# This file is the result of combining several RDB files, specifically # T0333.t04.dssp-ebghstl.rdb (weight 1.53986) # T0333.t04.stride-ebghtl.rdb (weight 1.24869) # T0333.t04.str2.rdb (weight 1.54758) # T0333.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 T0333.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0333 # 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 T0333.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 2239 # # ============================================ # Comments from T0333.t04.stride-ebghtl.rdb # ============================================ # TARGET T0333 # 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 T0333.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 2239 # # ============================================ # Comments from T0333.t04.str2.rdb # ============================================ # TARGET T0333 # 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 T0333.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 2239 # # ============================================ # Comments from T0333.t04.alpha.rdb # ============================================ # TARGET T0333 # 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 T0333.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 2239 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2058 0.0106 0.7836 2 L 0.7266 0.0100 0.2633 3 F 0.8277 0.0101 0.1622 4 V 0.7641 0.0127 0.2232 5 S 0.4938 0.0280 0.4782 6 S 0.1922 0.0381 0.7697 7 P 0.0683 0.0912 0.8405 8 G 0.0659 0.1243 0.8099 9 I 0.0534 0.2827 0.6639 10 G 0.0590 0.3462 0.5949 11 H 0.0678 0.4059 0.5263 12 L 0.0637 0.6065 0.3298 13 F 0.0143 0.8716 0.1141 14 P 0.0075 0.9207 0.0718 15 L 0.0048 0.9545 0.0407 16 I 0.0047 0.9595 0.0358 17 Q 0.0047 0.9612 0.0341 18 L 0.0047 0.9600 0.0353 19 A 0.0047 0.9600 0.0354 20 W 0.0047 0.9603 0.0351 21 G 0.0047 0.9595 0.0358 22 F 0.0048 0.9566 0.0387 23 R 0.0049 0.9453 0.0498 24 T 0.0060 0.8788 0.1152 25 A 0.0388 0.3548 0.6064 26 G 0.0420 0.0164 0.9416 27 H 0.0897 0.0091 0.9012 28 D 0.5470 0.0152 0.4378 29 V 0.9079 0.0035 0.0886 30 L 0.9299 0.0034 0.0667 31 I 0.9291 0.0033 0.0676 32 A 0.8755 0.0065 0.1180 33 V 0.5231 0.0116 0.4653 34 A 0.1248 0.1320 0.7432 35 E 0.0737 0.2251 0.7012 36 H 0.0592 0.4036 0.5372 37 A 0.0264 0.6747 0.2989 38 D 0.0196 0.7676 0.2128 39 R 0.0257 0.8256 0.1487 40 A 0.0351 0.8328 0.1321 41 A 0.0288 0.7907 0.1805 42 A 0.0275 0.7416 0.2309 43 A 0.0496 0.3219 0.6284 44 G 0.0516 0.0516 0.8968 45 L 0.1837 0.0229 0.7935 46 E 0.5439 0.0249 0.4311 47 V 0.7384 0.0311 0.2304 48 V 0.7077 0.0265 0.2658 49 D 0.6734 0.0245 0.3021 50 V 0.3984 0.0325 0.5691 51 A 0.1292 0.0304 0.8404 52 P 0.0318 0.1173 0.8509 53 D 0.0510 0.0690 0.8800 54 Y 0.1666 0.0537 0.7797 55 S 0.2687 0.0631 0.6682 56 A 0.5534 0.1553 0.2914 57 V 0.6120 0.1638 0.2242 58 K 0.6687 0.1491 0.1822 59 V 0.5590 0.1783 0.2627 60 F 0.4043 0.2320 0.3637 61 E 0.2693 0.3676 0.3631 62 Q 0.1842 0.4244 0.3915 63 V 0.1547 0.4179 0.4274 64 A 0.1236 0.3204 0.5560 65 K 0.0629 0.2307 0.7063 66 D 0.0482 0.1459 0.8059 67 N 0.0876 0.0527 0.8597 68 P 0.0552 0.2334 0.7113 69 R 0.0840 0.2868 0.6292 70 F 0.1203 0.3209 0.5587 71 A 0.1347 0.3590 0.5063 72 E 0.1543 0.3606 0.4851 73 T 0.1836 0.3210 0.4954 74 V 0.1732 0.2822 0.5446 75 A 0.1494 0.2048 0.6458 76 T 0.1296 0.1553 0.7150 77 R 0.1028 0.0890 0.8082 78 P 0.0840 0.1331 0.7829 79 A 0.1161 0.1767 0.7073 80 I 0.1446 0.1060 0.7494 81 D 0.1370 0.0637 0.7993 82 L 0.0110 0.8582 0.1308 83 E 0.0065 0.9145 0.0789 84 E 0.0071 0.9240 0.0689 85 W 0.0086 0.9155 0.0758 86 G 0.0106 0.9076 0.0818 87 V 0.0083 0.9290 0.0628 88 Q 0.0084 0.9301 0.0615 89 I 0.0072 0.9342 0.0586 90 A 0.0082 0.9221 0.0698 91 A 0.0103 0.8815 0.1082 92 V 0.0116 0.7957 0.1927 93 N 0.0192 0.6996 0.2813 94 R 0.0088 0.8606 0.1306 95 P 0.0054 0.8900 0.1046 96 L 0.0053 0.9144 0.0803 97 V 0.0051 0.9293 0.0656 98 D 0.0049 0.9361 0.0590 99 G 0.0051 0.9253 0.0697 100 T 0.0049 0.9422 0.0529 101 M 0.0047 0.9534 0.0419 102 A 0.0048 0.9483 0.0469 103 L 0.0052 0.9387 0.0561 104 V 0.0066 0.9089 0.0845 105 D 0.0073 0.7808 0.2119 106 D 0.0115 0.5905 0.3980 107 Y 0.0635 0.2584 0.6780 108 R 0.0873 0.0268 0.8860 109 P 0.1220 0.0171 0.8609 110 D 0.2934 0.0431 0.6635 111 L 0.9210 0.0039 0.0751 112 V 0.9315 0.0032 0.0652 113 V 0.9240 0.0046 0.0714 114 Y 0.8346 0.0142 0.1513 115 E 0.3192 0.0209 0.6599 116 Q 0.0788 0.0998 0.8214 117 G 0.0603 0.1514 0.7883 118 A 0.0549 0.3401 0.6050 119 T 0.0250 0.7505 0.2245 120 V 0.0091 0.9118 0.0791 121 G 0.0068 0.9471 0.0462 122 L 0.0052 0.9587 0.0361 123 L 0.0048 0.9598 0.0355 124 A 0.0047 0.9593 0.0359 125 A 0.0050 0.9575 0.0375 126 D 0.0051 0.9515 0.0433 127 R 0.0072 0.9163 0.0765 128 A 0.0453 0.4530 0.5017 129 G 0.0400 0.0162 0.9439 130 V 0.0612 0.0083 0.9306 131 P 0.1792 0.0089 0.8120 132 A 0.8205 0.0116 0.1679 133 V 0.9044 0.0078 0.0878 134 Q 0.9118 0.0074 0.0808 135 R 0.8469 0.0231 0.1300 136 N 0.6207 0.0238 0.3555 137 Q 0.2894 0.0744 0.6362 138 S 0.1588 0.0977 0.7435 139 A 0.1207 0.1878 0.6914 140 W 0.0998 0.2284 0.6718 141 R 0.0855 0.2614 0.6530 142 T 0.0802 0.3584 0.5613 143 R 0.0765 0.3738 0.5498 144 G 0.0889 0.3229 0.5881 145 M 0.1062 0.3401 0.5538 146 H 0.0824 0.4170 0.5006 147 R 0.0354 0.6706 0.2940 148 S 0.0384 0.7161 0.2455 149 I 0.0143 0.8570 0.1287 150 A 0.0108 0.8667 0.1225 151 S 0.0087 0.8671 0.1242 152 F 0.0093 0.8762 0.1144 153 L 0.0082 0.8913 0.1005 154 T 0.0068 0.9155 0.0776 155 D 0.0067 0.8890 0.1043 156 L 0.0085 0.8496 0.1419 157 M 0.0319 0.7125 0.2556 158 D 0.0355 0.5271 0.4374 159 K 0.0492 0.4591 0.4917 160 H 0.0967 0.3578 0.5455 161 Q 0.1554 0.2842 0.5604 162 V 0.1755 0.2245 0.6001 163 S 0.1428 0.1453 0.7119 164 L 0.0940 0.0453 0.8607 165 P 0.0687 0.0875 0.8438 166 E 0.0966 0.0945 0.8090 167 P 0.1033 0.2227 0.6739 168 V 0.1428 0.2961 0.5611 169 A 0.2584 0.2797 0.4619 170 T 0.3308 0.2411 0.4281 171 I 0.3797 0.2147 0.4056 172 E 0.3313 0.1776 0.4911 173 S 0.2060 0.1438 0.6502 174 F 0.1215 0.0621 0.8164 175 P 0.0733 0.0677 0.8590 176 P 0.0507 0.2946 0.6548 177 S 0.0697 0.3916 0.5387 178 L 0.1081 0.4100 0.4819 179 L 0.1611 0.3583 0.4806 180 L 0.1947 0.3803 0.4250 181 E 0.2105 0.3385 0.4510 182 A 0.2154 0.2637 0.5210 183 E 0.1370 0.0867 0.7763 184 P 0.0829 0.1409 0.7762 185 E 0.0873 0.1451 0.7677 186 G 0.1041 0.1514 0.7445 187 W 0.1974 0.1381 0.6645 188 F 0.2696 0.1110 0.6194 189 M 0.2062 0.2069 0.5869 190 R 0.2487 0.1591 0.5922 191 W 0.4102 0.1141 0.4757 192 V 0.4661 0.0518 0.4821 193 P 0.4048 0.0606 0.5346 194 Y 0.3006 0.1056 0.5938 195 G 0.1910 0.0926 0.7164 196 G 0.1290 0.1182 0.7528 197 G 0.1366 0.2459 0.6175 198 A 0.1708 0.2964 0.5328 199 V 0.1944 0.3068 0.4987 200 L 0.1436 0.2923 0.5641 201 G 0.0660 0.4473 0.4867 202 D 0.0605 0.4655 0.4740 203 R 0.0891 0.3582 0.5526 204 L 0.1085 0.0665 0.8250 205 P 0.0769 0.0494 0.8736 206 P 0.0874 0.0645 0.8481 207 V 0.0755 0.0496 0.8749 208 P 0.0432 0.1268 0.8300 209 A 0.0445 0.1055 0.8500 210 R 0.0838 0.0218 0.8944 211 P 0.1310 0.0100 0.8591 212 E 0.7088 0.0057 0.2855 213 V 0.9233 0.0033 0.0734 214 A 0.9331 0.0032 0.0637 215 I 0.9300 0.0033 0.0667 216 T 0.8842 0.0048 0.1109 217 M 0.5430 0.0205 0.4365 218 G 0.2502 0.0329 0.7169 219 T 0.2222 0.0990 0.6788 220 I 0.1565 0.3509 0.4925 221 E 0.1693 0.4386 0.3921 222 L 0.1162 0.5528 0.3310 223 Q 0.0822 0.5291 0.3887 224 A 0.0650 0.4444 0.4906 225 F 0.0746 0.2676 0.6579 226 G 0.0579 0.2209 0.7212 227 I 0.0171 0.7293 0.2536 228 G 0.0180 0.7842 0.1978 229 A 0.0139 0.8451 0.1410 230 V 0.0063 0.9225 0.0711 231 E 0.0050 0.9536 0.0414 232 P 0.0049 0.9582 0.0369 233 I 0.0047 0.9593 0.0359 234 I 0.0047 0.9585 0.0368 235 A 0.0048 0.9527 0.0424 236 A 0.0052 0.9356 0.0592 237 A 0.0091 0.8898 0.1011 238 G 0.0078 0.7309 0.2613 239 E 0.0140 0.4724 0.5136 240 V 0.0592 0.1156 0.8252 241 D 0.0616 0.0325 0.9058 242 A 0.1863 0.0120 0.8017 243 D 0.5931 0.0083 0.3986 244 F 0.9203 0.0033 0.0763 245 V 0.9308 0.0032 0.0660 246 L 0.9286 0.0034 0.0680 247 A 0.9043 0.0039 0.0918 248 L 0.6213 0.0174 0.3613 249 G 0.1714 0.0248 0.8038 250 D 0.1045 0.0531 0.8424 251 L 0.0907 0.1159 0.7934 252 D 0.1163 0.0898 0.7939 253 I 0.0844 0.2625 0.6531 254 S 0.0550 0.3593 0.5857 255 P 0.0621 0.4467 0.4912 256 L 0.0766 0.4216 0.5018 257 G 0.0779 0.2412 0.6809 258 T 0.1066 0.1777 0.7158 259 L 0.1054 0.0295 0.8651 260 P 0.0923 0.0694 0.8383 261 R 0.0617 0.1476 0.7907 262 N 0.2068 0.0714 0.7218 263 V 0.6997 0.0098 0.2905 264 R 0.8837 0.0059 0.1105 265 A 0.8918 0.0054 0.1028 266 V 0.6941 0.0389 0.2670 267 G 0.4105 0.0267 0.5628 268 W 0.2440 0.0421 0.7139 269 T 0.1674 0.0281 0.8045 270 P 0.1496 0.0422 0.8082 271 L 0.0070 0.9057 0.0874 272 H 0.0058 0.9394 0.0548 273 T 0.0057 0.9411 0.0532 274 L 0.0108 0.9152 0.0740 275 L 0.0151 0.8695 0.1154 276 R 0.0149 0.6943 0.2908 277 T 0.0392 0.3514 0.6094 278 C 0.1512 0.0405 0.8083 279 T 0.1238 0.0615 0.8147 280 A 0.8852 0.0109 0.1039 281 V 0.9275 0.0046 0.0679 282 V 0.9202 0.0059 0.0739 283 H 0.7968 0.0183 0.1850 284 H 0.2115 0.0449 0.7436 285 G 0.0616 0.0926 0.8458 286 G 0.0518 0.1528 0.7954 287 G 0.0295 0.6040 0.3666 288 G 0.0123 0.8654 0.1223 289 T 0.0138 0.9111 0.0752 290 V 0.0056 0.9540 0.0404 291 M 0.0071 0.9543 0.0386 292 T 0.0103 0.9505 0.0392 293 A 0.0073 0.9497 0.0430 294 I 0.0070 0.9438 0.0492 295 D 0.0104 0.8951 0.0945 296 A 0.0449 0.4513 0.5039 297 G 0.0363 0.0260 0.9378 298 I 0.0901 0.0111 0.8988 299 P 0.2679 0.0092 0.7229 300 Q 0.8379 0.0088 0.1533 301 L 0.9121 0.0049 0.0831 302 L 0.8939 0.0090 0.0970 303 A 0.7293 0.0080 0.2626 304 P 0.3165 0.0162 0.6672 305 D 0.1035 0.0167 0.8797 306 P 0.0200 0.4817 0.4983 307 R 0.0110 0.5760 0.4130 308 D 0.0177 0.6345 0.3478 309 Q 0.0237 0.7102 0.2661 310 F 0.0145 0.7731 0.2124 311 Q 0.0156 0.7852 0.1992 312 H 0.0134 0.7755 0.2111 313 T 0.0165 0.7504 0.2330 314 A 0.0138 0.7605 0.2257 315 R 0.0108 0.8577 0.1314 316 E 0.0100 0.8969 0.0931 317 A 0.0134 0.8905 0.0961 318 V 0.0265 0.8569 0.1166 319 S 0.0315 0.8573 0.1112 320 R 0.0368 0.8074 0.1558 321 R 0.0591 0.3717 0.5692 322 G 0.0524 0.0493 0.8983 323 I 0.1357 0.0468 0.8175 324 G 0.3166 0.0402 0.6432 325 L 0.4567 0.0347 0.5086 326 V 0.3250 0.0177 0.6573 327 S 0.1863 0.0397 0.7740 328 T 0.1057 0.0182 0.8761 329 S 0.0105 0.6819 0.3076 330 D 0.0106 0.6245 0.3649 331 K 0.0200 0.6648 0.3152 332 V 0.1028 0.2999 0.5974 333 D 0.0794 0.2634 0.6572 334 A 0.0051 0.9444 0.0505 335 D 0.0049 0.9560 0.0390 336 L 0.0047 0.9576 0.0377 337 L 0.0047 0.9600 0.0353 338 R 0.0047 0.9591 0.0362 339 R 0.0049 0.9548 0.0403 340 L 0.0054 0.9241 0.0705 341 I 0.0105 0.7840 0.2055 342 G 0.0253 0.3676 0.6071 343 D 0.0812 0.0257 0.8931 344 E 0.0053 0.9128 0.0819 345 S 0.0048 0.9376 0.0575 346 L 0.0047 0.9562 0.0391 347 R 0.0047 0.9608 0.0346 348 T 0.0046 0.9601 0.0353 349 A 0.0047 0.9584 0.0370 350 A 0.0047 0.9600 0.0353 351 R 0.0047 0.9595 0.0358 352 E 0.0047 0.9568 0.0385 353 V 0.0049 0.9495 0.0456 354 R 0.0050 0.9506 0.0444 355 E 0.0049 0.9467 0.0484 356 E 0.0055 0.9352 0.0593 357 M 0.0078 0.9022 0.0900 358 V 0.0123 0.7973 0.1903 359 A 0.0195 0.5473 0.4332 360 L 0.0577 0.0955 0.8468 361 P 0.0436 0.0630 0.8934 362 T 0.0680 0.0368 0.8953 363 P 0.0622 0.2001 0.7377 364 A 0.0051 0.9350 0.0600 365 E 0.0047 0.9571 0.0382 366 T 0.0048 0.9576 0.0376 367 V 0.0047 0.9595 0.0358 368 R 0.0047 0.9608 0.0345 369 R 0.0047 0.9599 0.0354 370 I 0.0050 0.9575 0.0375 371 V 0.0048 0.9532 0.0420 372 E 0.0054 0.9315 0.0631 373 R 0.0084 0.8446 0.1470 374 I 0.0417 0.6192 0.3391 375 S 0.0324 0.2032 0.7644 376 G 0.0279 0.0500 0.9221