# This file is the result of combining several RDB files, specifically # T0296.t06.dssp-ebghstl.rdb (weight 1.53986) # T0296.t06.stride-ebghtl.rdb (weight 1.24869) # T0296.t06.str2.rdb (weight 1.54758) # T0296.t06.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 T0296.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0296 # 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 T0296.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 7.03749 # # ============================================ # Comments from T0296.t06.stride-ebghtl.rdb # ============================================ # TARGET T0296 # 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 T0296.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 7.03749 # # ============================================ # Comments from T0296.t06.str2.rdb # ============================================ # TARGET T0296 # 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 T0296.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 7.03749 # # ============================================ # Comments from T0296.t06.alpha.rdb # ============================================ # TARGET T0296 # 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 T0296.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 7.03749 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.1151 0.0513 0.8336 2 L 0.2233 0.0710 0.7057 3 S 0.3176 0.0485 0.6339 4 L 0.3058 0.0533 0.6409 5 A 0.1650 0.0264 0.8086 6 P 0.1430 0.0390 0.8180 7 T 0.1183 0.0283 0.8534 8 P 0.0531 0.1508 0.7961 9 A 0.0457 0.1579 0.7964 10 V 0.0597 0.1863 0.7539 11 G 0.0481 0.1081 0.8438 12 D 0.0477 0.3019 0.6504 13 S 0.1598 0.4866 0.3536 14 V 0.0145 0.9188 0.0667 15 A 0.0054 0.9546 0.0400 16 R 0.0050 0.9605 0.0346 17 V 0.0047 0.9604 0.0350 18 L 0.0047 0.9572 0.0381 19 E 0.0051 0.9468 0.0482 20 E 0.0078 0.8866 0.1056 21 M 0.0433 0.6015 0.3552 22 G 0.0570 0.2489 0.6941 23 L 0.0955 0.2728 0.6317 24 E 0.1703 0.3975 0.4322 25 T 0.2628 0.3561 0.3811 26 V 0.2067 0.2441 0.5493 27 G 0.0963 0.1046 0.7991 28 T 0.0785 0.1567 0.7648 29 H 0.0510 0.3316 0.6174 30 G 0.0454 0.4197 0.5349 31 T 0.0301 0.8117 0.1582 32 T 0.0058 0.9516 0.0426 33 A 0.0048 0.9596 0.0356 34 A 0.0047 0.9604 0.0349 35 L 0.0047 0.9604 0.0350 36 A 0.0047 0.9595 0.0358 37 L 0.0048 0.9494 0.0457 38 L 0.0051 0.9372 0.0577 39 N 0.0212 0.8984 0.0805 40 D 0.0059 0.9279 0.0662 41 Q 0.0062 0.9210 0.0729 42 V 0.0148 0.8780 0.1072 43 K 0.0164 0.8521 0.1315 44 K 0.0187 0.7562 0.2252 45 G 0.0389 0.5483 0.4129 46 G 0.0997 0.4279 0.4724 47 V 0.2794 0.4096 0.3110 48 M 0.3451 0.4080 0.2469 49 A 0.3847 0.3453 0.2700 50 C 0.3918 0.2663 0.3418 51 N 0.3249 0.2268 0.4484 52 Q 0.3612 0.1671 0.4716 53 V 0.3933 0.1523 0.4544 54 G 0.2749 0.1143 0.6107 55 G 0.2446 0.0938 0.6615 56 L 0.3054 0.1098 0.5849 57 S 0.2783 0.1381 0.5836 58 G 0.3003 0.1621 0.5376 59 A 0.5349 0.1043 0.3608 60 F 0.6803 0.0482 0.2715 61 I 0.5337 0.0289 0.4374 62 P 0.3818 0.0290 0.5891 63 V 0.1979 0.2928 0.5093 64 S 0.1112 0.4515 0.4373 65 E 0.0500 0.5070 0.4430 66 D 0.0579 0.5353 0.4069 67 E 0.0070 0.9183 0.0747 68 G 0.0072 0.9344 0.0584 69 M 0.0051 0.9530 0.0419 70 I 0.0052 0.9565 0.0383 71 A 0.0049 0.9591 0.0361 72 A 0.0050 0.9575 0.0375 73 V 0.0056 0.9510 0.0433 74 Q 0.0074 0.9185 0.0741 75 N 0.0401 0.5575 0.4024 76 G 0.0245 0.1227 0.8528 77 S 0.0715 0.0697 0.8588 78 L 0.2315 0.0335 0.7350 79 N 0.1692 0.0323 0.7985 80 L 0.0104 0.8915 0.0981 81 E 0.0055 0.9188 0.0757 82 K 0.0062 0.9215 0.0723 83 L 0.0121 0.9072 0.0807 84 E 0.0124 0.8816 0.1060 85 A 0.0168 0.8628 0.1204 86 M 0.0348 0.8045 0.1607 87 T 0.0536 0.7945 0.1520 88 A 0.1084 0.7379 0.1537 89 I 0.1789 0.6693 0.1518 90 C 0.1869 0.5891 0.2240 91 S 0.2270 0.3838 0.3892 92 V 0.1648 0.3135 0.5217 93 G 0.2304 0.1838 0.5858 94 L 0.3153 0.1689 0.5158 95 D 0.3707 0.1627 0.4667 96 M 0.6201 0.1089 0.2710 97 I 0.6660 0.0374 0.2965 98 A 0.6933 0.0271 0.2797 99 I 0.3639 0.0228 0.6133 100 P 0.1114 0.1435 0.7451 101 E 0.0238 0.1631 0.8131 102 D 0.0606 0.1699 0.7695 103 T 0.0644 0.0297 0.9059 104 P 0.0587 0.1160 0.8253 105 A 0.0055 0.9300 0.0645 106 E 0.0047 0.9487 0.0465 107 T 0.0047 0.9557 0.0396 108 I 0.0047 0.9589 0.0365 109 A 0.0047 0.9585 0.0368 110 A 0.0047 0.9507 0.0446 111 M 0.0048 0.9466 0.0486 112 I 0.0055 0.9394 0.0551 113 A 0.0056 0.9114 0.0830 114 D 0.0080 0.8695 0.1225 115 E 0.0079 0.9147 0.0773 116 A 0.0084 0.9210 0.0706 117 A 0.0134 0.9237 0.0629 118 I 0.0196 0.9160 0.0644 119 G 0.0560 0.8499 0.0941 120 V 0.0885 0.7809 0.1305 121 I 0.0911 0.6416 0.2674 122 N 0.0710 0.2439 0.6850 123 M 0.0590 0.0766 0.8644 124 K 0.2242 0.0201 0.7557 125 T 0.4611 0.0098 0.5291 126 T 0.7426 0.0182 0.2392 127 A 0.9037 0.0038 0.0925 128 V 0.9218 0.0035 0.0746 129 R 0.9248 0.0038 0.0714 130 I 0.8975 0.0043 0.0982 131 I 0.7466 0.0064 0.2470 132 P 0.4358 0.0165 0.5476 133 K 0.1172 0.0620 0.8209 134 G 0.0538 0.0328 0.9133 135 K 0.0822 0.0321 0.8857 136 E 0.0941 0.0443 0.8615 137 G 0.1091 0.0324 0.8586 138 D 0.3118 0.0301 0.6581 139 M 0.8383 0.0133 0.1484 140 I 0.8778 0.0117 0.1105 141 E 0.8828 0.0137 0.1035 142 F 0.7704 0.0411 0.1885 143 G 0.3488 0.0575 0.5937 144 G 0.1619 0.0630 0.7751 145 L 0.2967 0.1076 0.5957 146 L 0.3251 0.1154 0.5595 147 G 0.2066 0.0609 0.7325 148 T 0.3001 0.0351 0.6647 149 A 0.3474 0.0150 0.6376 150 P 0.4002 0.0192 0.5806 151 V 0.7198 0.0358 0.2444 152 M 0.7854 0.0292 0.1854 153 K 0.8081 0.0261 0.1658 154 V 0.6408 0.0384 0.3208 155 N 0.3170 0.0627 0.6204 156 G 0.1440 0.0528 0.8032 157 A 0.1680 0.0697 0.7623 158 S 0.1830 0.0743 0.7426 159 S 0.1400 0.3516 0.5083 160 V 0.1280 0.5191 0.3529 161 D 0.1876 0.5670 0.2454 162 F 0.2627 0.5451 0.1922 163 I 0.2976 0.4762 0.2263 164 S 0.2406 0.4197 0.3397 165 R 0.1273 0.2478 0.6249 166 G 0.1002 0.0805 0.8193 167 G 0.1418 0.0504 0.8078 168 Q 0.3684 0.0324 0.5992 169 I 0.3424 0.0197 0.6378 170 P 0.3246 0.0264 0.6490 171 A 0.3067 0.0540 0.6393 172 P 0.2836 0.0828 0.6336 173 I 0.1922 0.3672 0.4406 174 H 0.1380 0.4614 0.4006 175 S 0.1672 0.3886 0.4442 176 F 0.1868 0.2123 0.6009 177 K 0.1328 0.1362 0.7310 178 N 0.0690 0.0474 0.8836