# This file is the result of combining several RDB files, specifically # T0152.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0152.t2k.stride-ebghtl.rdb (weight 1.24869) # T0152.t2k.str.rdb (weight 1.53983) # T0152.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 T0152.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0152 # 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 T0152.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 28 # # ============================================ # Comments from T0152.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0152 # 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 T0152.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 28 # # ============================================ # Comments from T0152.t2k.str.rdb # ============================================ # TARGET T0152 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0152.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 28 # # ============================================ # Comments from T0152.t2k.alpha.rdb # ============================================ # TARGET T0152 # 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 T0152.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 28 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0586 0.0330 0.9084 2 T 0.1413 0.0765 0.7822 3 K 0.1466 0.0997 0.7537 4 P 0.1240 0.1525 0.7235 5 T 0.1302 0.1608 0.7091 6 S 0.1219 0.1636 0.7145 7 A 0.0751 0.1706 0.7543 8 G 0.0515 0.2385 0.7100 9 Q 0.0536 0.3134 0.6330 10 A 0.0501 0.4591 0.4908 11 D 0.0388 0.5543 0.4069 12 D 0.0362 0.5484 0.4154 13 A 0.0383 0.5676 0.3941 14 L 0.0451 0.5600 0.3949 15 V 0.0417 0.6004 0.3579 16 R 0.0564 0.4814 0.4623 17 L 0.0956 0.3931 0.5113 18 A 0.2053 0.2539 0.5408 19 R 0.2683 0.1962 0.5356 20 E 0.2238 0.0779 0.6983 21 R 0.1405 0.0602 0.7993 22 F 0.1214 0.0616 0.8170 23 D 0.1056 0.0405 0.8539 24 L 0.0719 0.0295 0.8986 25 P 0.0867 0.0437 0.8696 26 D 0.0933 0.0562 0.8505 27 Q 0.0913 0.1062 0.8025 28 V 0.1095 0.1682 0.7223 29 R 0.1858 0.1582 0.6561 30 R 0.2606 0.1243 0.6151 31 L 0.2922 0.0967 0.6111 32 A 0.2275 0.0600 0.7126 33 R 0.1658 0.0670 0.7672 34 P 0.1583 0.0534 0.7883 35 P 0.1905 0.0675 0.7420 36 V 0.1482 0.0650 0.7869 37 P 0.0917 0.2163 0.6920 38 S 0.1079 0.2039 0.6882 39 L 0.1380 0.1727 0.6893 40 E 0.0848 0.1134 0.8019 41 P 0.1013 0.0740 0.8247 42 P 0.3141 0.0357 0.6502 43 Y 0.6953 0.0092 0.2955 44 G 0.8002 0.0083 0.1915 45 L 0.8402 0.0066 0.1532 46 R 0.7451 0.0075 0.2474 47 V 0.6975 0.0067 0.2958 48 A 0.3669 0.0104 0.6226 49 Q 0.1783 0.0136 0.8081 50 L 0.0181 0.6452 0.3367 51 T 0.0077 0.6999 0.2924 52 D 0.0142 0.7220 0.2638 53 A 0.0046 0.9098 0.0855 54 E 0.0045 0.9236 0.0719 55 M 0.0045 0.9342 0.0613 56 L 0.0045 0.9492 0.0464 57 A 0.0047 0.9454 0.0499 58 E 0.0050 0.9157 0.0794 59 W 0.0059 0.8705 0.1236 60 M 0.0122 0.7279 0.2599 61 N 0.0203 0.5228 0.4570 62 R 0.0488 0.2327 0.7185 63 P 0.0143 0.6509 0.3348 64 H 0.0238 0.6687 0.3075 65 L 0.0395 0.8131 0.1474 66 A 0.0364 0.8388 0.1248 67 A 0.0271 0.8442 0.1286 68 A 0.0265 0.7907 0.1828 69 W 0.0411 0.6624 0.2965 70 E 0.0371 0.4816 0.4813 71 Y 0.0405 0.3149 0.6446 72 D 0.0440 0.1973 0.7587 73 W 0.0481 0.1207 0.8312 74 P 0.0500 0.1606 0.7894 75 A 0.0128 0.8033 0.1839 76 S 0.0091 0.8863 0.1046 77 R 0.0088 0.9135 0.0777 78 W 0.0070 0.9260 0.0670 79 R 0.0055 0.9296 0.0649 80 Q 0.0056 0.9271 0.0673 81 H 0.0052 0.9260 0.0687 82 L 0.0061 0.9265 0.0674 83 N 0.0062 0.9192 0.0746 84 A 0.0070 0.9060 0.0870 85 Q 0.0122 0.8644 0.1233 86 L 0.0246 0.6998 0.2756 87 E 0.0329 0.3955 0.5716 88 G 0.0469 0.0864 0.8667 89 T 0.0433 0.0982 0.8585 90 Y 0.0700 0.0801 0.8498 91 S 0.2100 0.0481 0.7419 92 L 0.4375 0.0215 0.5409 93 P 0.6737 0.0188 0.3075 94 L 0.8485 0.0091 0.1424 95 I 0.8910 0.0076 0.1013 96 G 0.8992 0.0059 0.0948 97 S 0.8798 0.0079 0.1124 98 W 0.7614 0.0211 0.2175 99 H 0.0933 0.0328 0.8739 100 G 0.0452 0.0466 0.9082 101 T 0.5123 0.0143 0.4734 102 D 0.7560 0.0111 0.2329 103 G 0.7877 0.0138 0.1985 104 G 0.8647 0.0143 0.1209 105 Y 0.8863 0.0110 0.1027 106 L 0.8947 0.0130 0.0923 107 E 0.8919 0.0141 0.0940 108 L 0.8636 0.0215 0.1149 109 Y 0.7447 0.0356 0.2197 110 W 0.5314 0.0474 0.4212 111 A 0.2206 0.2074 0.5720 112 A 0.0852 0.3250 0.5897 113 K 0.0643 0.3202 0.6155 114 D 0.0994 0.1847 0.7159 115 L 0.1135 0.2221 0.6645 116 I 0.1438 0.2090 0.6472 117 S 0.1609 0.2058 0.6332 118 H 0.1565 0.2188 0.6247 119 Y 0.1841 0.2136 0.6023 120 Y 0.2029 0.1392 0.6579 121 D 0.2004 0.0910 0.7086 122 A 0.1280 0.0610 0.8110 123 D 0.0770 0.0309 0.8922 124 P 0.0362 0.1112 0.8526 125 Y 0.0459 0.0731 0.8810 126 D 0.1994 0.0352 0.7654 127 L 0.4177 0.0863 0.4960 128 G 0.6575 0.0780 0.2645 129 L 0.7720 0.0511 0.1769 130 H 0.7657 0.0579 0.1764 131 A 0.7967 0.0478 0.1555 132 A 0.7828 0.0382 0.1791 133 I 0.6587 0.0437 0.2976 134 A 0.4456 0.0238 0.5306 135 D 0.1778 0.0641 0.7581 136 L 0.0371 0.4561 0.5068 137 S 0.0344 0.5191 0.4465 138 K 0.0511 0.4822 0.4667 139 V 0.0486 0.2399 0.7115 140 N 0.0583 0.1339 0.8079 141 R 0.0411 0.2891 0.6698 142 G 0.0410 0.3793 0.5797 143 F 0.0377 0.6210 0.3413 144 G 0.0127 0.8159 0.1714 145 P 0.0046 0.9315 0.0639 146 L 0.0045 0.9465 0.0491 147 L 0.0044 0.9520 0.0435 148 L 0.0044 0.9556 0.0400 149 P 0.0044 0.9577 0.0380 150 R 0.0044 0.9564 0.0391 151 I 0.0044 0.9570 0.0386 152 V 0.0045 0.9545 0.0410 153 A 0.0046 0.9477 0.0477 154 S 0.0056 0.9254 0.0690 155 V 0.0082 0.8885 0.1032 156 F 0.0185 0.7360 0.2455 157 A 0.0281 0.4043 0.5676 158 N 0.0326 0.1590 0.8084 159 E 0.0684 0.0487 0.8828 160 P 0.0353 0.1773 0.7875 161 R 0.0719 0.1586 0.7695 162 C 0.3399 0.0646 0.5955 163 R 0.5478 0.0522 0.4000 164 R 0.8332 0.0131 0.1537 165 I 0.8724 0.0091 0.1185 166 M 0.8350 0.0132 0.1518 167 F 0.6794 0.0168 0.3038 168 D 0.3211 0.0198 0.6591 169 P 0.1249 0.0499 0.8252 170 D 0.0917 0.0615 0.8467 171 H 0.0274 0.3457 0.6269 172 R 0.0219 0.4219 0.5562 173 N 0.0164 0.6666 0.3170 174 T 0.0073 0.8982 0.0945 175 A 0.0076 0.9365 0.0560 176 T 0.0091 0.9422 0.0488 177 R 0.0097 0.9459 0.0444 178 R 0.0087 0.9417 0.0495 179 L 0.0066 0.9317 0.0617 180 C 0.0101 0.8884 0.1015 181 E 0.0165 0.8315 0.1519 182 W 0.0124 0.6961 0.2915 183 A 0.0502 0.3356 0.6142 184 G 0.0617 0.0360 0.9023 185 C 0.2089 0.0209 0.7702 186 K 0.4727 0.0212 0.5061 187 F 0.5158 0.0327 0.4514 188 L 0.4094 0.1230 0.4676 189 G 0.4274 0.0968 0.4758 190 E 0.5147 0.0623 0.4230 191 H 0.5359 0.0298 0.4343 192 D 0.4324 0.0335 0.5341 193 T 0.1895 0.0325 0.7780 194 T 0.0721 0.0798 0.8481 195 N 0.0603 0.0698 0.8699 196 R 0.1592 0.0922 0.7485 197 R 0.3050 0.1466 0.5484 198 M 0.5614 0.1450 0.2936 199 A 0.7252 0.1281 0.1467 200 L 0.7981 0.0947 0.1072 201 Y 0.7684 0.1103 0.1214 202 A 0.7581 0.1157 0.1262 203 L 0.5902 0.1399 0.2699 204 E 0.3882 0.1274 0.4844 205 A 0.1789 0.3278 0.4933 206 P 0.1626 0.3950 0.4425 207 T 0.1345 0.4395 0.4261 208 T 0.1353 0.3231 0.5416 209 A 0.1090 0.2036 0.6874 210 A 0.0387 0.0426 0.9188