# This file is the result of combining several RDB files, specifically # T0344.t06.dssp-ebghstl.rdb (weight 1.53986) # T0344.t06.stride-ebghtl.rdb (weight 1.24869) # T0344.t06.str2.rdb (weight 1.54758) # T0344.t06.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 T0344.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0344 # Using neural net t06-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 T0344.t06-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 2.6722 # # ============================================ # Comments from T0344.t06.stride-ebghtl.rdb # ============================================ # TARGET T0344 # Using neural net t06-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 T0344.t06-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 2.6722 # # ============================================ # Comments from T0344.t06.str2.rdb # ============================================ # TARGET T0344 # Using neural net t06-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 T0344.t06-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 2.6722 # # ============================================ # Comments from T0344.t06.alpha.rdb # ============================================ # TARGET T0344 # Using neural net t06-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 T0344.t06-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 2.6722 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1700 0.0130 0.8170 2 R 0.7333 0.0112 0.2555 3 I 0.8929 0.0091 0.0980 4 V 0.8815 0.0167 0.1018 5 A 0.8312 0.0211 0.1476 6 A 0.6223 0.0628 0.3149 7 D 0.3401 0.0641 0.5958 8 T 0.1562 0.0586 0.7853 9 G 0.1056 0.0961 0.7982 10 G 0.1598 0.1444 0.6959 11 A 0.3551 0.1972 0.4477 12 V 0.4876 0.1982 0.3142 13 L 0.4415 0.1957 0.3628 14 D 0.2171 0.2130 0.5700 15 E 0.0491 0.3916 0.5593 16 T 0.0547 0.3013 0.6440 17 F 0.1170 0.2167 0.6663 18 E 0.1133 0.1830 0.7037 19 P 0.1672 0.3398 0.4930 20 I 0.1897 0.4707 0.3397 21 G 0.3428 0.4083 0.2489 22 L 0.4528 0.3945 0.1527 23 I 0.5059 0.3425 0.1516 24 A 0.5871 0.2434 0.1695 25 T 0.6448 0.1960 0.1592 26 V 0.6278 0.2501 0.1221 27 A 0.5738 0.3252 0.1010 28 V 0.5505 0.3509 0.0986 29 L 0.5469 0.3372 0.1159 30 V 0.5245 0.2709 0.2047 31 E 0.4133 0.2118 0.3749 32 K 0.2172 0.0904 0.6924 33 P 0.1351 0.1236 0.7413 34 Y 0.1293 0.1775 0.6931 35 R 0.1244 0.1813 0.6943 36 S 0.1235 0.1661 0.7103 37 A 0.1071 0.4203 0.4726 38 K 0.1685 0.3927 0.4388 39 E 0.3996 0.2867 0.3137 40 V 0.5517 0.2016 0.2467 41 M 0.6785 0.1464 0.1750 42 V 0.7061 0.1181 0.1758 43 K 0.6872 0.1165 0.1963 44 Y 0.6023 0.0668 0.3309 45 A 0.3169 0.0529 0.6302 46 N 0.1518 0.0162 0.8320 47 P 0.0455 0.1946 0.7599 48 Y 0.0872 0.1868 0.7261 49 D 0.1542 0.1935 0.6523 50 Y 0.2213 0.1575 0.6213 51 D 0.2376 0.1286 0.6338 52 L 0.1062 0.3154 0.5784 53 T 0.1046 0.3169 0.5785 54 G 0.0593 0.4197 0.5211 55 R 0.0660 0.6527 0.2812 56 Q 0.0940 0.7219 0.1841 57 A 0.0943 0.7401 0.1656 58 I 0.0723 0.7740 0.1537 59 R 0.0367 0.8414 0.1220 60 D 0.0174 0.8929 0.0896 61 E 0.0099 0.9383 0.0518 62 V 0.0091 0.9489 0.0420 63 L 0.0078 0.9550 0.0372 64 L 0.0074 0.9548 0.0379 65 A 0.0076 0.9541 0.0382 66 I 0.0114 0.9488 0.0398 67 E 0.0124 0.9427 0.0449 68 L 0.0093 0.9254 0.0653 69 A 0.0118 0.8849 0.1033 70 R 0.0206 0.8030 0.1764 71 K 0.0395 0.6105 0.3500 72 V 0.0955 0.2791 0.6254 73 K 0.0920 0.0328 0.8752 74 P 0.0839 0.0824 0.8337 75 D 0.1418 0.1024 0.7559 76 V 0.7726 0.0349 0.1925 77 I 0.8709 0.0160 0.1131 78 H 0.8547 0.0159 0.1295 79 L 0.6607 0.0460 0.2933 80 D 0.2930 0.0727 0.6343 81 S 0.1533 0.1525 0.6941 82 T 0.1586 0.1807 0.6606 83 L 0.2148 0.1685 0.6167 84 G 0.1414 0.1050 0.7536 85 G 0.3163 0.0821 0.6017 86 I 0.6228 0.0694 0.3078 87 E 0.7209 0.0706 0.2086 88 L 0.6568 0.1150 0.2282 89 R 0.5712 0.1346 0.2942 90 K 0.4641 0.1078 0.4282 91 L 0.2024 0.0838 0.7138 92 D 0.1081 0.0604 0.8315 93 E 0.0542 0.4623 0.4835 94 P 0.0577 0.5524 0.3899 95 T 0.0747 0.6256 0.2997 96 I 0.0896 0.7043 0.2061 97 D 0.1147 0.6406 0.2446 98 A 0.1292 0.6288 0.2420 99 L 0.1884 0.4062 0.4054 100 G 0.2250 0.1269 0.6480 101 I 0.2948 0.0810 0.6242 102 S 0.2170 0.0995 0.6835 103 D 0.0868 0.2245 0.6887 104 K 0.0464 0.2495 0.7041 105 G 0.0432 0.2595 0.6973 106 K 0.0645 0.6322 0.3033 107 E 0.1747 0.6672 0.1581 108 V 0.1157 0.7495 0.1348 109 W 0.0797 0.8034 0.1169 110 K 0.0462 0.8410 0.1128 111 E 0.0463 0.7935 0.1602 112 L 0.0235 0.7496 0.2269 113 S 0.0255 0.6746 0.2998 114 K 0.0093 0.6442 0.3465 115 D 0.0144 0.5473 0.4382 116 L 0.0181 0.6701 0.3118 117 Q 0.0098 0.7878 0.2024 118 P 0.0066 0.8920 0.1014 119 L 0.0060 0.9159 0.0781 120 A 0.0106 0.9051 0.0843 121 R 0.0106 0.9010 0.0885 122 K 0.0134 0.8737 0.1129 123 F 0.0236 0.8456 0.1308 124 W 0.0367 0.8305 0.1329 125 E 0.0250 0.8397 0.1353 126 E 0.0362 0.7615 0.2023 127 T 0.0663 0.3777 0.5560 128 N 0.0940 0.0337 0.8723 129 I 0.3787 0.0080 0.6132 130 E 0.7859 0.0058 0.2083 131 I 0.9177 0.0042 0.0781 132 V 0.9018 0.0095 0.0887 133 A 0.8957 0.0073 0.0969 134 I 0.7307 0.0272 0.2421 135 G 0.3374 0.0233 0.6393 136 K 0.1686 0.0998 0.7316 137 S 0.1401 0.1000 0.7599 138 S 0.2018 0.1061 0.6921 139 V 0.2920 0.0761 0.6319 140 P 0.3434 0.1242 0.5324 141 V 0.4380 0.2623 0.2997 142 R 0.4881 0.2732 0.2386 143 I 0.3386 0.5210 0.1403 144 A 0.2741 0.6073 0.1185 145 E 0.3059 0.5903 0.1039 146 I 0.2517 0.6302 0.1182 147 Y 0.1800 0.6631 0.1569 148 A 0.1119 0.6375 0.2507 149 G 0.1082 0.5540 0.3378 150 I 0.1882 0.5750 0.2368 151 Y 0.2201 0.5776 0.2023 152 S 0.2197 0.5595 0.2208 153 A 0.1252 0.7074 0.1675 154 K 0.1101 0.7529 0.1370 155 W 0.1863 0.6324 0.1813 156 G 0.2576 0.5298 0.2126 157 I 0.2648 0.5301 0.2051 158 E 0.2630 0.4839 0.2531 159 N 0.2692 0.4696 0.2612 160 V 0.3041 0.4172 0.2788 161 E 0.2525 0.4100 0.3375 162 K 0.2086 0.3816 0.4098 163 E 0.0653 0.1159 0.8188 164 G 0.0553 0.0397 0.9050 165 H 0.4197 0.0172 0.5631 166 L 0.8534 0.0060 0.1406 167 I 0.8961 0.0066 0.0973 168 I 0.8389 0.0206 0.1405 169 G 0.6805 0.0186 0.3009 170 L 0.4216 0.0209 0.5575 171 P 0.2908 0.0690 0.6402 172 R 0.3491 0.1089 0.5421 173 Y 0.6494 0.0546 0.2960 174 M 0.7796 0.0150 0.2053 175 E 0.8640 0.0082 0.1278 176 V 0.8669 0.0060 0.1271 177 N 0.8701 0.0057 0.1242 178 I 0.7542 0.0108 0.2350 179 K 0.4701 0.0283 0.5016 180 D 0.1117 0.0589 0.8295 181 G 0.1056 0.0490 0.8454 182 K 0.5788 0.0340 0.3872 183 I 0.8037 0.0146 0.1817 184 I 0.6784 0.0367 0.2849 185 G 0.4574 0.0403 0.5022 186 R 0.4308 0.0520 0.5172 187 S 0.4745 0.0340 0.4914 188 L 0.3788 0.0267 0.5945 189 D 0.2004 0.0124 0.7872 190 P 0.0246 0.2829 0.6925 191 R 0.0314 0.2592 0.7094 192 E 0.0928 0.2538 0.6534 193 G 0.1068 0.0929 0.8003 194 G 0.2164 0.0742 0.7094 195 L 0.5387 0.0570 0.4043 196 Y 0.5701 0.0504 0.3795 197 G 0.5510 0.0312 0.4178 198 S 0.6818 0.0247 0.2935 199 A 0.7826 0.0216 0.1958 200 E 0.8384 0.0149 0.1467 201 V 0.8105 0.0149 0.1747 202 S 0.7249 0.0158 0.2592 203 V 0.3952 0.0228 0.5820 204 P 0.1766 0.0677 0.7557 205 E 0.0733 0.0913 0.8353 206 G 0.1290 0.0633 0.8077 207 V 0.4791 0.0150 0.5059 208 K 0.7473 0.0129 0.2399 209 W 0.8404 0.0161 0.1435 210 E 0.8389 0.0210 0.1401 211 I 0.7948 0.0266 0.1787 212 Y 0.4923 0.0175 0.4902 213 P 0.1895 0.0482 0.7623 214 N 0.1101 0.0574 0.8325 215 P 0.0294 0.5756 0.3950 216 V 0.0412 0.6611 0.2977 217 A 0.0980 0.6734 0.2287 218 R 0.1577 0.6315 0.2107 219 R 0.3343 0.4652 0.2005 220 F 0.4826 0.3530 0.1645 221 M 0.5696 0.3121 0.1183 222 I 0.6405 0.2672 0.0923 223 F 0.6405 0.2541 0.1054 224 E 0.6627 0.2255 0.1118 225 I 0.6002 0.2413 0.1585 226 F 0.4512 0.1978 0.3510 227 S 0.2945 0.1328 0.5727 228 K 0.1226 0.1157 0.7617 229 R 0.0499 0.0328 0.9173