# This file is the result of combining several RDB files, specifically # T0280.t04.dssp-ebghstl.rdb (weight 1.53986) # T0280.t04.stride-ebghtl.rdb (weight 1.24869) # T0280.t04.str2.rdb (weight 1.54758) # T0280.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 T0280.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0280 # 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 T0280.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 396 # # ============================================ # Comments from T0280.t04.stride-ebghtl.rdb # ============================================ # TARGET T0280 # 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 T0280.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 396 # # ============================================ # Comments from T0280.t04.str2.rdb # ============================================ # TARGET T0280 # 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 T0280.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 396 # # ============================================ # Comments from T0280.t04.alpha.rdb # ============================================ # TARGET T0280 # 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 T0280.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 396 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1438 0.0278 0.8285 2 R 0.3426 0.0497 0.6077 3 F 0.3187 0.0855 0.5958 4 R 0.1900 0.1495 0.6604 5 D 0.1200 0.1230 0.7570 6 R 0.0440 0.3145 0.6416 7 R 0.0405 0.6471 0.3124 8 H 0.0217 0.7989 0.1794 9 A 0.0089 0.8955 0.0955 10 G 0.0068 0.9321 0.0611 11 A 0.0052 0.9547 0.0401 12 L 0.0050 0.9553 0.0397 13 L 0.0048 0.9526 0.0426 14 A 0.0049 0.9521 0.0430 15 E 0.0052 0.9385 0.0563 16 A 0.0063 0.9123 0.0814 17 L 0.0226 0.8331 0.1443 18 A 0.0173 0.6996 0.2831 19 P 0.0214 0.5997 0.3789 20 L 0.0447 0.3064 0.6489 21 G 0.0356 0.0759 0.8885 22 L 0.0696 0.0526 0.8778 23 E 0.0598 0.0783 0.8619 24 A 0.1030 0.0427 0.8543 25 P 0.1861 0.0725 0.7414 26 V 0.5300 0.1012 0.3689 27 V 0.6674 0.1223 0.2103 28 L 0.5828 0.1358 0.2814 29 G 0.4028 0.0823 0.5149 30 L 0.2003 0.0374 0.7624 31 P 0.1174 0.1157 0.7668 32 R 0.0584 0.3593 0.5822 33 G 0.0514 0.4390 0.5096 34 G 0.0636 0.5881 0.3483 35 V 0.0660 0.8047 0.1293 36 V 0.0660 0.8342 0.0998 37 V 0.0205 0.9166 0.0630 38 A 0.0094 0.9454 0.0452 39 D 0.0054 0.9585 0.0361 40 E 0.0049 0.9606 0.0345 41 V 0.0047 0.9606 0.0348 42 A 0.0047 0.9585 0.0367 43 R 0.0049 0.9503 0.0448 44 R 0.0079 0.8896 0.1025 45 L 0.0477 0.5244 0.4280 46 G 0.0316 0.0433 0.9251 47 G 0.0482 0.0257 0.9261 48 E 0.1236 0.0410 0.8354 49 L 0.3057 0.0265 0.6678 50 D 0.4230 0.0473 0.5298 51 V 0.8923 0.0113 0.0964 52 V 0.9209 0.0050 0.0741 53 L 0.9204 0.0040 0.0756 54 V 0.8580 0.0066 0.1354 55 R 0.6262 0.0153 0.3585 56 K 0.4061 0.0465 0.5474 57 V 0.1877 0.0706 0.7417 58 G 0.0994 0.0501 0.8506 59 A 0.0901 0.0250 0.8849 60 P 0.1279 0.0507 0.8214 61 G 0.1362 0.0522 0.8116 62 N 0.0960 0.0379 0.8660 63 P 0.0372 0.2545 0.7082 64 E 0.0612 0.2613 0.6774 65 F 0.1376 0.1943 0.6681 66 A 0.2049 0.0950 0.7002 67 L 0.5029 0.0719 0.4253 68 G 0.6581 0.0433 0.2986 69 A 0.7845 0.0253 0.1902 70 V 0.6705 0.0463 0.2832 71 G 0.3558 0.0602 0.5841 72 E 0.1311 0.1697 0.6991 73 G 0.0640 0.2078 0.7282 74 G 0.0897 0.3192 0.5911 75 E 0.1516 0.4343 0.4141 76 L 0.2063 0.5050 0.2887 77 V 0.1966 0.4888 0.3146 78 L 0.1562 0.5302 0.3135 79 M 0.1216 0.4573 0.4211 80 P 0.0275 0.7841 0.1884 81 Y 0.0301 0.7807 0.1892 82 A 0.0422 0.7565 0.2013 83 L 0.0627 0.6737 0.2636 84 R 0.0697 0.5704 0.3599 85 Y 0.0843 0.3867 0.5289 86 A 0.0878 0.1599 0.7522 87 D 0.0888 0.1183 0.7929 88 Q 0.0464 0.5398 0.4138 89 S 0.0578 0.5810 0.3612 90 Y 0.1087 0.6567 0.2347 91 L 0.2367 0.4742 0.2891 92 E 0.3016 0.4273 0.2711 93 R 0.3118 0.5219 0.1663 94 E 0.3058 0.5302 0.1640 95 A 0.2876 0.5152 0.1972 96 A 0.2198 0.5111 0.2691 97 R 0.1634 0.4380 0.3986 98 Q 0.0967 0.3658 0.5374 99 R 0.0588 0.5432 0.3980 100 D 0.0654 0.5855 0.3492 101 V 0.0931 0.6177 0.2892 102 L 0.1204 0.5717 0.3078 103 R 0.0946 0.5797 0.3257 104 K 0.0977 0.5746 0.3276 105 R 0.1120 0.6102 0.2778 106 A 0.1407 0.6582 0.2011 107 E 0.1874 0.6282 0.1844 108 R 0.2633 0.5720 0.1648 109 Y 0.3135 0.4917 0.1947 110 R 0.3171 0.4170 0.2659 111 R 0.2917 0.3167 0.3916 112 V 0.2361 0.1426 0.6213 113 R 0.1409 0.0355 0.8236 114 P 0.1096 0.0683 0.8221 115 K 0.1208 0.2230 0.6562 116 A 0.1667 0.3132 0.5201 117 A 0.1402 0.3334 0.5265 118 R 0.1745 0.2628 0.5628 119 K 0.0652 0.0963 0.8385 120 G 0.0486 0.0347 0.9166 121 R 0.1530 0.0115 0.8355 122 D 0.5327 0.0086 0.4588 123 V 0.9185 0.0036 0.0779 124 V 0.9328 0.0033 0.0639 125 L 0.9313 0.0032 0.0655 126 V 0.8752 0.0060 0.1188 127 D 0.4659 0.0177 0.5163 128 D 0.2104 0.0763 0.7133 129 G 0.2980 0.0980 0.6040 130 V 0.3243 0.1766 0.4992 131 A 0.2513 0.1592 0.5895 132 T 0.0906 0.1509 0.7585 133 G 0.0276 0.3763 0.5961 134 A 0.0159 0.8105 0.1735 135 S 0.0087 0.9064 0.0849 136 M 0.0047 0.9610 0.0343 137 E 0.0046 0.9616 0.0338 138 A 0.0046 0.9613 0.0341 139 A 0.0047 0.9609 0.0344 140 L 0.0047 0.9611 0.0342 141 S 0.0046 0.9617 0.0337 142 V 0.0047 0.9608 0.0345 143 V 0.0047 0.9597 0.0356 144 F 0.0049 0.9487 0.0464 145 Q 0.0070 0.8571 0.1360 146 E 0.0417 0.4533 0.5050 147 G 0.0425 0.0356 0.9218 148 P 0.0793 0.0219 0.8988 149 R 0.1315 0.0680 0.8005 150 R 0.8190 0.0144 0.1665 151 V 0.9243 0.0032 0.0725 152 V 0.9301 0.0037 0.0662 153 V 0.9308 0.0033 0.0659 154 A 0.9233 0.0034 0.0733 155 V 0.8945 0.0045 0.1010 156 P 0.7572 0.0081 0.2347 157 V 0.4493 0.0404 0.5103 158 A 0.1470 0.0284 0.8246 159 S 0.0634 0.0251 0.9115 160 P 0.0077 0.7735 0.2187 161 E 0.0086 0.8590 0.1324 162 A 0.0082 0.9003 0.0914 163 V 0.0098 0.9072 0.0830 164 E 0.0153 0.8753 0.1094 165 R 0.0152 0.8215 0.1633 166 L 0.0335 0.6385 0.3280 167 K 0.0339 0.4603 0.5057 168 A 0.0650 0.3517 0.5833 169 R 0.1413 0.1126 0.7460 170 A 0.2189 0.0499 0.7312 171 E 0.4015 0.0529 0.5457 172 V 0.8882 0.0099 0.1019 173 V 0.9079 0.0095 0.0826 174 A 0.8906 0.0133 0.0961 175 L 0.7871 0.0244 0.1885 176 S 0.4964 0.0221 0.4815 177 V 0.2722 0.0172 0.7106 178 P 0.1692 0.0301 0.8007 179 Q 0.1022 0.1190 0.7788 180 D 0.1098 0.1558 0.7344 181 F 0.0753 0.5391 0.3856 182 A 0.1330 0.4360 0.4310 183 A 0.2600 0.3884 0.3516 184 V 0.4412 0.2315 0.3273 185 G 0.5757 0.1126 0.3118 186 A 0.7130 0.0737 0.2133 187 Y 0.7966 0.0404 0.1630 188 Y 0.7098 0.0268 0.2634 189 L 0.4460 0.0500 0.5040 190 D 0.2527 0.0466 0.7007 191 F 0.0740 0.4200 0.5061 192 G 0.0577 0.4309 0.5114 193 E 0.0763 0.4258 0.4979 194 V 0.1603 0.1521 0.6876 195 T 0.0772 0.0869 0.8359 196 D 0.0255 0.6213 0.3532 197 E 0.0060 0.9458 0.0482 198 D 0.0064 0.9519 0.0417 199 V 0.0054 0.9580 0.0366 200 E 0.0066 0.9588 0.0347 201 A 0.0068 0.9582 0.0350 202 I 0.0082 0.9533 0.0385 203 L 0.0074 0.9476 0.0450 204 L 0.0083 0.9351 0.0566 205 E 0.0095 0.8903 0.1002 206 W 0.0164 0.7896 0.1940 207 A 0.0520 0.4328 0.5152 208 G 0.0363 0.0741 0.8896