# This file is the result of combining several RDB files, specifically # T0585.t04.dssp-ebghstl.rdb (weight 1.53986) # T0585.t04.stride-ebghtl.rdb (weight 1.24869) # T0585.t04.str2.rdb (weight 1.54758) # T0585.t04.alpha.rdb (weight 0.659012) # T0585.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0585.t2k.stride-ebghtl.rdb (weight 1.24869) # T0585.t2k.str2.rdb (weight 1.54758) # T0585.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 T0585.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0585 # 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 T0585.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 1016.66 # # ============================================ # Comments from T0585.t04.stride-ebghtl.rdb # ============================================ # TARGET T0585 # 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 T0585.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 1016.66 # # ============================================ # Comments from T0585.t04.str2.rdb # ============================================ # TARGET T0585 # 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 T0585.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 1016.66 # # ============================================ # Comments from T0585.t04.alpha.rdb # ============================================ # TARGET T0585 # 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 T0585.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 1016.66 # # ============================================ # Comments from T0585.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0585 # 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 T0585.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 1553 # # ============================================ # Comments from T0585.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0585 # 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 T0585.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 1553 # # ============================================ # Comments from T0585.t2k.str2.rdb # ============================================ # TARGET T0585 # 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 T0585.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 1553 # # ============================================ # Comments from T0585.t2k.alpha.rdb # ============================================ # TARGET T0585 # 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 T0585.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 1553 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0528 0.0587 0.8886 2 N 0.0908 0.1021 0.8071 3 A 0.0731 0.1474 0.7795 4 S 0.0724 0.0993 0.8283 5 F 0.2519 0.0175 0.7306 6 R 0.7142 0.0037 0.2821 7 V 0.9068 0.0035 0.0897 8 V 0.9186 0.0034 0.0780 9 L 0.8830 0.0079 0.1091 10 D 0.5990 0.0091 0.3919 11 P 0.0947 0.0974 0.8079 12 G 0.0659 0.0807 0.8534 13 H 0.0906 0.0968 0.8126 14 G 0.0814 0.0797 0.8389 15 G 0.1425 0.0784 0.7791 16 I 0.1742 0.1033 0.7225 17 D 0.1549 0.0911 0.7540 18 G 0.0796 0.1842 0.7362 19 G 0.0913 0.1487 0.7600 20 A 0.2795 0.1150 0.6055 21 R 0.4736 0.0437 0.4827 22 G 0.2281 0.0380 0.7340 23 V 0.0683 0.1112 0.8205 24 T 0.0425 0.0688 0.8887 25 G 0.0670 0.0775 0.8555 26 I 0.2242 0.0917 0.6841 27 L 0.4070 0.1732 0.4198 28 E 0.1652 0.6363 0.1985 29 K 0.0475 0.8306 0.1219 30 D 0.0380 0.8590 0.1030 31 V 0.0204 0.9104 0.0692 32 T 0.0116 0.9335 0.0549 33 L 0.0050 0.9560 0.0390 34 A 0.0047 0.9595 0.0358 35 F 0.0047 0.9586 0.0367 36 A 0.0047 0.9603 0.0350 37 R 0.0047 0.9593 0.0360 38 A 0.0047 0.9587 0.0366 39 L 0.0047 0.9566 0.0386 40 R 0.0047 0.9556 0.0397 41 D 0.0048 0.9508 0.0444 42 E 0.0050 0.9390 0.0560 43 L 0.0060 0.9164 0.0776 44 Q 0.0059 0.8785 0.1156 45 K 0.0105 0.7344 0.2551 46 G 0.0592 0.1968 0.7440 47 S 0.0261 0.0803 0.8936 48 H 0.0285 0.0411 0.9304 49 T 0.3006 0.0108 0.6886 50 I 0.7873 0.0039 0.2088 51 V 0.9223 0.0031 0.0747 52 A 0.9195 0.0040 0.0765 53 L 0.9035 0.0037 0.0928 54 T 0.6883 0.0072 0.3046 55 R 0.2713 0.0137 0.7150 56 D 0.0709 0.0832 0.8459 57 S 0.0464 0.1017 0.8519 58 D 0.0900 0.0874 0.8226 59 I 0.1038 0.1201 0.7761 60 F 0.1479 0.0643 0.7877 61 L 0.1345 0.0365 0.8290 62 R 0.0827 0.0307 0.8866 63 L 0.0057 0.8979 0.0964 64 S 0.0049 0.9319 0.0632 65 E 0.0050 0.9446 0.0504 66 R 0.0047 0.9521 0.0432 67 V 0.0049 0.9516 0.0435 68 K 0.0051 0.9475 0.0474 69 K 0.0048 0.9473 0.0479 70 A 0.0049 0.9393 0.0558 71 Q 0.0056 0.8927 0.1018 72 E 0.0089 0.7688 0.2223 73 F 0.0434 0.4285 0.5281 74 D 0.0527 0.0450 0.9023 75 A 0.0958 0.0112 0.8931 76 D 0.1301 0.0406 0.8293 77 L 0.9176 0.0036 0.0788 78 F 0.9312 0.0033 0.0654 79 I 0.9304 0.0033 0.0663 80 S 0.9168 0.0040 0.0792 81 I 0.7815 0.0093 0.2092 82 H 0.5129 0.0211 0.4660 83 A 0.3449 0.0700 0.5851 84 D 0.2300 0.0840 0.6860 85 T 0.1587 0.1111 0.7302 86 I 0.1148 0.1069 0.7782 87 D 0.0789 0.1076 0.8136 88 V 0.0879 0.0836 0.8285 89 H 0.0746 0.1682 0.7572 90 S 0.1184 0.1215 0.7602 91 L 0.2337 0.0821 0.6843 92 R 0.3129 0.0564 0.6307 93 G 0.4779 0.0319 0.4902 94 A 0.7583 0.0112 0.2305 95 T 0.8919 0.0056 0.1025 96 V 0.9097 0.0041 0.0862 97 Y 0.8871 0.0056 0.1073 98 T 0.8144 0.0076 0.1780 99 I 0.5172 0.0235 0.4593 100 S 0.1698 0.0447 0.7855 101 D 0.0529 0.1236 0.8236 102 E 0.0492 0.1810 0.7698 103 A 0.0510 0.2392 0.7098 104 S 0.0446 0.3341 0.6213 105 D 0.0258 0.5546 0.4196 106 A 0.0134 0.7861 0.2005 107 I 0.0099 0.8550 0.1351 108 A 0.0080 0.8941 0.0979 109 K 0.0070 0.9140 0.0789 110 S 0.0061 0.9256 0.0682 111 L 0.0056 0.9265 0.0679 112 A 0.0059 0.9098 0.0843 113 E 0.0062 0.8901 0.1036 114 S 0.0089 0.8515 0.1396 115 E 0.0180 0.7377 0.2443 116 N 0.0249 0.6236 0.3515 117 K 0.0283 0.6333 0.3383 118 V 0.0242 0.6702 0.3055 119 D 0.0288 0.6794 0.2918 120 L 0.0254 0.7013 0.2733 121 L 0.0333 0.6837 0.2830 122 D 0.0478 0.4904 0.4618 123 G 0.0537 0.2469 0.6995 124 L 0.0900 0.2102 0.6998 125 P 0.1060 0.2302 0.6637 126 K 0.0701 0.2716 0.6583 127 E 0.0564 0.2532 0.6905 128 E 0.0720 0.2032 0.7248 129 S 0.0564 0.2565 0.6871 130 L 0.0642 0.3176 0.6183 131 E 0.0169 0.7453 0.2378 132 L 0.0130 0.8474 0.1397 133 T 0.0089 0.8984 0.0927 134 D 0.0087 0.9086 0.0828 135 I 0.0109 0.9005 0.0886 136 L 0.0112 0.9029 0.0859 137 L 0.0128 0.8796 0.1076 138 D 0.0122 0.8513 0.1364 139 L 0.0126 0.8443 0.1431 140 T 0.0114 0.8390 0.1496 141 R 0.0179 0.7749 0.2071 142 R 0.0198 0.7207 0.2595 143 E 0.0259 0.6595 0.3146 144 T 0.0242 0.6172 0.3586 145 H 0.0280 0.5616 0.4103 146 A 0.0236 0.6923 0.2842 147 F 0.0151 0.7962 0.1888 148 S 0.0108 0.8357 0.1535 149 I 0.0088 0.8779 0.1133 150 N 0.0056 0.9337 0.0607 151 F 0.0057 0.9418 0.0526 152 A 0.0050 0.9439 0.0511 153 N 0.0050 0.9510 0.0440 154 N 0.0048 0.9510 0.0442 155 V 0.0048 0.9519 0.0433 156 V 0.0048 0.9505 0.0446 157 S 0.0049 0.9452 0.0499 158 N 0.0053 0.9347 0.0600 159 L 0.0058 0.9225 0.0716 160 S 0.0089 0.9026 0.0885 161 K 0.0098 0.8752 0.1150 162 S 0.0121 0.8241 0.1639 163 H 0.0229 0.7194 0.2577 164 I 0.0672 0.3526 0.5802 165 N 0.0804 0.1481 0.7715 166 L 0.1240 0.1542 0.7218 167 I 0.1115 0.1867 0.7019 168 N 0.1026 0.1882 0.7092 169 N 0.1267 0.1457 0.7277 170 P 0.1854 0.1356 0.6790 171 H 0.3587 0.1068 0.5345 172 R 0.3664 0.1274 0.5062 173 Y 0.3300 0.1433 0.5267 174 A 0.2190 0.1214 0.6596 175 D 0.2117 0.0801 0.7082 176 F 0.6994 0.0422 0.2583 177 Q 0.8484 0.0234 0.1282 178 V 0.8702 0.0260 0.1038 179 L 0.7818 0.0464 0.1718 180 K 0.5367 0.0798 0.3835 181 A 0.2471 0.0885 0.6644 182 P 0.1192 0.0782 0.8026 183 D 0.0907 0.0457 0.8636 184 V 0.1209 0.0188 0.8604 185 P 0.2082 0.0233 0.7685 186 S 0.7294 0.0178 0.2528 187 V 0.9021 0.0107 0.0873 188 L 0.9103 0.0108 0.0790 189 I 0.8767 0.0143 0.1090 190 E 0.8231 0.0200 0.1569 191 I 0.5722 0.0516 0.3762 192 G 0.4714 0.0641 0.4645 193 Y 0.4436 0.0883 0.4681 194 L 0.3136 0.0756 0.6108 195 S 0.1391 0.0523 0.8086 196 N 0.0618 0.0562 0.8820 197 K 0.0067 0.8615 0.1318 198 E 0.0060 0.8978 0.0962 199 D 0.0054 0.9244 0.0702 200 E 0.0057 0.9245 0.0698 201 K 0.0067 0.8807 0.1126 202 L 0.0099 0.8008 0.1894 203 L 0.0251 0.5931 0.3818 204 N 0.0351 0.3782 0.5867 205 N 0.0539 0.1019 0.8442 206 P 0.0061 0.9012 0.0928 207 Q 0.0050 0.9332 0.0618 208 W 0.0052 0.9381 0.0567 209 R 0.0047 0.9567 0.0386 210 K 0.0047 0.9573 0.0380 211 Q 0.0048 0.9564 0.0389 212 M 0.0047 0.9586 0.0367 213 A 0.0047 0.9599 0.0354 214 A 0.0047 0.9602 0.0350 215 S 0.0047 0.9603 0.0351 216 I 0.0047 0.9599 0.0355 217 A 0.0047 0.9597 0.0356 218 Y 0.0047 0.9579 0.0374 219 S 0.0047 0.9569 0.0384 220 I 0.0047 0.9576 0.0377 221 R 0.0048 0.9562 0.0389 222 Q 0.0050 0.9500 0.0451 223 F 0.0057 0.9315 0.0628 224 A 0.0167 0.8672 0.1161 225 E 0.0126 0.7064 0.2809 226 Y 0.0299 0.4419 0.5281 227 R 0.0600 0.1000 0.8400 228 Q 0.0452 0.1302 0.8246 229 K 0.0367 0.1956 0.7678 230 I 0.0601 0.1450 0.7949 231 M 0.0835 0.0598 0.8567 232 Q 0.0975 0.0499 0.8526 233 P 0.1047 0.0388 0.8565 234 L 0.0427 0.0413 0.9160