# This file is the result of combining several RDB files, specifically # T0301.t06.dssp-ebghstl.rdb (weight 1.53986) # T0301.t06.stride-ebghtl.rdb (weight 1.24869) # T0301.t06.str2.rdb (weight 1.54758) # T0301.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 T0301.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0301 # 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 T0301.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 15.2178 # # ============================================ # Comments from T0301.t06.stride-ebghtl.rdb # ============================================ # TARGET T0301 # 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 T0301.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 15.2178 # # ============================================ # Comments from T0301.t06.str2.rdb # ============================================ # TARGET T0301 # 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 T0301.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 15.2178 # # ============================================ # Comments from T0301.t06.alpha.rdb # ============================================ # TARGET T0301 # 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 T0301.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 15.2178 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.0596 0.0555 0.8850 2 G 0.1127 0.0419 0.8454 3 V 0.2131 0.0280 0.7589 4 T 0.2122 0.0290 0.7588 5 F 0.1378 0.0640 0.7982 6 P 0.1033 0.0970 0.7996 7 A 0.1323 0.1351 0.7325 8 A 0.2895 0.0700 0.6405 9 E 0.5179 0.0378 0.4443 10 I 0.8263 0.0115 0.1622 11 V 0.8792 0.0093 0.1114 12 L 0.8814 0.0109 0.1077 13 E 0.8613 0.0146 0.1241 14 F 0.7943 0.0151 0.1905 15 L 0.5586 0.0191 0.4223 16 D 0.2741 0.0098 0.7161 17 P 0.0801 0.0887 0.8312 18 S 0.0496 0.0754 0.8750 19 D 0.0449 0.1223 0.8327 20 D 0.0597 0.0776 0.8627 21 G 0.0776 0.0520 0.8704 22 E 0.0756 0.1563 0.7680 23 D 0.1926 0.1400 0.6674 24 G 0.1726 0.1498 0.6777 25 G 0.1548 0.1305 0.7146 26 A 0.3469 0.0764 0.5767 27 I 0.6077 0.0549 0.3373 28 F 0.2944 0.0388 0.6668 29 P 0.1693 0.0557 0.7750 30 T 0.1387 0.0472 0.8141 31 G 0.0853 0.0723 0.8424 32 N 0.1359 0.0596 0.8045 33 L 0.3418 0.1143 0.5439 34 V 0.4797 0.0847 0.4357 35 D 0.4965 0.1076 0.3959 36 D 0.7254 0.0480 0.2266 37 L 0.8462 0.0150 0.1388 38 E 0.8300 0.0092 0.1608 39 V 0.5322 0.0120 0.4558 40 P 0.1308 0.0562 0.8130 41 G 0.0782 0.0416 0.8802 42 V 0.1862 0.0533 0.7605 43 G 0.1652 0.0448 0.7901 44 T 0.4018 0.0315 0.5667 45 F 0.6444 0.0069 0.3488 46 K 0.7691 0.0060 0.2250 47 A 0.8933 0.0080 0.0988 48 T 0.9035 0.0108 0.0858 49 M 0.8876 0.0181 0.0944 50 I 0.7826 0.0643 0.1530 51 N 0.5096 0.1124 0.3780 52 A 0.1801 0.1370 0.6829 53 G 0.1542 0.1045 0.7413 54 I 0.1633 0.0716 0.7652 55 P 0.2609 0.0719 0.6673 56 T 0.6941 0.0640 0.2419 57 V 0.8841 0.0212 0.0947 58 F 0.9064 0.0136 0.0801 59 V 0.8346 0.0244 0.1410 60 N 0.5561 0.0133 0.4306 61 A 0.0271 0.7369 0.2361 62 E 0.0107 0.8044 0.1849 63 E 0.0131 0.8229 0.1640 64 I 0.0807 0.5041 0.4152 65 G 0.0632 0.1279 0.8089 66 Y 0.1281 0.1404 0.7314 67 R 0.1228 0.1518 0.7255 68 G 0.0788 0.1407 0.7805 69 T 0.0924 0.3275 0.5800 70 E 0.1495 0.4259 0.4245 71 L 0.0849 0.5578 0.3572 72 R 0.0166 0.8482 0.1352 73 E 0.0098 0.8646 0.1256 74 E 0.0099 0.8396 0.1505 75 I 0.0358 0.6291 0.3351 76 N 0.0405 0.3356 0.6239 77 G 0.0357 0.1595 0.8048 78 D 0.0844 0.0273 0.8883 79 P 0.0051 0.9257 0.0692 80 Q 0.0049 0.9418 0.0533 81 Q 0.0049 0.9497 0.0454 82 L 0.0047 0.9566 0.0387 83 A 0.0047 0.9565 0.0387 84 R 0.0048 0.9551 0.0402 85 F 0.0047 0.9570 0.0383 86 E 0.0047 0.9604 0.0349 87 R 0.0047 0.9608 0.0346 88 I 0.0047 0.9597 0.0357 89 R 0.0047 0.9597 0.0356 90 V 0.0047 0.9593 0.0359 91 A 0.0048 0.9554 0.0397 92 G 0.0047 0.9548 0.0405 93 A 0.0048 0.9545 0.0407 94 L 0.0060 0.9488 0.0451 95 R 0.0069 0.9216 0.0715 96 M 0.0453 0.6059 0.3487 97 G 0.0407 0.1124 0.8469 98 L 0.0794 0.1387 0.7820 99 I 0.1240 0.0891 0.7869 100 K 0.0762 0.0674 0.8564 101 T 0.0834 0.0285 0.8881 102 P 0.0079 0.8348 0.1573 103 E 0.0060 0.8683 0.1258 104 E 0.0087 0.8751 0.1162 105 A 0.0224 0.8071 0.1705 106 A 0.0273 0.6616 0.3111 107 T 0.0417 0.4442 0.5142 108 R 0.0800 0.1426 0.7774 109 Q 0.0821 0.0921 0.8257 110 H 0.1334 0.0491 0.8175 111 T 0.1887 0.0195 0.7919 112 P 0.2300 0.0165 0.7535 113 K 0.6008 0.0174 0.3818 114 I 0.8460 0.0095 0.1445 115 A 0.8904 0.0094 0.1003 116 F 0.9089 0.0063 0.0847 117 V 0.8155 0.0131 0.1713 118 A 0.4653 0.0149 0.5198 119 P 0.1832 0.0167 0.8001 120 P 0.0981 0.1236 0.7783 121 R 0.0698 0.3026 0.6276 122 D 0.1012 0.3499 0.5488 123 Y 0.1503 0.4025 0.4472 124 R 0.2498 0.3102 0.4401 125 T 0.2262 0.2655 0.5083 126 A 0.1715 0.2370 0.5915 127 S 0.0984 0.1419 0.7597 128 G 0.1235 0.1123 0.7642 129 K 0.4371 0.1182 0.4447 130 L 0.6365 0.1121 0.2513 131 V 0.4022 0.1372 0.4606 132 A 0.3112 0.1258 0.5629 133 A 0.0979 0.2741 0.6279 134 G 0.0582 0.1471 0.7947 135 D 0.1258 0.1143 0.7599 136 I 0.2616 0.0605 0.6779 137 D 0.3463 0.0774 0.5764 138 L 0.7237 0.0913 0.1850 139 L 0.8076 0.0921 0.1003 140 V 0.7946 0.1066 0.0988 141 R 0.7436 0.1328 0.1236 142 A 0.6803 0.1337 0.1860 143 L 0.4760 0.1433 0.3807 144 S 0.2796 0.0967 0.6237 145 M 0.0906 0.2170 0.6923 146 G 0.0474 0.2014 0.7512 147 K 0.0928 0.1910 0.7163 148 L 0.1344 0.2427 0.6229 149 H 0.1011 0.3320 0.5669 150 H 0.0428 0.5690 0.3882 151 A 0.0531 0.6176 0.3293 152 M 0.0559 0.6380 0.3061 153 M 0.0314 0.7465 0.2221 154 G 0.0188 0.8266 0.1547 155 T 0.0086 0.9196 0.0719 156 A 0.0051 0.9538 0.0412 157 A 0.0047 0.9588 0.0365 158 V 0.0047 0.9596 0.0357 159 A 0.0047 0.9590 0.0363 160 I 0.0048 0.9579 0.0373 161 G 0.0050 0.9506 0.0444 162 T 0.0058 0.9366 0.0575 163 A 0.0073 0.8996 0.0931 164 A 0.0182 0.7905 0.1913 165 A 0.0443 0.6346 0.3210 166 I 0.0783 0.1808 0.7409 167 P 0.0331 0.1942 0.7728 168 G 0.0478 0.1694 0.7828 169 T 0.1425 0.3886 0.4689 170 L 0.0793 0.7594 0.1613 171 V 0.0621 0.7984 0.1395 172 N 0.0762 0.7464 0.1774 173 L 0.0638 0.7469 0.1892 174 A 0.0736 0.6127 0.3137 175 A 0.0758 0.4202 0.5041 176 G 0.0624 0.1774 0.7602 177 G 0.0623 0.0747 0.8631 178 G 0.0721 0.0553 0.8726 179 E 0.1424 0.0669 0.7907 180 R 0.2151 0.0819 0.7030 181 S 0.3193 0.0557 0.6250 182 A 0.7355 0.0184 0.2461 183 V 0.8705 0.0061 0.1234 184 R 0.9009 0.0053 0.0939 185 F 0.8341 0.0122 0.1537 186 G 0.6265 0.0186 0.3549 187 H 0.3150 0.0183 0.6667 188 P 0.1361 0.0757 0.7882 189 S 0.1713 0.0525 0.7762 190 G 0.4376 0.0340 0.5284 191 T 0.7744 0.0104 0.2152 192 L 0.9005 0.0049 0.0946 193 R 0.9130 0.0046 0.0824 194 V 0.9088 0.0058 0.0855 195 G 0.8888 0.0082 0.1030 196 A 0.8812 0.0081 0.1107 197 E 0.8871 0.0091 0.1038 198 A 0.8707 0.0135 0.1158 199 S 0.8088 0.0186 0.1726 200 Q 0.6810 0.0601 0.2588 201 A 0.4145 0.0847 0.5008 202 N 0.0923 0.0458 0.8618 203 G 0.0735 0.0400 0.8865 204 E 0.3921 0.0313 0.5766 205 W 0.7473 0.0092 0.2435 206 T 0.8460 0.0112 0.1428 207 V 0.8751 0.0126 0.1123 208 T 0.7840 0.0486 0.1674 209 K 0.8086 0.0559 0.1355 210 A 0.7654 0.1174 0.1172 211 I 0.7279 0.1707 0.1014 212 M 0.5824 0.3058 0.1118 213 S 0.3850 0.4528 0.1622 214 R 0.1786 0.5855 0.2360 215 S 0.1184 0.6628 0.2188 216 A 0.0475 0.8457 0.1068 217 R 0.0644 0.8364 0.0992 218 I 0.0848 0.8220 0.0932 219 L 0.1496 0.7113 0.1390 220 M 0.2552 0.5239 0.2209 221 E 0.2947 0.3071 0.3982 222 G 0.3722 0.1894 0.4383 223 W 0.6460 0.1163 0.2377 224 V 0.8019 0.0375 0.1605 225 R 0.7572 0.0235 0.2193 226 V 0.4886 0.0134 0.4980 227 P 0.2081 0.0339 0.7580 228 G 0.0630 0.2119 0.7251 229 D 0.0665 0.2453 0.6882 230 A 0.0753 0.2480 0.6767 231 F 0.0582 0.0472 0.8946