# This file is the result of combining several RDB files, specifically # T0252.t04.dssp-ebghstl.rdb (weight 1.53986) # T0252.t04.stride-ebghtl.rdb (weight 1.24869) # T0252.t04.str2.rdb (weight 1.54758) # T0252.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 T0252.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0252 # 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 T0252.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 17.5609 # # ============================================ # Comments from T0252.t04.stride-ebghtl.rdb # ============================================ # TARGET T0252 # 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 T0252.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 17.5609 # # ============================================ # Comments from T0252.t04.str2.rdb # ============================================ # TARGET T0252 # 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 T0252.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 17.5609 # # ============================================ # Comments from T0252.t04.alpha.rdb # ============================================ # TARGET T0252 # 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 T0252.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 17.5609 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0779 0.0649 0.8572 2 L 0.1016 0.1119 0.7865 3 D 0.0844 0.1118 0.8038 4 A 0.0254 0.5707 0.4039 5 N 0.0211 0.7258 0.2531 6 K 0.0192 0.7414 0.2394 7 L 0.0070 0.9069 0.0861 8 Q 0.0057 0.9482 0.0461 9 Q 0.0047 0.9578 0.0375 10 A 0.0047 0.9574 0.0379 11 V 0.0047 0.9565 0.0387 12 D 0.0047 0.9550 0.0403 13 Q 0.0048 0.9486 0.0466 14 A 0.0051 0.9350 0.0598 15 Y 0.0068 0.9190 0.0742 16 T 0.0090 0.8909 0.1001 17 Q 0.0134 0.8241 0.1624 18 F 0.0465 0.7035 0.2500 19 H 0.1375 0.5119 0.3506 20 S 0.2019 0.4055 0.3926 21 L 0.1332 0.2568 0.6099 22 N 0.0779 0.1565 0.7656 23 G 0.0466 0.0604 0.8930 24 G 0.0830 0.0519 0.8651 25 Q 0.2872 0.0687 0.6441 26 N 0.4711 0.0830 0.4459 27 A 0.3963 0.1704 0.4334 28 D 0.4134 0.2206 0.3660 29 Y 0.4359 0.2581 0.3060 30 I 0.2812 0.3332 0.3855 31 P 0.1674 0.4968 0.3358 32 F 0.1714 0.5582 0.2705 33 L 0.1413 0.6325 0.2262 34 A 0.1175 0.4735 0.4090 35 N 0.0841 0.2287 0.6872 36 V 0.1047 0.0372 0.8581 37 P 0.0846 0.0257 0.8897 38 G 0.0294 0.2628 0.7078 39 Q 0.0484 0.2592 0.6924 40 L 0.2953 0.1845 0.5202 41 A 0.7107 0.0170 0.2723 42 A 0.9000 0.0041 0.0959 43 V 0.9274 0.0033 0.0694 44 A 0.9276 0.0036 0.0688 45 I 0.9268 0.0035 0.0697 46 V 0.9143 0.0051 0.0807 47 T 0.8262 0.0075 0.1663 48 C 0.3495 0.0494 0.6011 49 D 0.0649 0.0213 0.9138 50 G 0.0745 0.0324 0.8932 51 N 0.5605 0.0208 0.4187 52 V 0.8897 0.0078 0.1025 53 Y 0.8394 0.0187 0.1418 54 S 0.8034 0.0136 0.1830 55 A 0.5915 0.0438 0.3648 56 G 0.3417 0.0418 0.6165 57 D 0.2678 0.0746 0.6576 58 S 0.2033 0.1408 0.6559 59 D 0.2615 0.1095 0.6290 60 Y 0.4927 0.0370 0.4704 61 R 0.6106 0.0261 0.3634 62 F 0.7441 0.0169 0.2390 63 A 0.7392 0.0302 0.2306 64 L 0.7038 0.0933 0.2029 65 E 0.6068 0.1559 0.2373 66 S 0.5530 0.1763 0.2706 67 I 0.2591 0.3599 0.3810 68 S 0.1338 0.4770 0.3892 69 K 0.0301 0.8095 0.1604 70 V 0.0124 0.9201 0.0675 71 C 0.0103 0.9387 0.0510 72 T 0.0091 0.9523 0.0386 73 L 0.0077 0.9549 0.0374 74 A 0.0071 0.9568 0.0361 75 L 0.0080 0.9540 0.0380 76 A 0.0091 0.9446 0.0463 77 L 0.0123 0.9201 0.0676 78 E 0.0163 0.8663 0.1174 79 D 0.0239 0.6977 0.2784 80 V 0.0597 0.4695 0.4707 81 G 0.0512 0.0812 0.8676 82 P 0.0135 0.8299 0.1566 83 Q 0.0074 0.9249 0.0678 84 A 0.0097 0.9361 0.0542 85 V 0.0096 0.9437 0.0467 86 Q 0.0103 0.9342 0.0554 87 D 0.0119 0.9148 0.0732 88 K 0.0193 0.8378 0.1430 89 I 0.0681 0.5227 0.4092 90 G 0.0678 0.0994 0.8329 91 A 0.1109 0.0602 0.8289 92 D 0.1358 0.0403 0.8239 93 P 0.0748 0.1174 0.8078 94 T 0.0937 0.0609 0.8454 95 G 0.0560 0.0589 0.8850 96 L 0.0708 0.0415 0.8877 97 P 0.0928 0.1297 0.7775 98 F 0.1119 0.2009 0.6872 99 N 0.1241 0.2454 0.6304 100 S 0.1490 0.4523 0.3987 101 V 0.2497 0.5293 0.2210 102 I 0.4377 0.3983 0.1640 103 A 0.4425 0.3999 0.1576 104 L 0.4502 0.3655 0.1842 105 E 0.4761 0.2989 0.2249 106 L 0.3039 0.3080 0.3881 107 H 0.1374 0.1599 0.7027 108 G 0.0404 0.0414 0.9183 109 G 0.0438 0.0362 0.9200 110 K 0.1568 0.0167 0.8265 111 P 0.2799 0.0236 0.6965 112 L 0.2406 0.0473 0.7120 113 S 0.1671 0.0577 0.7753 114 P 0.0869 0.3707 0.5424 115 L 0.1656 0.4803 0.3541 116 V 0.2650 0.5095 0.2255 117 N 0.2028 0.5376 0.2597 118 A 0.1189 0.6689 0.2123 119 G 0.0995 0.6462 0.2543 120 A 0.1773 0.6977 0.1251 121 I 0.2102 0.6954 0.0943 122 A 0.2521 0.6522 0.0957 123 T 0.1905 0.6751 0.1344 124 T 0.1156 0.6899 0.1945 125 S 0.0804 0.6170 0.3026 126 L 0.0632 0.5495 0.3873 127 I 0.1112 0.3085 0.5803 128 N 0.0679 0.2155 0.7166 129 A 0.0313 0.3766 0.5920 130 E 0.0347 0.4174 0.5480 131 N 0.0581 0.3755 0.5664 132 V 0.0086 0.8772 0.1141 133 E 0.0057 0.9368 0.0576 134 Q 0.0049 0.9461 0.0490 135 R 0.0048 0.9479 0.0474 136 W 0.0047 0.9542 0.0411 137 Q 0.0048 0.9569 0.0383 138 R 0.0048 0.9563 0.0389 139 I 0.0047 0.9580 0.0372 140 L 0.0047 0.9600 0.0353 141 H 0.0047 0.9602 0.0351 142 I 0.0047 0.9593 0.0361 143 Q 0.0047 0.9567 0.0386 144 Q 0.0053 0.9527 0.0420 145 Q 0.0071 0.9332 0.0597 146 L 0.0119 0.8656 0.1225 147 A 0.0395 0.5947 0.3658 148 G 0.0292 0.2026 0.7681 149 E 0.0618 0.1040 0.8343 150 Q 0.1437 0.1167 0.7396 151 V 0.2851 0.0834 0.6315 152 A 0.3649 0.0734 0.5618 153 L 0.3475 0.1361 0.5165 154 S 0.1420 0.1823 0.6757 155 D 0.0189 0.7409 0.2402 156 E 0.0535 0.7737 0.1728 157 V 0.0844 0.7588 0.1568 158 N 0.0895 0.7119 0.1986 159 Q 0.0872 0.6244 0.2885 160 S 0.0746 0.5723 0.3531 161 E 0.0517 0.6776 0.2707 162 Q 0.0587 0.5852 0.3561 163 T 0.0610 0.5211 0.4179 164 T 0.0484 0.4370 0.5147 165 N 0.0261 0.5334 0.4406 166 F 0.0197 0.8060 0.1742 167 H 0.0095 0.8987 0.0918 168 N 0.0064 0.9360 0.0576 169 R 0.0048 0.9553 0.0399 170 A 0.0047 0.9595 0.0358 171 I 0.0047 0.9595 0.0359 172 A 0.0047 0.9603 0.0350 173 W 0.0047 0.9585 0.0367 174 L 0.0048 0.9570 0.0382 175 L 0.0050 0.9509 0.0441 176 Y 0.0066 0.9322 0.0611 177 S 0.0089 0.8817 0.1094 178 A 0.0432 0.4227 0.5341 179 G 0.0278 0.0799 0.8923 180 Y 0.0904 0.0710 0.8386 181 L 0.1929 0.0992 0.7079 182 Y 0.1369 0.1476 0.7155 183 C 0.0675 0.2429 0.6896 184 D 0.0757 0.3101 0.6142 185 A 0.0113 0.8920 0.0967 186 M 0.0115 0.9181 0.0704 187 E 0.0128 0.9269 0.0603 188 A 0.0093 0.9397 0.0510 189 C 0.0138 0.9212 0.0650 190 D 0.0135 0.9105 0.0760 191 V 0.0126 0.9182 0.0691 192 Y 0.0208 0.9026 0.0767 193 T 0.0234 0.8731 0.1035 194 R 0.0346 0.8130 0.1524 195 Q 0.0490 0.7392 0.2118 196 C 0.0706 0.6219 0.3074 197 S 0.1345 0.5221 0.3434 198 T 0.2111 0.4677 0.3212 199 L 0.4151 0.3077 0.2772 200 L 0.4495 0.1510 0.3995 201 N 0.2609 0.1259 0.6132 202 T 0.0086 0.9381 0.0532 203 I 0.0047 0.9575 0.0379 204 E 0.0046 0.9609 0.0345 205 L 0.0047 0.9608 0.0345 206 A 0.0047 0.9607 0.0347 207 T 0.0046 0.9616 0.0338 208 L 0.0046 0.9609 0.0344 209 G 0.0047 0.9600 0.0353 210 A 0.0047 0.9592 0.0361 211 T 0.0047 0.9571 0.0382 212 L 0.0051 0.9461 0.0488 213 A 0.0066 0.8979 0.0955 214 A 0.0295 0.6061 0.3644 215 G 0.0442 0.1644 0.7913 216 G 0.0447 0.0444 0.9110 217 V 0.1778 0.0337 0.7885 218 N 0.2086 0.0195 0.7719 219 P 0.0706 0.1444 0.7850 220 L 0.0718 0.1290 0.7992 221 T 0.0975 0.0983 0.8043 222 H 0.0856 0.1251 0.7892 223 K 0.2661 0.1195 0.6143 224 R 0.5432 0.0866 0.3702 225 V 0.5116 0.0800 0.4084 226 L 0.4084 0.0417 0.5499 227 Q 0.1544 0.0405 0.8052 228 A 0.0103 0.7038 0.2859 229 D 0.0111 0.6198 0.3692 230 N 0.0206 0.6373 0.3421 231 V 0.0326 0.5794 0.3880 232 P 0.0271 0.7073 0.2656 233 Y 0.0737 0.7950 0.1313 234 I 0.1345 0.7659 0.0996 235 L 0.1808 0.6885 0.1308 236 A 0.1462 0.6797 0.1741 237 E 0.1579 0.6682 0.1739 238 M 0.2057 0.6162 0.1782 239 M 0.2075 0.5446 0.2479 240 M 0.1879 0.4979 0.3142 241 E 0.0996 0.4760 0.4245 242 G 0.0829 0.3425 0.5745 243 L 0.1294 0.3752 0.4955 244 Y 0.1605 0.3771 0.4624 245 G 0.0623 0.3755 0.5621 246 R 0.0378 0.4207 0.5414 247 S 0.0640 0.4144 0.5216 248 G 0.0590 0.3892 0.5518 249 D 0.1112 0.4907 0.3981 250 W 0.2809 0.4957 0.2234 251 A 0.3943 0.4455 0.1602 252 Y 0.4764 0.3727 0.1508 253 R 0.5499 0.2835 0.1667 254 V 0.4999 0.1755 0.3246 255 G 0.2970 0.0841 0.6189 256 L 0.2860 0.0501 0.6639 257 P 0.2695 0.0736 0.6570 258 G 0.2035 0.0964 0.7001 259 K 0.1997 0.1021 0.6982 260 S 0.1973 0.1015 0.7012 261 G 0.1903 0.0901 0.7196 262 V 0.2678 0.0983 0.6338 263 G 0.3147 0.0896 0.5957 264 G 0.3838 0.0795 0.5367 265 G 0.6388 0.0564 0.3048 266 I 0.8114 0.0436 0.1450 267 L 0.8736 0.0359 0.0905 268 A 0.8899 0.0230 0.0871 269 V 0.8677 0.0219 0.1104 270 V 0.6158 0.0187 0.3655 271 P 0.2187 0.0564 0.7249 272 G 0.0983 0.0503 0.8513 273 V 0.3505 0.0433 0.6062 274 M 0.7294 0.0142 0.2564 275 G 0.8796 0.0060 0.1144 276 I 0.9201 0.0038 0.0761 277 A 0.9178 0.0046 0.0776 278 A 0.8984 0.0070 0.0946 279 F 0.8122 0.0095 0.1783 280 S 0.4482 0.0157 0.5361 281 P 0.1732 0.0599 0.7670 282 P 0.1493 0.1093 0.7414 283 L 0.2031 0.1056 0.6913 284 D 0.0641 0.0436 0.8923 285 E 0.0117 0.1903 0.7980 286 D 0.0472 0.0697 0.8831 287 G 0.0704 0.0895 0.8401 288 N 0.0965 0.0863 0.8172 289 S 0.1732 0.2940 0.5329 290 V 0.0523 0.7303 0.2174 291 R 0.0220 0.8425 0.1356 292 G 0.0056 0.9329 0.0615 293 Q 0.0047 0.9598 0.0355 294 K 0.0046 0.9614 0.0340 295 M 0.0046 0.9613 0.0340 296 V 0.0047 0.9608 0.0345 297 A 0.0046 0.9616 0.0337 298 S 0.0046 0.9608 0.0345 299 V 0.0046 0.9605 0.0349 300 A 0.0047 0.9595 0.0359 301 K 0.0049 0.9482 0.0469 302 Q 0.0067 0.9100 0.0833 303 L 0.0444 0.5516 0.4040 304 G 0.0450 0.0758 0.8792 305 Y 0.0688 0.1442 0.7869 306 N 0.0980 0.2276 0.6743 307 V 0.1374 0.2536 0.6090 308 F 0.1430 0.1491 0.7079 309 K 0.0954 0.1028 0.8018 310 G 0.0425 0.0355 0.9219