# This file is the result of combining several RDB files, specifically # T0448.t04.dssp-ebghstl.rdb (weight 1.53986) # T0448.t04.stride-ebghtl.rdb (weight 1.24869) # T0448.t04.str2.rdb (weight 1.54758) # T0448.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 T0448.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0448 # 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 T0448.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 2322 # # ============================================ # Comments from T0448.t04.stride-ebghtl.rdb # ============================================ # TARGET T0448 # 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 T0448.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 2322 # # ============================================ # Comments from T0448.t04.str2.rdb # ============================================ # TARGET T0448 # 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 T0448.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 2322 # # ============================================ # Comments from T0448.t04.alpha.rdb # ============================================ # TARGET T0448 # 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 T0448.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 2322 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1676 0.2437 0.5887 2 I 0.2770 0.3346 0.3884 3 A 0.3346 0.4064 0.2590 4 M 0.3829 0.4170 0.2001 5 I 0.4047 0.4061 0.1891 6 V 0.3275 0.4109 0.2616 7 K 0.1735 0.4848 0.3417 8 G 0.0939 0.4396 0.4665 9 G 0.0939 0.4425 0.4636 10 L 0.1330 0.5346 0.3324 11 A 0.1299 0.5993 0.2708 12 M 0.1238 0.6072 0.2691 13 A 0.1446 0.5248 0.3306 14 I 0.1412 0.4185 0.4403 15 S 0.1016 0.2832 0.6152 16 N 0.0731 0.1842 0.7428 17 G 0.0642 0.1150 0.8207 18 H 0.1003 0.1328 0.7668 19 V 0.1211 0.1053 0.7737 20 S 0.1126 0.0837 0.8037 21 F 0.1328 0.0624 0.8048 22 K 0.1500 0.0482 0.8018 23 R 0.3763 0.0141 0.6096 24 P 0.6783 0.0091 0.3125 25 A 0.8752 0.0085 0.1163 26 W 0.8937 0.0082 0.0981 27 L 0.8120 0.0333 0.1547 28 G 0.4734 0.0440 0.4826 29 D 0.2584 0.0943 0.6472 30 S 0.2182 0.2362 0.5456 31 I 0.1768 0.3863 0.4369 32 T 0.1806 0.3939 0.4255 33 A 0.1512 0.3522 0.4966 34 N 0.1157 0.2151 0.6692 35 N 0.0967 0.1487 0.7546 36 G 0.0889 0.1113 0.7998 37 L 0.0924 0.1271 0.7805 38 A 0.0636 0.1651 0.7714 39 T 0.0497 0.2015 0.7488 40 V 0.0552 0.2536 0.6911 41 H 0.0886 0.3481 0.5633 42 Y 0.0197 0.8196 0.1607 43 H 0.0069 0.9346 0.0585 44 D 0.0047 0.9570 0.0383 45 I 0.0047 0.9583 0.0370 46 L 0.0049 0.9518 0.0433 47 A 0.0057 0.9319 0.0624 48 A 0.0073 0.8238 0.1689 49 D 0.0125 0.5968 0.3907 50 W 0.0630 0.1787 0.7583 51 D 0.0743 0.0463 0.8795 52 V 0.0693 0.1341 0.7965 53 E 0.0555 0.1930 0.7515 54 R 0.1241 0.1671 0.7088 55 S 0.1817 0.1568 0.6614 56 D 0.2984 0.1560 0.5457 57 N 0.4105 0.1676 0.4219 58 L 0.4470 0.1258 0.4273 59 G 0.4811 0.0762 0.4428 60 I 0.4336 0.0737 0.4927 61 S 0.2425 0.0905 0.6670 62 G 0.0948 0.1767 0.7285 63 S 0.1048 0.2685 0.6267 64 T 0.1391 0.3431 0.5178 65 I 0.0760 0.5061 0.4179 66 G 0.0322 0.6100 0.3578 67 S 0.0299 0.6776 0.2925 68 R 0.0129 0.8579 0.1293 69 Y 0.0094 0.9128 0.0778 70 D 0.0065 0.9242 0.0694 71 A 0.0064 0.9327 0.0609 72 M 0.0072 0.9334 0.0594 73 A 0.0079 0.9318 0.0603 74 V 0.0073 0.9324 0.0603 75 R 0.0088 0.9190 0.0722 76 Y 0.0145 0.8909 0.0947 77 Q 0.0145 0.8101 0.1755 78 A 0.0229 0.5738 0.4033 79 I 0.0714 0.0606 0.8680 80 P 0.0332 0.1213 0.8455 81 E 0.0403 0.1312 0.8285 82 D 0.0996 0.0561 0.8443 83 A 0.1773 0.0257 0.7970 84 D 0.2351 0.0532 0.7117 85 F 0.9100 0.0056 0.0844 86 I 0.9308 0.0035 0.0656 87 A 0.9331 0.0032 0.0637 88 V 0.9158 0.0052 0.0789 89 F 0.8462 0.0083 0.1455 90 G 0.5584 0.0391 0.4026 91 G 0.3390 0.0506 0.6104 92 V 0.2637 0.1505 0.5857 93 N 0.1655 0.2584 0.5761 94 D 0.1421 0.2941 0.5638 95 Y 0.1014 0.2666 0.6320 96 G 0.1005 0.1619 0.7376 97 R 0.1021 0.1011 0.7968 98 D 0.0925 0.0726 0.8349 99 Q 0.0920 0.0631 0.8449 100 P 0.1053 0.1001 0.7946 101 L 0.0950 0.1742 0.7308 102 G 0.0711 0.1350 0.7938 103 Q 0.0928 0.1515 0.7557 104 Y 0.1171 0.1421 0.7408 105 G 0.0792 0.1022 0.8187 106 D 0.1042 0.0621 0.8337 107 C 0.1520 0.0204 0.8276 108 D 0.0900 0.0208 0.8892 109 M 0.0049 0.9435 0.0516 110 T 0.0047 0.9596 0.0357 111 T 0.0047 0.9601 0.0352 112 F 0.0047 0.9586 0.0368 113 Y 0.0047 0.9583 0.0370 114 G 0.0047 0.9575 0.0378 115 A 0.0047 0.9584 0.0370 116 L 0.0047 0.9606 0.0347 117 M 0.0046 0.9615 0.0339 118 M 0.0046 0.9618 0.0336 119 L 0.0046 0.9613 0.0340 120 L 0.0047 0.9610 0.0344 121 T 0.0046 0.9607 0.0346 122 G 0.0047 0.9573 0.0380 123 L 0.0049 0.9485 0.0466 124 Q 0.0055 0.9269 0.0676 125 T 0.0074 0.8668 0.1258 126 N 0.0156 0.6633 0.3211 127 W 0.0836 0.0446 0.8718 128 P 0.0115 0.1298 0.8587 129 T 0.0208 0.0522 0.9270 130 V 0.1067 0.0167 0.8767 131 P 0.2958 0.0086 0.6955 132 K 0.9101 0.0034 0.0865 133 L 0.9287 0.0038 0.0675 134 F 0.9320 0.0032 0.0648 135 I 0.9076 0.0063 0.0861 136 S 0.7837 0.0078 0.2085 137 A 0.4613 0.0183 0.5204 138 I 0.2769 0.0380 0.6851 139 H 0.2528 0.0481 0.6991 140 I 0.1499 0.0821 0.7680 141 G 0.1000 0.0755 0.8245 142 S 0.0682 0.1751 0.7567 143 D 0.0735 0.1851 0.7414 144 F 0.0766 0.1864 0.7371 145 G 0.0699 0.1192 0.8110 146 G 0.0855 0.1133 0.8012 147 S 0.1212 0.1645 0.7144 148 F 0.1356 0.2503 0.6141 149 S 0.1307 0.2696 0.5997 150 A 0.1129 0.3540 0.5331 151 V 0.1434 0.3277 0.5290 152 T 0.1203 0.3299 0.5499 153 N 0.0670 0.3059 0.6271 154 G 0.0580 0.2933 0.6486 155 L 0.0844 0.3027 0.6129 156 G 0.0576 0.2735 0.6689 157 Y 0.0786 0.4165 0.5049 158 R 0.0821 0.4883 0.4296 159 Q 0.0308 0.6993 0.2699 160 S 0.0119 0.8432 0.1449 161 D 0.0129 0.8833 0.1038 162 Y 0.0048 0.9516 0.0437 163 E 0.0047 0.9603 0.0351 164 A 0.0046 0.9615 0.0338 165 A 0.0046 0.9615 0.0339 166 I 0.0047 0.9606 0.0347 167 A 0.0046 0.9609 0.0345 168 Q 0.0047 0.9599 0.0354 169 M 0.0047 0.9603 0.0350 170 T 0.0047 0.9580 0.0372 171 A 0.0049 0.9447 0.0504 172 D 0.0063 0.9023 0.0914 173 Y 0.0453 0.5009 0.4538 174 G 0.0436 0.0180 0.9384 175 V 0.0740 0.0090 0.9170 176 P 0.2511 0.0248 0.7242 177 H 0.8189 0.0240 0.1571 178 L 0.8290 0.0228 0.1482 179 S 0.7345 0.0302 0.2354 180 L 0.3759 0.2021 0.4220 181 Y 0.1598 0.3021 0.5381 182 R 0.0550 0.5486 0.3965 183 D 0.0419 0.5789 0.3791 184 A 0.0734 0.4769 0.4497 185 G 0.0561 0.3734 0.5705 186 M 0.0711 0.3917 0.5372 187 T 0.0678 0.4396 0.4926 188 F 0.0659 0.3516 0.5825 189 A 0.0746 0.2332 0.6922 190 I 0.0785 0.1259 0.7955 191 P 0.0725 0.2144 0.7131 192 A 0.0765 0.2941 0.6293 193 Q 0.0867 0.3256 0.5878 194 A 0.0691 0.4824 0.4484 195 A 0.0813 0.4590 0.4597 196 I 0.1380 0.3656 0.4964 197 Y 0.1836 0.2269 0.5895 198 S 0.1678 0.1610 0.6712 199 V 0.1212 0.1723 0.7065 200 D 0.1421 0.1068 0.7511 201 T 0.1527 0.1086 0.7387 202 L 0.1953 0.0718 0.7329 203 H 0.1781 0.0461 0.7758 204 P 0.0712 0.1112 0.8176 205 N 0.0598 0.0767 0.8635 206 N 0.0084 0.7159 0.2757 207 A 0.0052 0.8939 0.1010 208 G 0.0047 0.9383 0.0570 209 H 0.0047 0.9563 0.0390 210 R 0.0046 0.9615 0.0338 211 V 0.0046 0.9614 0.0339 212 I 0.0047 0.9601 0.0352 213 A 0.0047 0.9603 0.0350 214 R 0.0047 0.9593 0.0360 215 K 0.0047 0.9533 0.0420 216 L 0.0049 0.9467 0.0485 217 Q 0.0047 0.9523 0.0430 218 S 0.0047 0.9457 0.0495 219 F 0.0050 0.9389 0.0560 220 L 0.0054 0.9117 0.0829 221 D 0.0054 0.8789 0.1157 222 S 0.0056 0.8324 0.1621 223 H 0.0075 0.7892 0.2033 224 F 0.0149 0.6828 0.3023 225 L 0.0153 0.5946 0.3901 226 E 0.0224 0.5013 0.4763 227 H 0.0436 0.3942 0.5622 228 H 0.0561 0.2644 0.6795 229 H 0.0557 0.2063 0.7380 230 H 0.0639 0.1488 0.7873 231 H 0.0654 0.0603 0.8743 232 H 0.0465 0.0416 0.9119