# This file is the result of combining several RDB files, specifically # T0425.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0425.t2k.stride-ebghtl.rdb (weight 1.24869) # T0425.t2k.str.rdb (weight 1.53983) # 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 T0425.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0425 # 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 T0425.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 431 # # ============================================ # Comments from T0425.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0425 # 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 T0425.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 431 # # ============================================ # Comments from T0425.t2k.str.rdb # ============================================ # TARGET T0425 # 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 T0425.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 431 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0265 0.0162 0.9573 2 S 0.1310 0.0127 0.8563 3 K 0.6388 0.0057 0.3555 4 I 0.9423 0.0026 0.0551 5 I 0.9729 0.0024 0.0246 6 C 0.9635 0.0025 0.0341 7 L 0.9209 0.0027 0.0764 8 T 0.5165 0.0065 0.4770 9 A 0.1108 0.0415 0.8476 10 G 0.0769 0.0753 0.8479 11 H 0.0587 0.0963 0.8450 12 S 0.0570 0.0653 0.8777 13 N 0.1220 0.0709 0.8071 14 T 0.1708 0.1118 0.7175 15 D 0.1400 0.1258 0.7342 16 P 0.0664 0.2262 0.7074 17 G 0.0634 0.1977 0.7390 18 A 0.2396 0.2080 0.5524 19 V 0.2643 0.1495 0.5862 20 N 0.1420 0.1221 0.7359 21 G 0.0194 0.1310 0.8496 22 S 0.0293 0.1077 0.8631 23 D 0.1466 0.2310 0.6223 24 R 0.2231 0.2981 0.4789 25 E 0.0892 0.7415 0.1693 26 A 0.0233 0.8508 0.1259 27 D 0.0146 0.8924 0.0930 28 L 0.0087 0.9426 0.0487 29 A 0.0037 0.9692 0.0270 30 Q 0.0037 0.9729 0.0234 31 D 0.0037 0.9747 0.0216 32 M 0.0037 0.9750 0.0213 33 R 0.0037 0.9766 0.0197 34 N 0.0037 0.9759 0.0204 35 I 0.0037 0.9732 0.0230 36 V 0.0037 0.9739 0.0224 37 A 0.0037 0.9748 0.0215 38 S 0.0037 0.9715 0.0248 39 I 0.0037 0.9699 0.0263 40 L 0.0041 0.9618 0.0341 41 R 0.0052 0.9117 0.0832 42 N 0.0069 0.7535 0.2396 43 D 0.0076 0.3358 0.6566 44 Y 0.0116 0.0212 0.9672 45 G 0.0579 0.0142 0.9279 46 L 0.5535 0.0080 0.4386 47 T 0.9302 0.0027 0.0672 48 V 0.9602 0.0024 0.0373 49 K 0.9593 0.0025 0.0382 50 T 0.9234 0.0026 0.0739 51 D 0.7045 0.0058 0.2896 52 G 0.3604 0.0143 0.6252 53 T 0.0869 0.0331 0.8801 54 G 0.0416 0.0552 0.9032 55 K 0.0581 0.0624 0.8795 56 G 0.2212 0.0558 0.7230 57 N 0.3389 0.0378 0.6233 58 M 0.2718 0.0278 0.7004 59 P 0.1240 0.0324 0.8436 60 L 0.0112 0.7940 0.1948 61 R 0.0076 0.8526 0.1398 62 D 0.0100 0.8971 0.0929 63 A 0.0193 0.8733 0.1074 64 V 0.0265 0.8545 0.1190 65 K 0.0298 0.8372 0.1330 66 L 0.0237 0.8183 0.1580 67 I 0.0247 0.7003 0.2750 68 R 0.0229 0.3803 0.5968 69 G 0.0220 0.0735 0.9044 70 S 0.0541 0.0223 0.9237 71 D 0.1529 0.0126 0.8345 72 V 0.9234 0.0028 0.0739 73 A 0.9770 0.0024 0.0206 74 I 0.9790 0.0024 0.0186 75 E 0.9706 0.0028 0.0267 76 F 0.8796 0.0069 0.1135 77 H 0.7075 0.0143 0.2782 78 T 0.4525 0.0433 0.5041 79 N 0.2562 0.0743 0.6695 80 A 0.1287 0.0861 0.7851 81 A 0.0795 0.1010 0.8195 82 A 0.0613 0.0823 0.8563 83 N 0.0556 0.0746 0.8698 84 K 0.0814 0.1258 0.7929 85 T 0.1086 0.1135 0.7779 86 A 0.1992 0.0770 0.7238 87 T 0.2388 0.0362 0.7250 88 G 0.4550 0.0232 0.5217 89 I 0.8027 0.0068 0.1905 90 E 0.9455 0.0029 0.0515 91 A 0.9577 0.0028 0.0394 92 L 0.9449 0.0032 0.0519 93 S 0.8954 0.0036 0.1010 94 T 0.6561 0.0089 0.3350 95 P 0.1887 0.0249 0.7864 96 K 0.0320 0.0655 0.9025 97 N 0.0199 0.1386 0.8416 98 K 0.0164 0.2625 0.7210 99 R 0.0163 0.3643 0.6195 100 W 0.0172 0.5683 0.4145 101 C 0.0129 0.7936 0.1935 102 Q 0.0122 0.8601 0.1277 103 V 0.0101 0.9030 0.0869 104 L 0.0070 0.9267 0.0663 105 G 0.0051 0.9371 0.0579 106 K 0.0046 0.9347 0.0607 107 A 0.0044 0.9279 0.0677 108 V 0.0044 0.9262 0.0694 109 A 0.0047 0.9173 0.0780 110 K 0.0058 0.9202 0.0740 111 K 0.0084 0.9163 0.0753 112 T 0.0088 0.9181 0.0731 113 G 0.0101 0.9088 0.0810 114 W 0.0160 0.8865 0.0974 115 K 0.0249 0.8416 0.1335 116 L 0.0304 0.7631 0.2065 117 R 0.0377 0.6400 0.3223 118 G 0.0566 0.3388 0.6046 119 E 0.0912 0.1511 0.7577 120 D 0.1354 0.1313 0.7333 121 G 0.1255 0.1211 0.7534 122 F 0.1098 0.1358 0.7544 123 K 0.1136 0.1344 0.7520 124 P 0.1638 0.1196 0.7166 125 D 0.3527 0.0946 0.5528 126 N 0.3768 0.0953 0.5279 127 A 0.3208 0.1081 0.5711 128 G 0.2341 0.0914 0.6745 129 Q 0.2362 0.0592 0.7046 130 H 0.7123 0.0342 0.2536 131 S 0.8975 0.0146 0.0880 132 R 0.9178 0.0184 0.0638 133 L 0.8751 0.0231 0.1018 134 A 0.7072 0.0381 0.2547 135 Y 0.3821 0.0449 0.5730 136 A 0.1329 0.0426 0.8245 137 Q 0.0679 0.0260 0.9060 138 A 0.1004 0.0167 0.8828 139 G 0.1935 0.0172 0.7893 140 G 0.8281 0.0126 0.1592 141 I 0.9440 0.0102 0.0457 142 V 0.9578 0.0102 0.0320 143 F 0.9428 0.0124 0.0448 144 E 0.8933 0.0174 0.0894 145 P 0.7154 0.0491 0.2355 146 F 0.5479 0.0754 0.3767 147 F 0.5117 0.0756 0.4127 148 I 0.4053 0.0564 0.5383 149 S 0.1385 0.0317 0.8298 150 N 0.0229 0.0553 0.9218 151 D 0.0038 0.9156 0.0806 152 T 0.0038 0.9365 0.0598 153 D 0.0038 0.9529 0.0433 154 L 0.0038 0.9482 0.0480 155 A 0.0042 0.9035 0.0923 156 L 0.0054 0.8098 0.1848 157 F 0.0087 0.5894 0.4018 158 K 0.0112 0.3393 0.6495 159 T 0.0101 0.0832 0.9067 160 T 0.0042 0.8611 0.1347 161 K 0.0038 0.9162 0.0799 162 W 0.0038 0.9513 0.0449 163 G 0.0037 0.9698 0.0264 164 I 0.0037 0.9723 0.0239 165 C 0.0037 0.9734 0.0229 166 R 0.0037 0.9748 0.0215 167 A 0.0037 0.9759 0.0204 168 I 0.0037 0.9759 0.0204 169 A 0.0037 0.9752 0.0211 170 D 0.0037 0.9752 0.0211 171 A 0.0037 0.9741 0.0222 172 I 0.0037 0.9653 0.0310 173 A 0.0038 0.9507 0.0456 174 M 0.0037 0.9695 0.0267 175 E 0.0037 0.9705 0.0258 176 L 0.0038 0.9596 0.0366 177 G 0.0038 0.9405 0.0557 178 A 0.0042 0.8833 0.1125 179 A 0.0045 0.6991 0.2965 180 K 0.0096 0.4981 0.4922 181 V 0.0089 0.0563 0.9348