0.0840 0.7906 218 A 0.2032 0.1187 0.6780 219 I 0.2744 0.1280 0.5977 220 D 0.4216 0.1094 0.4690 221 V 0.6647 0.0937 0.2416 222 Y 0.7824 0.0478 0.1698 223 K 0.8221 0.0374 0.1405 224 I 0.7542 0.0526 0.1933 225 M 0.5738 0.0724 0.3538 226 E 0.4679 0.1078 0.4243 227 K 0.4847 0.0865 0.4288 228 V 0.5089 0.0505 0.4407 229 D 0.3891 0.0438 0.5671 230 Y 0.3274 0.0360 0.6366 231 P 0.3720 0.0420 0.5860 232 R 0.4298 0.0650 0.5052 233 N 0.2707 0.0766 0.6527 234 E 0.1486 0.1331 0.7182 235 S 0.0946 0.0579 0.8476 236 G 0.0912 0.0449 0.8639 237 D 0.3516 0.0340 0.6145 238 V 0.7465 0.0318 0.2217 239 A 0.8002 0.0487 0.1511 240 A 0.8622 0.0331 0.1047 241 V 0.8414 0.0344 0.1242 242 I 0.7791 0.0298 0.1911 243 H 0.3891 0.0307 0.5802 244 P 0.1167 0.1827 0.7007 245 N 0.0672 0.1669 0.7660 246 L 0.0776 0.1943 0.7281 247 Q 0.0640 0.1407 0.7953 248 D 0.0862 0.1309 0.7829 249 Q 0.0847 0.1443 0.7710 250 D 0.1515 0.0900 0.7585 251 W 0.3699 0.0521 0.5780 252 K 0.5317 0.0209 0.4475 253 P 0.6555 0.0179 0.3266 254 L 0.4031 0.0263 0.5706 255 H 0.1510 0.0181 0.8308 256 P 0.0394 0.0623 0.8983 257 G 0.0244 0.0393 0.9363 258 D 0.1692 0.0150 0.8157 259 P 0.5373 0.0109 0.4518 260 V 0.8539 0.0102 0.1359 261 F 0.9053 0.0061 0.0886 262 V 0.9036 0.0093 0.0871 263 S 0.8547 0.0076 0.1377 264 L 0.5784 0.0443 0.3773 265 D 0.1821 0.0244 0.7935 266 G 0.1194 0.0357 0.8449 267 K 0.5218 0.0112 0.4670 268 V 0.7995 0.0047 0.1958 269 I 0.7616 0.0065 0.2320 270 P 0.6580 0.0089 0.3331 271 L 0.3148 0.0456 0.6395 272 G 0.1018 0.0523 0.8459 273 G 0.0839 0.0506 0.8655 274 D 0.2409 0.0400 0.7191 275 C 0.6847 0.0170 0.2984 276 T 0.8538 0.0090 0.1373 277 V 0.8686 0.0133 0.1182 278 Y 0.7616 0.0139 0.2244 279 P 0.5117 0.0509 0.4374 280 V 0.3935 0.0808 0.5257 281 F 0.3300 0.1312 0.5388 282 V 0.2173 0.2241 0.5586 283 N 0.1253 0.2749 0.5998 284 E 0.0563 0.6812 0.2626 285 A 0.0447 0.8279 0.1274 286 A 0.0423 0.8472 0.1106 287 Y 0.0510 0.8450 0.1040 288 Y 0.0622 0.8078 0.1300 289 E 0.0493 0.7862 0.1645 290 K 0.0362 0.7625 0.2013 291 K 0.0461 0.7286 0.2253 292 E 0.0614 0.7062 0.2324 293 A 0.0678 0.7085 0.2237 294 F 0.0961 0.6579 0.2460 295 A 0.1838 0.5265 0.2897 296 K 0.2594 0.4361 0.3045 297 T 0.3418 0.3495 0.3087 298 T 0.4171 0.2718 0.3111 299 K 0.4806 0.1573 0.3622 300 L 0.5736 0.0923 0.3341 301 T 0.5747 0.0701 0.3552 302 L 0.4610 0.0540 0.4849 303 N 0.3387 0.0468 0.6145 304 A 0.1476 0.3620 0.4904 305 K 0.0808 0.5175 0.4018 306 S 0.0633 0.5793 0.3573 307 I 0.1070 0.6074 0.2856 308 R 0.1034 0.6128 0.2838 309 S 0.1043 0.5482 0.3475 310 T 0.1002 0.4355 0.4643 311 L 0.0984 0.2570 0.6447 312 H 0.0525 0.0726 0.8749