# This file is the result of combining several RDB files, specifically # T0454.t04.dssp-ebghstl.rdb (weight 1.53986) # T0454.t04.stride-ebghtl.rdb (weight 1.24869) # T0454.t04.str2.rdb (weight 1.54758) # T0454.t04.alpha.rdb (weight 0.659012) # T0454.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0454.t2k.stride-ebghtl.rdb (weight 1.24869) # T0454.t2k.str2.rdb (weight 1.54758) # T0454.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 T0454.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0454 # 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 T0454.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 2180 # # ============================================ # Comments from T0454.t04.stride-ebghtl.rdb # ============================================ # TARGET T0454 # 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 T0454.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 2180 # # ============================================ # Comments from T0454.t04.str2.rdb # ============================================ # TARGET T0454 # 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 T0454.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 2180 # # ============================================ # Comments from T0454.t04.alpha.rdb # ============================================ # TARGET T0454 # 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 T0454.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 2180 # # ============================================ # Comments from T0454.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0454 # 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 T0454.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 5302 # # ============================================ # Comments from T0454.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0454 # 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 T0454.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 5302 # # ============================================ # Comments from T0454.t2k.str2.rdb # ============================================ # TARGET T0454 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0454.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 5302 # # ============================================ # Comments from T0454.t2k.alpha.rdb # ============================================ # TARGET T0454 # 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 T0454.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 5302 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0457 0.0529 0.9014 2 T 0.0476 0.1572 0.7952 3 R 0.0351 0.4616 0.5033 4 A 0.0184 0.7194 0.2622 5 D 0.0158 0.7823 0.2018 6 C 0.0155 0.8272 0.1573 7 R 0.0048 0.9457 0.0495 8 S 0.0049 0.9548 0.0403 9 R 0.0047 0.9568 0.0384 10 L 0.0047 0.9589 0.0364 11 M 0.0047 0.9604 0.0349 12 E 0.0047 0.9604 0.0349 13 V 0.0046 0.9601 0.0352 14 A 0.0047 0.9598 0.0355 15 T 0.0047 0.9594 0.0359 16 E 0.0047 0.9591 0.0362 17 L 0.0047 0.9583 0.0370 18 F 0.0047 0.9554 0.0398 19 A 0.0050 0.9425 0.0525 20 Q 0.0121 0.8302 0.1577 21 K 0.0400 0.4808 0.4792 22 G 0.0388 0.1168 0.8444 23 F 0.0587 0.1066 0.8346 24 Y 0.0932 0.1996 0.7072 25 G 0.2448 0.1579 0.5973 26 V 0.4108 0.0294 0.5598 27 S 0.2845 0.0272 0.6883 28 I 0.0055 0.9379 0.0566 29 R 0.0047 0.9554 0.0399 30 E 0.0048 0.9581 0.0371 31 L 0.0047 0.9586 0.0367 32 A 0.0047 0.9568 0.0385 33 Q 0.0052 0.9340 0.0609 34 A 0.0062 0.8796 0.1142 35 A 0.0463 0.4172 0.5365 36 G 0.0361 0.0388 0.9250 37 A 0.0813 0.0197 0.8990 38 S 0.0879 0.0270 0.8851 39 I 0.0269 0.7079 0.2652 40 S 0.0301 0.7988 0.1711 41 M 0.0582 0.8293 0.1126 42 I 0.0721 0.8370 0.0908 43 S 0.0940 0.7670 0.1391 44 Y 0.0920 0.6664 0.2416 45 H 0.0947 0.4955 0.4097 46 F 0.1278 0.1614 0.7109 47 G 0.0466 0.0886 0.8647 48 G 0.0758 0.0425 0.8817 49 K 0.0072 0.8817 0.1111 50 E 0.0059 0.9392 0.0549 51 G 0.0052 0.9496 0.0452 52 L 0.0048 0.9579 0.0373 53 Y 0.0047 0.9585 0.0367 54 A 0.0047 0.9593 0.0360 55 A 0.0047 0.9588 0.0365 56 V 0.0047 0.9580 0.0373 57 L 0.0048 0.9533 0.0419 58 Q 0.0051 0.9401 0.0549 59 E 0.0055 0.9185 0.0760 60 Q 0.0061 0.9031 0.0909 61 F 0.0058 0.8914 0.1028 62 A 0.0062 0.8909 0.1030 63 C 0.0060 0.8884 0.1055 64 F 0.0061 0.9004 0.0935 65 G 0.0063 0.9062 0.0875 66 Q 0.0065 0.9027 0.0908 67 L 0.0065 0.8999 0.0937 68 D 0.0086 0.8772 0.1142 69 D 0.0094 0.8470 0.1436 70 I 0.0103 0.7799 0.2097 71 R 0.0161 0.6655 0.3185 72 G 0.0292 0.4745 0.4963 73 Q 0.0292 0.2888 0.6820 74 A 0.0432 0.1380 0.8188 75 G 0.0498 0.0703 0.8798 76 D 0.0558 0.0604 0.8838 77 P 0.0130 0.8651 0.1219 78 L 0.0050 0.9375 0.0575 79 A 0.0048 0.9493 0.0458 80 V 0.0048 0.9532 0.0420 81 M 0.0047 0.9559 0.0393 82 T 0.0047 0.9576 0.0377 83 A 0.0047 0.9578 0.0375 84 Y 0.0047 0.9576 0.0377 85 L 0.0047 0.9576 0.0377 86 R 0.0047 0.9575 0.0378 87 W 0.0048 0.9550 0.0403 88 T 0.0048 0.9538 0.0415 89 I 0.0048 0.9464 0.0488 90 Q 0.0051 0.9209 0.0739 91 R 0.0065 0.8664 0.1271 92 H 0.0129 0.7914 0.1957 93 R 0.0153 0.6686 0.3161 94 N 0.0237 0.4649 0.5114 95 N 0.0531 0.2326 0.7143 96 P 0.0216 0.5490 0.4294 97 Q 0.0217 0.7060 0.2722 98 L 0.0200 0.8533 0.1267 99 L 0.0244 0.9052 0.0705 100 R 0.0281 0.9158 0.0561 101 F 0.0314 0.9173 0.0513 102 Y 0.0225 0.9236 0.0539 103 T 0.0199 0.9169 0.0632 104 S 0.0186 0.8916 0.0898 105 E 0.0160 0.8339 0.1501 106 L 0.0216 0.7270 0.2515 107 T 0.0280 0.5539 0.4181 108 N 0.0359 0.3493 0.6148 109 P 0.0447 0.2101 0.7452 110 T 0.0455 0.2615 0.6930 111 P 0.0104 0.7937 0.1959 112 C 0.0074 0.8573 0.1353 113 F 0.0066 0.8886 0.1048 114 A 0.0059 0.9165 0.0776 115 A 0.0060 0.9252 0.0688 116 I 0.0055 0.9307 0.0637 117 V 0.0058 0.9245 0.0697 118 S 0.0058 0.9233 0.0709 119 P 0.0060 0.9060 0.0880 120 A 0.0069 0.8834 0.1097 121 I 0.0064 0.9005 0.0932 122 A 0.0058 0.9115 0.0827 123 S 0.0055 0.9205 0.0740 124 V 0.0051 0.9326 0.0623 125 I 0.0048 0.9476 0.0475 126 R 0.0048 0.9516 0.0436 127 L 0.0048 0.9531 0.0421 128 L 0.0048 0.9554 0.0398 129 A 0.0047 0.9582 0.0371 130 E 0.0047 0.9579 0.0374 131 S 0.0047 0.9569 0.0383 132 I 0.0047 0.9555 0.0397 133 E 0.0048 0.9473 0.0480 134 A 0.0052 0.9292 0.0656 135 G 0.0056 0.9012 0.0932 136 M 0.0085 0.8701 0.1214 137 T 0.0084 0.8212 0.1704 138 R 0.0433 0.4082 0.5484 139 G 0.0313 0.0933 0.8754 140 L 0.0834 0.0870 0.8296 141 F 0.1841 0.0687 0.7472 142 R 0.0932 0.0827 0.8241 143 R 0.0347 0.2078 0.7575 144 D 0.0457 0.1264 0.8279 145 L 0.0831 0.0517 0.8652 146 H 0.0744 0.0312 0.8944 147 A 0.0058 0.9168 0.0774 148 V 0.0049 0.9431 0.0521 149 N 0.0048 0.9536 0.0416 150 S 0.0047 0.9593 0.0360 151 A 0.0047 0.9598 0.0356 152 L 0.0047 0.9594 0.0359 153 A 0.0047 0.9594 0.0360 154 L 0.0047 0.9593 0.0360 155 A 0.0047 0.9586 0.0367 156 G 0.0048 0.9554 0.0399 157 M 0.0048 0.9512 0.0439 158 V 0.0049 0.9465 0.0486 159 N 0.0055 0.9314 0.0631 160 Y 0.0062 0.9207 0.0731 161 F 0.0075 0.9308 0.0616 162 F 0.0107 0.9264 0.0629 163 L 0.0147 0.9011 0.0842 164 S 0.0176 0.8660 0.1164 165 T 0.0209 0.8208 0.1583 166 L 0.0279 0.7378 0.2343 167 A 0.0415 0.5841 0.3744 168 T 0.0598 0.3137 0.6264 169 E 0.0465 0.2025 0.7511 170 G 0.0558 0.1670 0.7772 171 L 0.0615 0.1770 0.7616 172 T 0.0541 0.1821 0.7638 173 S 0.0629 0.1787 0.7584 174 H 0.0367 0.4030 0.5603 175 S 0.0324 0.4698 0.4978 176 P 0.0131 0.7387 0.2482 177 D 0.0130 0.7864 0.2005 178 Q 0.0105 0.8476 0.1419 179 D 0.0053 0.9302 0.0645 180 E 0.0051 0.9427 0.0522 181 E 0.0048 0.9526 0.0426 182 L 0.0047 0.9557 0.0396 183 I 0.0047 0.9583 0.0370 184 R 0.0047 0.9576 0.0377 185 Q 0.0047 0.9545 0.0407 186 Y 0.0048 0.9536 0.0417 187 V 0.0048 0.9509 0.0442 188 A 0.0054 0.9374 0.0572 189 I 0.0073 0.9110 0.0818 190 F 0.0181 0.8528 0.1292 191 T 0.0260 0.7267 0.2473 192 R 0.0412 0.4279 0.5309 193 G 0.0554 0.2570 0.6876 194 I 0.1396 0.2009 0.6595 195 M 0.1155 0.1408 0.7436 196 A 0.0889 0.1060 0.8051 197 D 0.0680 0.1141 0.8178 198 G 0.0510 0.1991 0.7499 199 G 0.0460 0.2312 0.7228 200 A 0.0589 0.2138 0.7274 201 A 0.0698 0.1689 0.7613 202 P 0.0659 0.1377 0.7965 203 A 0.0476 0.0741 0.8783