# This file is the result of combining several RDB files, specifically # T0611.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0611.t2k.stride-ebghtl.rdb (weight 1.24869) # T0611.t2k.str2.rdb (weight 1.54758) # T0611.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 T0611.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0611 # 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 T0611.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 6598 # # ============================================ # Comments from T0611.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0611 # 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 T0611.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 6598 # # ============================================ # Comments from T0611.t2k.str2.rdb # ============================================ # TARGET T0611 # 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 T0611.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 6598 # # ============================================ # Comments from T0611.t2k.alpha.rdb # ============================================ # TARGET T0611 # 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 T0611.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 6598 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0471 0.0788 0.8740 2 T 0.0419 0.3209 0.6372 3 M 0.0162 0.7105 0.2732 4 K 0.0145 0.7640 0.2215 5 T 0.0175 0.8098 0.1727 6 R 0.0047 0.9451 0.0502 7 D 0.0047 0.9552 0.0400 8 K 0.0047 0.9574 0.0379 9 I 0.0047 0.9595 0.0358 10 L 0.0047 0.9603 0.0350 11 L 0.0047 0.9603 0.0350 12 S 0.0046 0.9601 0.0353 13 S 0.0047 0.9592 0.0361 14 L 0.0047 0.9592 0.0361 15 E 0.0047 0.9581 0.0372 16 L 0.0047 0.9567 0.0385 17 F 0.0048 0.9533 0.0420 18 N 0.0051 0.9362 0.0587 19 D 0.0126 0.8191 0.1682 20 K 0.0404 0.4758 0.4837 21 G 0.0382 0.1121 0.8496 22 E 0.0646 0.1318 0.8036 23 R 0.1074 0.2212 0.6715 24 N 0.2299 0.1455 0.6247 25 I 0.4003 0.0266 0.5731 26 T 0.2894 0.0248 0.6859 27 T 0.0052 0.9393 0.0555 28 N 0.0047 0.9568 0.0385 29 H 0.0048 0.9582 0.0371 30 I 0.0047 0.9587 0.0366 31 A 0.0047 0.9566 0.0386 32 A 0.0052 0.9354 0.0594 33 H 0.0064 0.8843 0.1093 34 L 0.0469 0.4286 0.5245 35 A 0.0384 0.0389 0.9227 36 I 0.0839 0.0189 0.8972 37 S 0.0965 0.0232 0.8803 38 P 0.0399 0.5464 0.4137 39 G 0.0539 0.6310 0.3151 40 N 0.1530 0.6501 0.1969 41 L 0.2150 0.6427 0.1423 42 Y 0.2861 0.5316 0.1823 43 Y 0.2602 0.4588 0.2810 44 H 0.2127 0.3185 0.4688 45 F 0.1626 0.0853 0.7521 46 R 0.0453 0.0846 0.8701 47 N 0.0808 0.0244 0.8948 48 K 0.0080 0.8693 0.1227 49 S 0.0066 0.9337 0.0596 50 D 0.0053 0.9480 0.0467 51 I 0.0048 0.9579 0.0374 52 I 0.0047 0.9581 0.0372 53 Y 0.0047 0.9579 0.0374 54 E 0.0048 0.9573 0.0380 55 I 0.0048 0.9562 0.0391 56 F 0.0048 0.9508 0.0443 57 Q 0.0051 0.9377 0.0572 58 E 0.0055 0.9174 0.0771 59 Y 0.0061 0.9054 0.0885 60 E 0.0057 0.9065 0.0878 61 K 0.0061 0.9070 0.0869 62 L 0.0058 0.9101 0.0841 63 V 0.0062 0.9173 0.0765 64 D 0.0063 0.9164 0.0773 65 Y 0.0069 0.9072 0.0859 66 Y 0.0071 0.8886 0.1043 67 L 0.0153 0.8212 0.1635 68 D 0.0156 0.7437 0.2408 69 I 0.0199 0.6024 0.3777 70 P 0.0315 0.3562 0.6123 71 E 0.0419 0.2872 0.6710 72 D 0.0337 0.2198 0.7465 73 R 0.0455 0.1366 0.8179 74 P 0.0529 0.0932 0.8539 75 I 0.0610 0.0825 0.8565 76 T 0.0144 0.8466 0.1390 77 L 0.0050 0.9343 0.0607 78 E 0.0048 0.9470 0.0482 79 D 0.0048 0.9528 0.0424 80 M 0.0047 0.9565 0.0388 81 T 0.0047 0.9583 0.0370 82 F 0.0047 0.9584 0.0369 83 Y 0.0047 0.9584 0.0369 84 L 0.0047 0.9587 0.0366 85 E 0.0047 0.9580 0.0373 86 S 0.0047 0.9552 0.0400 87 V 0.0048 0.9536 0.0417 88 F 0.0048 0.9484 0.0468 89 D 0.0051 0.9279 0.0670 90 G 0.0061 0.8852 0.1087 91 L 0.0102 0.8380 0.1518 92 W 0.0105 0.7384 0.2511 93 S 0.0171 0.5770 0.4059 94 Y 0.0507 0.3477 0.6016 95 R 0.0135 0.7276 0.2589 96 F 0.0113 0.8143 0.1744 97 F 0.0107 0.8831 0.1062 98 H 0.0144 0.9089 0.0767 99 R 0.0182 0.9156 0.0662 100 D 0.0198 0.9161 0.0641 101 L 0.0168 0.9150 0.0682 102 E 0.0162 0.8969 0.0869 103 Y 0.0165 0.8364 0.1470 104 L 0.0187 0.7287 0.2526 105 L 0.0348 0.5340 0.4312 106 D 0.0370 0.3671 0.5959 107 S 0.0443 0.2446 0.7112 108 D 0.0508 0.2179 0.7313 109 P 0.0110 0.7856 0.2034 110 R 0.0096 0.8341 0.1563 111 L 0.0075 0.8784 0.1142 112 R 0.0065 0.9080 0.0855 113 Q 0.0064 0.9206 0.0730 114 D 0.0058 0.9279 0.0663 115 Y 0.0058 0.9308 0.0634 116 R 0.0055 0.9337 0.0608 117 E 0.0054 0.9268 0.0678 118 F 0.0057 0.9155 0.0787 119 T 0.0060 0.9230 0.0711 120 N 0.0055 0.9262 0.0683 121 R 0.0055 0.9281 0.0663 122 C 0.0051 0.9362 0.0587 123 L 0.0048 0.9482 0.0470 124 A 0.0048 0.9521 0.0431 125 A 0.0048 0.9538 0.0415 126 I 0.0048 0.9556 0.0396 127 N 0.0047 0.9593 0.0360 128 R 0.0047 0.9586 0.0367 129 I 0.0047 0.9581 0.0372 130 F 0.0047 0.9558 0.0395 131 A 0.0048 0.9462 0.0490 132 K 0.0053 0.9212 0.0735 133 L 0.0064 0.8894 0.1042 134 A 0.0093 0.8560 0.1347 135 D 0.0086 0.8135 0.1779 136 A 0.0437 0.4072 0.5491 137 G 0.0325 0.0775 0.8900 138 I 0.0849 0.0660 0.8491 139 I 0.1878 0.0477 0.7645 140 Q 0.0851 0.0493 0.8656 141 P 0.0569 0.1214 0.8217 142 Q 0.0418 0.0965 0.8618 143 P 0.0624 0.0791 0.8586 144 E 0.0087 0.8911 0.1001 145 D 0.0049 0.9360 0.0590 146 L 0.0048 0.9502 0.0450 147 R 0.0047 0.9584 0.0369 148 S 0.0047 0.9596 0.0357 149 A 0.0047 0.9600 0.0353 150 M 0.0047 0.9601 0.0353 151 S 0.0047 0.9596 0.0357 152 L 0.0047 0.9589 0.0365 153 N 0.0047 0.9568 0.0385 154 V 0.0047 0.9556 0.0397 155 W 0.0048 0.9539 0.0413 156 L 0.0048 0.9501 0.0451 157 V 0.0051 0.9461 0.0488 158 I 0.0054 0.9487 0.0458 159 T 0.0075 0.9442 0.0483 160 N 0.0092 0.9336 0.0572 161 W 0.0106 0.9146 0.0748 162 M 0.0139 0.8804 0.1057 163 A 0.0221 0.7951 0.1829 164 F 0.0374 0.5954 0.3671 165 L 0.0495 0.2713 0.6792 166 K 0.0408 0.1564 0.8028 167 T 0.0506 0.1253 0.8241 168 A 0.0562 0.1368 0.8070 169 H 0.0602 0.1190 0.8208 170 A 0.0641 0.0999 0.8360 171 A 0.0080 0.8745 0.1175 172 E 0.0057 0.9122 0.0821 173 E 0.0058 0.9249 0.0693 174 P 0.0050 0.9403 0.0547 175 A 0.0048 0.9509 0.0443 176 S 0.0048 0.9531 0.0421 177 L 0.0047 0.9547 0.0405 178 S 0.0047 0.9566 0.0387 179 L 0.0047 0.9573 0.0380 180 T 0.0048 0.9543 0.0409 181 E 0.0051 0.9468 0.0481 182 L 0.0056 0.9345 0.0600 183 K 0.0072 0.8876 0.1052 184 Q 0.0153 0.6863 0.2984 185 G 0.0272 0.5355 0.4373 186 I 0.0899 0.3898 0.5203 187 Y 0.1165 0.2302 0.6534 188 Q 0.1300 0.1738 0.6962 189 V 0.1228 0.2085 0.6687 190 L 0.0952 0.1970 0.7078 191 T 0.0931 0.1613 0.7456 192 L 0.0675 0.2320 0.7004 193 E 0.0771 0.1987 0.7243 194 V 0.0854 0.1677 0.7469 195 P 0.0854 0.1594 0.7553 196 Y 0.1009 0.1443 0.7548 197 L 0.0978 0.1406 0.7616 198 T 0.0699 0.1102 0.8200 199 P 0.0555 0.2244 0.7200 200 E 0.0593 0.2396 0.7011 201 Y 0.0699 0.2271 0.7030 202 R 0.0793 0.2659 0.6548 203 E 0.0771 0.2830 0.6399 204 R 0.0830 0.3098 0.6071 205 V 0.0763 0.3500 0.5738 206 L 0.0640 0.3391 0.5969 207 A 0.0517 0.3242 0.6241 208 L 0.0592 0.2535 0.6873 209 R 0.0745 0.2182 0.7073 210 E 0.0453 0.2638 0.6909 211 K 0.0432 0.2141 0.7427 212 Y 0.0868 0.1517 0.7615 213 R 0.0977 0.0772 0.8251 214 P 0.0709 0.0610 0.8681 215 T 0.0845 0.0840 0.8315 216 L 0.0611 0.1429 0.7960 217 P 0.0475 0.2197 0.7328 218 E 0.0461 0.3069 0.6469 219 A 0.0560 0.2606 0.6835 220 Q 0.0651 0.1884 0.7465 221 G 0.0751 0.1393 0.7856 222 I 0.0965 0.0796 0.8239 223 S 0.0862 0.0648 0.8490 224 G 0.0919 0.1706 0.7375 225 V 0.0852 0.2029 0.7119 226 E 0.0826 0.1766 0.7408 227 A 0.0502 0.0510 0.8988