# This file is the result of combining several RDB files, specifically # T0272.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0272.t2k.stride-ebghtl.rdb (weight 1.24869) # T0272.t2k.str2.rdb (weight 1.54758) # T0272.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 T0272.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0272 # 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 T0272.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 18 # # ============================================ # Comments from T0272.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0272 # 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 T0272.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 18 # # ============================================ # Comments from T0272.t2k.str2.rdb # ============================================ # TARGET T0272 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0272.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 18 # # ============================================ # Comments from T0272.t2k.alpha.rdb # ============================================ # TARGET T0272 # 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 T0272.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 18 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1799 0.0136 0.8064 2 W 0.5583 0.0220 0.4197 3 L 0.6890 0.0236 0.2874 4 T 0.7109 0.0323 0.2568 5 K 0.7763 0.0193 0.2044 6 L 0.8123 0.0138 0.1739 7 V 0.7982 0.0119 0.1898 8 L 0.5646 0.0164 0.4190 9 N 0.1686 0.0157 0.8157 10 P 0.0232 0.3017 0.6751 11 A 0.0206 0.3394 0.6400 12 S 0.0467 0.3938 0.5595 13 R 0.0588 0.3881 0.5531 14 A 0.0728 0.3597 0.5674 15 A 0.0302 0.7547 0.2151 16 R 0.0303 0.7702 0.1995 17 R 0.0345 0.7619 0.2036 18 D 0.0445 0.7007 0.2548 19 L 0.0585 0.4889 0.4526 20 A 0.0440 0.3531 0.6029 21 N 0.0670 0.1562 0.7768 22 P 0.0145 0.7770 0.2084 23 Y 0.0112 0.8786 0.1103 24 E 0.0074 0.9302 0.0624 25 M 0.0057 0.9369 0.0573 26 H 0.0066 0.9398 0.0536 27 R 0.0099 0.9418 0.0483 28 T 0.0093 0.9415 0.0492 29 L 0.0064 0.9370 0.0567 30 S 0.0069 0.9026 0.0904 31 K 0.0076 0.8078 0.1846 32 A 0.0185 0.6534 0.3281 33 V 0.0811 0.1479 0.7710 34 S 0.0394 0.1380 0.8226 35 R 0.0641 0.0757 0.8601 36 A 0.0560 0.2238 0.7202 37 L 0.0354 0.4246 0.5399 38 E 0.0243 0.4947 0.4811 39 E 0.0369 0.4259 0.5371 40 G 0.0487 0.3097 0.6416 41 R 0.0706 0.2297 0.6997 42 E 0.1056 0.1539 0.7405 43 R 0.1754 0.0902 0.7344 44 L 0.5808 0.0528 0.3664 45 L 0.7465 0.0426 0.2109 46 W 0.7998 0.0283 0.1719 47 R 0.7472 0.0276 0.2252 48 L 0.5825 0.0615 0.3561 49 E 0.4210 0.0932 0.4858 50 P 0.3087 0.1239 0.5674 51 A 0.1384 0.1716 0.6899 52 R 0.0730 0.1742 0.7528 53 G 0.0710 0.1785 0.7505 54 L 0.0937 0.1297 0.7766 55 E 0.1011 0.0712 0.8276 56 P 0.1453 0.0287 0.8259 57 P 0.3164 0.0105 0.6731 58 V 0.8361 0.0042 0.1597 59 V 0.9256 0.0034 0.0710 60 L 0.9248 0.0035 0.0717 61 V 0.9266 0.0032 0.0703 62 Q 0.8420 0.0107 0.1473 63 T 0.4322 0.0081 0.5597 64 L 0.1678 0.0509 0.7813 65 T 0.1081 0.0500 0.8419 66 E 0.0890 0.0607 0.8503 67 P 0.0999 0.0911 0.8090 68 D 0.1457 0.1638 0.6905 69 W 0.1352 0.2687 0.5960 70 S 0.1211 0.3165 0.5623 71 V 0.1081 0.3563 0.5357 72 L 0.1042 0.3244 0.5714 73 D 0.0909 0.2794 0.6297 74 E 0.1097 0.2123 0.6781 75 G 0.1939 0.1265 0.6796 76 Y 0.3265 0.1030 0.5705 77 A 0.5575 0.0795 0.3631 78 Q 0.6982 0.0437 0.2581 79 V 0.7074 0.0429 0.2497 80 F 0.5792 0.0453 0.3754 81 P 0.4318 0.0447 0.5235 82 P 0.2956 0.0691 0.6353 83 K 0.2702 0.0705 0.6593 84 P 0.2118 0.1149 0.6733 85 F 0.1550 0.1377 0.7072 86 H 0.0959 0.2824 0.6217 87 P 0.0474 0.4942 0.4584 88 A 0.0666 0.4466 0.4869 89 L 0.1651 0.2105 0.6244 90 K 0.0983 0.0909 0.8107 91 P 0.0274 0.1033 0.8693 92 G 0.0256 0.0481 0.9263 93 Q 0.2648 0.0195 0.7157 94 R 0.7432 0.0046 0.2522 95 L 0.8796 0.0047 0.1158 96 R 0.9104 0.0034 0.0862 97 F 0.9075 0.0039 0.0886 98 R 0.9102 0.0044 0.0854 99 L 0.9021 0.0035 0.0944 100 R 0.8634 0.0069 0.1296 101 A 0.7634 0.0081 0.2285 102 N 0.3714 0.0162 0.6124 103 P 0.2694 0.0939 0.6367 104 A 0.4875 0.0707 0.4418 105 K 0.6190 0.0549 0.3261 106 R 0.5249 0.0529 0.4221 107 L 0.3516 0.1562 0.4923 108 A 0.1899 0.1215 0.6886 109 A 0.1110 0.1075 0.7814 110 T 0.0820 0.1239 0.7941 111 G 0.1000 0.0930 0.8070 112 K 0.1477 0.0694 0.7829 113 R 0.3329 0.0590 0.6081 114 V 0.3088 0.0783 0.6130 115 A 0.2102 0.1227 0.6671 116 L 0.1474 0.2398 0.6128 117 K 0.0827 0.3149 0.6024 118 T 0.0711 0.3293 0.5995 119 P 0.0154 0.7646 0.2200 120 A 0.0130 0.8476 0.1394 121 E 0.0107 0.8702 0.1191 122 K 0.0101 0.8696 0.1202 123 V 0.0116 0.8713 0.1171 124 A 0.0097 0.8753 0.1150 125 W 0.0088 0.8929 0.0982 126 L 0.0076 0.9102 0.0822 127 E 0.0068 0.9136 0.0796 128 R 0.0074 0.9068 0.0858 129 R 0.0080 0.9055 0.0865 130 L 0.0104 0.8769 0.1127 131 E 0.0090 0.8597 0.1313 132 E 0.0166 0.8069 0.1765 133 G 0.0351 0.5393 0.4256 134 G 0.0391 0.2515 0.7094 135 F 0.1386 0.2357 0.6257 136 R 0.3366 0.2685 0.3949 137 L 0.3321 0.3750 0.2929 138 L 0.2733 0.3860 0.3407 139 E 0.2259 0.3539 0.4202 140 G 0.1248 0.3504 0.5248 141 E 0.1072 0.2612 0.6316 142 R 0.0737 0.3886 0.5377 143 G 0.0672 0.3862 0.5466 144 P 0.0609 0.4694 0.4697 145 W 0.0793 0.5982 0.3225 146 V 0.1085 0.6112 0.2803 147 Q 0.1331 0.5969 0.2699 148 I 0.1482 0.5666 0.2852 149 L 0.1152 0.5775 0.3073 150 Q 0.0879 0.5902 0.3219 151 D 0.0743 0.6076 0.3180 152 T 0.0697 0.6462 0.2841 153 F 0.0773 0.6307 0.2920 154 L 0.0784 0.6004 0.3212 155 E 0.1000 0.5646 0.3354 156 V 0.1517 0.5052 0.3431 157 R 0.2211 0.4005 0.3784 158 R 0.2631 0.3197 0.4172 159 K 0.2983 0.2699 0.4318 160 K 0.3335 0.2056 0.4609 161 D 0.3783 0.1910 0.4306 162 G 0.3480 0.1515 0.5005 163 E 0.1831 0.1906 0.6263 164 E 0.1049 0.1526 0.7425 165 A 0.0873 0.0942 0.8185 166 G 0.0956 0.0508 0.8536 167 K 0.4061 0.0133 0.5806 168 L 0.7357 0.0052 0.2591 169 L 0.8533 0.0044 0.1423 170 Q 0.8763 0.0058 0.1180 171 V 0.8050 0.0077 0.1873 172 Q 0.7284 0.0344 0.2372 173 A 0.8234 0.0093 0.1673 174 V 0.8733 0.0046 0.1221 175 L 0.8751 0.0058 0.1190 176 F 0.8573 0.0124 0.1303 177 E 0.7579 0.0341 0.2080 178 G 0.7649 0.0126 0.2225 179 R 0.8461 0.0094 0.1445 180 L 0.8780 0.0088 0.1132 181 E 0.8807 0.0051 0.1143 182 V 0.7288 0.0134 0.2579 183 V 0.3306 0.0237 0.6457 184 D 0.1833 0.0123 0.8044 185 P 0.0062 0.8437 0.1501 186 E 0.0054 0.9293 0.0653 187 R 0.0050 0.9476 0.0474 188 A 0.0049 0.9534 0.0418 189 L 0.0048 0.9531 0.0421 190 A 0.0054 0.9480 0.0466 191 T 0.0054 0.9424 0.0522 192 L 0.0076 0.9262 0.0662 193 R 0.0085 0.8525 0.1390 194 R 0.0219 0.5901 0.3880 195 G 0.0313 0.3057 0.6630 196 V 0.0795 0.2211 0.6994 197 G 0.0764 0.1809 0.7426 198 P 0.0534 0.4144 0.5322 199 G 0.0727 0.5031 0.4242 200 K 0.1458 0.4827 0.3715 201 A 0.2324 0.3597 0.4078 202 L 0.1888 0.2554 0.5558 203 G 0.1748 0.1642 0.6610 204 L 0.1974 0.2063 0.5964 205 G 0.2214 0.2386 0.5401 206 L 0.2895 0.3693 0.3412 207 L 0.3872 0.3124 0.3004 208 S 0.4335 0.2351 0.3314 209 V 0.3572 0.0859 0.5569 210 A 0.1818 0.0294 0.7888 211 P 0.0576 0.0230 0.9194