# This file is the result of combining several RDB files, specifically # T0509.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0509.t2k.stride-ebghtl.rdb (weight 1.24869) # T0509.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 T0509.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0509 # 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 T0509.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 69 # # ============================================ # Comments from T0509.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0509 # 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 T0509.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 69 # # ============================================ # Comments from T0509.t2k.str.rdb # ============================================ # TARGET T0509 # 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 T0509.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 69 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0163 0.0136 0.9701 2 S 0.0464 0.0815 0.8721 3 N 0.0286 0.1077 0.8637 4 A 0.0056 0.5486 0.4457 5 F 0.0051 0.6881 0.3067 6 E 0.0058 0.8174 0.1769 7 Y 0.0063 0.9082 0.0854 8 L 0.0044 0.9509 0.0446 9 R 0.0041 0.9630 0.0329 10 T 0.0037 0.9587 0.0376 11 Y 0.0038 0.9540 0.0422 12 V 0.0052 0.9331 0.0617 13 E 0.0056 0.8417 0.1527 14 S 0.0087 0.6580 0.3333 15 T 0.0335 0.3561 0.6104 16 T 0.0534 0.1425 0.8040 17 E 0.0335 0.1167 0.8499 18 T 0.0158 0.1409 0.8434 19 D 0.0117 0.2162 0.7721 20 A 0.0067 0.8085 0.1847 21 A 0.0053 0.8885 0.1062 22 V 0.0060 0.9265 0.0675 23 A 0.0044 0.9408 0.0548 24 R 0.0041 0.9457 0.0501 25 A 0.0042 0.9565 0.0394 26 R 0.0045 0.9520 0.0435 27 E 0.0042 0.9498 0.0460 28 D 0.0046 0.9284 0.0671 29 A 0.0044 0.9045 0.0910 30 A 0.0051 0.8648 0.1301 31 E 0.0063 0.7568 0.2369 32 F 0.0063 0.6255 0.3682 33 G 0.0089 0.3905 0.6006 34 L 0.0139 0.3246 0.6615 35 P 0.0260 0.3176 0.6564 36 A 0.0348 0.3257 0.6395 37 P 0.0405 0.3888 0.5707 38 D 0.0596 0.3833 0.5571 39 E 0.0969 0.3032 0.5999 40 M 0.1221 0.1641 0.7138 41 T 0.0239 0.0768 0.8993 42 G 0.0039 0.8457 0.1504 43 Q 0.0041 0.8971 0.0988 44 L 0.0037 0.9579 0.0384 45 L 0.0037 0.9692 0.0270 46 T 0.0037 0.9730 0.0232 47 T 0.0037 0.9762 0.0200 48 L 0.0037 0.9766 0.0197 49 A 0.0037 0.9766 0.0197 50 A 0.0037 0.9766 0.0197 51 T 0.0037 0.9766 0.0197 52 T 0.0037 0.9737 0.0226 53 N 0.0038 0.9576 0.0386 54 G 0.0039 0.8835 0.1126 55 N 0.0066 0.5448 0.4486 56 G 0.0132 0.0792 0.9076 57 S 0.0279 0.0532 0.9189 58 T 0.0702 0.0767 0.8531 59 G 0.4692 0.0546 0.4762 60 A 0.9203 0.0085 0.0712 61 I 0.9631 0.0038 0.0331 62 A 0.9655 0.0035 0.0310 63 I 0.8770 0.0074 0.1155 64 T 0.5443 0.0317 0.4240 65 P 0.1732 0.1375 0.6893 66 A 0.0676 0.2496 0.6828 67 A 0.0274 0.4104 0.5622 68 G 0.0223 0.4886 0.4890 69 L 0.0110 0.8803 0.1088 70 V 0.0122 0.9264 0.0614 71 G 0.0055 0.9678 0.0267 72 L 0.0055 0.9706 0.0239 73 Y 0.0048 0.9671 0.0281 74 I 0.0052 0.9543 0.0405 75 L 0.0069 0.9113 0.0818 76 N 0.0122 0.6470 0.3408 77 G 0.0382 0.2575 0.7044 78 L 0.1358 0.0499 0.8143 79 A 0.0522 0.0454 0.9024 80 D 0.0200 0.0832 0.8968 81 N 0.0374 0.0545 0.9081 82 T 0.3751 0.0200 0.6049 83 T 0.8572 0.0028 0.1400 84 L 0.9692 0.0024 0.0284 85 T 0.9568 0.0024 0.0408 86 C 0.9167 0.0028 0.0805 87 I 0.6812 0.0043 0.3146 88 D 0.3003 0.0070 0.6926 89 P 0.0354 0.0411 0.9235 90 E 0.0184 0.0991 0.8825 91 S 0.0053 0.7939 0.2008 92 E 0.0054 0.8601 0.1345 93 H 0.0065 0.9183 0.0753 94 Q 0.0038 0.9602 0.0360 95 R 0.0038 0.9661 0.0301 96 Q 0.0037 0.9663 0.0299 97 A 0.0038 0.9659 0.0303 98 K 0.0037 0.9704 0.0259 99 A 0.0037 0.9693 0.0270 100 L 0.0037 0.9721 0.0242 101 F 0.0037 0.9723 0.0239 102 R 0.0038 0.9648 0.0315 103 E 0.0038 0.9298 0.0664 104 A 0.0044 0.6378 0.3578 105 G 0.0110 0.0425 0.9465 106 Y 0.0374 0.0214 0.9412 107 S 0.0770 0.0612 0.8618 108 P 0.0774 0.2085 0.7141 109 S 0.1900 0.2092 0.6008 110 R 0.5370 0.1319 0.3311 111 V 0.7115 0.1053 0.1832 112 R 0.7686 0.0997 0.1317 113 F 0.6835 0.0901 0.2264 114 L 0.3566 0.1001 0.5433 115 L 0.0763 0.1664 0.7573 116 S 0.0224 0.3295 0.6481 117 R 0.0254 0.4741 0.5005 118 P 0.0106 0.7767 0.2127 119 L 0.0081 0.7894 0.2025 120 D 0.0114 0.8007 0.1878 121 V 0.0151 0.7981 0.1868 122 M 0.0121 0.8086 0.1793 123 S 0.0132 0.7716 0.2151 124 R 0.0122 0.7680 0.2198 125 L 0.0174 0.7202 0.2624 126 A 0.0155 0.5846 0.3999 127 N 0.0127 0.2271 0.7602 128 D 0.0194 0.0772 0.9033 129 S 0.0698 0.0333 0.8969 130 Y 0.2085 0.0145 0.7770 131 Q 0.4368 0.0095 0.5537 132 L 0.9343 0.0026 0.0632 133 V 0.9769 0.0024 0.0207 134 F 0.9771 0.0024 0.0204 135 G 0.9482 0.0025 0.0492 136 Q 0.5833 0.0047 0.4120 137 V 0.1106 0.0276 0.8618 138 S 0.0417 0.0421 0.9162 139 P 0.0098 0.5091 0.4811 140 M 0.0067 0.4554 0.5379 141 D 0.0122 0.4720 0.5158 142 L 0.0087 0.6181 0.3732 143 K 0.0038 0.9606 0.0356 144 A 0.0038 0.9688 0.0275 145 L 0.0037 0.9725 0.0238 146 V 0.0037 0.9738 0.0225 147 D 0.0037 0.9700 0.0263 148 A 0.0041 0.9561 0.0398 149 A 0.0041 0.9425 0.0534 150 W 0.0053 0.9146 0.0802 151 P 0.0061 0.8626 0.1313 152 L 0.0112 0.6926 0.2962 153 L 0.0954 0.4379 0.4667 154 R 0.1109 0.1293 0.7598 155 R 0.0547 0.0769 0.8683 156 G 0.0614 0.0281 0.9105 157 G 0.6101 0.0110 0.3788 158 A 0.8690 0.0045 0.1265 159 L 0.9599 0.0045 0.0355 160 V 0.9406 0.0077 0.0517 161 L 0.8757 0.0109 0.1134 162 A 0.4359 0.0833 0.4808 163 D 0.1773 0.2039 0.6188 164 A 0.1770 0.3548 0.4681 165 L 0.1966 0.3846 0.4188 166 L 0.1620 0.2992 0.5388 167 D 0.0692 0.1431 0.7877 168 G 0.0809 0.0430 0.8761 169 T 0.2810 0.0441 0.6749 170 I 0.5067 0.0342 0.4591 171 A 0.2668 0.0332 0.7001 172 D 0.0785 0.0331 0.8884 173 Q 0.0173 0.4731 0.5096 174 T 0.0104 0.4443 0.5454 175 R 0.0217 0.3995 0.5789 176 K 0.0290 0.1129 0.8581 177 D 0.0207 0.0871 0.8921 178 R 0.0048 0.8128 0.1824 179 D 0.0039 0.9020 0.0941 180 T 0.0037 0.9584 0.0379 181 Q 0.0041 0.9691 0.0268 182 A 0.0037 0.9702 0.0261 183 A 0.0037 0.9734 0.0229 184 R 0.0037 0.9727 0.0236 185 D 0.0037 0.9706 0.0257 186 A 0.0037 0.9671 0.0292 187 D 0.0037 0.9679 0.0284 188 E 0.0038 0.9611 0.0351 189 Y 0.0041 0.9457 0.0502 190 I 0.0042 0.9163 0.0795 191 R 0.0062 0.7782 0.2156 192 S 0.0076 0.5491 0.4433 193 I 0.0150 0.1589 0.8261 194 E 0.0191 0.1621 0.8188 195 G 0.0738 0.1502 0.7760 196 A 0.4355 0.0626 0.5019 197 H 0.6977 0.0421 0.2602 198 V 0.8460 0.0435 0.1105 199 A 0.8679 0.0311 0.1010 200 R 0.8424 0.0222 0.1353 201 L 0.6547 0.0147 0.3306 202 P 0.5338 0.0203 0.4459 203 L 0.2599 0.0663 0.6738 204 G 0.0800 0.1521 0.7679 205 A 0.0583 0.1578 0.7840 206 G 0.2636 0.1491 0.5873 207 L 0.6419 0.1306 0.2275 208 T 0.7940 0.0980 0.1080 209 V 0.8517 0.0774 0.0709 210 V 0.8435 0.0561 0.1004 211 T 0.7953 0.0376 0.1671 212 K 0.5098 0.0309 0.4593 213 A 0.0220 0.0056 0.9724