# This file is the result of combining several RDB files, specifically # T0148.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0148.t2k.stride-ebghtl.rdb (weight 1.24869) # T0148.t2k.str.rdb (weight 1.53983) # T0148.t2k.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 T0148.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0148 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0148.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ # Comments from T0148.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0148 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0148.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ # Comments from T0148.t2k.str.rdb # ============================================ # TARGET T0148 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0148.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ # Comments from T0148.t2k.alpha.rdb # ============================================ # TARGET T0148 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0148.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0574 0.0303 0.9123 2 P 0.1168 0.0276 0.8556 3 S 0.1996 0.0483 0.7521 4 F 0.2865 0.0606 0.6528 5 D 0.3600 0.0607 0.5793 6 I 0.4405 0.1056 0.4540 7 V 0.3915 0.1372 0.4713 8 S 0.3225 0.1648 0.5126 9 E 0.2484 0.1382 0.6134 10 I 0.1381 0.0818 0.7800 11 T 0.0850 0.1114 0.8036 12 L 0.0104 0.8689 0.1207 13 H 0.0052 0.9338 0.0610 14 E 0.0049 0.9434 0.0517 15 V 0.0047 0.9458 0.0495 16 R 0.0047 0.9432 0.0521 17 N 0.0046 0.9408 0.0546 18 A 0.0046 0.9349 0.0605 19 V 0.0045 0.9480 0.0475 20 E 0.0050 0.9432 0.0518 21 N 0.0053 0.9353 0.0594 22 A 0.0061 0.9353 0.0586 23 N 0.0080 0.9016 0.0904 24 R 0.0102 0.8579 0.1319 25 V 0.0246 0.7666 0.2087 26 L 0.0547 0.6476 0.2977 27 S 0.0572 0.4826 0.4602 28 T 0.1063 0.3203 0.5734 29 R 0.1624 0.2955 0.5421 30 Y 0.2927 0.1885 0.5188 31 D 0.2718 0.1409 0.5873 32 F 0.1676 0.1370 0.6954 33 R 0.0647 0.1024 0.8329 34 G 0.0567 0.0557 0.8875 35 V 0.2683 0.0234 0.7083 36 E 0.5197 0.0209 0.4594 37 A 0.7502 0.0091 0.2407 38 V 0.8681 0.0065 0.1254 39 I 0.8931 0.0058 0.1011 40 E 0.8973 0.0050 0.0977 41 L 0.7901 0.0105 0.1994 42 N 0.3769 0.0268 0.5963 43 E 0.0525 0.1353 0.8121 44 K 0.0539 0.0855 0.8606 45 N 0.1486 0.0431 0.8083 46 E 0.5608 0.0138 0.4254 47 T 0.8791 0.0036 0.1173 48 I 0.9097 0.0038 0.0864 49 K 0.9027 0.0037 0.0935 50 I 0.8722 0.0048 0.1230 51 T 0.7404 0.0119 0.2478 52 T 0.4183 0.0180 0.5637 53 E 0.0931 0.1136 0.7933 54 S 0.0738 0.1502 0.7760 55 D 0.0255 0.5986 0.3760 56 F 0.0401 0.7050 0.2549 57 Q 0.0585 0.7602 0.1813 58 L 0.0196 0.9016 0.0788 59 E 0.0177 0.9092 0.0731 60 Q 0.0112 0.9227 0.0660 61 L 0.0072 0.9380 0.0548 62 I 0.0052 0.9507 0.0441 63 E 0.0046 0.9522 0.0433 64 I 0.0044 0.9543 0.0413 65 L 0.0046 0.9436 0.0518 66 I 0.0045 0.9422 0.0533 67 G 0.0047 0.9396 0.0556 68 S 0.0048 0.9391 0.0561 69 C 0.0049 0.9331 0.0620 70 I 0.0052 0.9204 0.0744 71 K 0.0065 0.8579 0.1357 72 R 0.0444 0.4016 0.5539 73 G 0.0538 0.0320 0.9142 74 I 0.0931 0.0201 0.8868 75 E 0.1251 0.0364 0.8385 76 H 0.0674 0.6009 0.3317 77 S 0.0603 0.6437 0.2960 78 S 0.1219 0.6195 0.2586 79 L 0.2811 0.3228 0.3961 80 D 0.2927 0.1627 0.5446 81 I 0.1666 0.1818 0.6516 82 P 0.0644 0.2164 0.7192 83 A 0.0894 0.2791 0.6315 84 E 0.2024 0.2654 0.5321 85 S 0.2551 0.2562 0.4888 86 E 0.2506 0.2464 0.5030 87 H 0.2270 0.2042 0.5688 88 H 0.1591 0.1051 0.7358 89 G 0.1104 0.0614 0.8282 90 K 0.1865 0.0750 0.7385 91 L 0.5895 0.0379 0.3726 92 Y 0.7668 0.0247 0.2085 93 S 0.8305 0.0217 0.1479 94 K 0.8550 0.0247 0.1203 95 E 0.8560 0.0171 0.1269 96 I 0.8326 0.0194 0.1480 97 K 0.8411 0.0205 0.1384 98 L 0.7352 0.0720 0.1929 99 K 0.4528 0.1194 0.4279 100 Q 0.1941 0.1728 0.6331 101 G 0.1024 0.1415 0.7561 102 I 0.1391 0.1705 0.6905 103 E 0.0561 0.2284 0.7156 104 T 0.0086 0.8528 0.1386 105 E 0.0075 0.8936 0.0990 106 M 0.0060 0.9178 0.0762 107 A 0.0049 0.9357 0.0594 108 K 0.0058 0.9405 0.0537 109 K 0.0059 0.9389 0.0552 110 I 0.0049 0.9516 0.0435 111 T 0.0054 0.9515 0.0431 112 K 0.0060 0.9451 0.0490 113 L 0.0077 0.9355 0.0568 114 V 0.0133 0.9033 0.0835 115 K 0.0131 0.8462 0.1407 116 D 0.0206 0.7078 0.2716 117 S 0.0230 0.5104 0.4666 118 K 0.0338 0.1176 0.8486 119 I 0.1394 0.0738 0.7869 120 K 0.3801 0.0971 0.5228 121 V 0.6383 0.1043 0.2574 122 Q 0.6803 0.1183 0.2014 123 T 0.7238 0.0854 0.1908 124 Q 0.7114 0.0851 0.2034 125 I 0.5945 0.0992 0.3063 126 Q 0.3045 0.0814 0.6141 127 G 0.1264 0.0537 0.8200 128 E 0.2881 0.0693 0.6426 129 Q 0.7491 0.0192 0.2317 130 V 0.8359 0.0108 0.1533 131 R 0.8411 0.0096 0.1493 132 V 0.7642 0.0159 0.2199 133 T 0.4670 0.0423 0.4906 134 G 0.1944 0.0810 0.7246 135 K 0.1100 0.1417 0.7483 136 S 0.0838 0.2098 0.7064 137 R 0.0115 0.7512 0.2373 138 D 0.0085 0.8377 0.1538 139 D 0.0082 0.8700 0.1219 140 L 0.0045 0.9523 0.0433 141 Q 0.0044 0.9592 0.0364 142 A 0.0044 0.9598 0.0358 143 V 0.0044 0.9594 0.0362 144 I 0.0044 0.9581 0.0375 145 Q 0.0044 0.9493 0.0463 146 L 0.0047 0.9178 0.0775 147 V 0.0223 0.8182 0.1595 148 K 0.0423 0.6063 0.3514 149 S 0.0184 0.5597 0.4220 150 A 0.0172 0.4383 0.5445 151 E 0.0353 0.3371 0.6276 152 L 0.0638 0.1843 0.7518 153 G 0.0384 0.1004 0.8612 154 Q 0.0814 0.0495 0.8691 155 P 0.1771 0.0546 0.7683 156 F 0.4324 0.0758 0.4918 157 Q 0.5353 0.0804 0.3843 158 F 0.5552 0.1261 0.3187 159 N 0.4541 0.1554 0.3905 160 N 0.3586 0.1332 0.5081 161 F 0.2615 0.1419 0.5966 162 R 0.1689 0.0784 0.7527 163 D 0.0609 0.0282 0.9109