# This file is the result of combining several RDB files, specifically # T0232.t04.dssp-ebghstl.rdb (weight 1.53986) # T0232.t04.stride-ebghtl.rdb (weight 1.24869) # T0232.t04.str2.rdb (weight 1.54758) # T0232.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 T0232.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0232 # Using neural net t04-2621-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 T0232.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 1765 # # ============================================ # Comments from T0232.t04.stride-ebghtl.rdb # ============================================ # TARGET T0232 # 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 T0232.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 1765 # # ============================================ # Comments from T0232.t04.str2.rdb # ============================================ # TARGET T0232 # Using neural net t04-2621-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 T0232.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 1765 # # ============================================ # Comments from T0232.t04.alpha.rdb # ============================================ # TARGET T0232 # 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 T0232.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 1765 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0632 0.0590 0.8778 2 E 0.0678 0.1051 0.8270 3 D 0.0493 0.1529 0.7978 4 G 0.0433 0.1133 0.8435 5 M 0.0929 0.0441 0.8629 6 N 0.1460 0.0459 0.8081 7 T 0.4064 0.0265 0.5671 8 F 0.7116 0.0076 0.2808 9 D 0.8775 0.0054 0.1171 10 L 0.9005 0.0045 0.0949 11 Y 0.8576 0.0085 0.1339 12 Y 0.7038 0.0127 0.2834 13 W 0.3529 0.0127 0.6344 14 P 0.1613 0.0271 0.8116 15 V 0.0946 0.0273 0.8782 16 P 0.0713 0.0565 0.8722 17 F 0.0314 0.3829 0.5857 18 R 0.0273 0.5994 0.3733 19 G 0.0170 0.8429 0.1401 20 Q 0.0085 0.9385 0.0530 21 L 0.0054 0.9579 0.0367 22 I 0.0054 0.9597 0.0349 23 R 0.0046 0.9614 0.0340 24 G 0.0047 0.9613 0.0341 25 I 0.0047 0.9608 0.0345 26 L 0.0048 0.9592 0.0360 27 A 0.0052 0.9519 0.0429 28 H 0.0074 0.9182 0.0744 29 C 0.0442 0.4330 0.5228 30 G 0.0360 0.0196 0.9444 31 C 0.0663 0.0081 0.9256 32 S 0.2069 0.0077 0.7854 33 W 0.4987 0.0651 0.4362 34 D 0.6760 0.0545 0.2695 35 E 0.8250 0.0360 0.1391 36 H 0.8284 0.0206 0.1510 37 D 0.7877 0.0114 0.2009 38 V 0.5782 0.0265 0.3953 39 D 0.3537 0.0321 0.6142 40 A 0.1144 0.2688 0.6167 41 I 0.0737 0.3758 0.5506 42 E 0.0617 0.3144 0.6239 43 G 0.0484 0.2301 0.7216 44 L 0.1347 0.2904 0.5749 45 M 0.1151 0.2843 0.6005 46 D 0.0852 0.2264 0.6884 47 C 0.0734 0.1583 0.7682 48 G 0.0587 0.1011 0.8402 49 A 0.0175 0.5717 0.4108 50 E 0.0287 0.5325 0.4387 51 K 0.0447 0.5515 0.4039 52 Q 0.0946 0.2717 0.6338 53 P 0.0790 0.3374 0.5837 54 V 0.1328 0.3341 0.5332 55 A 0.1600 0.1656 0.6744 56 F 0.0651 0.1671 0.7678 57 M 0.0959 0.0899 0.8142 58 G 0.0871 0.0290 0.8839 59 P 0.1349 0.0119 0.8532 60 P 0.3541 0.0160 0.6299 61 V 0.8235 0.0079 0.1686 62 L 0.9132 0.0036 0.0832 63 I 0.9084 0.0047 0.0869 64 D 0.7109 0.0061 0.2830 65 R 0.0320 0.1020 0.8660 66 E 0.0280 0.0985 0.8736 67 R 0.0549 0.0417 0.9034 68 N 0.1055 0.0255 0.8691 69 F 0.5509 0.0114 0.4377 70 A 0.7928 0.0112 0.1961 71 I 0.7342 0.0457 0.2200 72 S 0.4917 0.1022 0.4061 73 Q 0.1961 0.1382 0.6657 74 M 0.0494 0.5687 0.3819 75 P 0.0056 0.9336 0.0607 76 A 0.0053 0.9549 0.0398 77 I 0.0047 0.9596 0.0357 78 A 0.0047 0.9602 0.0352 79 I 0.0047 0.9582 0.0371 80 Y 0.0048 0.9520 0.0432 81 L 0.0050 0.9474 0.0476 82 G 0.0060 0.9342 0.0598 83 E 0.0069 0.9039 0.0892 84 R 0.0108 0.8278 0.1615 85 L 0.0581 0.4432 0.4988 86 D 0.0359 0.1508 0.8134 87 I 0.0684 0.0903 0.8413 88 L 0.0822 0.0265 0.8913 89 P 0.0557 0.0919 0.8524 90 A 0.0545 0.1033 0.8423 91 T 0.0655 0.0699 0.8646 92 V 0.0070 0.8998 0.0932 93 E 0.0061 0.9253 0.0686 94 G 0.0057 0.9336 0.0607 95 R 0.0052 0.9461 0.0487 96 T 0.0049 0.9484 0.0467 97 L 0.0047 0.9525 0.0428 98 S 0.0047 0.9577 0.0376 99 A 0.0047 0.9581 0.0371 100 K 0.0048 0.9572 0.0380 101 I 0.0048 0.9525 0.0427 102 V 0.0056 0.9414 0.0530 103 N 0.0060 0.9271 0.0668 104 D 0.0077 0.8906 0.1017 105 A 0.0085 0.8755 0.1160 106 N 0.0147 0.8261 0.1592 107 D 0.0132 0.7885 0.1984 108 V 0.0190 0.7929 0.1881 109 L 0.0348 0.7839 0.1813 110 D 0.0283 0.7932 0.1785 111 E 0.0085 0.8942 0.0973 112 L 0.0139 0.8595 0.1266 113 T 0.0264 0.8015 0.1720 114 L 0.0443 0.7244 0.2313 115 N 0.0561 0.5406 0.4034 116 G 0.0664 0.3267 0.6070 117 G 0.0855 0.1890 0.7256 118 R 0.1093 0.1511 0.7396 119 E 0.0944 0.1518 0.7538 120 M 0.0864 0.1328 0.7808 121 W 0.1066 0.0860 0.8074 122 T 0.0695 0.0399 0.8905 123 P 0.0087 0.8747 0.1166 124 E 0.0066 0.9012 0.0921 125 K 0.0080 0.9069 0.0850 126 W 0.0076 0.9181 0.0744 127 Q 0.0068 0.9160 0.0772 128 E 0.0076 0.8545 0.1379 129 F 0.0094 0.8145 0.1761 130 V 0.0094 0.8607 0.1299 131 P 0.0049 0.9298 0.0653 132 R 0.0050 0.9229 0.0722 133 L 0.0049 0.9516 0.0436 134 Q 0.0047 0.9580 0.0373 135 K 0.0047 0.9579 0.0374 136 W 0.0048 0.9566 0.0386 137 I 0.0047 0.9597 0.0356 138 R 0.0047 0.9606 0.0347 139 I 0.0047 0.9580 0.0373 140 F 0.0047 0.9540 0.0413 141 A 0.0048 0.9499 0.0453 142 D 0.0052 0.9278 0.0670 143 T 0.0127 0.8642 0.1231 144 G 0.0163 0.7544 0.2294 145 A 0.0160 0.6637 0.3204 146 R 0.0254 0.5541 0.4205 147 N 0.0580 0.2311 0.7109 148 G 0.0466 0.1357 0.8177 149 L 0.1053 0.1953 0.6994 150 S 0.1622 0.1948 0.6429 151 A 0.1059 0.2125 0.6816 152 A 0.1133 0.1493 0.7375 153 S 0.1466 0.0841 0.7693 154 G 0.1980 0.0830 0.7190 155 F 0.5320 0.0771 0.3910 156 M 0.6333 0.0615 0.3052 157 L 0.5135 0.0603 0.4262 158 G 0.3207 0.0467 0.6326 159 T 0.2151 0.0593 0.7256 160 E 0.1570 0.1033 0.7398 161 K 0.3734 0.0802 0.5464 162 I 0.5242 0.0629 0.4129 163 G 0.5210 0.0942 0.3848 164 V 0.2818 0.5160 0.2022 165 A 0.2034 0.5895 0.2071 166 D 0.1555 0.5963 0.2482 167 I 0.0692 0.7427 0.1881 168 V 0.0600 0.7837 0.1563 169 T 0.0443 0.8209 0.1348 170 A 0.0635 0.8168 0.1197 171 I 0.0802 0.8325 0.0872 172 L 0.0668 0.8319 0.1013 173 W 0.0712 0.7778 0.1510 174 T 0.0942 0.6837 0.2220 175 T 0.1233 0.6032 0.2735 176 V 0.1365 0.5261 0.3374 177 A 0.1072 0.3853 0.5074 178 D 0.0737 0.2592 0.6670 179 R 0.0586 0.2557 0.6857 180 F 0.0585 0.2479 0.6936 181 P 0.0204 0.5547 0.4249 182 A 0.0201 0.6158 0.3640 183 I 0.0318 0.6410 0.3272 184 K 0.0271 0.6379 0.3350 185 G 0.0250 0.5461 0.4288 186 I 0.0480 0.4686 0.4834 187 I 0.0396 0.5318 0.4285 188 E 0.0224 0.5732 0.4044 189 D 0.0189 0.5124 0.4687 190 T 0.0294 0.4433 0.5273 191 S 0.0509 0.3885 0.5607 192 P 0.0106 0.8677 0.1217 193 I 0.0112 0.9097 0.0791 194 I 0.0050 0.9543 0.0407 195 W 0.0050 0.9590 0.0361 196 G 0.0052 0.9597 0.0351 197 L 0.0050 0.9578 0.0372 198 S 0.0047 0.9588 0.0365 199 R 0.0047 0.9587 0.0366 200 R 0.0048 0.9550 0.0402 201 V 0.0050 0.9390 0.0560 202 V 0.0059 0.8580 0.1362 203 A 0.0101 0.6688 0.3211 204 T 0.0469 0.5326 0.4205 205 A 0.0092 0.7546 0.2362 206 P 0.0098 0.8064 0.1838 207 L 0.0105 0.8935 0.0960 208 A 0.0097 0.9096 0.0807 209 A 0.0108 0.8551 0.1341 210 L 0.0140 0.7243 0.2617 211 N 0.0377 0.3968 0.5654 212 S 0.0138 0.5321 0.4541 213 K 0.0175 0.5590 0.4235 214 S 0.0323 0.5409 0.4268 215 F 0.0478 0.5132 0.4390 216 E 0.0541 0.5486 0.3973 217 E 0.0651 0.4797 0.4552 218 Y 0.1031 0.3501 0.5468 219 G 0.1316 0.2189 0.6495 220 N 0.1164 0.2124 0.6712 221 A 0.0684 0.3085 0.6231 222 Y 0.0928 0.2536 0.6536 223 C 0.1130 0.1732 0.7138 224 G 0.1001 0.1161 0.7839 225 G 0.0991 0.1217 0.7792 226 E 0.1557 0.1561 0.6883 227 I 0.1112 0.2456 0.6432 228 E 0.0754 0.2618 0.6628 229 K 0.0169 0.6829 0.3002 230 S 0.0297 0.6237 0.3466 231 L 0.0363 0.6510 0.3127 232 R 0.0222 0.5395 0.4383 233 K 0.0537 0.4522 0.4941 234 V 0.1009 0.2150 0.6842 235 A 0.0644 0.0872 0.8485 236 S 0.0535 0.0584 0.8881