# This file is the result of combining several RDB files, specifically # T0250.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0250.t2k.stride-ebghtl.rdb (weight 1.24869) # T0250.t2k.str2.rdb (weight 1.54758) # T0250.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 T0250.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0250 # 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 T0250.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 48 # # ============================================ # Comments from T0250.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0250 # 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 T0250.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 48 # # ============================================ # Comments from T0250.t2k.str2.rdb # ============================================ # TARGET T0250 # 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 T0250.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 48 # # ============================================ # Comments from T0250.t2k.alpha.rdb # ============================================ # TARGET T0250 # 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 T0250.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 48 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0611 0.0505 0.8883 2 T 0.0991 0.1021 0.7988 3 N 0.1355 0.1858 0.6787 4 V 0.3497 0.3989 0.2514 5 L 0.4113 0.4315 0.1572 6 Y 0.3895 0.4359 0.1746 7 Q 0.3049 0.5208 0.1744 8 H 0.1242 0.6783 0.1975 9 G 0.0584 0.7846 0.1570 10 T 0.0194 0.8813 0.0993 11 L 0.0070 0.9452 0.0478 12 G 0.0076 0.9482 0.0443 13 T 0.0058 0.9472 0.0470 14 L 0.0067 0.9352 0.0582 15 M 0.0088 0.9019 0.0893 16 A 0.0215 0.7220 0.2565 17 G 0.0283 0.5089 0.4628 18 L 0.0798 0.4553 0.4649 19 L 0.1268 0.3600 0.5132 20 E 0.0835 0.1955 0.7210 21 G 0.1095 0.1283 0.7622 22 T 0.2990 0.0873 0.6137 23 A 0.5420 0.0283 0.4297 24 T 0.4008 0.0470 0.5521 25 I 0.0062 0.9295 0.0643 26 N 0.0051 0.9470 0.0479 27 E 0.0049 0.9453 0.0499 28 L 0.0068 0.9389 0.0543 29 L 0.0115 0.9078 0.0806 30 E 0.0161 0.8159 0.1680 31 H 0.0491 0.5305 0.4204 32 G 0.0607 0.1292 0.8101 33 N 0.0687 0.0737 0.8576 34 L 0.2248 0.0724 0.7028 35 G 0.3685 0.0691 0.5624 36 I 0.5246 0.1016 0.3738 37 A 0.5839 0.0790 0.3372 38 T 0.5060 0.0821 0.4119 39 L 0.3031 0.1645 0.5324 40 T 0.1781 0.1897 0.6323 41 G 0.1558 0.1544 0.6898 42 S 0.1843 0.0758 0.7399 43 D 0.2047 0.0622 0.7331 44 G 0.3922 0.0631 0.5447 45 E 0.6797 0.0507 0.2697 46 V 0.8158 0.0524 0.1318 47 I 0.8605 0.0414 0.0981 48 F 0.8257 0.0444 0.1299 49 L 0.6665 0.0459 0.2876 50 D 0.2504 0.0273 0.7223 51 G 0.2091 0.0458 0.7452 52 K 0.6237 0.0307 0.3457 53 A 0.8355 0.0177 0.1467 54 Y 0.8549 0.0186 0.1265 55 H 0.8778 0.0089 0.1133 56 A 0.8502 0.0074 0.1424 57 N 0.5238 0.0245 0.4517 58 E 0.1377 0.0900 0.7723 59 H 0.0640 0.0194 0.9166 60 K 0.1706 0.0288 0.8005 61 E 0.6653 0.0093 0.3253 62 F 0.9051 0.0038 0.0911 63 I 0.8709 0.0061 0.1230 64 E 0.8505 0.0051 0.1444 65 L 0.5191 0.0088 0.4721 66 K 0.1942 0.0206 0.7853 67 G 0.0251 0.1862 0.7887 68 D 0.0415 0.1501 0.8084 69 E 0.2325 0.1366 0.6309 70 K 0.4604 0.0537 0.4859 71 V 0.4513 0.0194 0.5294 72 P 0.4468 0.0291 0.5241 73 Y 0.6687 0.0323 0.2990 74 A 0.7915 0.0190 0.1894 75 S 0.8702 0.0102 0.1195 76 I 0.8544 0.0087 0.1369 77 T 0.7233 0.0171 0.2596 78 N 0.5800 0.0274 0.3926 79 F 0.3953 0.0408 0.5640 80 K 0.2568 0.0269 0.7163 81 A 0.1842 0.1296 0.6862 82 S 0.2613 0.1495 0.5892 83 K 0.4891 0.0961 0.4148 84 T 0.5996 0.0548 0.3456 85 F 0.6767 0.0259 0.2974 86 P 0.5967 0.0237 0.3796 87 L 0.3215 0.0439 0.6346 88 Q 0.1851 0.0550 0.7599 89 Q 0.1589 0.0588 0.7823 90 L 0.1602 0.0343 0.8055 91 S 0.1077 0.0199 0.8723 92 Q 0.0067 0.8925 0.1007 93 D 0.0050 0.9309 0.0642 94 D 0.0054 0.9431 0.0515 95 V 0.0047 0.9530 0.0423 96 F 0.0047 0.9542 0.0411 97 A 0.0048 0.9501 0.0451 98 Q 0.0048 0.9462 0.0490 99 I 0.0054 0.9356 0.0590 100 K 0.0057 0.9036 0.0907 101 N 0.0072 0.8155 0.1772 102 E 0.0144 0.6932 0.2924 103 M 0.0798 0.1830 0.7372 104 L 0.0427 0.1061 0.8512 105 S 0.0811 0.0917 0.8272 106 E 0.1312 0.1282 0.7406 107 N 0.2869 0.0841 0.6290 108 L 0.5357 0.0886 0.3757 109 F 0.6499 0.0861 0.2641 110 S 0.7254 0.0874 0.1872 111 A 0.8478 0.0330 0.1193 112 V 0.8942 0.0118 0.0940 113 K 0.9042 0.0069 0.0888 114 I 0.8920 0.0112 0.0967 115 Y 0.7877 0.0363 0.1760 116 G 0.7053 0.0226 0.2722 117 T 0.7316 0.0266 0.2419 118 F 0.6734 0.0410 0.2856 119 K 0.4897 0.0916 0.4187 120 H 0.5709 0.0361 0.3930 121 M 0.7113 0.0108 0.2779 122 H 0.8341 0.0072 0.1587 123 V 0.8735 0.0061 0.1204 124 R 0.8219 0.0135 0.1646 125 M 0.7115 0.0128 0.2757 126 M 0.3759 0.0230 0.6011 127 P 0.1889 0.1381 0.6730 128 A 0.1118 0.2232 0.6649 129 Q 0.1399 0.1775 0.6826 130 Q 0.0952 0.0825 0.8222 131 P 0.0610 0.0800 0.8591 132 P 0.0664 0.1027 0.8310 133 Y 0.0609 0.1611 0.7780 134 T 0.0406 0.4359 0.5234 135 R 0.0391 0.5589 0.4020 136 L 0.0100 0.8679 0.1221 137 I 0.0084 0.9095 0.0821 138 D 0.0085 0.9240 0.0676 139 S 0.0082 0.9097 0.0821 140 A 0.0137 0.8735 0.1128 141 R 0.0149 0.6672 0.3179 142 R 0.0303 0.3797 0.5901 143 Q 0.0913 0.0855 0.8232 144 P 0.1255 0.1215 0.7530 145 E 0.3372 0.1553 0.5074 146 E 0.4709 0.1171 0.4120 147 K 0.5744 0.0795 0.3461 148 R 0.4349 0.1585 0.4066 149 Q 0.2301 0.1794 0.5905 150 D 0.2010 0.0973 0.7016 151 I 0.3730 0.0397 0.5873 152 R 0.5154 0.0401 0.4445 153 G 0.7552 0.0131 0.2317 154 A 0.8522 0.0093 0.1385 155 I 0.8928 0.0086 0.0986 156 V 0.8355 0.0229 0.1416 157 G 0.7796 0.0260 0.1945 158 F 0.7234 0.0396 0.2371 159 F 0.5410 0.0460 0.4130 160 T 0.2480 0.0489 0.7032 161 P 0.1063 0.4397 0.4539 162 E 0.0482 0.5731 0.3786 163 L 0.0517 0.6111 0.3372 164 F 0.1197 0.4057 0.4746 165 H 0.0844 0.3202 0.5954 166 G 0.1079 0.1681 0.7241 167 V 0.2100 0.1122 0.6778 168 G 0.2647 0.0792 0.6561 169 S 0.2039 0.0956 0.7005 170 A 0.1303 0.1252 0.7445 171 G 0.2201 0.1011 0.6787 172 F 0.5198 0.0710 0.4092 173 H 0.6721 0.0476 0.2803 174 I 0.7542 0.0462 0.1996 175 H 0.7977 0.0295 0.1728 176 F 0.7708 0.0262 0.2030 177 A 0.6692 0.0269 0.3039 178 D 0.3173 0.0371 0.6456 179 D 0.0698 0.1519 0.7783 180 E 0.0714 0.1123 0.8163 181 R 0.1148 0.0976 0.7876 182 A 0.1856 0.0713 0.7431 183 Y 0.2474 0.0558 0.6968 184 G 0.2163 0.0415 0.7422 185 G 0.3808 0.0395 0.5798 186 H 0.5917 0.0315 0.3768 187 V 0.7246 0.0320 0.2434 188 L 0.7695 0.0238 0.2067 189 D 0.8021 0.0145 0.1835 190 F 0.8691 0.0072 0.1237 191 E 0.8807 0.0046 0.1146 192 V 0.8397 0.0082 0.1521 193 D 0.6649 0.0392 0.2960 194 D 0.6144 0.0253 0.3603 195 V 0.7736 0.0061 0.2203 196 V 0.9068 0.0033 0.0899 197 V 0.9243 0.0035 0.0723 198 E 0.9204 0.0040 0.0755 199 I 0.8936 0.0058 0.1005 200 Q 0.7068 0.0099 0.2832 201 N 0.4970 0.0353 0.4677 202 F 0.3870 0.0786 0.5344 203 E 0.3222 0.1177 0.5601 204 T 0.4049 0.1025 0.4926 205 F 0.6932 0.0348 0.2720 206 Q 0.7794 0.0212 0.1994 207 Q 0.7682 0.0254 0.2063 208 H 0.6852 0.0285 0.2863 209 F 0.3907 0.0199 0.5894 210 P 0.2445 0.0287 0.7267 211 V 0.1597 0.0872 0.7531 212 N 0.1158 0.0631 0.8211 213 N 0.0852 0.0482 0.8666 214 E 0.0086 0.7843 0.2070 215 T 0.0084 0.7920 0.1996 216 F 0.0123 0.8421 0.1457 217 V 0.0222 0.7692 0.2086 218 K 0.0406 0.5130 0.4463 219 A 0.0588 0.3746 0.5666 220 K 0.0795 0.1792 0.7413 221 I 0.1114 0.0760 0.8127 222 D 0.0807 0.0306 0.8887 223 Y 0.0130 0.7695 0.2175 224 K 0.0073 0.8350 0.1577 225 D 0.0128 0.8285 0.1587 226 V 0.0085 0.8882 0.1034 227 A 0.0072 0.9181 0.0748 228 E 0.0074 0.9158 0.0767 229 E 0.0083 0.9062 0.0854 230 I 0.0134 0.8902 0.0964 231 R 0.0150 0.8462 0.1388 232 E 0.0187 0.6873 0.2940 233 A 0.0304 0.4205 0.5491 234 E 0.0220 0.1528 0.8253