# This file is the result of combining several RDB files, specifically # T0293.t04.dssp-ebghstl.rdb (weight 1.53986) # T0293.t04.stride-ebghtl.rdb (weight 1.24869) # T0293.t04.str2.rdb (weight 1.54758) # T0293.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 T0293.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0293 # 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 T0293.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 2149 # # ============================================ # Comments from T0293.t04.stride-ebghtl.rdb # ============================================ # TARGET T0293 # 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 T0293.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 2149 # # ============================================ # Comments from T0293.t04.str2.rdb # ============================================ # TARGET T0293 # 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 T0293.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 2149 # # ============================================ # Comments from T0293.t04.alpha.rdb # ============================================ # TARGET T0293 # 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 T0293.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 2149 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.1412 0.1001 0.7588 2 S 0.2111 0.1857 0.6032 3 L 0.1884 0.2693 0.5422 4 N 0.1568 0.2573 0.5859 5 F 0.1534 0.2262 0.6204 6 K 0.1241 0.1469 0.7291 7 D 0.1072 0.0377 0.8551 8 P 0.0096 0.6857 0.3047 9 E 0.0099 0.6970 0.2931 10 A 0.0156 0.7684 0.2160 11 V 0.0568 0.6064 0.3369 12 R 0.1568 0.4991 0.3441 13 A 0.2164 0.5426 0.2410 14 L 0.1153 0.6933 0.1914 15 T 0.1222 0.6881 0.1897 16 C 0.1396 0.7020 0.1583 17 T 0.1632 0.6583 0.1785 18 L 0.1474 0.5578 0.2948 19 L 0.1633 0.3498 0.4869 20 R 0.1128 0.3529 0.5343 21 E 0.0557 0.5114 0.4329 22 D 0.0536 0.4826 0.4638 23 F 0.0963 0.2648 0.6388 24 G 0.0965 0.0750 0.8285 25 L 0.2069 0.0328 0.7604 26 S 0.3614 0.0282 0.6104 27 I 0.4467 0.0253 0.5280 28 D 0.4216 0.0169 0.5615 29 I 0.2737 0.0177 0.7086 30 P 0.1370 0.0198 0.8432 31 L 0.0220 0.4127 0.5654 32 E 0.0297 0.3974 0.5729 33 R 0.1509 0.4167 0.4324 34 L 0.4014 0.1089 0.4898 35 I 0.2570 0.0717 0.6714 36 P 0.1621 0.0853 0.7526 37 T 0.1359 0.0852 0.7789 38 V 0.1472 0.0723 0.7805 39 P 0.1171 0.1164 0.7665 40 L 0.1139 0.1465 0.7397 41 R 0.0884 0.1527 0.7589 42 L 0.0330 0.4293 0.5377 43 N 0.0398 0.4929 0.4674 44 Y 0.0515 0.7056 0.2429 45 I 0.0336 0.8537 0.1128 46 H 0.0243 0.8957 0.0800 47 W 0.0145 0.9182 0.0673 48 V 0.0066 0.9466 0.0467 49 E 0.0059 0.9491 0.0451 50 D 0.0061 0.9407 0.0532 51 L 0.0075 0.9121 0.0804 52 I 0.0160 0.8001 0.1838 53 G 0.0170 0.5371 0.4459 54 H 0.0205 0.4053 0.5742 55 Q 0.0314 0.3407 0.6279 56 D 0.0468 0.2495 0.7038 57 S 0.0467 0.2404 0.7130 58 D 0.0549 0.2064 0.7388 59 K 0.0484 0.2797 0.6720 60 S 0.0588 0.2487 0.6925 61 T 0.0672 0.2304 0.7024 62 L 0.1311 0.0907 0.7782 63 R 0.2254 0.0462 0.7284 64 R 0.7396 0.0162 0.2443 65 G 0.9042 0.0053 0.0905 66 I 0.9161 0.0047 0.0792 67 D 0.8792 0.0066 0.1143 68 I 0.6416 0.0481 0.3103 69 G 0.2508 0.0490 0.7002 70 T 0.1170 0.0946 0.7884 71 G 0.0714 0.1588 0.7698 72 A 0.0380 0.4961 0.4659 73 S 0.0158 0.7572 0.2270 74 C 0.0105 0.8854 0.1041 75 I 0.0060 0.9319 0.0621 76 Y 0.0051 0.9514 0.0435 77 P 0.0050 0.9551 0.0399 78 L 0.0052 0.9523 0.0425 79 L 0.0050 0.9395 0.0555 80 G 0.0052 0.9082 0.0866 81 A 0.0066 0.8283 0.1651 82 T 0.0143 0.6899 0.2958 83 L 0.0707 0.1617 0.7676 84 N 0.0372 0.1019 0.8609 85 G 0.0644 0.0547 0.8809 86 W 0.4586 0.0162 0.5252 87 Y 0.8869 0.0059 0.1072 88 F 0.9232 0.0033 0.0735 89 L 0.9096 0.0070 0.0834 90 A 0.8969 0.0056 0.0975 91 T 0.8401 0.0101 0.1499 92 E 0.6723 0.0113 0.3164 93 V 0.1582 0.0328 0.8089 94 D 0.0760 0.0162 0.9078 95 D 0.0052 0.9035 0.0913 96 M 0.0050 0.9323 0.0628 97 C 0.0049 0.9505 0.0446 98 F 0.0047 0.9576 0.0377 99 N 0.0047 0.9581 0.0372 100 Y 0.0047 0.9582 0.0370 101 A 0.0047 0.9588 0.0365 102 K 0.0047 0.9580 0.0373 103 K 0.0051 0.9550 0.0400 104 N 0.0050 0.9540 0.0410 105 V 0.0049 0.9529 0.0423 106 E 0.0050 0.9403 0.0546 107 Q 0.0068 0.8537 0.1395 108 N 0.0475 0.3870 0.5655 109 N 0.0447 0.0390 0.9163 110 L 0.0633 0.1337 0.8030 111 S 0.0545 0.3848 0.5607 112 D 0.0869 0.3418 0.5713 113 L 0.4136 0.1077 0.4787 114 I 0.7124 0.0117 0.2760 115 K 0.9007 0.0056 0.0937 116 V 0.9197 0.0039 0.0764 117 V 0.8888 0.0069 0.1043 118 K 0.8049 0.0070 0.1880 119 V 0.3265 0.0154 0.6582 120 P 0.0965 0.0509 0.8525 121 Q 0.0368 0.3548 0.6084 122 A 0.0173 0.7339 0.2487 123 T 0.0190 0.8168 0.1642 124 L 0.0252 0.8626 0.1123 125 L 0.0280 0.8690 0.1030 126 M 0.0248 0.8642 0.1111 127 D 0.0238 0.8295 0.1467 128 A 0.0226 0.8032 0.1742 129 L 0.0492 0.6675 0.2833 130 K 0.0637 0.5409 0.3955 131 E 0.0427 0.4797 0.4775 132 E 0.0503 0.3553 0.5944 133 S 0.0452 0.3364 0.6184 134 E 0.0453 0.1964 0.7583 135 I 0.1499 0.0851 0.7650 136 I 0.4363 0.0221 0.5417 137 Y 0.6365 0.0057 0.3578 138 D 0.6718 0.0175 0.3107 139 F 0.9236 0.0036 0.0728 140 C 0.9309 0.0033 0.0658 141 M 0.9213 0.0048 0.0740 142 C 0.7692 0.0149 0.2159 143 N 0.1896 0.0234 0.7871 144 P 0.0688 0.2283 0.7028 145 P 0.0473 0.4157 0.5370 146 F 0.0795 0.4996 0.4209 147 F 0.1010 0.4481 0.4509 148 A 0.0649 0.4068 0.5283 149 N 0.0701 0.3388 0.5912 150 Q 0.0728 0.3915 0.5357 151 L 0.0609 0.4769 0.4623 152 E 0.0695 0.4776 0.4529 153 A 0.0425 0.6155 0.3420 154 K 0.0454 0.5821 0.3725 155 G 0.0434 0.4865 0.4700 156 V 0.0639 0.4509 0.4853 157 N 0.0914 0.2900 0.6187 158 S 0.0621 0.2323 0.7056 159 R 0.0653 0.1992 0.7355 160 N 0.1041 0.0564 0.8395 161 P 0.0684 0.1276 0.8040 162 R 0.1298 0.0870 0.7832 163 R 0.1619 0.0316 0.8065 164 P 0.1006 0.0157 0.8837 165 P 0.0741 0.0160 0.9099 166 P 0.0504 0.1282 0.8214 167 S 0.0564 0.1503 0.7934 168 S 0.1505 0.1849 0.6646 169 V 0.2662 0.1796 0.5542 170 N 0.3231 0.1687 0.5082 171 T 0.1856 0.1961 0.6183 172 G 0.0814 0.2630 0.6557 173 G 0.1207 0.3533 0.5259 174 I 0.1049 0.6745 0.2206 175 T 0.0807 0.7329 0.1865 176 E 0.0906 0.7746 0.1349 177 I 0.1073 0.7780 0.1147 178 M 0.1616 0.6688 0.1696 179 A 0.1002 0.5553 0.3444 180 E 0.0248 0.2863 0.6889 181 G 0.0346 0.0994 0.8660 182 G 0.0734 0.0730 0.8535 183 E 0.2934 0.1558 0.5507 184 L 0.3116 0.4355 0.2529 185 E 0.1493 0.6866 0.1642 186 F 0.0984 0.8029 0.0987 187 V 0.0442 0.8749 0.0809 188 K 0.0212 0.9158 0.0631 189 R 0.0140 0.9198 0.0662 190 I 0.0093 0.9097 0.0810 191 I 0.0081 0.9040 0.0879 192 H 0.0060 0.9115 0.0824 193 D 0.0061 0.9003 0.0937 194 S 0.0063 0.9090 0.0846 195 L 0.0070 0.9090 0.0841 196 Q 0.0079 0.8652 0.1269 197 L 0.0130 0.7619 0.2251 198 G 0.0285 0.5903 0.3812 199 K 0.0386 0.5247 0.4367 200 R 0.0547 0.5451 0.4002 201 L 0.1294 0.3628 0.5077 202 R 0.2925 0.1964 0.5111 203 W 0.6030 0.1390 0.2580 204 Y 0.7289 0.1193 0.1517 205 S 0.7408 0.1189 0.1403 206 C 0.6925 0.1511 0.1563 207 M 0.6720 0.1501 0.1779 208 L 0.4545 0.1955 0.3501 209 G 0.1990 0.1437 0.6573 210 K 0.1389 0.2308 0.6303 211 A 0.0896 0.3296 0.5808 212 C 0.0626 0.2980 0.6394 213 S 0.0567 0.2537 0.6896 214 L 0.0341 0.5325 0.4335 215 A 0.0115 0.8839 0.1046 216 P 0.0065 0.9434 0.0501 217 L 0.0058 0.9523 0.0419 218 K 0.0047 0.9595 0.0358 219 E 0.0047 0.9595 0.0358 220 E 0.0047 0.9593 0.0360 221 L 0.0048 0.9562 0.0390 222 R 0.0050 0.9438 0.0511 223 I 0.0071 0.8765 0.1165 224 Q 0.0428 0.4297 0.5274 225 G 0.0377 0.0269 0.9355 226 V 0.0648 0.0116 0.9235 227 P 0.0925 0.0732 0.8343 228 K 0.3541 0.0720 0.5739 229 V 0.6944 0.0170 0.2887 230 T 0.8588 0.0105 0.1308 231 Y 0.8586 0.0161 0.1253 232 T 0.7633 0.0297 0.2070 233 E 0.6668 0.0500 0.2832 234 F 0.3829 0.1418 0.4753 235 C 0.2450 0.1850 0.5700 236 Q 0.1005 0.1174 0.7821 237 G 0.0710 0.0635 0.8655 238 R 0.2508 0.0516 0.6976 239 T 0.5339 0.0455 0.4206 240 M 0.7740 0.0339 0.1921 241 R 0.8726 0.0278 0.0996 242 W 0.9011 0.0236 0.0753 243 A 0.8896 0.0313 0.0791 244 L 0.8580 0.0327 0.1093 245 A 0.7733 0.0554 0.1713 246 W 0.6092 0.1064 0.2844 247 S 0.4029 0.1656 0.4315 248 F 0.2186 0.1925 0.5889 249 Y 0.1420 0.0755 0.7824 250 D 0.0651 0.0290 0.9059