# This file is the result of combining several RDB files, specifically # T0280.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0280.t2k.stride-ebghtl.rdb (weight 1.24869) # T0280.t2k.str2.rdb (weight 1.54758) # T0280.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 T0280.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0280 # 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 T0280.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 705 # # ============================================ # Comments from T0280.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0280 # 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 T0280.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 705 # # ============================================ # Comments from T0280.t2k.str2.rdb # ============================================ # TARGET T0280 # 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 T0280.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 705 # # ============================================ # Comments from T0280.t2k.alpha.rdb # ============================================ # TARGET T0280 # 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 T0280.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 705 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0626 0.0829 0.8546 2 R 0.0562 0.1853 0.7585 3 F 0.0357 0.5758 0.3885 4 R 0.0194 0.7606 0.2200 5 D 0.0235 0.8045 0.1720 6 R 0.0085 0.8984 0.0931 7 R 0.0066 0.9200 0.0734 8 H 0.0063 0.9165 0.0773 9 A 0.0054 0.9112 0.0835 10 G 0.0049 0.9347 0.0604 11 A 0.0048 0.9463 0.0489 12 L 0.0048 0.9500 0.0452 13 L 0.0050 0.9506 0.0444 14 A 0.0050 0.9453 0.0497 15 E 0.0055 0.9341 0.0603 16 A 0.0057 0.9097 0.0845 17 L 0.0119 0.8615 0.1266 18 A 0.0152 0.8181 0.1667 19 P 0.0227 0.6890 0.2883 20 L 0.0561 0.3743 0.5697 21 G 0.0550 0.1329 0.8121 22 L 0.0506 0.1169 0.8326 23 E 0.0554 0.0937 0.8509 24 A 0.1416 0.0280 0.8304 25 P 0.4506 0.0171 0.5324 26 V 0.8966 0.0040 0.0995 27 V 0.9235 0.0033 0.0732 28 L 0.8947 0.0078 0.0975 29 G 0.7729 0.0074 0.2196 30 L 0.4061 0.0250 0.5689 31 P 0.1191 0.0802 0.8007 32 R 0.0493 0.1676 0.7831 33 G 0.0368 0.1802 0.7831 34 G 0.0394 0.2990 0.6615 35 V 0.0338 0.7514 0.2148 36 V 0.0153 0.8900 0.0947 37 V 0.0092 0.9153 0.0756 38 A 0.0060 0.9394 0.0546 39 D 0.0056 0.9517 0.0428 40 E 0.0049 0.9559 0.0392 41 V 0.0048 0.9558 0.0394 42 A 0.0049 0.9520 0.0431 43 R 0.0053 0.9311 0.0635 44 R 0.0073 0.8738 0.1190 45 L 0.0477 0.5434 0.4089 46 G 0.0396 0.0940 0.8664 47 G 0.0596 0.0642 0.8762 48 E 0.0934 0.1548 0.7518 49 L 0.1457 0.2142 0.6401 50 D 0.2238 0.1913 0.5849 51 V 0.5839 0.0822 0.3339 52 V 0.7160 0.0498 0.2341 53 L 0.7885 0.0372 0.1743 54 V 0.7345 0.0450 0.2204 55 R 0.5532 0.0770 0.3698 56 K 0.3471 0.0682 0.5846 57 V 0.1139 0.0996 0.7866 58 G 0.0816 0.0684 0.8500 59 A 0.1366 0.0560 0.8075 60 P 0.1622 0.0594 0.7784 61 G 0.1361 0.0933 0.7707 62 N 0.1320 0.0883 0.7797 63 P 0.1883 0.2022 0.6095 64 E 0.3611 0.2194 0.4195 65 F 0.4770 0.2038 0.3193 66 A 0.5401 0.1760 0.2839 67 L 0.5157 0.2733 0.2110 68 G 0.5123 0.2912 0.1965 69 A 0.5547 0.2565 0.1888 70 V 0.5179 0.2614 0.2207 71 G 0.4089 0.2722 0.3189 72 E 0.2234 0.3242 0.4524 73 G 0.1268 0.2141 0.6590 74 G 0.1135 0.1593 0.7272 75 E 0.1507 0.2025 0.6468 76 L 0.2407 0.2350 0.5242 77 V 0.2791 0.2376 0.4833 78 L 0.2974 0.1751 0.5275 79 M 0.1151 0.1560 0.7289 80 P 0.0231 0.7546 0.2223 81 Y 0.0191 0.8256 0.1553 82 A 0.0157 0.8597 0.1247 83 L 0.0243 0.8295 0.1462 84 R 0.0295 0.7249 0.2455 85 Y 0.0424 0.6285 0.3291 86 A 0.0890 0.3392 0.5719 87 D 0.1032 0.1659 0.7309 88 Q 0.0811 0.4112 0.5077 89 S 0.0776 0.4000 0.5223 90 Y 0.1518 0.4102 0.4380 91 L 0.2409 0.2957 0.4634 92 E 0.2474 0.2500 0.5025 93 R 0.2646 0.3761 0.3594 94 E 0.3140 0.3903 0.2957 95 A 0.3081 0.3935 0.2984 96 A 0.2583 0.3610 0.3807 97 R 0.1525 0.3234 0.5241 98 Q 0.0885 0.4435 0.4680 99 R 0.0531 0.5830 0.3639 100 D 0.0367 0.6763 0.2870 101 V 0.0463 0.6713 0.2824 102 L 0.0539 0.6297 0.3164 103 R 0.0679 0.5312 0.4010 104 K 0.0648 0.4574 0.4778 105 R 0.0777 0.3313 0.5910 106 A 0.0960 0.2217 0.6824 107 E 0.1793 0.2664 0.5544 108 R 0.3042 0.3184 0.3775 109 Y 0.3852 0.2904 0.3244 110 R 0.4125 0.2760 0.3116 111 R 0.3830 0.2221 0.3949 112 V 0.3300 0.1413 0.5287 113 R 0.2654 0.1127 0.6219 114 P 0.1936 0.0880 0.7184 115 K 0.1464 0.1388 0.7149 116 A 0.1609 0.2529 0.5861 117 A 0.1611 0.2577 0.5812 118 R 0.1283 0.2098 0.6620 119 K 0.0506 0.1360 0.8134 120 G 0.0344 0.0501 0.9155 121 R 0.2500 0.0156 0.7344 122 D 0.6871 0.0047 0.3081 123 V 0.9132 0.0041 0.0827 124 V 0.9251 0.0035 0.0714 125 L 0.9195 0.0035 0.0770 126 V 0.8257 0.0186 0.1557 127 D 0.5594 0.0140 0.4266 128 D 0.4839 0.0730 0.4431 129 G 0.5475 0.1656 0.2869 130 V 0.4481 0.2566 0.2953 131 A 0.1925 0.2232 0.5843 132 T 0.0899 0.2005 0.7096 133 G 0.0393 0.2797 0.6810 134 A 0.0267 0.6787 0.2946 135 S 0.0168 0.8453 0.1379 136 M 0.0047 0.9574 0.0378 137 E 0.0047 0.9605 0.0348 138 A 0.0046 0.9610 0.0344 139 A 0.0047 0.9605 0.0349 140 L 0.0047 0.9601 0.0352 141 S 0.0047 0.9592 0.0362 142 V 0.0047 0.9570 0.0384 143 V 0.0048 0.9502 0.0450 144 F 0.0051 0.9341 0.0608 145 Q 0.0070 0.8393 0.1537 146 E 0.0394 0.3096 0.6510 147 G 0.0471 0.0244 0.9285 148 P 0.0922 0.0144 0.8935 149 R 0.3220 0.0239 0.6542 150 R 0.8555 0.0048 0.1397 151 V 0.9172 0.0032 0.0796 152 V 0.9258 0.0039 0.0703 153 V 0.9295 0.0031 0.0674 154 A 0.9084 0.0036 0.0880 155 V 0.8432 0.0053 0.1515 156 P 0.7844 0.0075 0.2081 157 V 0.5473 0.0375 0.4152 158 A 0.2568 0.0315 0.7117 159 S 0.0916 0.0985 0.8099 160 P 0.0343 0.3683 0.5973 161 E 0.0388 0.4581 0.5031 162 A 0.0571 0.4865 0.4564 163 V 0.0977 0.4580 0.4443 164 E 0.1076 0.4077 0.4847 165 R 0.1402 0.2956 0.5642 166 L 0.1400 0.1583 0.7017 167 K 0.1334 0.1089 0.7577 168 A 0.1992 0.1177 0.6830 169 R 0.1706 0.0864 0.7430 170 A 0.1414 0.0339 0.8247 171 E 0.1668 0.0438 0.7894 172 V 0.6508 0.0266 0.3226 173 V 0.7854 0.0183 0.1963 174 A 0.7782 0.0194 0.2024 175 L 0.7263 0.0244 0.2493 176 S 0.5628 0.0321 0.4051 177 V 0.3041 0.0244 0.6715 178 P 0.2088 0.0437 0.7475 179 Q 0.0803 0.2723 0.6475 180 D 0.0713 0.4102 0.5185 181 F 0.1032 0.4716 0.4252 182 A 0.1229 0.4418 0.4353 183 A 0.1436 0.4034 0.4530 184 V 0.1398 0.2946 0.5656 185 G 0.1904 0.1513 0.6582 186 A 0.3638 0.1162 0.5200 187 Y 0.3857 0.1048 0.5095 188 Y 0.0628 0.5281 0.4090 189 L 0.0142 0.7088 0.2770 190 D 0.0166 0.6696 0.3138 191 F 0.0334 0.6954 0.2711 192 G 0.0445 0.5697 0.3858 193 E 0.0439 0.4583 0.4978 194 V 0.0633 0.3116 0.6250 195 T 0.0748 0.1311 0.7941 196 D 0.0539 0.2112 0.7350 197 E 0.0050 0.9318 0.0631 198 D 0.0048 0.9437 0.0516 199 V 0.0047 0.9547 0.0406 200 E 0.0047 0.9594 0.0359 201 A 0.0047 0.9564 0.0389 202 I 0.0048 0.9521 0.0431 203 L 0.0053 0.9413 0.0534 204 L 0.0053 0.9251 0.0696 205 E 0.0081 0.8794 0.1126 206 W 0.0150 0.7503 0.2347 207 A 0.0433 0.4065 0.5502 208 G 0.0325 0.0949 0.8725