# This file is the result of combining several RDB files, specifically # T0357.t04.dssp-ebghstl.rdb (weight 1.53986) # T0357.t04.stride-ebghtl.rdb (weight 1.24869) # T0357.t04.str2.rdb (weight 1.54758) # T0357.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 T0357.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.107 # # ============================================ # Comments from T0357.t04.stride-ebghtl.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.107 # # ============================================ # Comments from T0357.t04.str2.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.107 # # ============================================ # Comments from T0357.t04.alpha.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.107 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1770 0.0294 0.7936 2 V 0.4462 0.0214 0.5324 3 K 0.7040 0.0229 0.2731 4 F 0.7586 0.0197 0.2216 5 A 0.7128 0.0215 0.2657 6 C 0.6949 0.0266 0.2785 7 R 0.7611 0.0348 0.2041 8 A 0.8282 0.0295 0.1423 9 I 0.7831 0.0387 0.1782 10 T 0.6938 0.0373 0.2689 11 R 0.3590 0.0707 0.5702 12 G 0.2917 0.0487 0.6595 13 R 0.6389 0.0438 0.3173 14 A 0.7941 0.0225 0.1834 15 E 0.7792 0.0320 0.1888 16 G 0.8079 0.0171 0.1750 17 E 0.8536 0.0183 0.1281 18 A 0.9106 0.0083 0.0811 19 L 0.9026 0.0097 0.0877 20 V 0.8605 0.0164 0.1231 21 T 0.6593 0.0278 0.3128 22 K 0.2648 0.0824 0.6528 23 E 0.2377 0.0776 0.6847 24 Y 0.3373 0.1233 0.5393 25 I 0.4455 0.1165 0.4380 26 S 0.4542 0.1250 0.4208 27 F 0.3610 0.2178 0.4212 28 L 0.2769 0.2158 0.5073 29 G 0.2044 0.1473 0.6483 30 G 0.2892 0.0781 0.6327 31 I 0.4451 0.0327 0.5221 32 D 0.2372 0.0179 0.7448 33 K 0.0158 0.1874 0.7969 34 E 0.0193 0.1539 0.8268 35 T 0.1047 0.1831 0.7121 36 G 0.2434 0.0614 0.6952 37 I 0.5360 0.0252 0.4389 38 V 0.6575 0.0186 0.3238 39 K 0.3204 0.0258 0.6539 40 E 0.0536 0.1639 0.7826 41 D 0.0618 0.1217 0.8164 42 C 0.1515 0.0868 0.7616 43 E 0.1090 0.2124 0.6786 44 I 0.1367 0.2311 0.6322 45 K 0.1059 0.1562 0.7379 46 G 0.1173 0.0671 0.8155 47 E 0.4276 0.0354 0.5370 48 S 0.6256 0.0277 0.3467 49 V 0.5734 0.0634 0.3632 50 A 0.2451 0.0671 0.6879 51 G 0.1945 0.0386 0.7669 52 R 0.6700 0.0098 0.3202 53 I 0.9156 0.0033 0.0811 54 L 0.9228 0.0035 0.0737 55 V 0.9051 0.0039 0.0909 56 F 0.7241 0.0073 0.2687 57 P 0.3076 0.0413 0.6511 58 G 0.1053 0.0468 0.8479 59 G 0.1255 0.0454 0.8291 60 K 0.1382 0.0778 0.7840 61 G 0.1353 0.0796 0.7851 62 S 0.1204 0.1434 0.7362 63 T 0.1069 0.2798 0.6133 64 V 0.0628 0.5321 0.4051 65 G 0.0183 0.8141 0.1676 66 S 0.0063 0.9358 0.0579 67 Y 0.0066 0.9536 0.0399 68 V 0.0077 0.9555 0.0368 69 L 0.0068 0.9556 0.0375 70 L 0.0061 0.9538 0.0401 71 N 0.0063 0.9520 0.0418 72 L 0.0084 0.9423 0.0493 73 R 0.0082 0.9203 0.0715 74 K 0.0160 0.8070 0.1770 75 N 0.0446 0.2352 0.7202 76 G 0.0353 0.0360 0.9288 77 V 0.1039 0.0269 0.8692 78 A 0.2293 0.0234 0.7473 79 P 0.2612 0.0766 0.6621 80 K 0.5581 0.1293 0.3126 81 A 0.8152 0.0713 0.1135 82 I 0.8660 0.0542 0.0798 83 I 0.8448 0.0503 0.1050 84 N 0.6969 0.0564 0.2467 85 K 0.3407 0.1052 0.5541 86 K 0.1866 0.0887 0.7247 87 T 0.1721 0.1362 0.6916 88 E 0.1850 0.1390 0.6760 89 T 0.3777 0.1216 0.5008 90 I 0.7095 0.1146 0.1760 91 I 0.8226 0.0676 0.1098 92 A 0.8240 0.0705 0.1055 93 V 0.7312 0.1064 0.1624 94 G 0.6925 0.0681 0.2394 95 A 0.8082 0.0536 0.1382 96 A 0.8434 0.0479 0.1087 97 M 0.8061 0.0456 0.1483 98 A 0.6008 0.0597 0.3395 99 E 0.3194 0.0582 0.6224 100 I 0.2542 0.0170 0.7288 101 P 0.3630 0.0194 0.6176 102 L 0.6743 0.0356 0.2901 103 V 0.7271 0.0353 0.2376 104 E 0.7183 0.0341 0.2476 105 V 0.4577 0.0500 0.4923 106 R 0.1975 0.0491 0.7534 107 D 0.0970 0.0877 0.8153 108 E 0.0141 0.8409 0.1449 109 K 0.0166 0.8588 0.1247 110 F 0.0107 0.9095 0.0798 111 F 0.0127 0.9193 0.0680 112 E 0.0171 0.9089 0.0740 113 A 0.0233 0.8784 0.0983 114 V 0.0531 0.7451 0.2019 115 K 0.0638 0.4848 0.4514 116 T 0.0455 0.1772 0.7773 117 G 0.0336 0.0380 0.9284 118 D 0.1197 0.0238 0.8564 119 R 0.7277 0.0074 0.2649 120 V 0.8786 0.0042 0.1172 121 V 0.9131 0.0039 0.0831 122 V 0.8894 0.0053 0.1053 123 N 0.6458 0.0068 0.3474 124 A 0.1265 0.0889 0.7846 125 D 0.0540 0.1335 0.8125 126 E 0.0646 0.1286 0.8068 127 G 0.1691 0.0815 0.7494 128 Y 0.5688 0.0796 0.3516 129 V 0.7266 0.0653 0.2082 130 E 0.7611 0.0684 0.1704 131 L 0.7487 0.1026 0.1487 132 I 0.5764 0.1548 0.2688 133 E 0.4700 0.1696 0.3604 134 L 0.2492 0.2788 0.4720 135 E 0.1661 0.2591 0.5748 136 H 0.1334 0.2635 0.6031 137 H 0.1080 0.2108 0.6812 138 H 0.0912 0.1630 0.7458 139 H 0.0731 0.1431 0.7839 140 H 0.0610 0.0838 0.8553 141 H 0.0468 0.0420 0.9112