# This file is the result of combining several RDB files, specifically # T0289.t06.dssp-ebghstl.rdb (weight 1.53986) # T0289.t06.stride-ebghtl.rdb (weight 1.24869) # T0289.t06.str2.rdb (weight 1.54758) # T0289.t06.alpha.rdb (weight 0.659012) # 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) # T0289.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0289.t2k.stride-ebghtl.rdb (weight 1.24869) # T0289.t2k.str2.rdb (weight 1.54758) # T0289.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 T0289.t06.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.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 880 # # ============================================ # Comments from T0289.t06.stride-ebghtl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 880 # # ============================================ # Comments from T0289.t06.str2.rdb # ============================================ # TARGET T0289 # 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 T0289.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 880 # # ============================================ # Comments from T0289.t06.alpha.rdb # ============================================ # TARGET T0289 # 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 T0289.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 880 # # ============================================ # 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 # # ============================================ # Comments from T0289.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 118 # # ============================================ # Comments from T0289.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 118 # # ============================================ # Comments from T0289.t2k.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.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 118 # # ============================================ # Comments from T0289.t2k.alpha.rdb # ============================================ # TARGET T0289 # 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 T0289.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 118 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1344 0.0294 0.8362 2 T 0.2868 0.0287 0.6844 3 S 0.3642 0.0267 0.6091 4 C 0.2639 0.0409 0.6952 5 V 0.1594 0.0631 0.7774 6 A 0.0961 0.0935 0.8104 7 E 0.0604 0.0771 0.8625 8 E 0.0812 0.0431 0.8756 9 P 0.1173 0.0543 0.8284 10 I 0.1562 0.0220 0.8218 11 K 0.1567 0.0473 0.7960 12 K 0.7331 0.0077 0.2592 13 I 0.9218 0.0037 0.0745 14 A 0.9299 0.0036 0.0666 15 I 0.9266 0.0037 0.0697 16 F 0.8721 0.0179 0.1099 17 G 0.6734 0.0189 0.3076 18 G 0.4096 0.0319 0.5585 19 T 0.2835 0.0625 0.6540 20 H 0.1678 0.0942 0.7380 21 G 0.0813 0.1435 0.7752 22 N 0.0725 0.1200 0.8075 23 E 0.1306 0.3551 0.5142 24 L 0.1179 0.4688 0.4134 25 T 0.0510 0.5283 0.4207 26 G 0.0165 0.7282 0.2553 27 V 0.0048 0.9535 0.0416 28 F 0.0059 0.9556 0.0385 29 L 0.0050 0.9582 0.0368 30 V 0.0047 0.9589 0.0364 31 T 0.0047 0.9581 0.0372 32 H 0.0048 0.9553 0.0399 33 W 0.0049 0.9474 0.0477 34 L 0.0053 0.9207 0.0740 35 K 0.0093 0.7848 0.2059 36 N 0.0257 0.5476 0.4267 37 G 0.0283 0.4836 0.4880 38 A 0.0198 0.5940 0.3861 39 E 0.0278 0.6251 0.3471 40 V 0.0475 0.5511 0.4014 41 H 0.0713 0.4722 0.4565 42 R 0.0758 0.3220 0.6022 43 A 0.0589 0.2367 0.7044 44 G 0.0603 0.0800 0.8597 45 L 0.2331 0.0309 0.7360 46 E 0.6427 0.0205 0.3368 47 V 0.8473 0.0127 0.1400 48 K 0.8438 0.0158 0.1404 49 P 0.8202 0.0184 0.1614 50 F 0.7188 0.0313 0.2499 51 I 0.4398 0.0676 0.4926 52 T 0.1641 0.0606 0.7753 53 N 0.0847 0.0425 0.8727 54 P 0.0179 0.7439 0.2382 55 R 0.0088 0.8972 0.0940 56 A 0.0083 0.9108 0.0809 57 V 0.0115 0.9087 0.0798 58 E 0.0131 0.9059 0.0810 59 K 0.0290 0.8020 0.1690 60 C 0.0438 0.6953 0.2609 61 T 0.0872 0.6369 0.2758 62 R 0.1380 0.5817 0.2804 63 Y 0.1526 0.4876 0.3598 64 I 0.1849 0.3141 0.5010 65 D 0.1604 0.1915 0.6482 66 C 0.1292 0.2810 0.5899 67 D 0.2024 0.2366 0.5609 68 L 0.0741 0.4946 0.4312 69 N 0.0928 0.4582 0.4490 70 R 0.1599 0.4312 0.4090 71 V 0.2380 0.2551 0.5070 72 F 0.2280 0.1108 0.6612 73 D 0.1235 0.0689 0.8076 74 L 0.0335 0.6065 0.3600 75 E 0.0235 0.7097 0.2668 76 N 0.0296 0.7001 0.2704 77 L 0.0466 0.5113 0.4422 78 S 0.0390 0.3473 0.6137 79 K 0.0533 0.2925 0.6542 80 E 0.0451 0.3560 0.5989 81 M 0.0521 0.3277 0.6203 82 S 0.0447 0.3437 0.6116 83 E 0.0346 0.3125 0.6529 84 D 0.0428 0.3503 0.6069 85 L 0.0184 0.5780 0.4035 86 P 0.0080 0.8512 0.1408 87 Y 0.0059 0.9258 0.0683 88 E 0.0060 0.9363 0.0577 89 V 0.0069 0.9372 0.0559 90 R 0.0068 0.9400 0.0532 91 R 0.0084 0.9368 0.0548 92 A 0.0056 0.9411 0.0533 93 Q 0.0061 0.9406 0.0533 94 E 0.0052 0.9414 0.0534 95 I 0.0051 0.9388 0.0561 96 N 0.0054 0.9280 0.0666 97 H 0.0058 0.9041 0.0901 98 L 0.0078 0.8552 0.1370 99 F 0.0233 0.6801 0.2966 100 G 0.0545 0.2960 0.6496 101 P 0.0530 0.1775 0.7695 102 K 0.0457 0.2618 0.6924 103 N 0.0372 0.2415 0.7212 104 S 0.0506 0.2003 0.7490 105 D 0.0574 0.1394 0.8032 106 D 0.0747 0.1392 0.7861 107 A 0.1818 0.1397 0.6785 108 Y 0.4115 0.0561 0.5324 109 D 0.6332 0.0476 0.3192 110 V 0.8970 0.0144 0.0887 111 V 0.9105 0.0127 0.0768 112 F 0.9019 0.0134 0.0847 113 D 0.8139 0.0175 0.1686 114 L 0.3444 0.1134 0.5422 115 H 0.1716 0.1309 0.6976 116 N 0.1354 0.1561 0.7084 117 T 0.1532 0.1863 0.6605 118 T 0.1263 0.1775 0.6962 119 S 0.0583 0.2411 0.7006 120 N 0.0550 0.1958 0.7492 121 M 0.1065 0.1941 0.6993 122 G 0.1745 0.1180 0.7075 123 C 0.3563 0.1007 0.5430 124 T 0.6071 0.0676 0.3252 125 L 0.7282 0.0462 0.2256 126 I 0.7309 0.0423 0.2268 127 L 0.5826 0.0492 0.3683 128 E 0.3212 0.0658 0.6130 129 D 0.1146 0.1061 0.7792 130 S 0.0596 0.1206 0.8197 131 R 0.0488 0.1460 0.8051 132 N 0.0401 0.2833 0.6766 133 D 0.0432 0.4006 0.5562 134 F 0.0285 0.6388 0.3326 135 L 0.0201 0.7597 0.2202 136 I 0.0151 0.8281 0.1568 137 Q 0.0116 0.8702 0.1182 138 M 0.0122 0.8813 0.1065 139 F 0.0107 0.8751 0.1142 140 H 0.0152 0.8588 0.1260 141 Y 0.0165 0.8371 0.1464 142 I 0.0248 0.8209 0.1543 143 K 0.0252 0.8150 0.1598 144 T 0.0274 0.7789 0.1937 145 C 0.0443 0.6694 0.2863 146 M 0.0845 0.4489 0.4666 147 A 0.0879 0.3000 0.6120 148 P 0.1116 0.3054 0.5830 149 L 0.1479 0.3019 0.5502 150 P 0.1953 0.2526 0.5521 151 C 0.3219 0.1799 0.4982 152 S 0.4831 0.1525 0.3644 153 V 0.4845 0.1758 0.3397 154 Y 0.4838 0.1602 0.3560 155 L 0.4430 0.1098 0.4472 156 I 0.3043 0.0904 0.6053 157 E 0.2031 0.0980 0.6989 158 H 0.1349 0.0901 0.7749 159 P 0.0982 0.1344 0.7674 160 S 0.1005 0.2358 0.6638 161 L 0.0959 0.3643 0.5398 162 K 0.1039 0.3622 0.5339 163 Y 0.1682 0.3430 0.4888 164 A 0.2253 0.3029 0.4717 165 T 0.2464 0.2910 0.4626 166 T 0.1326 0.6051 0.2623 167 R 0.0882 0.6779 0.2339 168 S 0.0993 0.6026 0.2981 169 I 0.1328 0.4458 0.4213 170 A 0.1481 0.2505 0.6014 171 K 0.1398 0.1867 0.6735 172 Y 0.1988 0.0832 0.7180 173 P 0.4430 0.0430 0.5140 174 V 0.8049 0.0139 0.1812 175 G 0.9050 0.0068 0.0882 176 I 0.9025 0.0059 0.0915 177 E 0.8742 0.0077 0.1181 178 V 0.6754 0.0224 0.3022 179 G 0.4097 0.0166 0.5737 180 P 0.3049 0.0298 0.6652 181 Q 0.2258 0.0234 0.7508 182 P 0.1053 0.0746 0.8201 183 H 0.0497 0.1051 0.8452 184 G 0.0596 0.1124 0.8280 185 V 0.1104 0.2201 0.6695 186 L 0.1081 0.2459 0.6460 187 R 0.0591 0.3370 0.6038 188 A 0.0085 0.8750 0.1165 189 D 0.0089 0.8931 0.0980 190 I 0.0054 0.9408 0.0538 191 L 0.0047 0.9545 0.0408 192 D 0.0047 0.9567 0.0386 193 Q 0.0047 0.9580 0.0373 194 M 0.0047 0.9598 0.0356 195 R 0.0047 0.9601 0.0352 196 R 0.0047 0.9602 0.0351 197 M 0.0047 0.9601 0.0352 198 L 0.0047 0.9592 0.0361 199 K 0.0047 0.9575 0.0378 200 H 0.0048 0.9493 0.0459 201 A 0.0048 0.9422 0.0530 202 L 0.0051 0.9207 0.0742 203 D 0.0058 0.8604 0.1338 204 F 0.0086 0.7758 0.2156 205 I 0.0475 0.6002 0.3523 206 Q 0.0477 0.4580 0.4943 207 R 0.0536 0.4563 0.4900 208 F 0.0742 0.4410 0.4848 209 N 0.0608 0.3272 0.6120 210 E 0.0587 0.2385 0.7028 211 G 0.0521 0.1769 0.7710 212 K 0.0876 0.1484 0.7641 213 E 0.1048 0.1058 0.7894 214 F 0.0851 0.0946 0.8203 215 P 0.0884 0.1301 0.7815 216 P 0.1126 0.1994 0.6880 217 C 0.2141 0.2193 0.5666 218 A 0.4263 0.1706 0.4031 219 I 0.5816 0.1608 0.2576 220 D 0.6612 0.1539 0.1849 221 V 0.6809 0.1490 0.1701 222 Y 0.6766 0.1457 0.1776 223 K 0.6548 0.1365 0.2088 224 I 0.6348 0.1189 0.2463 225 M 0.5968 0.1016 0.3016 226 E 0.5973 0.0862 0.3165 227 K 0.6088 0.0614 0.3298 228 V 0.5757 0.0363 0.3881 229 D 0.4179 0.0276 0.5545 230 Y 0.2781 0.0491 0.6728 231 P 0.1697 0.0969 0.7334 232 R 0.1716 0.1563 0.6721 233 N 0.1731 0.1697 0.6572 234 E 0.1655 0.1719 0.6626 235 S 0.1406 0.1375 0.7219 236 G 0.1201 0.0893 0.7906 237 D 0.1492 0.0928 0.7581 238 V 0.1670 0.2157 0.6173 239 A 0.2088 0.2627 0.5285 240 A 0.4036 0.2547 0.3416 241 V 0.5734 0.1682 0.2584 242 I 0.5604 0.1166 0.3230 243 H 0.3459 0.0728 0.5813 244 P 0.1122 0.3384 0.5494 245 N 0.0791 0.4021 0.5188 246 L 0.0709 0.4610 0.4682 247 Q 0.1328 0.2492 0.6180 248 D 0.1170 0.1736 0.7093 249 Q 0.0701 0.1700 0.7599 250 D 0.1246 0.1149 0.7604 251 W 0.2287 0.1305 0.6408 252 K 0.3540 0.0662 0.5798 253 P 0.5144 0.0441 0.4415 254 L 0.2541 0.0315 0.7145 255 H 0.1153 0.0259 0.8588 256 P 0.0480 0.0685 0.8836 257 G 0.0424 0.0379 0.9197 258 D 0.2698 0.0189 0.7113 259 P 0.7132 0.0100 0.2768 260 V 0.8021 0.0262 0.1717 261 F 0.8633 0.0141 0.1226 262 V 0.8593 0.0121 0.1286 263 S 0.6515 0.0250 0.3234 264 L 0.1515 0.0803 0.7682 265 D 0.0667 0.0271 0.9062 266 G 0.1427 0.0371 0.8202 267 K 0.4913 0.0155 0.4932 268 V 0.8444 0.0061 0.1495 269 I 0.8421 0.0071 0.1508 270 P 0.7901 0.0095 0.2004 271 L 0.5085 0.0414 0.4501 272 G 0.2069 0.0504 0.7426 273 G 0.0661 0.0735 0.8604 274 D 0.1008 0.0505 0.8487 275 C 0.4260 0.0179 0.5561 276 T 0.7485 0.0082 0.2433 277 V 0.8341 0.0064 0.1595 278 Y 0.7577 0.0092 0.2331 279 P 0.4600 0.0149 0.5251 280 V 0.1581 0.0592 0.7827 281 F 0.1055 0.0367 0.8578 282 V 0.0413 0.4028 0.5559 283 N 0.0348 0.4632 0.5019 284 E 0.0284 0.6832 0.2884 285 A 0.0186 0.8358 0.1456 286 A 0.0150 0.8521 0.1329 287 Y 0.0271 0.8179 0.1550 288 Y 0.0324 0.8255 0.1421 289 E 0.0476 0.8223 0.1300 290 K 0.0465 0.6293 0.3241 291 K 0.0687 0.4378 0.4935 292 E 0.1909 0.3895 0.4195 293 A 0.3735 0.2756 0.3509 294 F 0.5231 0.2029 0.2740 295 A 0.6217 0.1209 0.2574 296 K 0.5798 0.1443 0.2759 297 T 0.5884 0.0828 0.3289 298 T 0.6018 0.0670 0.3312 299 K 0.6233 0.0537 0.3230 300 L 0.7239 0.0362 0.2399 301 T 0.7399 0.0198 0.2404 302 L 0.7489 0.0088 0.2423 303 N 0.6276 0.0135 0.3589 304 A 0.2821 0.2567 0.4611 305 K 0.1374 0.4366 0.4260 306 S 0.1545 0.5147 0.3308 307 I 0.4253 0.3135 0.2612 308 R 0.5009 0.2131 0.2860 309 S 0.4724 0.1845 0.3431 310 T 0.3150 0.1486 0.5364 311 L 0.2122 0.0929 0.6949 312 H 0.0689 0.0361 0.8950