# This file is the result of combining several RDB files, specifically # T0323.t04.dssp-ebghstl.rdb (weight 1.53986) # T0323.t04.stride-ebghtl.rdb (weight 1.24869) # T0323.t04.str2.rdb (weight 1.54758) # T0323.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 T0323.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0323 # Using neural net t06-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 T0323.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 1224 # # ============================================ # Comments from T0323.t04.stride-ebghtl.rdb # ============================================ # TARGET T0323 # 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 T0323.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 1224 # # ============================================ # Comments from T0323.t04.str2.rdb # ============================================ # TARGET T0323 # Using neural net t06-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 T0323.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 1224 # # ============================================ # Comments from T0323.t04.alpha.rdb # ============================================ # TARGET T0323 # 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 T0323.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 1224 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0909 0.0390 0.8701 2 R 0.1544 0.0816 0.7640 3 Y 0.1683 0.1029 0.7288 4 F 0.1141 0.1312 0.7546 5 S 0.0866 0.1247 0.7887 6 T 0.0521 0.1266 0.8213 7 D 0.0562 0.0783 0.8655 8 S 0.0346 0.4491 0.5163 9 P 0.0074 0.7984 0.1943 10 E 0.0099 0.8707 0.1195 11 V 0.0143 0.8853 0.1004 12 K 0.0154 0.8852 0.0994 13 T 0.0182 0.8742 0.1076 14 I 0.0162 0.8816 0.1022 15 V 0.0173 0.8696 0.1131 16 A 0.0174 0.8008 0.1818 17 Q 0.0241 0.7026 0.2734 18 D 0.0441 0.5951 0.3608 19 S 0.0051 0.8575 0.1374 20 R 0.0056 0.8856 0.1088 21 L 0.0052 0.9362 0.0586 22 F 0.0050 0.9527 0.0423 23 Q 0.0050 0.9557 0.0393 24 F 0.0049 0.9543 0.0408 25 I 0.0055 0.9490 0.0456 26 E 0.0067 0.9158 0.0774 27 I 0.0152 0.7824 0.2023 28 A 0.0538 0.4453 0.5009 29 G 0.0324 0.1248 0.8428 30 E 0.0667 0.0992 0.8341 31 V 0.1454 0.0441 0.8106 32 Q 0.1840 0.0347 0.7814 33 L 0.1345 0.0230 0.8425 34 P 0.0982 0.0374 0.8644 35 T 0.0795 0.0571 0.8634 36 K 0.0787 0.0326 0.8887 37 P 0.0545 0.0401 0.9054 38 N 0.0763 0.0561 0.8676 39 P 0.0059 0.9106 0.0835 40 F 0.0048 0.9456 0.0495 41 Q 0.0047 0.9562 0.0391 42 S 0.0050 0.9594 0.0357 43 L 0.0047 0.9604 0.0349 44 V 0.0047 0.9611 0.0342 45 S 0.0046 0.9614 0.0340 46 S 0.0046 0.9608 0.0345 47 I 0.0047 0.9574 0.0379 48 V 0.0048 0.9459 0.0493 49 E 0.0050 0.9078 0.0871 50 Q 0.0078 0.8347 0.1575 51 Q 0.0182 0.7235 0.2583 52 L 0.0517 0.5641 0.3842 53 S 0.0733 0.4247 0.5021 54 I 0.0068 0.9426 0.0507 55 K 0.0059 0.9529 0.0412 56 A 0.0057 0.9511 0.0432 57 A 0.0051 0.9528 0.0421 58 S 0.0047 0.9565 0.0388 59 A 0.0047 0.9521 0.0432 60 I 0.0048 0.9465 0.0487 61 Y 0.0047 0.9506 0.0446 62 G 0.0047 0.9549 0.0404 63 R 0.0047 0.9552 0.0401 64 V 0.0048 0.9547 0.0406 65 E 0.0049 0.9547 0.0404 66 Q 0.0055 0.9441 0.0504 67 L 0.0110 0.8980 0.0909 68 V 0.0471 0.6782 0.2747 69 G 0.0278 0.1709 0.8012 70 G 0.0385 0.1245 0.8370 71 A 0.0788 0.1616 0.7596 72 L 0.1021 0.0647 0.8332 73 E 0.0812 0.0465 0.8723 74 K 0.0769 0.0294 0.8937 75 P 0.0054 0.9184 0.0762 76 E 0.0050 0.9394 0.0556 77 Q 0.0058 0.9255 0.0688 78 L 0.0094 0.8839 0.1066 79 Y 0.0144 0.6258 0.3598 80 R 0.0262 0.2245 0.7493 81 V 0.0697 0.0430 0.8873 82 S 0.0673 0.0211 0.9116 83 D 0.0052 0.8972 0.0976 84 E 0.0048 0.9233 0.0719 85 A 0.0048 0.9351 0.0601 86 L 0.0083 0.9236 0.0682 87 R 0.0102 0.8730 0.1168 88 Q 0.0110 0.8358 0.1532 89 A 0.0454 0.5259 0.4287 90 G 0.0414 0.1669 0.7917 91 V 0.0651 0.1582 0.7767 92 S 0.0539 0.2932 0.6528 93 K 0.0079 0.8496 0.1425 94 R 0.0088 0.8932 0.0980 95 K 0.0063 0.9332 0.0605 96 I 0.0059 0.9529 0.0412 97 E 0.0049 0.9581 0.0370 98 Y 0.0047 0.9587 0.0366 99 I 0.0047 0.9597 0.0356 100 R 0.0047 0.9609 0.0345 101 H 0.0047 0.9610 0.0343 102 V 0.0047 0.9596 0.0357 103 C 0.0047 0.9597 0.0356 104 E 0.0047 0.9601 0.0353 105 H 0.0047 0.9580 0.0373 106 V 0.0048 0.9538 0.0414 107 E 0.0054 0.9322 0.0624 108 S 0.0346 0.6802 0.2852 109 G 0.0258 0.1892 0.7850 110 R 0.0574 0.1136 0.8290 111 L 0.0768 0.0672 0.8560 112 D 0.0925 0.0499 0.8576 113 F 0.0186 0.7793 0.2021 114 T 0.0100 0.8469 0.1430 115 E 0.0142 0.8556 0.1303 116 L 0.0287 0.7697 0.2017 117 E 0.0210 0.5346 0.4444 118 G 0.0248 0.2451 0.7302 119 A 0.0627 0.0339 0.9034 120 E 0.0765 0.0477 0.8758 121 A 0.0071 0.8425 0.1504 122 T 0.0048 0.9342 0.0610 123 T 0.0048 0.9492 0.0460 124 V 0.0048 0.9551 0.0401 125 I 0.0047 0.9579 0.0374 126 E 0.0047 0.9583 0.0370 127 K 0.0050 0.9496 0.0453 128 L 0.0051 0.9295 0.0654 129 T 0.0062 0.8422 0.1515 130 A 0.0126 0.6030 0.3845 131 I 0.0709 0.2036 0.7255 132 K 0.0258 0.2456 0.7286 133 G 0.0470 0.1624 0.7906 134 I 0.0978 0.2157 0.6866 135 G 0.0529 0.3111 0.6361 136 Q 0.0074 0.8734 0.1193 137 W 0.0059 0.9303 0.0638 138 T 0.0051 0.9501 0.0448 139 A 0.0047 0.9593 0.0361 140 E 0.0047 0.9609 0.0344 141 M 0.0046 0.9608 0.0345 142 F 0.0047 0.9606 0.0348 143 M 0.0047 0.9602 0.0351 144 M 0.0048 0.9577 0.0376 145 F 0.0057 0.9410 0.0533 146 S 0.0076 0.8821 0.1103 147 L 0.0438 0.4642 0.4920 148 G 0.0251 0.0817 0.8932 149 R 0.0748 0.0377 0.8875 150 L 0.1281 0.0603 0.8117 151 D 0.1997 0.0698 0.7305 152 V 0.5925 0.0308 0.3767 153 L 0.6789 0.0210 0.3000 154 S 0.5706 0.0317 0.3978 155 V 0.2542 0.2209 0.5249 156 G 0.0948 0.1978 0.7074 157 D 0.0685 0.4968 0.4347 158 V 0.0261 0.7622 0.2116 159 G 0.0242 0.8610 0.1148 160 L 0.0165 0.9240 0.0594 161 Q 0.0135 0.9450 0.0415 162 R 0.0118 0.9490 0.0393 163 G 0.0092 0.9494 0.0414 164 A 0.0139 0.9372 0.0489 165 K 0.0212 0.9192 0.0596 166 W 0.0180 0.8906 0.0914 167 L 0.0292 0.7854 0.1854 168 Y 0.0467 0.4381 0.5152 169 G 0.0562 0.1752 0.7686 170 N 0.0774 0.0883 0.8343 171 G 0.0569 0.0851 0.8580 172 E 0.0597 0.0925 0.8478 173 G 0.0523 0.0725 0.8752 174 D 0.0453 0.1428 0.8119 175 G 0.0528 0.1911 0.7560 176 K 0.0131 0.8884 0.0985 177 K 0.0101 0.9354 0.0545 178 L 0.0091 0.9425 0.0485 179 L 0.0090 0.9447 0.0464 180 I 0.0118 0.9395 0.0487 181 Y 0.0135 0.9177 0.0688 182 H 0.0086 0.8910 0.1004 183 G 0.0126 0.8340 0.1534 184 K 0.0144 0.7830 0.2025 185 A 0.0183 0.6804 0.3013 186 W 0.0403 0.4807 0.4790 187 A 0.0590 0.0649 0.8762 188 P 0.0500 0.1068 0.8432 189 Y 0.0295 0.5138 0.4567 190 E 0.0341 0.6396 0.3264 191 T 0.0424 0.7374 0.2202 192 V 0.0311 0.8803 0.0886 193 A 0.0410 0.8813 0.0777 194 C 0.0538 0.8648 0.0814 195 L 0.0703 0.8372 0.0925 196 Y 0.1091 0.7679 0.1230 197 L 0.1222 0.7382 0.1396 198 W 0.1341 0.6923 0.1736 199 K 0.1672 0.6066 0.2262 200 A 0.1730 0.5111 0.3159 201 A 0.1278 0.3248 0.5474 202 G 0.1011 0.1692 0.7297 203 T 0.1950 0.1839 0.6211 204 F 0.2348 0.2211 0.5441 205 A 0.1332 0.3583 0.5086 206 E 0.1067 0.3869 0.5064 207 E 0.0899 0.3885 0.5216 208 Y 0.0842 0.2737 0.6421 209 R 0.0716 0.2632 0.6652 210 S 0.0655 0.3388 0.5957 211 L 0.0528 0.4578 0.4894 212 E 0.0227 0.7465 0.2307 213 E 0.0176 0.7656 0.2168 214 L 0.0240 0.7081 0.2680 215 L 0.0270 0.5675 0.4054 216 H 0.0377 0.4497 0.5127 217 H 0.0654 0.2613 0.6734 218 G 0.0473 0.2615 0.6913 219 N 0.0626 0.2227 0.7148 220 Q 0.0813 0.1751 0.7436 221 C 0.0786 0.0862 0.8353