# This file is the result of combining several RDB files, specifically # T0640.t04.dssp-ebghstl.rdb (weight 1.53986) # T0640.t04.stride-ebghtl.rdb (weight 1.24869) # T0640.t04.str2.rdb (weight 1.54758) # T0640.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 T0640.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0640 # 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 T0640.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 22.1141 # # ============================================ # Comments from T0640.t04.stride-ebghtl.rdb # ============================================ # TARGET T0640 # 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 T0640.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 22.1141 # # ============================================ # Comments from T0640.t04.str2.rdb # ============================================ # TARGET T0640 # 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 T0640.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 22.1141 # # ============================================ # Comments from T0640.t04.alpha.rdb # ============================================ # TARGET T0640 # 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 T0640.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 22.1141 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0983 0.0178 0.8839 2 S 0.1285 0.0322 0.8394 3 L 0.0614 0.3223 0.6163 4 E 0.0469 0.3481 0.6050 5 K 0.0541 0.2767 0.6692 6 Q 0.0991 0.0780 0.8229 7 K 0.1512 0.0636 0.7851 8 G 0.3054 0.0351 0.6595 9 L 0.8022 0.0064 0.1914 10 A 0.9199 0.0037 0.0764 11 I 0.9278 0.0034 0.0688 12 I 0.8978 0.0047 0.0976 13 T 0.6034 0.0358 0.3608 14 G 0.1671 0.0396 0.7934 15 A 0.0821 0.1598 0.7582 16 S 0.0888 0.2431 0.6681 17 Q 0.0504 0.2601 0.6895 18 G 0.0319 0.5754 0.3927 19 I 0.0092 0.8989 0.0919 20 G 0.0065 0.9347 0.0587 21 A 0.0047 0.9597 0.0356 22 V 0.0047 0.9611 0.0342 23 I 0.0047 0.9604 0.0349 24 A 0.0047 0.9606 0.0347 25 A 0.0047 0.9599 0.0355 26 G 0.0047 0.9571 0.0383 27 L 0.0048 0.9533 0.0419 28 A 0.0050 0.9336 0.0614 29 T 0.0065 0.8553 0.1382 30 D 0.0363 0.3317 0.6320 31 G 0.0377 0.0257 0.9366 32 Y 0.1396 0.0073 0.8531 33 R 0.7645 0.0063 0.2292 34 V 0.9283 0.0032 0.0685 35 V 0.9310 0.0034 0.0656 36 L 0.9291 0.0033 0.0676 37 I 0.8695 0.0091 0.1215 38 A 0.4605 0.0147 0.5247 39 R 0.1065 0.0503 0.8432 40 S 0.0761 0.0298 0.8941 41 K 0.0078 0.8185 0.1737 42 Q 0.0066 0.8864 0.1070 43 N 0.0073 0.8952 0.0976 44 L 0.0048 0.9498 0.0455 45 E 0.0047 0.9573 0.0380 46 K 0.0048 0.9560 0.0393 47 V 0.0048 0.9548 0.0404 48 H 0.0047 0.9590 0.0364 49 D 0.0047 0.9593 0.0361 50 E 0.0047 0.9589 0.0364 51 I 0.0047 0.9572 0.0380 52 M 0.0050 0.9463 0.0487 53 R 0.0062 0.9075 0.0863 54 S 0.0325 0.5258 0.4418 55 N 0.0359 0.0929 0.8713 56 K 0.0503 0.0616 0.8881 57 H 0.1349 0.0882 0.7768 58 V 0.1853 0.1029 0.7119 59 Q 0.1582 0.0791 0.7627 60 E 0.2553 0.0293 0.7155 61 P 0.4636 0.0250 0.5114 62 I 0.7420 0.0165 0.2415 63 V 0.8052 0.0119 0.1829 64 L 0.7450 0.0130 0.2420 65 P 0.6549 0.0175 0.3276 66 L 0.4203 0.0311 0.5486 67 D 0.3043 0.0267 0.6690 68 I 0.1208 0.1766 0.7027 69 T 0.0914 0.1764 0.7322 70 D 0.0917 0.1477 0.7605 71 C 0.0135 0.7988 0.1877 72 T 0.0082 0.8900 0.1018 73 K 0.0109 0.8993 0.0898 74 A 0.0068 0.9239 0.0693 75 D 0.0066 0.9402 0.0532 76 T 0.0050 0.9476 0.0473 77 E 0.0050 0.9482 0.0467 78 I 0.0047 0.9586 0.0367 79 K 0.0047 0.9606 0.0348 80 D 0.0047 0.9598 0.0355 81 I 0.0047 0.9582 0.0371 82 H 0.0049 0.9540 0.0411 83 Q 0.0054 0.9301 0.0645 84 K 0.0118 0.8476 0.1406 85 Y 0.0493 0.5791 0.3716 86 G 0.0362 0.0996 0.8642 87 A 0.0920 0.0899 0.8181 88 V 0.4002 0.0331 0.5667 89 D 0.5152 0.0807 0.4041 90 I 0.9180 0.0092 0.0727 91 L 0.9232 0.0096 0.0673 92 V 0.9093 0.0156 0.0750 93 N 0.7806 0.0436 0.1758 94 A 0.3905 0.0566 0.5529 95 A 0.2774 0.1225 0.6000 96 A 0.2836 0.1945 0.5220 97 M 0.3931 0.1846 0.4223 98 F 0.3689 0.1671 0.4640 99 M 0.2669 0.1566 0.5765 100 D 0.1061 0.1346 0.7594 101 G 0.0769 0.1256 0.7975 102 S 0.1185 0.1721 0.7094 103 L 0.1476 0.1652 0.6872 104 S 0.1118 0.0881 0.8001 105 E 0.0887 0.0224 0.8889 106 P 0.0689 0.0274 0.9037 107 V 0.0190 0.7186 0.2624 108 D 0.0138 0.7633 0.2229 109 N 0.0140 0.7953 0.1907 110 F 0.0155 0.8360 0.1485 111 R 0.0219 0.8220 0.1561 112 K 0.0680 0.8030 0.1289 113 I 0.1253 0.7714 0.1033 114 M 0.1628 0.7427 0.0945 115 E 0.1371 0.7577 0.1052 116 I 0.1655 0.7311 0.1034 117 N 0.1559 0.6829 0.1611 118 V 0.1820 0.6639 0.1541 119 I 0.1080 0.7559 0.1361 120 A 0.1194 0.7434 0.1373 121 Q 0.0746 0.8265 0.0989 122 Y 0.0512 0.8722 0.0765 123 G 0.0273 0.9006 0.0721 124 I 0.0163 0.9124 0.0713 125 L 0.0085 0.9321 0.0594 126 K 0.0053 0.9504 0.0443 127 T 0.0051 0.9485 0.0464 128 V 0.0052 0.9423 0.0525 129 T 0.0050 0.9477 0.0473 130 E 0.0048 0.9529 0.0423 131 I 0.0057 0.9446 0.0497 132 M 0.0096 0.9227 0.0677 133 K 0.0172 0.8904 0.0924 134 V 0.0240 0.8298 0.1462 135 Q 0.0514 0.5658 0.3827 136 K 0.0414 0.2290 0.7297 137 N 0.0805 0.0422 0.8773 138 G 0.1905 0.0201 0.7894 139 Y 0.6844 0.0069 0.3087 140 I 0.9241 0.0032 0.0728 141 F 0.9251 0.0041 0.0708 142 N 0.9107 0.0064 0.0828 143 V 0.8136 0.0223 0.1640 144 A 0.5357 0.0539 0.4104 145 S 0.3176 0.1109 0.5715 146 R 0.2165 0.2977 0.4859 147 A 0.2204 0.4037 0.3760 148 A 0.2084 0.4506 0.3409 149 K 0.2511 0.4221 0.3268 150 Y 0.2427 0.3336 0.4237 151 G 0.1677 0.2106 0.6217 152 F 0.1226 0.1319 0.7455 153 A 0.0555 0.2418 0.7027 154 D 0.0463 0.2477 0.7060 155 G 0.0766 0.3494 0.5740 156 G 0.1264 0.4923 0.3813 157 I 0.1460 0.6741 0.1798 158 Y 0.0876 0.7959 0.1165 159 G 0.0481 0.8566 0.0953 160 S 0.0289 0.8796 0.0914 161 T 0.0146 0.9056 0.0798 162 K 0.0059 0.9443 0.0498 163 F 0.0050 0.9521 0.0429 164 A 0.0047 0.9554 0.0399 165 L 0.0047 0.9566 0.0386 166 L 0.0048 0.9544 0.0408 167 G 0.0049 0.9458 0.0493 168 L 0.0052 0.9307 0.0640 169 A 0.0058 0.9282 0.0661 170 E 0.0047 0.9580 0.0373 171 S 0.0048 0.9567 0.0385 172 L 0.0050 0.9514 0.0436 173 Y 0.0050 0.9447 0.0503 174 R 0.0052 0.9264 0.0684 175 E 0.0072 0.8774 0.1154 176 L 0.0176 0.7754 0.2071 177 A 0.0292 0.5625 0.4083 178 P 0.0225 0.5626 0.4149 179 L 0.0475 0.2675 0.6850 180 G 0.0728 0.0245 0.9027 181 I 0.4601 0.0068 0.5330 182 R 0.8681 0.0048 0.1271 183 V 0.9082 0.0040 0.0878 184 T 0.8898 0.0059 0.1044 185 T 0.8507 0.0057 0.1436 186 L 0.6633 0.0101 0.3266 187 C 0.4324 0.0185 0.5491 188 P 0.1682 0.1082 0.7236 189 G 0.1317 0.1153 0.7529 190 W 0.2748 0.2187 0.5065 191 V 0.3066 0.1927 0.5007 192 N 0.2382 0.1696 0.5922 193 T 0.1071 0.3182 0.5747 194 D 0.0499 0.6392 0.3108 195 M 0.0330 0.7531 0.2139 196 A 0.0442 0.7340 0.2218 197 K 0.0357 0.6951 0.2692 198 K 0.0518 0.5561 0.3921 199 A 0.0785 0.2801 0.6414 200 G 0.0556 0.1111 0.8333 201 T 0.0679 0.1027 0.8294 202 P 0.0987 0.1615 0.7399 203 F 0.1114 0.1913 0.6973 204 K 0.1013 0.1749 0.7238 205 D 0.0747 0.1287 0.7967 206 E 0.0550 0.1075 0.8375 207 E 0.1206 0.0873 0.7922 208 M 0.2221 0.0660 0.7119 209 I 0.2376 0.0285 0.7340 210 Q 0.1197 0.0238 0.8566 211 P 0.0090 0.8744 0.1166 212 D 0.0058 0.9270 0.0672 213 D 0.0050 0.9448 0.0502 214 L 0.0050 0.9520 0.0430 215 L 0.0047 0.9574 0.0379 216 N 0.0047 0.9578 0.0375 217 T 0.0047 0.9577 0.0376 218 I 0.0056 0.9553 0.0391 219 R 0.0051 0.9527 0.0422 220 C 0.0053 0.9343 0.0604 221 L 0.0090 0.8771 0.1138 222 L 0.0371 0.6701 0.2928 223 N 0.0820 0.2382 0.6799 224 L 0.0247 0.4213 0.5541 225 S 0.0271 0.4195 0.5534 226 E 0.0343 0.4807 0.4850 227 N 0.0608 0.3706 0.5686 228 V 0.1247 0.2664 0.6088 229 C 0.3070 0.2088 0.4843 230 I 0.4626 0.1315 0.4059 231 K 0.3161 0.2011 0.4828 232 D 0.2392 0.1791 0.5817 233 I 0.5007 0.1626 0.3366 234 V 0.6289 0.1240 0.2471 235 F 0.5010 0.1031 0.3959 236 E 0.5067 0.1003 0.3930 237 M 0.3919 0.1494 0.4587 238 K 0.2721 0.1404 0.5875 239 K 0.2878 0.1353 0.5769 240 S 0.3800 0.1021 0.5179 241 I 0.4095 0.0601 0.5304 242 I 0.4301 0.0550 0.5149 243 E 0.2975 0.0759 0.6266 244 G 0.1585 0.0717 0.7698 245 H 0.2203 0.1029 0.6768 246 H 0.3980 0.1146 0.4875 247 H 0.4137 0.1027 0.4836 248 H 0.3076 0.0845 0.6079 249 H 0.1713 0.0511 0.7776 250 H 0.0698 0.0315 0.8987