# This file is the result of combining several RDB files, specifically # T0323.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0323.t2k.stride-ebghtl.rdb (weight 1.24869) # T0323.t2k.str2.rdb (weight 1.54758) # T0323.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 T0323.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0323 # 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 T0323.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 372 # # ============================================ # Comments from T0323.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0323 # 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 T0323.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 372 # # ============================================ # Comments from T0323.t2k.str2.rdb # ============================================ # TARGET T0323 # 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 T0323.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 372 # # ============================================ # Comments from T0323.t2k.alpha.rdb # ============================================ # TARGET T0323 # 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 T0323.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 372 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1170 0.1216 0.7613 2 R 0.1904 0.0886 0.7210 3 Y 0.1609 0.0709 0.7681 4 F 0.0568 0.2043 0.7388 5 S 0.0506 0.1975 0.7519 6 T 0.0371 0.2446 0.7183 7 D 0.0545 0.2112 0.7343 8 S 0.0140 0.5358 0.4502 9 P 0.0088 0.7776 0.2136 10 E 0.0072 0.8435 0.1492 11 V 0.0071 0.8908 0.1021 12 K 0.0062 0.9205 0.0733 13 T 0.0063 0.9171 0.0767 14 I 0.0061 0.9088 0.0851 15 V 0.0074 0.8844 0.1082 16 A 0.0095 0.8007 0.1898 17 Q 0.0179 0.6564 0.3256 18 D 0.0635 0.2385 0.6981 19 S 0.0060 0.7882 0.2059 20 R 0.0054 0.7910 0.2035 21 L 0.0082 0.8839 0.1079 22 F 0.0054 0.9388 0.0558 23 Q 0.0054 0.9414 0.0532 24 F 0.0051 0.9406 0.0543 25 I 0.0060 0.9298 0.0642 26 E 0.0057 0.8964 0.0979 27 I 0.0102 0.8163 0.1735 28 A 0.0560 0.4325 0.5115 29 G 0.0351 0.1528 0.8121 30 E 0.0570 0.1156 0.8274 31 V 0.1291 0.0945 0.7764 32 Q 0.1646 0.0766 0.7588 33 L 0.1502 0.0672 0.7826 34 P 0.0983 0.0799 0.8218 35 T 0.0666 0.0921 0.8413 36 K 0.0631 0.0541 0.8827 37 P 0.0482 0.0561 0.8957 38 N 0.0608 0.0728 0.8664 39 P 0.0061 0.9040 0.0899 40 F 0.0048 0.9463 0.0489 41 Q 0.0047 0.9568 0.0385 42 S 0.0047 0.9590 0.0363 43 L 0.0047 0.9600 0.0353 44 V 0.0047 0.9601 0.0353 45 S 0.0047 0.9609 0.0344 46 S 0.0047 0.9606 0.0347 47 I 0.0047 0.9549 0.0403 48 V 0.0049 0.9174 0.0777 49 E 0.0060 0.8059 0.1881 50 Q 0.0160 0.6564 0.3276 51 Q 0.0480 0.5704 0.3817 52 L 0.0677 0.4582 0.4740 53 S 0.0522 0.3968 0.5510 54 I 0.0050 0.9500 0.0450 55 K 0.0047 0.9558 0.0394 56 A 0.0048 0.9559 0.0394 57 A 0.0047 0.9575 0.0378 58 S 0.0047 0.9579 0.0374 59 A 0.0047 0.9579 0.0374 60 I 0.0047 0.9579 0.0374 61 Y 0.0047 0.9580 0.0373 62 G 0.0047 0.9560 0.0392 63 R 0.0047 0.9567 0.0386 64 V 0.0047 0.9552 0.0400 65 E 0.0049 0.9456 0.0495 66 Q 0.0055 0.9236 0.0709 67 L 0.0128 0.8300 0.1572 68 V 0.0550 0.4559 0.4890 69 G 0.0406 0.1024 0.8570 70 G 0.0537 0.1038 0.8425 71 A 0.0549 0.1524 0.7926 72 L 0.0819 0.1284 0.7898 73 E 0.0754 0.1458 0.7788 74 K 0.0647 0.1580 0.7773 75 P 0.0233 0.6216 0.3551 76 E 0.0142 0.6853 0.3005 77 Q 0.0211 0.7066 0.2723 78 L 0.0138 0.7455 0.2407 79 Y 0.0134 0.7094 0.2772 80 R 0.0176 0.6718 0.3106 81 V 0.0302 0.5501 0.4196 82 S 0.0252 0.5197 0.4551 83 D 0.0052 0.9181 0.0767 84 E 0.0052 0.9384 0.0564 85 A 0.0050 0.9420 0.0531 86 L 0.0059 0.9366 0.0576 87 R 0.0053 0.8981 0.0966 88 Q 0.0061 0.7753 0.2186 89 A 0.0443 0.4568 0.4989 90 G 0.0428 0.0605 0.8968 91 V 0.0600 0.0449 0.8952 92 S 0.0564 0.1325 0.8110 93 K 0.0111 0.7166 0.2723 94 R 0.0117 0.7617 0.2266 95 K 0.0075 0.9117 0.0808 96 I 0.0053 0.9486 0.0461 97 E 0.0055 0.9515 0.0430 98 Y 0.0053 0.9527 0.0421 99 I 0.0047 0.9587 0.0366 100 R 0.0047 0.9608 0.0345 101 H 0.0047 0.9605 0.0349 102 V 0.0047 0.9602 0.0352 103 C 0.0047 0.9582 0.0371 104 E 0.0047 0.9572 0.0381 105 H 0.0048 0.9524 0.0428 106 V 0.0054 0.9424 0.0523 107 E 0.0064 0.9108 0.0827 108 S 0.0367 0.4732 0.4902 109 G 0.0262 0.1468 0.8269 110 R 0.0593 0.0577 0.8831 111 L 0.1403 0.0357 0.8241 112 D 0.1105 0.0344 0.8551 113 F 0.0102 0.8304 0.1594 114 T 0.0077 0.8611 0.1312 115 E 0.0091 0.8570 0.1339 116 L 0.0212 0.7664 0.2124 117 E 0.0209 0.4122 0.5669 118 G 0.0275 0.1655 0.8070 119 A 0.0514 0.0653 0.8834 120 E 0.0673 0.0690 0.8637 121 A 0.0234 0.6930 0.2836 122 T 0.0061 0.9173 0.0766 123 T 0.0054 0.9369 0.0577 124 V 0.0052 0.9450 0.0498 125 I 0.0050 0.9519 0.0431 126 E 0.0048 0.9513 0.0439 127 K 0.0051 0.9429 0.0521 128 L 0.0075 0.9185 0.0740 129 T 0.0079 0.8844 0.1077 130 A 0.0141 0.7006 0.2853 131 I 0.0650 0.3493 0.5857 132 K 0.0284 0.2396 0.7321 133 G 0.0491 0.1323 0.8186 134 I 0.0821 0.1317 0.7862 135 G 0.0722 0.1517 0.7761 136 Q 0.0204 0.7538 0.2257 137 W 0.0198 0.8342 0.1459 138 T 0.0062 0.9370 0.0567 139 A 0.0047 0.9505 0.0447 140 E 0.0047 0.9585 0.0368 141 M 0.0047 0.9596 0.0357 142 F 0.0048 0.9601 0.0352 143 M 0.0048 0.9580 0.0372 144 M 0.0053 0.9536 0.0412 145 F 0.0073 0.9263 0.0664 146 S 0.0101 0.8080 0.1819 147 L 0.0365 0.4529 0.5106 148 G 0.0365 0.0954 0.8682 149 R 0.0756 0.0696 0.8547 150 L 0.0859 0.1208 0.7933 151 D 0.1634 0.1290 0.7077 152 V 0.2496 0.1027 0.6477 153 L 0.2709 0.0650 0.6641 154 S 0.2404 0.1029 0.6566 155 V 0.1360 0.4324 0.4316 156 G 0.0545 0.4996 0.4459 157 D 0.0320 0.6745 0.2935 158 V 0.0060 0.9324 0.0616 159 G 0.0052 0.9483 0.0466 160 L 0.0047 0.9573 0.0380 161 Q 0.0047 0.9589 0.0364 162 R 0.0047 0.9596 0.0358 163 G 0.0047 0.9591 0.0362 164 A 0.0048 0.9553 0.0399 165 K 0.0051 0.9473 0.0476 166 W 0.0069 0.9132 0.0799 167 L 0.0216 0.7472 0.2312 168 Y 0.0328 0.3032 0.6641 169 G 0.0404 0.1729 0.7867 170 N 0.0564 0.1318 0.8118 171 G 0.0468 0.1438 0.8094 172 E 0.0468 0.1445 0.8087 173 G 0.0664 0.1116 0.8221 174 D 0.0675 0.1167 0.8158 175 G 0.0574 0.1698 0.7728 176 K 0.0071 0.9089 0.0840 177 K 0.0057 0.9355 0.0588 178 L 0.0052 0.9442 0.0506 179 L 0.0050 0.9491 0.0458 180 I 0.0055 0.9416 0.0529 181 Y 0.0053 0.9298 0.0649 182 H 0.0061 0.9054 0.0885 183 G 0.0072 0.8618 0.1310 184 K 0.0075 0.7985 0.1940 185 A 0.0131 0.6933 0.2936 186 W 0.0398 0.4288 0.5313 187 A 0.0377 0.2206 0.7417 188 P 0.0235 0.5842 0.3923 189 Y 0.0168 0.7112 0.2720 190 E 0.0090 0.8734 0.1176 191 T 0.0079 0.9201 0.0720 192 V 0.0056 0.9496 0.0447 193 A 0.0050 0.9550 0.0400 194 C 0.0047 0.9583 0.0370 195 L 0.0047 0.9594 0.0359 196 Y 0.0047 0.9604 0.0349 197 L 0.0047 0.9596 0.0357 198 W 0.0047 0.9576 0.0377 199 K 0.0049 0.9515 0.0435 200 A 0.0060 0.9215 0.0725 201 A 0.0126 0.8244 0.1631 202 G 0.0187 0.6742 0.3071 203 T 0.0296 0.6550 0.3155 204 F 0.0376 0.7110 0.2514 205 A 0.0533 0.7001 0.2466 206 E 0.0687 0.6552 0.2761 207 E 0.0779 0.5781 0.3439 208 Y 0.0960 0.3982 0.5058 209 R 0.1048 0.2305 0.6647 210 S 0.1165 0.1688 0.7147 211 L 0.0860 0.2472 0.6668 212 E 0.0955 0.2253 0.6792 213 E 0.1232 0.2545 0.6223 214 L 0.1115 0.2688 0.6197 215 L 0.1136 0.1936 0.6928 216 H 0.1131 0.1618 0.7251 217 H 0.0666 0.1653 0.7681 218 G 0.0715 0.1684 0.7601 219 N 0.1020 0.1468 0.7512 220 Q 0.1519 0.1089 0.7391 221 C 0.0892 0.0472 0.8636