# This file is the result of combining several RDB files, specifically # T0253.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0253.t2k.stride-ebghtl.rdb (weight 1.24869) # T0253.t2k.str2.rdb (weight 1.54758) # T0253.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 T0253.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0253 # 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 T0253.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 398 # # ============================================ # Comments from T0253.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0253 # 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 T0253.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 398 # # ============================================ # Comments from T0253.t2k.str2.rdb # ============================================ # TARGET T0253 # 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 T0253.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 398 # # ============================================ # Comments from T0253.t2k.alpha.rdb # ============================================ # TARGET T0253 # 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 T0253.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 398 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0208 0.5201 0.4590 2 E 0.0126 0.8674 0.1200 3 A 0.0090 0.8805 0.1105 4 L 0.0063 0.9045 0.0892 5 K 0.0071 0.9200 0.0729 6 R 0.0077 0.9164 0.0759 7 K 0.0097 0.8804 0.1098 8 I 0.0309 0.7826 0.1866 9 E 0.0247 0.6972 0.2781 10 E 0.0374 0.4790 0.4835 11 E 0.0778 0.2077 0.7145 12 G 0.0813 0.1354 0.7833 13 V 0.1539 0.1181 0.7280 14 V 0.2755 0.0516 0.6729 15 L 0.1746 0.0478 0.7776 16 S 0.0947 0.0956 0.8097 17 D 0.0525 0.0853 0.8622 18 Q 0.1007 0.0612 0.8381 19 V 0.5857 0.0132 0.4011 20 L 0.7803 0.0089 0.2108 21 K 0.7549 0.0166 0.2285 22 V 0.6624 0.0332 0.3044 23 D 0.4433 0.0765 0.4803 24 S 0.2824 0.0813 0.6363 25 F 0.0911 0.4180 0.4909 26 L 0.0654 0.5396 0.3950 27 N 0.0437 0.6314 0.3250 28 H 0.0444 0.6122 0.3434 29 Q 0.0610 0.4810 0.4580 30 I 0.0535 0.3220 0.6244 31 D 0.0687 0.1440 0.7873 32 P 0.0055 0.9229 0.0717 33 L 0.0049 0.9399 0.0552 34 L 0.0050 0.9477 0.0473 35 M 0.0047 0.9573 0.0380 36 Q 0.0047 0.9577 0.0376 37 R 0.0048 0.9566 0.0387 38 I 0.0048 0.9548 0.0404 39 G 0.0047 0.9580 0.0373 40 D 0.0047 0.9572 0.0381 41 E 0.0047 0.9565 0.0388 42 F 0.0047 0.9536 0.0417 43 A 0.0048 0.9463 0.0489 44 S 0.0051 0.9209 0.0740 45 R 0.0060 0.8910 0.1030 46 F 0.0131 0.8426 0.1444 47 A 0.0083 0.7605 0.2312 48 K 0.0142 0.5391 0.4468 49 D 0.0559 0.2287 0.7154 50 G 0.0692 0.0430 0.8879 51 I 0.1425 0.0103 0.8472 52 T 0.2784 0.0410 0.6805 53 K 0.9039 0.0064 0.0896 54 I 0.9230 0.0056 0.0714 55 V 0.8940 0.0121 0.0939 56 T 0.7333 0.0236 0.2430 57 I 0.3253 0.1311 0.5436 58 E 0.1134 0.2663 0.6203 59 S 0.0591 0.3705 0.5704 60 S 0.0366 0.2558 0.7077 61 G 0.0373 0.2885 0.6742 62 I 0.0420 0.5553 0.4027 63 A 0.0212 0.8122 0.1666 64 P 0.0100 0.9015 0.0885 65 A 0.0059 0.9381 0.0560 66 V 0.0054 0.9510 0.0436 67 M 0.0051 0.9569 0.0380 68 T 0.0047 0.9578 0.0374 69 G 0.0048 0.9565 0.0386 70 L 0.0062 0.9398 0.0540 71 K 0.0081 0.8909 0.1009 72 L 0.0466 0.5003 0.4531 73 G 0.0414 0.0262 0.9324 74 V 0.0662 0.0104 0.9234 75 P 0.1718 0.0209 0.8073 76 V 0.7468 0.0110 0.2422 77 V 0.8622 0.0082 0.1296 78 F 0.8898 0.0062 0.1040 79 A 0.8263 0.0159 0.1578 80 R 0.6743 0.0221 0.3037 81 K 0.4093 0.0702 0.5205 82 H 0.2236 0.1304 0.6460 83 K 0.1696 0.1034 0.7271 84 S 0.2362 0.0738 0.6900 85 L 0.2839 0.0441 0.6719 86 T 0.1947 0.0716 0.7337 87 L 0.1294 0.0772 0.7934 88 T 0.1275 0.0921 0.7804 89 D 0.1144 0.0788 0.8068 90 N 0.1984 0.0571 0.7445 91 L 0.5649 0.0245 0.4106 92 L 0.7934 0.0145 0.1921 93 T 0.8282 0.0184 0.1533 94 A 0.7944 0.0187 0.1870 95 S 0.7552 0.0177 0.2272 96 V 0.7624 0.0272 0.2105 97 Y 0.7351 0.0367 0.2282 98 S 0.7118 0.0402 0.2479 99 F 0.5466 0.0985 0.3549 100 T 0.4116 0.1224 0.4660 101 K 0.2744 0.0999 0.6257 102 Q 0.2102 0.0538 0.7359 103 T 0.3814 0.0378 0.5808 104 E 0.5904 0.0240 0.3856 105 S 0.7422 0.0159 0.2420 106 Q 0.8594 0.0076 0.1330 107 I 0.8748 0.0059 0.1193 108 A 0.8929 0.0048 0.1023 109 V 0.8022 0.0086 0.1893 110 S 0.5201 0.0146 0.4653 111 G 0.0903 0.5170 0.3927 112 T 0.0522 0.5660 0.3818 113 H 0.0751 0.5368 0.3881 114 L 0.2003 0.1562 0.6434 115 S 0.0854 0.0679 0.8467 116 D 0.0253 0.1078 0.8669 117 Q 0.0232 0.0526 0.9242 118 D 0.1917 0.0212 0.7871 119 H 0.6066 0.0064 0.3870 120 V 0.8962 0.0037 0.1001 121 L 0.9163 0.0046 0.0791 122 I 0.9104 0.0064 0.0832 123 I 0.8250 0.0180 0.1570 124 D 0.5178 0.0495 0.4328 125 D 0.4315 0.1408 0.4277 126 F 0.3543 0.3364 0.3093 127 L 0.2168 0.4752 0.3079 128 A 0.0943 0.4330 0.4727 129 N 0.0618 0.3886 0.5496 130 G 0.0398 0.3937 0.5664 131 Q 0.0250 0.7103 0.2646 132 A 0.0164 0.8563 0.1272 133 A 0.0047 0.9543 0.0410 134 H 0.0047 0.9594 0.0360 135 G 0.0047 0.9578 0.0375 136 L 0.0047 0.9595 0.0358 137 V 0.0047 0.9599 0.0355 138 S 0.0047 0.9607 0.0347 139 I 0.0047 0.9603 0.0350 140 V 0.0047 0.9592 0.0360 141 K 0.0049 0.9500 0.0450 142 Q 0.0054 0.9019 0.0927 143 A 0.0428 0.3491 0.6081 144 G 0.0441 0.0154 0.9405 145 A 0.1075 0.0092 0.8834 146 S 0.6982 0.0069 0.2948 147 I 0.9047 0.0030 0.0923 148 A 0.8708 0.0166 0.1126 149 G 0.9202 0.0032 0.0766 150 I 0.9244 0.0032 0.0724 151 G 0.9237 0.0034 0.0729 152 I 0.9218 0.0036 0.0746 153 V 0.9134 0.0048 0.0819 154 I 0.8533 0.0102 0.1364 155 E 0.6073 0.0144 0.3783 156 K 0.2100 0.1602 0.6298 157 S 0.0470 0.2960 0.6569 158 F 0.0465 0.3627 0.5908 159 Q 0.0513 0.3616 0.5871 160 P 0.0555 0.2926 0.6519 161 G 0.0473 0.5145 0.4383 162 R 0.0632 0.6832 0.2536 163 D 0.0753 0.7273 0.1974 164 E 0.0514 0.8270 0.1216 165 L 0.0300 0.8716 0.0983 166 V 0.0163 0.8832 0.1005 167 K 0.0240 0.8297 0.1464 168 L 0.0500 0.3604 0.5897 169 G 0.0463 0.0199 0.9339 170 Y 0.1004 0.0087 0.8908 171 R 0.3955 0.0068 0.5977 172 V 0.8009 0.0103 0.1888 173 E 0.8535 0.0143 0.1322 174 S 0.8719 0.0106 0.1174 175 L 0.8707 0.0079 0.1214 176 A 0.8064 0.0093 0.1843 177 R 0.7342 0.0115 0.2543 178 I 0.5331 0.2180 0.2489 179 Q 0.4413 0.3343 0.2244 180 S 0.3622 0.3633 0.2745 181 L 0.3174 0.3672 0.3154 182 E 0.2076 0.3353 0.4571 183 E 0.0723 0.2062 0.7214 184 G 0.0687 0.0794 0.8519 185 K 0.3321 0.0231 0.6448 186 V 0.6854 0.0075 0.3071 187 S 0.8657 0.0046 0.1297 188 F 0.8739 0.0047 0.1214 189 V 0.8594 0.0053 0.1353 190 Q 0.7295 0.0099 0.2605 191 E 0.4560 0.0188 0.5252 192 V 0.1474 0.0509 0.8017 193 H 0.0635 0.0388 0.8978 194 S 0.0543 0.0273 0.9183