# This file is the result of combining several RDB files, specifically # T0295.t06.dssp-ebghstl.rdb (weight 1.53986) # T0295.t06.stride-ebghtl.rdb (weight 1.24869) # T0295.t06.str2.rdb (weight 1.54758) # T0295.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 T0295.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0295 # 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 T0295.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 3565 # # ============================================ # Comments from T0295.t06.stride-ebghtl.rdb # ============================================ # TARGET T0295 # 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 T0295.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 3565 # # ============================================ # Comments from T0295.t06.str2.rdb # ============================================ # TARGET T0295 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0295.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 3565 # # ============================================ # Comments from T0295.t06.alpha.rdb # ============================================ # TARGET T0295 # 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 T0295.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 3565 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 H 0.0811 0.0815 0.8373 2 L 0.1744 0.1407 0.6849 3 L 0.1811 0.1313 0.6876 4 K 0.1039 0.1084 0.7877 5 N 0.0772 0.0394 0.8834 6 P 0.0074 0.8422 0.1504 7 G 0.0075 0.8814 0.1110 8 I 0.0054 0.9403 0.0543 9 L 0.0047 0.9573 0.0380 10 D 0.0049 0.9587 0.0363 11 K 0.0050 0.9582 0.0368 12 I 0.0047 0.9572 0.0380 13 I 0.0050 0.9498 0.0452 14 Y 0.0062 0.9214 0.0725 15 A 0.0097 0.8541 0.1362 16 A 0.0549 0.5683 0.3768 17 K 0.0697 0.2025 0.7278 18 I 0.0899 0.1582 0.7518 19 K 0.0650 0.0931 0.8420 20 S 0.0435 0.1509 0.8056 21 S 0.0467 0.0857 0.8676 22 D 0.1389 0.0494 0.8117 23 I 0.7632 0.0073 0.2295 24 V 0.9090 0.0045 0.0865 25 L 0.9180 0.0047 0.0773 26 E 0.8791 0.0072 0.1137 27 I 0.5945 0.0361 0.3694 28 G 0.2321 0.0319 0.7360 29 C 0.1032 0.0748 0.8221 30 G 0.0739 0.0785 0.8477 31 T 0.0606 0.2964 0.6430 32 G 0.0200 0.7007 0.2793 33 N 0.0127 0.8975 0.0898 34 L 0.0079 0.9308 0.0614 35 T 0.0076 0.9329 0.0595 36 V 0.0070 0.9251 0.0679 37 K 0.0082 0.8840 0.1078 38 L 0.0105 0.8253 0.1641 39 L 0.0193 0.7834 0.1973 40 P 0.0101 0.7638 0.2261 41 L 0.0210 0.5734 0.4056 42 A 0.0920 0.2239 0.6841 43 K 0.0850 0.1031 0.8119 44 K 0.5007 0.0316 0.4676 45 V 0.8580 0.0088 0.1332 46 I 0.9059 0.0095 0.0846 47 T 0.9014 0.0070 0.0916 48 I 0.8443 0.0097 0.1460 49 D 0.5934 0.0140 0.3926 50 I 0.0989 0.0419 0.8592 51 D 0.0755 0.0227 0.9018 52 S 0.0052 0.8839 0.1109 53 R 0.0052 0.9183 0.0766 54 M 0.0051 0.9432 0.0518 55 I 0.0047 0.9569 0.0384 56 S 0.0047 0.9592 0.0361 57 E 0.0047 0.9594 0.0359 58 V 0.0047 0.9592 0.0361 59 K 0.0047 0.9589 0.0364 60 K 0.0050 0.9544 0.0407 61 R 0.0052 0.9451 0.0497 62 C 0.0062 0.9240 0.0698 63 L 0.0075 0.8943 0.0982 64 Y 0.0108 0.8434 0.1458 65 E 0.0421 0.4310 0.5270 66 G 0.0343 0.0528 0.9129 67 Y 0.0895 0.0485 0.8620 68 N 0.0819 0.0822 0.8359 69 N 0.3733 0.0440 0.5827 70 L 0.7492 0.0092 0.2416 71 E 0.9011 0.0061 0.0928 72 V 0.9235 0.0039 0.0725 73 Y 0.8848 0.0139 0.1012 74 E 0.7559 0.0239 0.2203 75 G 0.3511 0.0426 0.6063 76 D 0.2671 0.0687 0.6643 77 A 0.1513 0.4174 0.4312 78 I 0.1363 0.4737 0.3900 79 K 0.1285 0.4021 0.4694 80 T 0.1442 0.1240 0.7318 81 V 0.1362 0.0634 0.8004 82 F 0.0843 0.0575 0.8583 83 P 0.0451 0.1495 0.8054 84 K 0.0915 0.1382 0.7703 85 F 0.2849 0.0249 0.6902 86 D 0.3829 0.0464 0.5707 87 V 0.9136 0.0043 0.0821 88 C 0.9300 0.0032 0.0668 89 T 0.9266 0.0038 0.0696 90 A 0.8358 0.0101 0.1541 91 N 0.3722 0.0225 0.6053 92 I 0.1701 0.0371 0.7928 93 P 0.1515 0.1734 0.6751 94 Y 0.2020 0.2947 0.5033 95 K 0.1786 0.2894 0.5320 96 I 0.1205 0.2261 0.6534 97 S 0.0858 0.1331 0.7811 98 S 0.0502 0.3078 0.6420 99 P 0.0182 0.7720 0.2098 100 L 0.0063 0.9266 0.0670 101 I 0.0059 0.9421 0.0521 102 F 0.0065 0.9456 0.0479 103 K 0.0076 0.9382 0.0542 104 L 0.0079 0.9175 0.0745 105 I 0.0092 0.8595 0.1313 106 S 0.0116 0.7187 0.2696 107 H 0.0232 0.6700 0.3068 108 R 0.0371 0.5135 0.4494 109 P 0.0125 0.6321 0.3554 110 L 0.0288 0.6241 0.3471 111 F 0.1284 0.3484 0.5232 112 K 0.1291 0.1889 0.6821 113 C 0.0675 0.2421 0.6905 114 A 0.0778 0.1287 0.7935 115 V 0.5387 0.0722 0.3891 116 L 0.8086 0.0659 0.1255 117 M 0.8438 0.0674 0.0888 118 F 0.8204 0.0780 0.1016 119 Q 0.7108 0.1234 0.1658 120 K 0.5287 0.2223 0.2490 121 E 0.3670 0.3262 0.3068 122 F 0.1484 0.4764 0.3752 123 A 0.1153 0.5425 0.3422 124 E 0.1206 0.6360 0.2434 125 R 0.1015 0.6432 0.2553 126 M 0.1284 0.5858 0.2859 127 L 0.1344 0.5135 0.3522 128 A 0.1010 0.4076 0.4915 129 N 0.0930 0.2405 0.6665 130 V 0.0587 0.2492 0.6921 131 G 0.0485 0.1367 0.8149 132 D 0.0839 0.1404 0.7756 133 S 0.0562 0.2849 0.6589 134 N 0.0747 0.3118 0.6135 135 Y 0.1319 0.3232 0.5449 136 S 0.2022 0.3134 0.4844 137 R 0.2770 0.3704 0.3525 138 L 0.3797 0.3655 0.2548 139 T 0.4731 0.3386 0.1883 140 I 0.4962 0.3421 0.1616 141 N 0.4974 0.3241 0.1785 142 V 0.5146 0.3246 0.1608 143 K 0.4805 0.3270 0.1924 144 L 0.4254 0.3388 0.2358 145 F 0.4830 0.2118 0.3052 146 C 0.5412 0.1204 0.3385 147 K 0.5570 0.0776 0.3654 148 V 0.5983 0.0786 0.3231 149 T 0.6468 0.0711 0.2821 150 K 0.6811 0.0727 0.2462 151 V 0.6249 0.0881 0.2870 152 C 0.6271 0.0672 0.3058 153 N 0.5536 0.0389 0.4075 154 V 0.3792 0.0237 0.5970 155 N 0.1897 0.0322 0.7781 156 R 0.0254 0.5996 0.3750 157 S 0.0207 0.6282 0.3511 158 S 0.0412 0.5738 0.3850 159 F 0.1767 0.1203 0.7029 160 N 0.1094 0.0385 0.8521 161 P 0.0865 0.0172 0.8963 162 P 0.0750 0.0208 0.9042 163 P 0.1172 0.0507 0.8321 164 K 0.2374 0.0659 0.6967 165 V 0.4695 0.0355 0.4950 166 D 0.5326 0.0458 0.4216 167 S 0.8085 0.0128 0.1786 168 V 0.8836 0.0063 0.1101 169 I 0.9206 0.0047 0.0747 170 V 0.9158 0.0052 0.0791 171 K 0.8964 0.0057 0.0979 172 L 0.8331 0.0081 0.1588 173 I 0.6058 0.0091 0.3851 174 P 0.3598 0.0259 0.6143 175 K 0.1280 0.0526 0.8194 176 E 0.0785 0.0968 0.8247 177 S 0.0765 0.1331 0.7904 178 S 0.0460 0.2512 0.7027 179 F 0.0841 0.2212 0.6947 180 L 0.1581 0.1134 0.7285 181 T 0.0680 0.0533 0.8787