# This file is the result of combining several RDB files, specifically # T0298.t04.dssp-ebghstl.rdb (weight 1.53986) # T0298.t04.stride-ebghtl.rdb (weight 1.24869) # T0298.t04.str2.rdb (weight 1.54758) # T0298.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 T0298.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0298 # 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 T0298.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 82.659 # # ============================================ # Comments from T0298.t04.stride-ebghtl.rdb # ============================================ # TARGET T0298 # 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 T0298.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 82.659 # # ============================================ # Comments from T0298.t04.str2.rdb # ============================================ # TARGET T0298 # 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 T0298.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 82.659 # # ============================================ # Comments from T0298.t04.alpha.rdb # ============================================ # TARGET T0298 # 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 T0298.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 82.659 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0610 0.0341 0.9049 2 S 0.0877 0.0404 0.8719 3 Q 0.1193 0.0399 0.8408 4 P 0.2216 0.0267 0.7516 5 L 0.5479 0.0096 0.4425 6 N 0.7823 0.0050 0.2127 7 V 0.9204 0.0038 0.0758 8 A 0.9289 0.0034 0.0677 9 V 0.9300 0.0031 0.0669 10 V 0.8435 0.0182 0.1383 11 G 0.3537 0.0309 0.6154 12 A 0.1290 0.0746 0.7964 13 T 0.0895 0.1356 0.7748 14 G 0.0484 0.3300 0.6216 15 S 0.0269 0.8324 0.1407 16 V 0.0077 0.9303 0.0620 17 G 0.0052 0.9505 0.0443 18 E 0.0047 0.9603 0.0350 19 A 0.0047 0.9608 0.0346 20 L 0.0047 0.9592 0.0362 21 V 0.0050 0.9571 0.0378 22 G 0.0051 0.9492 0.0457 23 L 0.0059 0.9200 0.0742 24 L 0.0089 0.8765 0.1146 25 D 0.0132 0.6625 0.3243 26 E 0.0213 0.4848 0.4939 27 R 0.0473 0.1635 0.7892 28 D 0.0426 0.0477 0.9098 29 F 0.0920 0.0113 0.8967 30 P 0.2068 0.0153 0.7779 31 L 0.7102 0.0282 0.2616 32 H 0.7801 0.0547 0.1652 33 R 0.8573 0.0217 0.1210 34 L 0.8423 0.0303 0.1274 35 H 0.7697 0.0489 0.1814 36 L 0.7070 0.0630 0.2300 37 L 0.4722 0.0884 0.4394 38 A 0.2650 0.0678 0.6672 39 S 0.1264 0.0561 0.8176 40 A 0.0082 0.7978 0.1940 41 E 0.0101 0.7885 0.2014 42 S 0.0169 0.7883 0.1949 43 A 0.0373 0.7547 0.2080 44 G 0.0849 0.6362 0.2788 45 Q 0.1548 0.5931 0.2521 46 R 0.1779 0.6002 0.2218 47 M 0.2016 0.4904 0.3080 48 G 0.2142 0.2443 0.5415 49 F 0.2397 0.1804 0.5799 50 A 0.2221 0.1026 0.6753 51 E 0.1802 0.1086 0.7112 52 S 0.1940 0.1103 0.6957 53 S 0.4198 0.0821 0.4981 54 L 0.5941 0.0326 0.3733 55 R 0.6673 0.0212 0.3115 56 V 0.6249 0.0474 0.3277 57 G 0.4392 0.0465 0.5143 58 D 0.3195 0.0195 0.6609 59 V 0.0430 0.5681 0.3889 60 D 0.0355 0.5240 0.4405 61 S 0.0458 0.5529 0.4013 62 F 0.1350 0.1357 0.7293 63 D 0.1478 0.1052 0.7470 64 F 0.1012 0.3504 0.5485 65 S 0.0553 0.2422 0.7025 66 S 0.1105 0.1364 0.7532 67 V 0.3036 0.0110 0.6854 68 G 0.3646 0.0294 0.6059 69 L 0.9288 0.0034 0.0678 70 A 0.9336 0.0032 0.0632 71 F 0.9334 0.0032 0.0634 72 F 0.9037 0.0039 0.0923 73 A 0.5665 0.0173 0.4162 74 A 0.1731 0.0501 0.7768 75 A 0.0910 0.1454 0.7636 76 A 0.0600 0.3886 0.5514 77 E 0.0663 0.5096 0.4242 78 V 0.0826 0.4591 0.4582 79 S 0.0471 0.4687 0.4842 80 R 0.0056 0.9223 0.0721 81 A 0.0053 0.9296 0.0652 82 H 0.0055 0.9263 0.0681 83 A 0.0049 0.9442 0.0509 84 E 0.0047 0.9564 0.0389 85 R 0.0047 0.9564 0.0389 86 A 0.0047 0.9547 0.0406 87 R 0.0048 0.9435 0.0517 88 A 0.0056 0.8827 0.1117 89 A 0.0393 0.3096 0.6511 90 G 0.0372 0.0182 0.9446 91 C 0.1121 0.0079 0.8801 92 S 0.6451 0.0067 0.3482 93 V 0.9056 0.0037 0.0907 94 I 0.8850 0.0056 0.1094 95 D 0.7669 0.0070 0.2261 96 L 0.3623 0.0953 0.5424 97 S 0.1466 0.2072 0.6462 98 G 0.0873 0.2446 0.6681 99 A 0.1084 0.1343 0.7573 100 L 0.1265 0.0840 0.7896 101 E 0.0921 0.0581 0.8498 102 P 0.0291 0.3230 0.6478 103 S 0.0225 0.2882 0.6893 104 V 0.0460 0.2111 0.7429 105 A 0.0945 0.0340 0.8715 106 P 0.1306 0.0385 0.8310 107 P 0.4414 0.0569 0.5017 108 V 0.7073 0.0572 0.2355 109 M 0.7224 0.0519 0.2256 110 V 0.5837 0.1106 0.3057 111 S 0.4537 0.0851 0.4612 112 V 0.2528 0.0804 0.6668 113 N 0.1339 0.0666 0.7995 114 A 0.0089 0.8224 0.1687 115 E 0.0066 0.8499 0.1435 116 R 0.0088 0.8516 0.1395 117 L 0.0192 0.7761 0.2047 118 A 0.0211 0.6194 0.3596 119 S 0.0188 0.5174 0.4637 120 Q 0.0227 0.3833 0.5939 121 A 0.0524 0.2385 0.7091 122 A 0.0769 0.0783 0.8449 123 P 0.1068 0.1217 0.7715 124 F 0.4589 0.0914 0.4497 125 L 0.8298 0.0235 0.1467 126 L 0.8454 0.0145 0.1401 127 S 0.7228 0.0254 0.2518 128 S 0.2790 0.0252 0.6958 129 P 0.1080 0.1316 0.7604 130 C 0.1150 0.1505 0.7344 131 A 0.1404 0.2599 0.5998 132 V 0.1067 0.4004 0.4930 133 A 0.0607 0.5430 0.3964 134 A 0.0231 0.6226 0.3543 135 E 0.0267 0.7126 0.2607 136 L 0.0144 0.8291 0.1565 137 C 0.0187 0.8609 0.1204 138 E 0.0154 0.8750 0.1096 139 V 0.0131 0.8734 0.1135 140 L 0.0136 0.8909 0.0955 141 A 0.0067 0.9246 0.0688 142 P 0.0058 0.9350 0.0593 143 L 0.0067 0.9358 0.0575 144 L 0.0078 0.9153 0.0769 145 A 0.0072 0.8365 0.1563 146 T 0.0095 0.6750 0.3155 147 L 0.0655 0.1701 0.7644 148 D 0.0980 0.0373 0.8647 149 C 0.3808 0.0260 0.5932 150 R 0.5706 0.0505 0.3789 151 Q 0.8264 0.0211 0.1524 152 L 0.8732 0.0143 0.1125 153 N 0.8921 0.0110 0.0969 154 L 0.8486 0.0260 0.1255 155 T 0.7949 0.0342 0.1709 156 A 0.7632 0.0651 0.1717 157 C 0.7125 0.1392 0.1483 158 L 0.6620 0.1866 0.1515 159 S 0.4751 0.2624 0.2625 160 V 0.2684 0.2796 0.4520 161 S 0.1429 0.3038 0.5532 162 S 0.0457 0.3981 0.5562 163 L 0.0432 0.4226 0.5343 164 G 0.0334 0.4305 0.5361 165 R 0.0156 0.7157 0.2686 166 E 0.0125 0.7781 0.2094 167 G 0.0091 0.8414 0.1495 168 V 0.0050 0.9363 0.0587 169 K 0.0047 0.9545 0.0408 170 E 0.0047 0.9562 0.0391 171 L 0.0047 0.9539 0.0414 172 A 0.0047 0.9482 0.0472 173 R 0.0048 0.9227 0.0725 174 Q 0.0054 0.8905 0.1041 175 T 0.0134 0.8423 0.1443 176 A 0.0185 0.8013 0.1802 177 E 0.0338 0.8313 0.1349 178 L 0.0525 0.7941 0.1533 179 L 0.1164 0.5873 0.2964 180 N 0.1112 0.2968 0.5920 181 A 0.0637 0.1017 0.8346 182 R 0.0678 0.0733 0.8589 183 P 0.0738 0.1018 0.8243 184 L 0.0736 0.1092 0.8172 185 E 0.0794 0.1020 0.8185 186 P 0.0341 0.4464 0.5194 187 R 0.0389 0.4691 0.4920 188 L 0.0710 0.5096 0.4193 189 F 0.0780 0.3873 0.5346 190 D 0.0553 0.5076 0.4371 191 R 0.0679 0.6234 0.3087 192 Q 0.0878 0.6736 0.2386 193 I 0.1149 0.6676 0.2175 194 A 0.1554 0.6425 0.2022 195 F 0.2066 0.5621 0.2313 196 N 0.1933 0.4525 0.3542 197 L 0.2159 0.3926 0.3914 198 L 0.2322 0.3339 0.4339 199 A 0.2168 0.2817 0.5015 200 Q 0.2294 0.2438 0.5268 201 V 0.2114 0.2056 0.5831 202 G 0.1556 0.1349 0.7095 203 A 0.2136 0.1510 0.6353 204 V 0.2872 0.1374 0.5754 205 D 0.1426 0.1237 0.7337 206 A 0.0622 0.2207 0.7170 207 E 0.0595 0.1588 0.7816 208 G 0.0577 0.1301 0.8122 209 H 0.1030 0.1909 0.7060 210 S 0.1166 0.4366 0.4468 211 A 0.0506 0.7131 0.2363 212 I 0.0368 0.8627 0.1005 213 E 0.0325 0.8925 0.0750 214 R 0.0303 0.8881 0.0816 215 R 0.0294 0.8688 0.1018 216 I 0.0170 0.8796 0.1035 217 F 0.0121 0.9031 0.0848 218 A 0.0064 0.9389 0.0547 219 E 0.0057 0.9412 0.0530 220 V 0.0059 0.9329 0.0612 221 Q 0.0089 0.8886 0.1025 222 A 0.0099 0.8202 0.1698 223 L 0.0182 0.7449 0.2369 224 L 0.0573 0.4816 0.4611 225 G 0.0449 0.1964 0.7588 226 E 0.0684 0.1531 0.7785 227 R 0.0673 0.1376 0.7951 228 I 0.1069 0.0942 0.7989 229 G 0.1902 0.0259 0.7839 230 P 0.3348 0.0168 0.6485 231 L 0.7161 0.0078 0.2761 232 N 0.7349 0.0173 0.2478 233 V 0.8047 0.0074 0.1880 234 T 0.8102 0.0072 0.1826 235 C 0.8395 0.0063 0.1542 236 I 0.8246 0.0068 0.1686 237 Q 0.7852 0.0087 0.2060 238 A 0.6008 0.0119 0.3873 239 P 0.4926 0.0125 0.4950 240 V 0.4370 0.0258 0.5371 241 F 0.3443 0.0573 0.5984 242 F 0.3221 0.0461 0.6319 243 G 0.4176 0.0395 0.5428 244 D 0.5903 0.0291 0.3807 245 S 0.7619 0.0292 0.2089 246 L 0.8287 0.0183 0.1530 247 S 0.8746 0.0093 0.1161 248 V 0.8972 0.0065 0.0963 249 T 0.9090 0.0051 0.0859 250 L 0.8985 0.0057 0.0958 251 Q 0.8599 0.0059 0.1342 252 C 0.6445 0.0135 0.3420 253 A 0.2407 0.0392 0.7202 254 E 0.1556 0.0302 0.8142 255 P 0.1543 0.0247 0.8210 256 V 0.1829 0.0102 0.8069 257 D 0.1187 0.0099 0.8714 258 L 0.0049 0.9453 0.0498 259 A 0.0047 0.9577 0.0376 260 A 0.0047 0.9591 0.0362 261 V 0.0047 0.9599 0.0355 262 T 0.0047 0.9599 0.0354 263 R 0.0048 0.9580 0.0372 264 V 0.0049 0.9519 0.0432 265 L 0.0052 0.9291 0.0657 266 D 0.0062 0.8205 0.1733 267 A 0.0124 0.5492 0.4384 268 T 0.0700 0.1251 0.8049 269 K 0.0282 0.1335 0.8382 270 G 0.0935 0.1100 0.7965 271 I 0.5130 0.0460 0.4410 272 E 0.8057 0.0230 0.1712 273 W 0.8293 0.0186 0.1521 274 V 0.6646 0.0347 0.3008 275 G 0.3906 0.0310 0.5783 276 E 0.1528 0.0665 0.7806 277 G 0.0836 0.0659 0.8505 278 D 0.1069 0.0627 0.8304 279 Y 0.1407 0.0275 0.8318 280 P 0.1991 0.0407 0.7602 281 T 0.4208 0.0343 0.5449 282 V 0.5563 0.0224 0.4212 283 V 0.4821 0.0397 0.4782 284 G 0.4120 0.0923 0.4957 285 D 0.3401 0.1079 0.5520 286 A 0.3064 0.1399 0.5537 287 L 0.2122 0.0956 0.6923 288 G 0.1110 0.0412 0.8478 289 Q 0.1283 0.0488 0.8229 290 D 0.1682 0.0730 0.7588 291 E 0.3204 0.0833 0.5962 292 T 0.5780 0.0608 0.3612 293 Y 0.7324 0.0482 0.2194 294 V 0.7847 0.0547 0.1606 295 G 0.7617 0.0504 0.1880 296 R 0.7733 0.0369 0.1897 297 V 0.6852 0.0583 0.2565 298 R 0.5998 0.0619 0.3383 299 A 0.3694 0.1358 0.4948 300 G 0.2333 0.0968 0.6699 301 Q 0.2572 0.0789 0.6639 302 A 0.2491 0.0724 0.6785 303 D 0.1293 0.0401 0.8306 304 P 0.0362 0.1439 0.8198 305 C 0.1137 0.0918 0.7945 306 Q 0.6098 0.0316 0.3586 307 V 0.8412 0.0053 0.1535 308 N 0.9069 0.0049 0.0882 309 L 0.9261 0.0048 0.0692 310 W 0.9237 0.0079 0.0685 311 I 0.9192 0.0097 0.0712 312 V 0.8335 0.0543 0.1123 313 S 0.5942 0.1245 0.2812 314 D 0.2229 0.3263 0.4508 315 N 0.1088 0.5123 0.3789 316 V 0.0425 0.7417 0.2158 317 R 0.0237 0.8246 0.1516 318 K 0.0173 0.8290 0.1537 319 G 0.0154 0.7574 0.2272 320 A 0.0195 0.7783 0.2022 321 A 0.0125 0.8541 0.1334 322 L 0.0064 0.9027 0.0908 323 N 0.0060 0.9036 0.0905 324 A 0.0056 0.9425 0.0519 325 V 0.0061 0.9546 0.0393 326 L 0.0057 0.9567 0.0376 327 L 0.0052 0.9569 0.0380 328 G 0.0047 0.9582 0.0372 329 E 0.0049 0.9577 0.0374 330 L 0.0052 0.9559 0.0388 331 L 0.0051 0.9473 0.0475 332 I 0.0062 0.9178 0.0760 333 K 0.0080 0.8517 0.1403 334 H 0.0159 0.7002 0.2839 335 Y 0.0258 0.4830 0.4912 336 L 0.0416 0.0913 0.8672