# This file is the result of combining several RDB files, specifically # T0310.t04.dssp-ebghstl.rdb (weight 1.53986) # T0310.t04.stride-ebghtl.rdb (weight 1.24869) # T0310.t04.str2.rdb (weight 1.54758) # T0310.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 T0310.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0310 # 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 T0310.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 71.2378 # # ============================================ # Comments from T0310.t04.stride-ebghtl.rdb # ============================================ # TARGET T0310 # 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 T0310.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 71.2378 # # ============================================ # Comments from T0310.t04.str2.rdb # ============================================ # TARGET T0310 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0310.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 71.2378 # # ============================================ # Comments from T0310.t04.alpha.rdb # ============================================ # TARGET T0310 # 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 T0310.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 71.2378 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.0730 0.2476 0.6794 2 V 0.0080 0.9062 0.0858 3 E 0.0073 0.9341 0.0586 4 Q 0.0079 0.9395 0.0525 5 Q 0.0094 0.9420 0.0486 6 G 0.0057 0.9539 0.0404 7 E 0.0047 0.9582 0.0371 8 M 0.0048 0.9577 0.0375 9 A 0.0047 0.9582 0.0371 10 R 0.0048 0.9480 0.0472 11 S 0.0051 0.8934 0.1015 12 G 0.0113 0.8094 0.1793 13 G 0.0102 0.7189 0.2709 14 R 0.0136 0.7674 0.2190 15 M 0.0241 0.7708 0.2050 16 L 0.0268 0.7559 0.2173 17 A 0.0219 0.5911 0.3870 18 T 0.0316 0.2875 0.6809 19 L 0.0863 0.0554 0.8583 20 E 0.0564 0.0208 0.9227 21 P 0.0050 0.9448 0.0502 22 E 0.0047 0.9581 0.0372 23 Q 0.0047 0.9592 0.0361 24 R 0.0047 0.9595 0.0358 25 A 0.0047 0.9599 0.0354 26 E 0.0047 0.9600 0.0353 27 I 0.0047 0.9591 0.0362 28 I 0.0047 0.9591 0.0362 29 H 0.0047 0.9591 0.0362 30 H 0.0047 0.9497 0.0456 31 L 0.0048 0.9539 0.0412 32 A 0.0047 0.9576 0.0377 33 D 0.0047 0.9555 0.0398 34 L 0.0048 0.9487 0.0465 35 L 0.0048 0.9372 0.0580 36 T 0.0051 0.9157 0.0792 37 D 0.0080 0.8146 0.1775 38 Q 0.0095 0.7603 0.2303 39 R 0.0058 0.9165 0.0777 40 D 0.0050 0.9498 0.0452 41 E 0.0048 0.9562 0.0389 42 I 0.0048 0.9562 0.0390 43 L 0.0047 0.9562 0.0391 44 L 0.0048 0.9528 0.0424 45 A 0.0058 0.9338 0.0604 46 N 0.0101 0.8302 0.1597 47 K 0.0056 0.8168 0.1776 48 K 0.0072 0.8222 0.1706 49 D 0.0142 0.7822 0.2036 50 L 0.0064 0.9145 0.0791 51 E 0.0072 0.9245 0.0682 52 E 0.0088 0.9186 0.0726 53 A 0.0129 0.8852 0.1019 54 E 0.0205 0.7180 0.2615 55 G 0.0376 0.3028 0.6596 56 R 0.0370 0.1368 0.8262 57 L 0.0539 0.1902 0.7559 58 A 0.0412 0.2010 0.7577 59 A 0.0286 0.3831 0.5883 60 P 0.0214 0.7159 0.2627 61 L 0.0138 0.8350 0.1512 62 L 0.0143 0.8706 0.1151 63 K 0.0127 0.8709 0.1164 64 R 0.0150 0.8303 0.1547 65 L 0.0386 0.7057 0.2557 66 S 0.0379 0.6128 0.3493 67 L 0.0411 0.5344 0.4245 68 S 0.0464 0.4136 0.5400 69 T 0.0140 0.6631 0.3229 70 S 0.0177 0.6498 0.3325 71 K 0.0412 0.6785 0.2803 72 L 0.0201 0.9000 0.0800 73 N 0.0060 0.9319 0.0620 74 S 0.0090 0.9420 0.0490 75 L 0.0047 0.9574 0.0379 76 A 0.0047 0.9582 0.0372 77 I 0.0047 0.9516 0.0437 78 G 0.0047 0.9503 0.0449 79 L 0.0047 0.9584 0.0369 80 R 0.0047 0.9600 0.0353 81 Q 0.0047 0.9593 0.0360 82 I 0.0048 0.9536 0.0416 83 A 0.0049 0.9312 0.0639 84 A 0.0053 0.8598 0.1349 85 S 0.0090 0.7580 0.2330 86 S 0.0440 0.5042 0.4519 87 Q 0.0341 0.4146 0.5513 88 D 0.0541 0.2649 0.6810 89 S 0.0483 0.2797 0.6719 90 V 0.0835 0.1812 0.7353 91 G 0.1218 0.1145 0.7637 92 R 0.3398 0.0985 0.5617 93 V 0.6264 0.0641 0.3095 94 L 0.5545 0.0620 0.3836 95 R 0.4234 0.0713 0.5053 96 R 0.2523 0.1836 0.5641 97 T 0.2633 0.2389 0.4978 98 R 0.3452 0.2437 0.4111 99 I 0.3111 0.1856 0.5033 100 A 0.1480 0.1421 0.7099 101 K 0.0550 0.1585 0.7865 102 N 0.0637 0.0760 0.8603 103 L 0.3272 0.0335 0.6393 104 E 0.6617 0.0201 0.3182 105 L 0.8401 0.0133 0.1466 106 E 0.8520 0.0122 0.1358 107 Q 0.8903 0.0067 0.1030 108 V 0.8714 0.0065 0.1220 109 T 0.7931 0.0088 0.1981 110 V 0.5398 0.0115 0.4486 111 P 0.3423 0.0243 0.6334 112 I 0.4196 0.0426 0.5378 113 G 0.7045 0.0132 0.2823 114 V 0.8667 0.0069 0.1264 115 L 0.9175 0.0044 0.0781 116 L 0.9262 0.0035 0.0704 117 V 0.9233 0.0032 0.0735 118 I 0.8657 0.0083 0.1260 119 F 0.4922 0.0151 0.4926 120 E 0.1003 0.0914 0.8083 121 S 0.0486 0.0901 0.8613 122 R 0.0817 0.0500 0.8683 123 P 0.0333 0.2441 0.7226 124 D 0.0443 0.2863 0.6694 125 C 0.0873 0.3041 0.6086 126 L 0.0699 0.3867 0.5433 127 P 0.0302 0.5895 0.3803 128 Q 0.0205 0.8145 0.1650 129 V 0.0132 0.9069 0.0799 130 A 0.0080 0.9411 0.0509 131 A 0.0055 0.9521 0.0424 132 L 0.0056 0.9482 0.0462 133 A 0.0061 0.9439 0.0500 134 I 0.0074 0.9182 0.0743 135 A 0.0110 0.8047 0.1843 136 S 0.0543 0.3123 0.6334 137 G 0.0531 0.0874 0.8595 138 N 0.0918 0.0369 0.8713 139 G 0.6122 0.0305 0.3573 140 L 0.9020 0.0070 0.0910 141 L 0.9183 0.0062 0.0755 142 L 0.8422 0.0257 0.1321 143 K 0.5333 0.0511 0.4156 144 G 0.1909 0.0459 0.7632 145 G 0.0862 0.1631 0.7507 146 K 0.0521 0.3504 0.5975 147 E 0.0510 0.3913 0.5578 148 A 0.0354 0.3428 0.6218 149 A 0.0143 0.7602 0.2254 150 H 0.0083 0.8812 0.1105 151 S 0.0052 0.9423 0.0526 152 N 0.0047 0.9581 0.0372 153 R 0.0046 0.9612 0.0341 154 I 0.0046 0.9613 0.0341 155 L 0.0047 0.9606 0.0347 156 H 0.0046 0.9612 0.0342 157 L 0.0046 0.9602 0.0352 158 L 0.0047 0.9581 0.0372 159 T 0.0047 0.9552 0.0401 160 Q 0.0047 0.9532 0.0421 161 E 0.0050 0.9399 0.0551 162 A 0.0050 0.9307 0.0643 163 L 0.0067 0.8889 0.1044 164 S 0.0066 0.8343 0.1592 165 I 0.0111 0.7351 0.2538 166 H 0.0475 0.3578 0.5947 167 G 0.0409 0.0629 0.8962 168 V 0.0779 0.0400 0.8821 169 K 0.0658 0.1371 0.7971 170 E 0.4054 0.1294 0.4652 171 A 0.6793 0.0807 0.2401 172 V 0.7999 0.0497 0.1504 173 Q 0.8516 0.0401 0.1083 174 L 0.8632 0.0317 0.1051 175 V 0.7579 0.0310 0.2111 176 N 0.3532 0.0457 0.6011 177 T 0.0925 0.0467 0.8608 178 R 0.0259 0.5883 0.3858 179 E 0.0237 0.7647 0.2115 180 E 0.0315 0.7922 0.1763 181 V 0.0511 0.7598 0.1891 182 E 0.0587 0.5901 0.3512 183 L 0.0443 0.3476 0.6082 184 D 0.0963 0.1096 0.7941 185 K 0.0187 0.2837 0.6976 186 M 0.0692 0.1726 0.7582 187 I 0.3869 0.0791 0.5340 188 D 0.3499 0.0694 0.5807 189 L 0.8519 0.0139 0.1342 190 I 0.8866 0.0104 0.1030 191 I 0.8248 0.0137 0.1615 192 P 0.4804 0.0526 0.4670 193 R 0.2150 0.0434 0.7416 194 G 0.0759 0.0558 0.8682 195 S 0.0510 0.1813 0.7677 196 S 0.0092 0.8601 0.1307 197 Q 0.0050 0.9523 0.0426 198 L 0.0047 0.9573 0.0379 199 V 0.0047 0.9606 0.0347 200 R 0.0046 0.9617 0.0337 201 D 0.0046 0.9615 0.0339 202 I 0.0047 0.9598 0.0355 203 Q 0.0047 0.9568 0.0385 204 K 0.0052 0.9415 0.0534 205 A 0.0077 0.8619 0.1304 206 A 0.0474 0.5834 0.3693 207 K 0.0230 0.2668 0.7102 208 G 0.0477 0.0652 0.8870 209 I 0.1506 0.0299 0.8195 210 P 0.3948 0.0268 0.5785 211 V 0.6535 0.0474 0.2991 212 M 0.7361 0.0525 0.2114 213 G 0.6399 0.0773 0.2828 214 H 0.5271 0.0906 0.3823 215 S 0.3137 0.0938 0.5925 216 E 0.1947 0.0700 0.7353 217 G 0.1852 0.0574 0.7574 218 I 0.3450 0.0494 0.6056 219 C 0.3446 0.0320 0.6234 220 H 0.3809 0.0644 0.5547 221 M 0.6502 0.0479 0.3020 222 Y 0.8251 0.0226 0.1523 223 V 0.7408 0.0321 0.2270 224 D 0.2213 0.0296 0.7491 225 S 0.0191 0.1471 0.8338 226 E 0.0286 0.0984 0.8730 227 A 0.1131 0.0521 0.8347 228 S 0.1071 0.0351 0.8578 229 V 0.0058 0.9305 0.0637 230 D 0.0047 0.9546 0.0407 231 K 0.0051 0.9543 0.0406 232 V 0.0060 0.9535 0.0406 233 T 0.0055 0.9535 0.0410 234 R 0.0063 0.9483 0.0454 235 L 0.0072 0.9406 0.0522 236 V 0.0094 0.9239 0.0667 237 R 0.0128 0.8503 0.1369 238 D 0.0199 0.6275 0.3525 239 S 0.0284 0.4388 0.5329 240 K 0.0623 0.2218 0.7159 241 C 0.1434 0.1518 0.7048 242 E 0.1457 0.1169 0.7374 243 Y 0.1305 0.1206 0.7489 244 P 0.1179 0.2177 0.6645 245 A 0.2502 0.2572 0.4926 246 A 0.3772 0.2145 0.4083 247 C 0.3479 0.1928 0.4593 248 N 0.3137 0.1550 0.5313 249 A 0.2973 0.2348 0.4678 250 L 0.3183 0.3467 0.3350 251 E 0.3146 0.4047 0.2807 252 T 0.4305 0.4016 0.1679 253 L 0.5307 0.3536 0.1157 254 L 0.6294 0.2535 0.1171 255 I 0.5676 0.2185 0.2139 256 H 0.3121 0.2733 0.4146 257 R 0.0884 0.5235 0.3882 258 D 0.0557 0.5490 0.3954 259 L 0.0338 0.6170 0.3492 260 L 0.0489 0.3612 0.5899 261 R 0.0434 0.2180 0.7386 262 T 0.0355 0.2446 0.7199 263 P 0.0140 0.5153 0.4707 264 L 0.0118 0.7473 0.2409 265 F 0.0048 0.9472 0.0480 266 D 0.0047 0.9551 0.0401 267 Q 0.0047 0.9556 0.0396 268 I 0.0047 0.9582 0.0370 269 I 0.0047 0.9594 0.0359 270 D 0.0047 0.9554 0.0399 271 M 0.0052 0.9455 0.0493 272 L 0.0059 0.9286 0.0655 273 R 0.0072 0.9011 0.0916 274 V 0.0118 0.8577 0.1305 275 E 0.0582 0.7230 0.2188 276 Q 0.0884 0.5017 0.4098 277 V 0.1352 0.3525 0.5122 278 K 0.1073 0.2123 0.6804 279 I 0.1122 0.1590 0.7288 280 H 0.0747 0.1963 0.7289 281 A 0.0823 0.1520 0.7657 282 G 0.0678 0.0659 0.8662 283 P 0.0200 0.3123 0.6678 284 K 0.0292 0.2679 0.7028 285 F 0.0933 0.3065 0.6002 286 A 0.1765 0.1478 0.6757 287 S 0.2531 0.2169 0.5300 288 Y 0.2802 0.2775 0.4423 289 L 0.3144 0.2286 0.4570 290 T 0.2036 0.2086 0.5878 291 F 0.1003 0.3536 0.5462 292 V 0.0999 0.3594 0.5407 293 K 0.1198 0.3696 0.5107 294 S 0.1881 0.4126 0.3993 295 L 0.1920 0.5889 0.2191 296 R 0.2141 0.5677 0.2182 297 T 0.3000 0.4957 0.2043 298 E 0.3400 0.4404 0.2196 299 Y 0.3354 0.3275 0.3370 300 G 0.2047 0.1469 0.6484 301 D 0.2554 0.0732 0.6714 302 L 0.4707 0.0531 0.4763 303 E 0.7398 0.0338 0.2264 304 L 0.8132 0.0153 0.1714 305 C 0.8297 0.0099 0.1604 306 I 0.8658 0.0069 0.1273 307 E 0.8567 0.0066 0.1367 308 V 0.7812 0.0120 0.2068 309 V 0.4303 0.0304 0.5393 310 D 0.1152 0.0610 0.8238 311 N 0.0821 0.0524 0.8655 312 V 0.0048 0.9366 0.0586 313 Q 0.0047 0.9563 0.0390 314 D 0.0047 0.9558 0.0395 315 A 0.0050 0.9569 0.0381 316 I 0.0049 0.9580 0.0370 317 D 0.0047 0.9564 0.0389 318 H 0.0049 0.9471 0.0480 319 I 0.0054 0.9330 0.0616 320 H 0.0080 0.8106 0.1813 321 K 0.0124 0.5772 0.4104 322 Y 0.0524 0.2232 0.7244 323 G 0.0506 0.1068 0.8425 324 S 0.0919 0.1215 0.7866 325 S 0.1137 0.1533 0.7330 326 H 0.2208 0.1782 0.6009 327 T 0.3637 0.1539 0.4825 328 D 0.4908 0.1423 0.3669 329 V 0.8346 0.0398 0.1256 330 I 0.8777 0.0212 0.1011 331 V 0.8422 0.0246 0.1332 332 T 0.5317 0.0266 0.4417 333 E 0.0993 0.0837 0.8169 334 D 0.0995 0.0478 0.8527 335 E 0.0077 0.8763 0.1159 336 N 0.0058 0.9298 0.0643 337 T 0.0055 0.9465 0.0480 338 A 0.0047 0.9585 0.0368 339 E 0.0047 0.9601 0.0353 340 F 0.0047 0.9588 0.0365 341 F 0.0048 0.9556 0.0396 342 L 0.0051 0.9470 0.0480 343 Q 0.0058 0.8964 0.0978 344 H 0.0115 0.8139 0.1745 345 V 0.0647 0.5463 0.3889 346 D 0.0748 0.3373 0.5880 347 S 0.2357 0.2368 0.5275 348 A 0.4618 0.1682 0.3700 349 C 0.6862 0.0856 0.2282 350 V 0.8263 0.0561 0.1175 351 F 0.8734 0.0327 0.0938 352 W 0.8399 0.0276 0.1326 353 N 0.5407 0.0392 0.4201 354 A 0.3351 0.0649 0.6000 355 S 0.2260 0.1104 0.6636 356 T 0.1945 0.1061 0.6994 357 R 0.1724 0.1185 0.7090 358 F 0.1710 0.1026 0.7264 359 S 0.1103 0.0937 0.7960 360 D 0.0418 0.1666 0.7917 361 G 0.0517 0.1203 0.8280 362 Y 0.1387 0.0933 0.7680 363 R 0.2165 0.0967 0.6868 364 F 0.2317 0.1147 0.6536 365 G 0.1768 0.0872 0.7360 366 L 0.2054 0.0961 0.6984 367 G 0.2270 0.1111 0.6618 368 A 0.2181 0.1644 0.6175 369 E 0.2953 0.1458 0.5589 370 V 0.3304 0.1261 0.5435 371 G 0.3059 0.1021 0.5920 372 I 0.2917 0.1233 0.5850 373 S 0.2742 0.1245 0.6013 374 T 0.1275 0.3293 0.5432 375 S 0.0841 0.4921 0.4238 376 R 0.0672 0.5448 0.3881 377 I 0.0938 0.5345 0.3717 378 H 0.0937 0.3744 0.5318 379 A 0.0489 0.3280 0.6231 380 R 0.0451 0.3150 0.6399 381 G 0.0416 0.1128 0.8456 382 P 0.0253 0.5560 0.4187 383 V 0.0431 0.5795 0.3774 384 G 0.0468 0.6869 0.2663 385 L 0.0326 0.8280 0.1393 386 E 0.0266 0.8524 0.1209 387 G 0.0297 0.8319 0.1384 388 L 0.0625 0.7727 0.1648 389 L 0.1554 0.6369 0.2077 390 T 0.2752 0.4684 0.2565 391 T 0.4486 0.3057 0.2456 392 K 0.4883 0.2534 0.2583 393 W 0.6078 0.1691 0.2231 394 L 0.6555 0.1730 0.1715 395 L 0.7310 0.1067 0.1623 396 R 0.5191 0.0978 0.3831 397 G 0.2123 0.0530 0.7348 398 K 0.1392 0.0954 0.7653 399 D 0.1537 0.1270 0.7193 400 H 0.2996 0.1135 0.5870 401 V 0.4104 0.0993 0.4903 402 V 0.3519 0.1376 0.5105 403 S 0.1944 0.2272 0.5784 404 D 0.1429 0.2563 0.6008 405 F 0.1405 0.2985 0.5610 406 S 0.1441 0.2571 0.5988 407 E 0.1355 0.2097 0.6548 408 H 0.0841 0.2389 0.6770 409 G 0.0629 0.2208 0.7163 410 S 0.1079 0.3045 0.5877 411 L 0.1353 0.4348 0.4298 412 K 0.1656 0.4441 0.3902 413 Y 0.2284 0.4524 0.3192 414 L 0.2116 0.4976 0.2908 415 H 0.2115 0.4813 0.3072 416 E 0.1663 0.4454 0.3883 417 N 0.1331 0.2918 0.5752 418 L 0.1417 0.0539 0.8044 419 P 0.1368 0.0441 0.8191 420 I 0.1666 0.0727 0.7607 421 P 0.1488 0.1512 0.7000 422 Q 0.1728 0.2466 0.5806 423 R 0.1890 0.1739 0.6371 424 N 0.1375 0.0755 0.7871 425 T 0.0677 0.0401 0.8922