# This file is the result of combining several RDB files, specifically # T0263.t04.dssp-ebghstl.rdb (weight 1.53986) # T0263.t04.stride-ebghtl.rdb (weight 1.24869) # T0263.t04.str2.rdb (weight 1.54758) # T0263.t04.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 T0263.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0263 # 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 T0263.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 6.98393 # # ============================================ # Comments from T0263.t04.stride-ebghtl.rdb # ============================================ # TARGET T0263 # 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 T0263.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 6.98393 # # ============================================ # Comments from T0263.t04.str2.rdb # ============================================ # TARGET T0263 # 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 T0263.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 6.98393 # # ============================================ # Comments from T0263.t04.alpha.rdb # ============================================ # TARGET T0263 # 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 T0263.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 6.98393 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0892 0.2044 0.7064 2 A 0.2430 0.1449 0.6121 3 T 0.3704 0.1373 0.4923 4 L 0.7917 0.0554 0.1530 5 L 0.8712 0.0312 0.0976 6 Q 0.8998 0.0214 0.0788 7 L 0.8723 0.0240 0.1037 8 H 0.7948 0.0295 0.1758 9 F 0.6986 0.0314 0.2700 10 A 0.4857 0.0540 0.4604 11 F 0.3143 0.0599 0.6258 12 N 0.1580 0.0523 0.7897 13 G 0.0689 0.0281 0.9029 14 P 0.0780 0.0910 0.8310 15 F 0.0695 0.1774 0.7531 16 G 0.0413 0.4086 0.5501 17 D 0.0059 0.9091 0.0850 18 A 0.0078 0.9285 0.0637 19 M 0.0057 0.9343 0.0600 20 A 0.0054 0.9415 0.0531 21 E 0.0057 0.9124 0.0819 22 Q 0.0067 0.8679 0.1255 23 L 0.0095 0.8346 0.1559 24 K 0.0083 0.8266 0.1652 25 P 0.0056 0.8577 0.1367 26 L 0.0066 0.8824 0.1110 27 A 0.0061 0.9190 0.0749 28 E 0.0056 0.9108 0.0837 29 S 0.0065 0.8749 0.1187 30 I 0.0185 0.8020 0.1795 31 N 0.0264 0.5530 0.4206 32 Q 0.0446 0.3392 0.6163 33 E 0.0602 0.1162 0.8235 34 P 0.0384 0.1695 0.7921 35 G 0.0811 0.0947 0.8242 36 F 0.3462 0.0885 0.5653 37 L 0.5740 0.0571 0.3689 38 W 0.7876 0.0324 0.1799 39 K 0.8699 0.0188 0.1113 40 V 0.8710 0.0186 0.1104 41 W 0.8340 0.0251 0.1409 42 T 0.7944 0.0196 0.1860 43 E 0.6895 0.0456 0.2649 44 S 0.3506 0.0364 0.6131 45 E 0.0799 0.1748 0.7454 46 K 0.0497 0.1374 0.8130 47 N 0.0840 0.0754 0.8407 48 H 0.1473 0.0679 0.7848 49 E 0.4970 0.0646 0.4383 50 A 0.6079 0.0435 0.3486 51 G 0.5254 0.0332 0.4414 52 G 0.7432 0.0139 0.2429 53 I 0.8611 0.0086 0.1303 54 Y 0.8866 0.0083 0.1050 55 L 0.8526 0.0141 0.1333 56 F 0.6577 0.0307 0.3116 57 T 0.2550 0.0572 0.6877 58 D 0.1175 0.0544 0.8282 59 E 0.0091 0.8878 0.1031 60 K 0.0070 0.9315 0.0615 61 S 0.0072 0.9266 0.0662 62 A 0.0053 0.9430 0.0517 63 L 0.0053 0.9489 0.0458 64 A 0.0052 0.9391 0.0557 65 Y 0.0058 0.9234 0.0707 66 L 0.0076 0.9219 0.0706 67 E 0.0062 0.9188 0.0751 68 K 0.0059 0.9163 0.0778 69 H 0.0078 0.9060 0.0862 70 T 0.0090 0.9222 0.0687 71 A 0.0069 0.9407 0.0524 72 R 0.0070 0.9429 0.0501 73 L 0.0095 0.9292 0.0613 74 K 0.0101 0.9043 0.0857 75 N 0.0168 0.7649 0.2182 76 L 0.0447 0.4288 0.5265 77 G 0.0513 0.0762 0.8725 78 V 0.1177 0.1034 0.7789 79 E 0.2629 0.1807 0.5564 80 E 0.4997 0.1907 0.3096 81 V 0.7220 0.0940 0.1840 82 V 0.8367 0.0391 0.1242 83 A 0.8340 0.0274 0.1385 84 K 0.8086 0.0278 0.1635 85 V 0.8313 0.0325 0.1362 86 F 0.7642 0.0340 0.2018 87 D 0.7106 0.0279 0.2615 88 V 0.4114 0.0751 0.5135 89 N 0.2133 0.0784 0.7083 90 E 0.1295 0.0747 0.7958 91 P 0.1434 0.1721 0.6845 92 L 0.1183 0.3541 0.5277 93 S 0.1229 0.3549 0.5222 94 Q 0.1099 0.4737 0.4164 95 I 0.0985 0.5304 0.3711 96 N 0.0648 0.4633 0.4719 97 Q 0.0503 0.5139 0.4357 98 A 0.0881 0.5911 0.3208 99 K 0.0930 0.7191 0.1879 100 L 0.0848 0.7862 0.1290 101 A 0.0721 0.7840 0.1439 102 M 0.0290 0.8988 0.0721 103 A 0.0322 0.8947 0.0731 104 T 0.0350 0.8912 0.0738 105 L 0.0252 0.9015 0.0732 106 L 0.0309 0.8763 0.0929 107 Q 0.0426 0.8396 0.1177 108 L 0.0576 0.7919 0.1505 109 H 0.0771 0.7345 0.1884 110 F 0.1068 0.6215 0.2717 111 A 0.1325 0.5010 0.3665 112 F 0.1514 0.3463 0.5023 113 N 0.1069 0.2208 0.6723 114 G 0.0549 0.1222 0.8229 115 P 0.0511 0.2809 0.6679 116 F 0.0401 0.4501 0.5098 117 G 0.0268 0.6274 0.3458 118 D 0.0134 0.7961 0.1905 119 A 0.0219 0.8128 0.1653 120 M 0.0100 0.8968 0.0933 121 A 0.0078 0.9165 0.0757 122 E 0.0074 0.8962 0.0964 123 Q 0.0078 0.8263 0.1659 124 L 0.0170 0.7310 0.2521 125 K 0.0182 0.5900 0.3917 126 P 0.0185 0.6821 0.2994 127 L 0.0204 0.7747 0.2049 128 A 0.0225 0.8222 0.1553 129 E 0.0266 0.7853 0.1880 130 S 0.0252 0.7297 0.2451 131 I 0.0410 0.5993 0.3597 132 N 0.0662 0.3388 0.5950 133 Q 0.0605 0.2861 0.6534 134 E 0.0671 0.2086 0.7243 135 P 0.0482 0.2876 0.6642 136 G 0.1115 0.1777 0.7109 137 F 0.4127 0.1777 0.4096 138 L 0.5302 0.2007 0.2691 139 W 0.6320 0.1780 0.1900 140 K 0.6810 0.1822 0.1368 141 V 0.6436 0.1798 0.1766 142 W 0.5496 0.1586 0.2918 143 T 0.4059 0.1059 0.4881 144 E 0.2080 0.2251 0.5670 145 S 0.1301 0.2113 0.6585 146 E 0.0961 0.3552 0.5488 147 K 0.1201 0.3224 0.5575 148 N 0.1388 0.2700 0.5912 149 H 0.1072 0.3458 0.5469 150 E 0.1326 0.2832 0.5842 151 A 0.1594 0.1764 0.6642 152 G 0.1609 0.0762 0.7629 153 G 0.4372 0.0426 0.5202 154 I 0.7515 0.0342 0.2142 155 Y 0.8475 0.0334 0.1191 156 L 0.8364 0.0438 0.1197 157 F 0.7529 0.0483 0.1988 158 T 0.4125 0.0794 0.5080 159 D 0.1305 0.1334 0.7361 160 E 0.0255 0.6004 0.3741 161 K 0.0177 0.7887 0.1936 162 S 0.0202 0.8166 0.1632 163 A 0.0169 0.9025 0.0806 164 L 0.0111 0.9367 0.0523 165 A 0.0105 0.9396 0.0498 166 Y 0.0104 0.9380 0.0516 167 L 0.0096 0.9366 0.0539 168 E 0.0088 0.9289 0.0623 169 K 0.0118 0.9030 0.0852 170 H 0.0240 0.8446 0.1314 171 T 0.0325 0.8002 0.1673 172 A 0.0303 0.8374 0.1324 173 R 0.0433 0.8388 0.1179 174 L 0.0407 0.8219 0.1375 175 K 0.0254 0.7554 0.2192 176 N 0.0326 0.5675 0.4000 177 L 0.0705 0.4161 0.5134 178 G 0.1118 0.1157 0.7724 179 V 0.2321 0.3450 0.4229 180 E 0.3502 0.4194 0.2304 181 E 0.4443 0.4412 0.1145 182 V 0.5325 0.3941 0.0733 183 V 0.5913 0.3288 0.0799 184 A 0.5394 0.3382 0.1223 185 K 0.5048 0.2960 0.1992 186 V 0.5031 0.3017 0.1952 187 F 0.4667 0.2058 0.3275 188 D 0.3919 0.0802 0.5279 189 V 0.0895 0.1810 0.7295 190 N 0.0441 0.1548 0.8011 191 E 0.0604 0.0989 0.8407 192 P 0.0593 0.2505 0.6901 193 L 0.0379 0.6254 0.3367 194 S 0.0366 0.6467 0.3167 195 Q 0.0354 0.7258 0.2388 196 I 0.0548 0.6945 0.2507 197 N 0.0548 0.6395 0.3056 198 Q 0.0246 0.8208 0.1546 199 A 0.0303 0.8007 0.1689 200 K 0.0399 0.7266 0.2336 201 L 0.0449 0.5490 0.4061 202 A 0.0348 0.2766 0.6886