# This file is the result of combining several RDB files, specifically # T0373.t04.dssp-ebghstl.rdb (weight 1.53986) # T0373.t04.stride-ebghtl.rdb (weight 1.24869) # T0373.t04.str2.rdb (weight 1.54758) # T0373.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 T0373.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0373 # 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 T0373.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 151.605 # # ============================================ # Comments from T0373.t04.stride-ebghtl.rdb # ============================================ # TARGET T0373 # 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 T0373.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 151.605 # # ============================================ # Comments from T0373.t04.str2.rdb # ============================================ # TARGET T0373 # 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 T0373.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 151.605 # # ============================================ # Comments from T0373.t04.alpha.rdb # ============================================ # TARGET T0373 # 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 T0373.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 151.605 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0595 0.0148 0.9257 2 P 0.0628 0.0310 0.9062 3 T 0.0374 0.1262 0.8363 4 N 0.0377 0.2642 0.6981 5 Q 0.0230 0.5896 0.3874 6 D 0.0204 0.8013 0.1783 7 L 0.0079 0.9184 0.0737 8 Q 0.0065 0.9378 0.0556 9 L 0.0050 0.9473 0.0477 10 A 0.0047 0.9553 0.0400 11 A 0.0047 0.9597 0.0356 12 H 0.0047 0.9591 0.0362 13 L 0.0047 0.9596 0.0357 14 R 0.0047 0.9599 0.0354 15 S 0.0047 0.9593 0.0360 16 Q 0.0047 0.9589 0.0364 17 V 0.0047 0.9601 0.0352 18 T 0.0046 0.9605 0.0349 19 T 0.0047 0.9602 0.0351 20 L 0.0047 0.9590 0.0363 21 T 0.0047 0.9598 0.0355 22 R 0.0047 0.9590 0.0364 23 R 0.0047 0.9574 0.0379 24 L 0.0048 0.9519 0.0433 25 R 0.0051 0.9458 0.0491 26 R 0.0049 0.9412 0.0539 27 E 0.0055 0.9249 0.0696 28 A 0.0126 0.8719 0.1155 29 Q 0.0132 0.7214 0.2654 30 A 0.0204 0.4683 0.5114 31 D 0.0654 0.0831 0.8514 32 P 0.0370 0.0693 0.8937 33 V 0.1071 0.0276 0.8653 34 Q 0.0895 0.0343 0.8761 35 F 0.0062 0.9085 0.0853 36 S 0.0048 0.9385 0.0567 37 Q 0.0049 0.9517 0.0433 38 L 0.0047 0.9601 0.0353 39 V 0.0050 0.9602 0.0348 40 V 0.0047 0.9606 0.0347 41 L 0.0047 0.9607 0.0347 42 G 0.0047 0.9593 0.0360 43 A 0.0047 0.9556 0.0397 44 I 0.0049 0.9471 0.0479 45 D 0.0065 0.9213 0.0722 46 R 0.0098 0.8064 0.1838 47 L 0.0499 0.4019 0.5482 48 G 0.0416 0.0467 0.9117 49 G 0.0401 0.0402 0.9197 50 D 0.0870 0.0383 0.8747 51 V 0.1228 0.0112 0.8660 52 T 0.0789 0.0127 0.9084 53 P 0.0049 0.9471 0.0481 54 S 0.0047 0.9603 0.0350 55 E 0.0047 0.9607 0.0346 56 L 0.0047 0.9602 0.0351 57 A 0.0048 0.9552 0.0400 58 A 0.0053 0.9372 0.0575 59 A 0.0065 0.8842 0.1093 60 E 0.0377 0.5526 0.4097 61 R 0.0264 0.1911 0.7825 62 M 0.0723 0.0833 0.8443 63 R 0.0447 0.0947 0.8606 64 S 0.0186 0.6610 0.3205 65 S 0.0133 0.7370 0.2497 66 N 0.0196 0.7830 0.1974 67 L 0.0049 0.9430 0.0521 68 A 0.0047 0.9573 0.0381 69 A 0.0046 0.9595 0.0359 70 L 0.0047 0.9591 0.0362 71 L 0.0047 0.9598 0.0355 72 R 0.0047 0.9599 0.0354 73 E 0.0047 0.9596 0.0357 74 L 0.0049 0.9548 0.0403 75 E 0.0051 0.9284 0.0665 76 R 0.0111 0.7096 0.2792 77 G 0.0442 0.1559 0.7999 78 G 0.0391 0.0219 0.9390 79 L 0.2118 0.0174 0.7708 80 I 0.7844 0.0070 0.2087 81 V 0.8557 0.0075 0.1368 82 R 0.8492 0.0089 0.1420 83 H 0.6723 0.0092 0.3185 84 A 0.5356 0.0140 0.4504 85 D 0.1676 0.0115 0.8209 86 P 0.0141 0.1780 0.8079 87 Q 0.0191 0.1237 0.8572 88 D 0.0773 0.1228 0.7999 89 G 0.0879 0.0895 0.8225 90 R 0.3723 0.0569 0.5708 91 R 0.7501 0.0171 0.2328 92 T 0.8399 0.0135 0.1467 93 R 0.9107 0.0062 0.0831 94 V 0.9173 0.0073 0.0755 95 S 0.9012 0.0136 0.0852 96 L 0.7614 0.0174 0.2211 97 S 0.2191 0.0176 0.7632 98 S 0.0116 0.7323 0.2561 99 E 0.0080 0.8026 0.1893 100 G 0.0067 0.8897 0.1036 101 R 0.0081 0.9317 0.0602 102 R 0.0074 0.9372 0.0554 103 N 0.0059 0.9272 0.0669 104 L 0.0067 0.8989 0.0944 105 Y 0.0067 0.8110 0.1823 106 G 0.0092 0.7257 0.2651 107 N 0.0167 0.6400 0.3433 108 R 0.0096 0.7653 0.2251 109 A 0.0052 0.9082 0.0866 110 K 0.0051 0.9291 0.0658 111 R 0.0049 0.9441 0.0510 112 E 0.0048 0.9554 0.0398 113 E 0.0047 0.9603 0.0350 114 W 0.0047 0.9597 0.0356 115 L 0.0047 0.9594 0.0359 116 V 0.0047 0.9586 0.0367 117 R 0.0048 0.9519 0.0433 118 A 0.0050 0.9288 0.0662 119 M 0.0068 0.8817 0.1115 120 H 0.0083 0.7739 0.2177 121 A 0.0183 0.5078 0.4739 122 C 0.0275 0.2058 0.7666 123 L 0.0756 0.0229 0.9015 124 D 0.0558 0.0145 0.9297 125 E 0.0049 0.9452 0.0498 126 S 0.0047 0.9575 0.0379 127 E 0.0047 0.9594 0.0359 128 R 0.0046 0.9610 0.0344 129 A 0.0047 0.9588 0.0366 130 L 0.0047 0.9534 0.0419 131 L 0.0047 0.9497 0.0455 132 A 0.0053 0.9361 0.0585 133 A 0.0063 0.8683 0.1254 134 A 0.0144 0.8401 0.1455 135 G 0.0091 0.8100 0.1809 136 P 0.0055 0.8691 0.1253 137 L 0.0053 0.9229 0.0717 138 L 0.0047 0.9544 0.0408 139 T 0.0047 0.9585 0.0368 140 R 0.0047 0.9566 0.0387 141 L 0.0048 0.9498 0.0454 142 A 0.0053 0.9285 0.0662 143 Q 0.0068 0.8454 0.1478 144 F 0.0136 0.6847 0.3017 145 E 0.0392 0.4619 0.4990 146 E 0.0465 0.1574 0.7961 147 P 0.0507 0.1317 0.8176 148 M 0.0665 0.0335 0.9000 149 P 0.0532 0.0915 0.8553 150 T 0.0493 0.1882 0.7624 151 N 0.0589 0.2534 0.6877 152 Q 0.0531 0.4125 0.5344 153 D 0.0706 0.4725 0.4570 154 L 0.0792 0.5512 0.3695 155 Q 0.0940 0.5283 0.3778 156 L 0.0927 0.5091 0.3981 157 A 0.0798 0.5012 0.4190 158 A 0.0307 0.7036 0.2657 159 H 0.0369 0.5887 0.3744 160 L 0.0444 0.5894 0.3662 161 R 0.0359 0.6709 0.2933 162 S 0.0387 0.7080 0.2533 163 Q 0.0469 0.7905 0.1626 164 V 0.0569 0.8451 0.0980 165 T 0.0578 0.8553 0.0869 166 T 0.0486 0.8708 0.0806 167 L 0.0346 0.8855 0.0799 168 T 0.0246 0.8953 0.0801 169 R 0.0147 0.9171 0.0682 170 R 0.0175 0.9151 0.0674 171 L 0.0204 0.9061 0.0734 172 R 0.0192 0.8853 0.0955 173 R 0.0116 0.9073 0.0811 174 E 0.0124 0.8578 0.1299 175 A 0.0290 0.7153 0.2557 176 Q 0.0490 0.3678 0.5831 177 A 0.0486 0.1493 0.8021 178 D 0.0564 0.0575 0.8860 179 P 0.0498 0.1278 0.8224 180 V 0.1375 0.0864 0.7761 181 Q 0.2198 0.1004 0.6798 182 F 0.1005 0.6740 0.2255 183 S 0.0941 0.6998 0.2061 184 Q 0.1007 0.7322 0.1671 185 L 0.1681 0.6842 0.1477 186 V 0.1985 0.6607 0.1408 187 V 0.2843 0.5831 0.1326 188 L 0.2560 0.5719 0.1721 189 G 0.1555 0.5329 0.3116 190 A 0.1638 0.5275 0.3087 191 I 0.1923 0.5534 0.2543 192 D 0.1484 0.5288 0.3228 193 R 0.0938 0.5369 0.3693 194 L 0.1222 0.3514 0.5264 195 G 0.0523 0.1577 0.7901 196 G 0.0396 0.0841 0.8763 197 D 0.1071 0.0642 0.8287 198 V 0.1913 0.0587 0.7500 199 T 0.1042 0.0305 0.8653 200 P 0.0449 0.3215 0.6336 201 S 0.0120 0.8033 0.1847 202 E 0.0065 0.9012 0.0923 203 L 0.0055 0.9237 0.0708 204 A 0.0073 0.9195 0.0732 205 A 0.0088 0.8925 0.0987 206 A 0.0107 0.8275 0.1618 207 E 0.0194 0.6941 0.2865 208 R 0.0315 0.5363 0.4321 209 M 0.0427 0.3824 0.5749 210 R 0.0378 0.3534 0.6088 211 S 0.0318 0.4855 0.4827 212 S 0.0250 0.4794 0.4957 213 N 0.0894 0.4884 0.4222 214 L 0.3178 0.5248 0.1574 215 A 0.4160 0.5186 0.0653 216 A 0.4894 0.4558 0.0548 217 L 0.5297 0.3936 0.0767 218 L 0.4398 0.4028 0.1574 219 R 0.2633 0.3734 0.3633 220 E 0.1544 0.2611 0.5845 221 L 0.2969 0.1589 0.5442 222 E 0.3290 0.1235 0.5475 223 R 0.5104 0.0842 0.4054 224 G 0.5218 0.0344 0.4438 225 G 0.6676 0.0228 0.3096 226 L 0.8092 0.0135 0.1773 227 I 0.8737 0.0106 0.1158 228 V 0.8323 0.0113 0.1563 229 R 0.7865 0.0123 0.2013 230 H 0.5240 0.0213 0.4547 231 A 0.3037 0.0272 0.6691 232 D 0.1215 0.0121 0.8664 233 P 0.0253 0.1886 0.7861 234 Q 0.0269 0.1749 0.7982 235 D 0.1156 0.1981 0.6863 236 G 0.2861 0.1116 0.6023 237 R 0.5618 0.0897 0.3485 238 R 0.7705 0.0484 0.1810 239 T 0.7490 0.0388 0.2122 240 R 0.8794 0.0169 0.1037 241 V 0.9059 0.0082 0.0859 242 S 0.8980 0.0075 0.0946 243 L 0.7065 0.0131 0.2804 244 S 0.1968 0.0229 0.7803 245 S 0.0186 0.5789 0.4025 246 E 0.0094 0.6172 0.3734 247 G 0.0239 0.6366 0.3395 248 R 0.0331 0.5801 0.3868 249 R 0.0317 0.5583 0.4100 250 N 0.0245 0.5503 0.4252 251 L 0.0313 0.6033 0.3654 252 Y 0.0257 0.7251 0.2492 253 G 0.0116 0.8478 0.1406 254 N 0.0071 0.8965 0.0964 255 R 0.0077 0.9189 0.0733 256 A 0.0074 0.9307 0.0619 257 K 0.0067 0.9368 0.0565 258 R 0.0063 0.9428 0.0509 259 E 0.0062 0.9442 0.0496 260 E 0.0054 0.9544 0.0403 261 W 0.0057 0.9554 0.0389 262 L 0.0096 0.9447 0.0457 263 V 0.0113 0.9408 0.0479 264 R 0.0137 0.9328 0.0535 265 A 0.0112 0.9143 0.0745 266 M 0.0124 0.7724 0.2152 267 H 0.0158 0.5599 0.4243 268 A 0.0343 0.4370 0.5286 269 C 0.0522 0.3767 0.5712 270 L 0.0401 0.3604 0.5995 271 D 0.0366 0.3794 0.5841 272 E 0.0083 0.7855 0.2062 273 S 0.0060 0.8878 0.1061 274 E 0.0047 0.9468 0.0484 275 R 0.0047 0.9572 0.0381 276 A 0.0047 0.9566 0.0387 277 L 0.0047 0.9555 0.0398 278 L 0.0051 0.9508 0.0442 279 A 0.0073 0.9206 0.0721 280 A 0.0086 0.8305 0.1609 281 A 0.0178 0.6928 0.2894 282 G 0.0129 0.5103 0.4768 283 P 0.0084 0.6788 0.3129 284 L 0.0128 0.7062 0.2809 285 L 0.0242 0.7866 0.1892 286 T 0.0286 0.8040 0.1675 287 R 0.0258 0.7921 0.1820 288 L 0.0370 0.7185 0.2445 289 A 0.0619 0.5549 0.3832 290 Q 0.1295 0.3779 0.4926 291 F 0.1779 0.2553 0.5668 292 E 0.2322 0.1539 0.6140 293 E 0.1481 0.0403 0.8116 294 P 0.0658 0.0375 0.8967