# This file is the result of combining several RDB files, specifically # T0250.t04.dssp-ebghstl.rdb (weight 1.53986) # T0250.t04.stride-ebghtl.rdb (weight 1.24869) # T0250.t04.str2.rdb (weight 1.54758) # T0250.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 T0250.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0250 # 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 T0250.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 15.9438 # # ============================================ # Comments from T0250.t04.stride-ebghtl.rdb # ============================================ # TARGET T0250 # 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 T0250.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 15.9438 # # ============================================ # Comments from T0250.t04.str2.rdb # ============================================ # TARGET T0250 # 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 T0250.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 15.9438 # # ============================================ # Comments from T0250.t04.alpha.rdb # ============================================ # TARGET T0250 # 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 T0250.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 15.9438 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0866 0.0396 0.8738 2 T 0.1090 0.0982 0.7929 3 N 0.1775 0.1264 0.6961 4 V 0.5055 0.2048 0.2898 5 L 0.6565 0.2196 0.1239 6 Y 0.6084 0.2615 0.1301 7 Q 0.3786 0.4292 0.1922 8 H 0.1132 0.6013 0.2855 9 G 0.0747 0.5964 0.3288 10 T 0.0239 0.8388 0.1373 11 L 0.0050 0.9482 0.0468 12 G 0.0047 0.9568 0.0385 13 T 0.0047 0.9552 0.0401 14 L 0.0048 0.9481 0.0471 15 M 0.0055 0.9282 0.0663 16 A 0.0141 0.8254 0.1605 17 G 0.0135 0.6874 0.2990 18 L 0.0476 0.6018 0.3506 19 L 0.1180 0.4903 0.3917 20 E 0.0808 0.3241 0.5952 21 G 0.0577 0.1354 0.8069 22 T 0.1759 0.1183 0.7059 23 A 0.4208 0.0453 0.5339 24 T 0.3524 0.0680 0.5796 25 I 0.0057 0.9505 0.0438 26 N 0.0050 0.9578 0.0372 27 E 0.0047 0.9588 0.0365 28 L 0.0060 0.9550 0.0390 29 L 0.0068 0.9322 0.0609 30 E 0.0108 0.8218 0.1674 31 H 0.0508 0.3217 0.6275 32 G 0.0439 0.0575 0.8986 33 N 0.0857 0.0474 0.8668 34 L 0.2908 0.0753 0.6339 35 G 0.4570 0.0703 0.4728 36 I 0.5467 0.0743 0.3790 37 A 0.5314 0.0570 0.4116 38 T 0.4398 0.0526 0.5076 39 L 0.3418 0.0760 0.5822 40 T 0.2192 0.1022 0.6785 41 G 0.1588 0.1084 0.7328 42 S 0.2050 0.0987 0.6963 43 D 0.1872 0.0348 0.7780 44 G 0.3693 0.0292 0.6015 45 E 0.7068 0.0063 0.2869 46 V 0.9149 0.0033 0.0817 47 I 0.9238 0.0037 0.0726 48 F 0.9139 0.0047 0.0813 49 L 0.8258 0.0160 0.1583 50 D 0.3208 0.0192 0.6599 51 G 0.1383 0.0351 0.8267 52 K 0.6802 0.0327 0.2871 53 A 0.8475 0.0215 0.1310 54 Y 0.7875 0.0253 0.1872 55 H 0.8310 0.0145 0.1545 56 A 0.7393 0.0282 0.2325 57 N 0.3508 0.0483 0.6009 58 E 0.1330 0.1179 0.7490 59 H 0.0973 0.0364 0.8663 60 K 0.1775 0.0279 0.7946 61 E 0.5565 0.0115 0.4321 62 F 0.8937 0.0056 0.1007 63 I 0.8863 0.0065 0.1073 64 E 0.8984 0.0044 0.0972 65 L 0.6814 0.0089 0.3097 66 K 0.2712 0.0361 0.6927 67 G 0.0457 0.1182 0.8360 68 D 0.0508 0.1207 0.8285 69 E 0.2611 0.0861 0.6528 70 K 0.4508 0.0251 0.5240 71 V 0.3826 0.0106 0.6068 72 P 0.3668 0.0270 0.6062 73 Y 0.7021 0.0298 0.2681 74 A 0.8329 0.0137 0.1534 75 S 0.8850 0.0092 0.1058 76 I 0.8745 0.0108 0.1147 77 T 0.7356 0.0387 0.2257 78 N 0.5668 0.0302 0.4029 79 F 0.3679 0.0411 0.5910 80 K 0.3501 0.0411 0.6088 81 A 0.2511 0.1491 0.5998 82 S 0.2322 0.1678 0.6000 83 K 0.3768 0.1026 0.5206 84 T 0.5230 0.0331 0.4439 85 F 0.5575 0.0129 0.4296 86 P 0.4121 0.0161 0.5718 87 L 0.2074 0.1311 0.6615 88 Q 0.1461 0.1898 0.6642 89 Q 0.1478 0.1398 0.7124 90 L 0.1499 0.0383 0.8118 91 S 0.0750 0.0235 0.9015 92 Q 0.0053 0.9237 0.0710 93 D 0.0047 0.9541 0.0412 94 D 0.0048 0.9567 0.0385 95 V 0.0047 0.9589 0.0364 96 F 0.0047 0.9600 0.0353 97 A 0.0047 0.9599 0.0355 98 Q 0.0047 0.9581 0.0372 99 I 0.0048 0.9459 0.0493 100 K 0.0057 0.9282 0.0662 101 N 0.0068 0.8544 0.1388 102 E 0.0117 0.7903 0.1980 103 M 0.0286 0.6218 0.3496 104 L 0.0301 0.4990 0.4708 105 S 0.0301 0.5328 0.4371 106 E 0.0328 0.5138 0.4534 107 N 0.1030 0.2593 0.6378 108 L 0.2895 0.1907 0.5198 109 F 0.5984 0.0998 0.3018 110 S 0.6886 0.0815 0.2299 111 A 0.8546 0.0389 0.1065 112 V 0.8910 0.0205 0.0885 113 K 0.9061 0.0120 0.0819 114 I 0.8577 0.0264 0.1159 115 Y 0.6881 0.0406 0.2713 116 G 0.6883 0.0195 0.2921 117 T 0.7232 0.0216 0.2552 118 F 0.6565 0.0361 0.3074 119 K 0.5404 0.0719 0.3877 120 H 0.7165 0.0295 0.2540 121 M 0.8272 0.0087 0.1641 122 H 0.8930 0.0062 0.1008 123 V 0.9022 0.0062 0.0917 124 R 0.8599 0.0107 0.1293 125 M 0.7720 0.0118 0.2162 126 M 0.3279 0.0214 0.6507 127 P 0.1268 0.1409 0.7323 128 A 0.0697 0.1546 0.7756 129 Q 0.1186 0.0988 0.7826 130 Q 0.0856 0.0309 0.8835 131 P 0.0721 0.0369 0.8910 132 P 0.0806 0.1255 0.7938 133 Y 0.0682 0.3309 0.6009 134 T 0.0380 0.6726 0.2894 135 R 0.0334 0.7856 0.1811 136 L 0.0081 0.9211 0.0708 137 I 0.0061 0.9417 0.0523 138 D 0.0051 0.9469 0.0480 139 S 0.0058 0.9397 0.0545 140 A 0.0066 0.9053 0.0880 141 R 0.0100 0.7902 0.1998 142 R 0.0147 0.5235 0.4618 143 Q 0.0643 0.0543 0.8814 144 P 0.0571 0.0798 0.8631 145 E 0.0734 0.3560 0.5705 146 E 0.1245 0.3861 0.4895 147 K 0.1866 0.3510 0.4623 148 R 0.1586 0.3280 0.5134 149 Q 0.1335 0.2194 0.6471 150 D 0.1936 0.0852 0.7212 151 I 0.4415 0.0346 0.5238 152 R 0.4676 0.0383 0.4941 153 G 0.7946 0.0106 0.1948 154 A 0.8588 0.0056 0.1356 155 I 0.9136 0.0033 0.0831 156 V 0.8603 0.0197 0.1200 157 G 0.8160 0.0131 0.1709 158 F 0.6785 0.0284 0.2931 159 F 0.4756 0.0354 0.4890 160 T 0.1822 0.0354 0.7824 161 P 0.0591 0.4990 0.4419 162 E 0.0397 0.6320 0.3283 163 L 0.0571 0.6593 0.2836 164 F 0.1158 0.4701 0.4141 165 H 0.0704 0.3281 0.6015 166 G 0.0797 0.1722 0.7481 167 V 0.1647 0.1361 0.6992 168 G 0.1763 0.0993 0.7244 169 S 0.1605 0.1183 0.7212 170 A 0.1381 0.1539 0.7080 171 G 0.2332 0.1240 0.6428 172 F 0.4128 0.1142 0.4730 173 H 0.5689 0.1006 0.3305 174 I 0.6246 0.1076 0.2678 175 H 0.6480 0.0902 0.2618 176 F 0.6459 0.0699 0.2842 177 A 0.4971 0.0624 0.4404 178 D 0.2178 0.0627 0.7195 179 D 0.0539 0.3190 0.6271 180 E 0.0577 0.3243 0.6179 181 R 0.1134 0.2894 0.5972 182 A 0.1673 0.1744 0.6583 183 Y 0.2104 0.1154 0.6742 184 G 0.2295 0.0669 0.7037 185 G 0.3838 0.0477 0.5686 186 H 0.6573 0.0257 0.3170 187 V 0.7181 0.0479 0.2340 188 L 0.7650 0.0364 0.1986 189 D 0.8009 0.0245 0.1746 190 F 0.8374 0.0156 0.1470 191 E 0.8680 0.0101 0.1219 192 V 0.8498 0.0165 0.1337 193 D 0.6438 0.0509 0.3053 194 D 0.5253 0.0302 0.4445 195 V 0.8826 0.0047 0.1128 196 V 0.9260 0.0034 0.0706 197 V 0.9192 0.0034 0.0774 198 E 0.9066 0.0038 0.0897 199 I 0.8577 0.0071 0.1352 200 Q 0.6065 0.0345 0.3590 201 N 0.5134 0.0514 0.4352 202 F 0.3352 0.1880 0.4767 203 E 0.2856 0.2405 0.4739 204 T 0.4029 0.2114 0.3857 205 F 0.5767 0.1050 0.3183 206 Q 0.6913 0.0762 0.2325 207 Q 0.7571 0.0557 0.1871 208 H 0.6981 0.0599 0.2420 209 F 0.4039 0.0210 0.5751 210 P 0.2038 0.0255 0.7707 211 V 0.1157 0.0893 0.7949 212 N 0.0794 0.0728 0.8478 213 N 0.0816 0.0766 0.8418 214 E 0.0079 0.8219 0.1703 215 T 0.0121 0.8542 0.1336 216 F 0.0269 0.8360 0.1371 217 V 0.0604 0.7566 0.1830 218 K 0.0693 0.6588 0.2720 219 A 0.0991 0.4254 0.4755 220 K 0.1274 0.1554 0.7172 221 I 0.1544 0.0461 0.7995 222 D 0.1037 0.0295 0.8667 223 Y 0.0131 0.8244 0.1624 224 K 0.0067 0.8689 0.1244 225 D 0.0140 0.8462 0.1399 226 V 0.0074 0.8926 0.1000 227 A 0.0051 0.9381 0.0568 228 E 0.0048 0.9460 0.0492 229 E 0.0051 0.9418 0.0531 230 I 0.0059 0.9376 0.0565 231 R 0.0067 0.9179 0.0753 232 E 0.0096 0.8583 0.1321 233 A 0.0179 0.7254 0.2566 234 E 0.0314 0.4710 0.4977