# This file is the result of combining several RDB files, specifically # T0344.t04.dssp-ebghstl.rdb (weight 1.53986) # T0344.t04.stride-ebghtl.rdb (weight 1.24869) # T0344.t04.str2.rdb (weight 1.54758) # T0344.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 T0344.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.13026 # # ============================================ # Comments from T0344.t04.stride-ebghtl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.13026 # # ============================================ # Comments from T0344.t04.str2.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.13026 # # ============================================ # Comments from T0344.t04.alpha.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.13026 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2121 0.0120 0.7759 2 R 0.7340 0.0106 0.2554 3 I 0.8819 0.0083 0.1098 4 V 0.8713 0.0195 0.1092 5 A 0.8410 0.0195 0.1396 6 A 0.6553 0.0689 0.2758 7 D 0.3597 0.0677 0.5726 8 T 0.1678 0.0610 0.7712 9 G 0.1098 0.0727 0.8175 10 G 0.1937 0.1266 0.6797 11 A 0.4057 0.1520 0.4423 12 V 0.5315 0.1542 0.3143 13 L 0.4329 0.1751 0.3919 14 D 0.1992 0.2014 0.5994 15 E 0.0424 0.3583 0.5994 16 T 0.0606 0.2885 0.6510 17 F 0.1273 0.1934 0.6793 18 E 0.1164 0.1319 0.7517 19 P 0.1613 0.2665 0.5722 20 I 0.2238 0.3441 0.4321 21 G 0.4693 0.2307 0.3001 22 L 0.5790 0.2630 0.1580 23 I 0.6210 0.2276 0.1513 24 A 0.7000 0.1283 0.1717 25 T 0.6971 0.1358 0.1671 26 V 0.6846 0.1653 0.1501 27 A 0.6706 0.2246 0.1048 28 V 0.6570 0.2458 0.0972 29 L 0.6671 0.2188 0.1141 30 V 0.6711 0.1459 0.1830 31 E 0.5326 0.1332 0.3342 32 K 0.2311 0.0676 0.7013 33 P 0.1488 0.1059 0.7453 34 Y 0.1395 0.1395 0.7209 35 R 0.1338 0.1455 0.7208 36 S 0.1352 0.1188 0.7461 37 A 0.1082 0.4233 0.4685 38 K 0.1624 0.4099 0.4277 39 E 0.4011 0.3107 0.2882 40 V 0.5799 0.1955 0.2246 41 M 0.6838 0.1591 0.1572 42 V 0.7090 0.1295 0.1615 43 K 0.7043 0.1105 0.1853 44 Y 0.5904 0.0635 0.3461 45 A 0.2985 0.0517 0.6498 46 N 0.1367 0.0166 0.8468 47 P 0.0469 0.1661 0.7871 48 Y 0.0815 0.1477 0.7708 49 D 0.1606 0.1604 0.6791 50 Y 0.2356 0.1367 0.6277 51 D 0.2287 0.1209 0.6504 52 L 0.1089 0.3292 0.5619 53 T 0.0774 0.3620 0.5607 54 G 0.0449 0.4746 0.4805 55 R 0.0631 0.6887 0.2482 56 Q 0.0966 0.7471 0.1563 57 A 0.0924 0.7486 0.1590 58 I 0.0637 0.7969 0.1393 59 R 0.0272 0.8728 0.1000 60 D 0.0155 0.9049 0.0796 61 E 0.0107 0.9385 0.0508 62 V 0.0098 0.9488 0.0414 63 L 0.0085 0.9558 0.0357 64 L 0.0074 0.9569 0.0356 65 A 0.0081 0.9551 0.0368 66 I 0.0114 0.9516 0.0369 67 E 0.0109 0.9486 0.0404 68 L 0.0077 0.9386 0.0537 69 A 0.0089 0.9060 0.0851 70 R 0.0205 0.8301 0.1493 71 K 0.0354 0.6365 0.3281 72 V 0.0920 0.3086 0.5994 73 K 0.0910 0.0419 0.8672 74 P 0.1003 0.0682 0.8316 75 D 0.1633 0.1004 0.7362 76 V 0.7939 0.0316 0.1745 77 I 0.8834 0.0132 0.1034 78 H 0.8700 0.0147 0.1153 79 L 0.6760 0.0367 0.2873 80 D 0.3005 0.0744 0.6251 81 S 0.1375 0.1423 0.7202 82 T 0.1718 0.1810 0.6472 83 L 0.2471 0.1659 0.5870 84 G 0.1711 0.0892 0.7397 85 G 0.2996 0.0862 0.6142 86 I 0.6382 0.0527 0.3091 87 E 0.7627 0.0508 0.1865 88 L 0.7522 0.0667 0.1811 89 R 0.6484 0.0978 0.2538 90 K 0.4815 0.1000 0.4185 91 L 0.1991 0.0871 0.7137 92 D 0.0869 0.0578 0.8553 93 E 0.0583 0.4011 0.5406 94 P 0.0493 0.5237 0.4270 95 T 0.0902 0.5747 0.3351 96 I 0.1133 0.6529 0.2337 97 D 0.1793 0.5639 0.2568 98 A 0.2367 0.5411 0.2222 99 L 0.2711 0.3205 0.4085 100 G 0.2919 0.1173 0.5908 101 I 0.3894 0.0848 0.5258 102 S 0.3131 0.0923 0.5946 103 D 0.1142 0.1753 0.7104 104 K 0.0502 0.1978 0.7520 105 G 0.0477 0.2534 0.6989 106 K 0.0637 0.6161 0.3203 107 E 0.1572 0.7137 0.1291 108 V 0.1036 0.7953 0.1012 109 W 0.0596 0.8430 0.0974 110 K 0.0343 0.8837 0.0820 111 E 0.0308 0.8571 0.1122 112 L 0.0204 0.7992 0.1804 113 S 0.0209 0.7221 0.2570 114 K 0.0095 0.6844 0.3061 115 D 0.0140 0.5977 0.3883 116 L 0.0150 0.7364 0.2486 117 Q 0.0086 0.7916 0.1998 118 P 0.0049 0.9099 0.0851 119 L 0.0050 0.9296 0.0653 120 A 0.0069 0.9270 0.0661 121 R 0.0066 0.9155 0.0779 122 K 0.0084 0.8882 0.1034 123 F 0.0158 0.8658 0.1184 124 W 0.0221 0.8626 0.1153 125 E 0.0272 0.8375 0.1353 126 E 0.0397 0.7462 0.2142 127 T 0.0666 0.3618 0.5717 128 N 0.0999 0.0356 0.8644 129 I 0.3772 0.0109 0.6119 130 E 0.7948 0.0078 0.1974 131 I 0.9140 0.0042 0.0818 132 V 0.9087 0.0075 0.0839 133 A 0.8916 0.0070 0.1015 134 I 0.7857 0.0264 0.1880 135 G 0.4484 0.0225 0.5291 136 K 0.2432 0.0858 0.6710 137 S 0.1765 0.0752 0.7483 138 S 0.2311 0.0875 0.6814 139 V 0.3381 0.0557 0.6062 140 P 0.4689 0.0946 0.4365 141 V 0.5698 0.1763 0.2539 142 R 0.6003 0.1954 0.2043 143 I 0.3979 0.4933 0.1088 144 A 0.3802 0.5298 0.0899 145 E 0.4173 0.4848 0.0979 146 I 0.3794 0.5103 0.1102 147 Y 0.3087 0.5300 0.1613 148 A 0.2074 0.5187 0.2739 149 G 0.1835 0.4632 0.3533 150 I 0.2703 0.5205 0.2092 151 Y 0.2745 0.5487 0.1767 152 S 0.2396 0.5518 0.2086 153 A 0.1368 0.6953 0.1679 154 K 0.1317 0.7345 0.1338 155 W 0.2226 0.6223 0.1551 156 G 0.3005 0.5270 0.1725 157 I 0.2874 0.5395 0.1730 158 E 0.2578 0.5116 0.2306 159 N 0.2748 0.4614 0.2638 160 V 0.3582 0.3839 0.2579 161 E 0.2847 0.3798 0.3355 162 K 0.2562 0.3286 0.4152 163 E 0.0755 0.1120 0.8124 164 G 0.0759 0.0346 0.8895 165 H 0.4330 0.0133 0.5537 166 L 0.8646 0.0047 0.1307 167 I 0.8997 0.0061 0.0942 168 I 0.8268 0.0235 0.1498 169 G 0.6601 0.0197 0.3202 170 L 0.3661 0.0226 0.6113 171 P 0.2752 0.1193 0.6055 172 R 0.2518 0.2326 0.5157 173 Y 0.3692 0.2509 0.3799 174 M 0.4132 0.1418 0.4450 175 E 0.3651 0.0847 0.5501 176 V 0.1523 0.0375 0.8102