# This file is the result of combining several RDB files, specifically # T0327.t04.dssp-ebghstl.rdb (weight 1.53986) # T0327.t04.stride-ebghtl.rdb (weight 1.24869) # T0327.t04.str2.rdb (weight 1.54758) # T0327.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 T0327.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0327 # 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 T0327.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 2 # # ============================================ # Comments from T0327.t04.stride-ebghtl.rdb # ============================================ # TARGET T0327 # 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 T0327.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 2 # # ============================================ # Comments from T0327.t04.str2.rdb # ============================================ # TARGET T0327 # 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 T0327.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 2 # # ============================================ # Comments from T0327.t04.alpha.rdb # ============================================ # TARGET T0327 # 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 T0327.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0782 0.0973 0.8245 2 N 0.0750 0.1006 0.8244 3 K 0.0126 0.7073 0.2801 4 D 0.0111 0.7999 0.1890 5 K 0.0089 0.9157 0.0753 6 L 0.0120 0.9270 0.0610 7 R 0.0099 0.9408 0.0493 8 Y 0.0143 0.9408 0.0448 9 A 0.0230 0.9333 0.0436 10 I 0.0245 0.9296 0.0458 11 L 0.0248 0.9194 0.0559 12 K 0.0295 0.9084 0.0621 13 E 0.0287 0.8933 0.0780 14 I 0.0340 0.8428 0.1232 15 F 0.0843 0.6099 0.3058 16 E 0.1071 0.2876 0.6053 17 G 0.0815 0.0925 0.8260 18 N 0.0733 0.0545 0.8722 19 T 0.1230 0.0234 0.8536 20 P 0.1566 0.0309 0.8125 21 L 0.1390 0.0412 0.8197 22 S 0.1174 0.0481 0.8345 23 E 0.0409 0.4131 0.5460 24 N 0.0631 0.2735 0.6634 25 D 0.1187 0.2745 0.6068 26 I 0.2157 0.1686 0.6157 27 G 0.2244 0.0786 0.6970 28 V 0.2334 0.0565 0.7101 29 T 0.1542 0.0598 0.7860 30 E 0.0422 0.6043 0.3536 31 D 0.0358 0.6039 0.3603 32 Q 0.0378 0.6761 0.2861 33 F 0.0452 0.6664 0.2883 34 D 0.0221 0.7486 0.2293 35 D 0.0220 0.7958 0.1822 36 A 0.0279 0.8766 0.0955 37 V 0.0431 0.8735 0.0834 38 N 0.0522 0.8414 0.1064 39 F 0.0440 0.8390 0.1170 40 L 0.0686 0.7769 0.1545 41 K 0.0849 0.6807 0.2345 42 R 0.1058 0.5833 0.3109 43 E 0.1023 0.2603 0.6374 44 G 0.1371 0.0378 0.8251 45 Y 0.6059 0.0126 0.3815 46 I 0.8789 0.0038 0.1174 47 I 0.8252 0.0218 0.1530 48 G 0.8411 0.0088 0.1501 49 V 0.8383 0.0086 0.1531 50 H 0.7984 0.0095 0.1921 51 Y 0.5510 0.0257 0.4233 52 S 0.2190 0.0618 0.7192 53 D 0.0714 0.1065 0.8221 54 D 0.0571 0.0914 0.8515 55 R 0.0947 0.1044 0.8009 56 P 0.0981 0.3096 0.5923 57 H 0.1679 0.4044 0.4277 58 L 0.2341 0.4795 0.2863 59 Y 0.2919 0.4288 0.2793 60 K 0.3048 0.3376 0.3576 61 L 0.2456 0.2123 0.5421 62 G 0.0969 0.0790 0.8241 63 P 0.0646 0.3056 0.6299 64 E 0.1152 0.3847 0.5001 65 L 0.1844 0.3363 0.4793 66 T 0.1457 0.2697 0.5846 67 E 0.1164 0.3588 0.5247 68 K 0.0876 0.2918 0.6206 69 G 0.0929 0.1922 0.7149 70 E 0.1012 0.3609 0.5379 71 N 0.1684 0.4139 0.4176 72 Y 0.2096 0.4714 0.3190 73 L 0.2952 0.4041 0.3007 74 K 0.1790 0.4399 0.3811 75 E 0.1266 0.4293 0.4441 76 N 0.0627 0.1906 0.7466 77 G 0.0624 0.0471 0.8905 78 T 0.1783 0.0826 0.7391 79 W 0.2245 0.3222 0.4533 80 S 0.1096 0.5214 0.3690 81 K 0.0640 0.7504 0.1856 82 A 0.0746 0.7590 0.1664 83 Y 0.0941 0.7430 0.1629 84 K 0.0979 0.7419 0.1601 85 T 0.0843 0.7529 0.1627 86 I 0.0207 0.9092 0.0701 87 K 0.0112 0.9333 0.0555 88 E 0.0165 0.9219 0.0616 89 I 0.0146 0.9162 0.0692 90 K 0.0155 0.9008 0.0837 91 D 0.0250 0.8384 0.1367 92 W 0.0571 0.7975 0.1454 93 I 0.1431 0.6776 0.1793 94 K 0.2180 0.5410 0.2411 95 L 0.1675 0.5293 0.3032 96 E 0.1280 0.4358 0.4362 97 H 0.1345 0.3273 0.5383 98 H 0.1315 0.2463 0.6223 99 H 0.1234 0.2221 0.6544 100 H 0.1124 0.2500 0.6376 101 H 0.1160 0.2423 0.6417 102 H 0.1276 0.2201 0.6523 103 M 0.1300 0.1732 0.6969 104 N 0.0932 0.1377 0.7691 105 K 0.0176 0.6500 0.3324 106 D 0.0154 0.7538 0.2308 107 K 0.0159 0.8677 0.1165 108 L 0.0319 0.8744 0.0938 109 R 0.0307 0.8972 0.0721 110 Y 0.0414 0.9018 0.0568 111 A 0.0456 0.9006 0.0538 112 I 0.0513 0.8917 0.0569 113 L 0.0343 0.9030 0.0627 114 K 0.0314 0.9051 0.0635 115 E 0.0285 0.8983 0.0732 116 I 0.0317 0.8608 0.1074 117 F 0.0753 0.6779 0.2469 118 E 0.0876 0.3565 0.5559 119 G 0.0615 0.1082 0.8302 120 N 0.0656 0.0565 0.8779 121 T 0.1165 0.0215 0.8620 122 P 0.1770 0.0307 0.7923 123 L 0.1648 0.0454 0.7897 124 S 0.1344 0.0513 0.8143 125 E 0.0520 0.3918 0.5561 126 N 0.0695 0.2476 0.6830 127 D 0.1233 0.2642 0.6125 128 I 0.2469 0.1469 0.6063 129 G 0.2367 0.0786 0.6847 130 V 0.2488 0.0570 0.6942 131 T 0.1779 0.0639 0.7582 132 E 0.0492 0.6392 0.3116 133 D 0.0363 0.6499 0.3138 134 Q 0.0375 0.7142 0.2482 135 F 0.0465 0.6831 0.2704 136 D 0.0240 0.7407 0.2353 137 D 0.0236 0.7661 0.2103 138 A 0.0388 0.8321 0.1291 139 V 0.0530 0.8276 0.1194 140 N 0.0655 0.7898 0.1447 141 F 0.0747 0.7880 0.1373 142 L 0.1204 0.7111 0.1685 143 K 0.1330 0.6108 0.2561 144 R 0.1382 0.5241 0.3377 145 E 0.1128 0.2103 0.6770 146 G 0.1494 0.0409 0.8097 147 Y 0.5992 0.0161 0.3847 148 I 0.8680 0.0053 0.1266 149 I 0.8165 0.0208 0.1628 150 G 0.8225 0.0108 0.1667 151 V 0.8251 0.0095 0.1654 152 H 0.7839 0.0114 0.2047 153 Y 0.5512 0.0263 0.4225 154 S 0.2146 0.0654 0.7200 155 D 0.0626 0.1106 0.8268 156 D 0.0543 0.0962 0.8495 157 R 0.0991 0.0981 0.8028 158 P 0.0968 0.3171 0.5861 159 H 0.1537 0.4300 0.4163 160 L 0.2236 0.4944 0.2821 161 Y 0.2674 0.4490 0.2837 162 K 0.2906 0.3514 0.3580 163 L 0.2193 0.2535 0.5273 164 G 0.0943 0.0849 0.8208 165 P 0.0562 0.3636 0.5802 166 E 0.0916 0.4576 0.4508 167 L 0.1464 0.4362 0.4174 168 T 0.1194 0.3823 0.4983 169 E 0.0934 0.4445 0.4622 170 K 0.0777 0.3130 0.6093 171 G 0.0863 0.1861 0.7276 172 E 0.0923 0.3850 0.5227 173 N 0.1440 0.4669 0.3892 174 Y 0.1850 0.5333 0.2817 175 L 0.2612 0.4609 0.2779 176 K 0.1695 0.4829 0.3476 177 E 0.1084 0.4611 0.4305 178 N 0.0608 0.1688 0.7704 179 G 0.0608 0.0584 0.8808 180 T 0.1923 0.0996 0.7081 181 W 0.2455 0.3153 0.4392 182 S 0.1034 0.5539 0.3426 183 K 0.0655 0.7378 0.1967 184 A 0.0694 0.7508 0.1797 185 Y 0.0789 0.7360 0.1851 186 K 0.0900 0.7094 0.2006 187 T 0.0797 0.7318 0.1884 188 I 0.0241 0.8920 0.0839 189 K 0.0152 0.9196 0.0652 190 E 0.0234 0.9019 0.0746 191 I 0.0186 0.8989 0.0825 192 K 0.0200 0.8812 0.0989 193 D 0.0303 0.8168 0.1529 194 W 0.0584 0.7828 0.1588 195 I 0.1442 0.6586 0.1972 196 K 0.2005 0.5385 0.2609 197 L 0.1589 0.5209 0.3201 198 E 0.1427 0.4294 0.4279 199 H 0.1508 0.3433 0.5059 200 H 0.1342 0.2733 0.5924 201 H 0.1247 0.2156 0.6596 202 H 0.1069 0.1626 0.7305 203 H 0.0902 0.1042 0.8056 204 H 0.0592 0.0444 0.8964