# This file is the result of combining several RDB files, specifically # T0208.t04.dssp-ebghstl.rdb (weight 1.53986) # T0208.t04.stride-ebghtl.rdb (weight 1.24869) # T0208.t04.str2.rdb (weight 1.54758) # T0208.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 T0208.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0208 # 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 T0208.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 114.786 # # ============================================ # Comments from T0208.t04.stride-ebghtl.rdb # ============================================ # TARGET T0208 # 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 T0208.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 114.786 # # ============================================ # Comments from T0208.t04.str2.rdb # ============================================ # TARGET T0208 # 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 T0208.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 114.786 # # ============================================ # Comments from T0208.t04.alpha.rdb # ============================================ # TARGET T0208 # 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 T0208.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 114.786 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1338 0.0851 0.7811 2 K 0.2791 0.1338 0.5871 3 W 0.4104 0.1403 0.4493 4 G 0.5365 0.1016 0.3620 5 F 0.7134 0.0831 0.2036 6 R 0.7173 0.1246 0.1581 7 W 0.6828 0.1378 0.1794 8 Y 0.5181 0.1123 0.3697 9 G 0.2602 0.0670 0.6728 10 A 0.1383 0.0516 0.8101 11 A 0.0403 0.1078 0.8519 12 G 0.0275 0.0652 0.9073 13 D 0.1036 0.0538 0.8426 14 A 0.1603 0.0449 0.7948 15 I 0.2115 0.0192 0.7693 16 P 0.1678 0.0283 0.8039 17 L 0.0188 0.8399 0.1413 18 K 0.0143 0.8623 0.1233 19 H 0.0191 0.8554 0.1256 20 I 0.0589 0.7906 0.1505 21 R 0.1021 0.6347 0.2632 22 Q 0.1593 0.5261 0.3146 23 I 0.1324 0.2375 0.6301 24 P 0.0464 0.2577 0.6958 25 G 0.0414 0.1447 0.8139 26 I 0.0970 0.3185 0.5845 27 T 0.0903 0.4122 0.4975 28 G 0.1725 0.4618 0.3657 29 V 0.2746 0.4901 0.2353 30 V 0.3198 0.5187 0.1615 31 G 0.2339 0.5777 0.1884 32 T 0.1667 0.5883 0.2450 33 L 0.1255 0.5453 0.3292 34 L 0.1096 0.4714 0.4190 35 N 0.1421 0.2742 0.5838 36 K 0.1160 0.1118 0.7722 37 L 0.0981 0.0495 0.8524 38 P 0.0492 0.1413 0.8094 39 G 0.0405 0.1319 0.8277 40 D 0.1152 0.1917 0.6930 41 V 0.2416 0.1846 0.5738 42 W 0.2707 0.0932 0.6360 43 T 0.1679 0.1201 0.7120 44 V 0.0165 0.8434 0.1401 45 A 0.0067 0.9225 0.0708 46 E 0.0068 0.9360 0.0572 47 I 0.0047 0.9530 0.0423 48 Q 0.0047 0.9601 0.0352 49 A 0.0047 0.9587 0.0366 50 L 0.0047 0.9529 0.0424 51 K 0.0047 0.9583 0.0370 52 Q 0.0048 0.9570 0.0382 53 S 0.0048 0.9571 0.0381 54 V 0.0047 0.9553 0.0399 55 E 0.0052 0.9448 0.0500 56 Q 0.0058 0.9174 0.0768 57 E 0.0399 0.5704 0.3897 58 G 0.0359 0.1033 0.8609 59 L 0.1556 0.0503 0.7941 60 A 0.4816 0.0546 0.4638 61 L 0.6549 0.0854 0.2597 62 L 0.6737 0.0895 0.2368 63 G 0.8425 0.0405 0.1169 64 I 0.8413 0.0376 0.1211 65 E 0.7232 0.0492 0.2275 66 S 0.5231 0.0542 0.4227 67 V 0.2918 0.0664 0.6417 68 A 0.2618 0.0979 0.6403 69 I 0.1314 0.3291 0.5396 70 H 0.0672 0.5161 0.4167 71 D 0.0217 0.6404 0.3380 72 A 0.0193 0.6873 0.2934 73 I 0.0505 0.6738 0.2757 74 K 0.0597 0.5852 0.3551 75 A 0.0640 0.3358 0.6002 76 G 0.0585 0.1151 0.8265 77 T 0.0640 0.0890 0.8471 78 D 0.0521 0.2155 0.7323 79 Q 0.0394 0.3317 0.6288 80 R 0.0398 0.4515 0.5087 81 D 0.0441 0.4873 0.4686 82 H 0.0458 0.5638 0.3905 83 Y 0.0599 0.5726 0.3675 84 I 0.0342 0.7425 0.2233 85 D 0.0137 0.8533 0.1329 86 N 0.0081 0.9032 0.0887 87 Y 0.0053 0.9468 0.0479 88 R 0.0055 0.9533 0.0412 89 Q 0.0049 0.9574 0.0377 90 T 0.0052 0.9559 0.0389 91 L 0.0047 0.9585 0.0368 92 R 0.0047 0.9553 0.0400 93 N 0.0048 0.9529 0.0423 94 L 0.0050 0.9428 0.0523 95 G 0.0063 0.8988 0.0949 96 K 0.0087 0.8443 0.1469 97 C 0.0437 0.4482 0.5081 98 G 0.0529 0.0375 0.9097 99 I 0.2087 0.0153 0.7760 100 S 0.6450 0.0109 0.3441 101 L 0.8041 0.0104 0.1855 102 V 0.8266 0.0122 0.1612 103 C 0.8020 0.0168 0.1812 104 Y 0.5502 0.0447 0.4051 105 S 0.2377 0.0438 0.7186 106 F 0.1981 0.0604 0.7415 107 K 0.2145 0.0529 0.7326 108 P 0.3023 0.0913 0.6065 109 I 0.2634 0.1623 0.5743 110 F 0.2443 0.2022 0.5535 111 G 0.1530 0.2548 0.5922 112 W 0.1481 0.3411 0.5108 113 A 0.1941 0.3485 0.4574 114 K 0.1747 0.4167 0.4086 115 T 0.1486 0.3386 0.5128 116 D 0.1540 0.3199 0.5261 117 L 0.1121 0.4927 0.3952 118 A 0.1484 0.4820 0.3696 119 Y 0.2203 0.4052 0.3745 120 E 0.2476 0.2791 0.4733 121 N 0.1368 0.0886 0.7746 122 E 0.0509 0.1530 0.7961 123 D 0.0629 0.0828 0.8543 124 G 0.0911 0.0934 0.8156 125 S 0.2704 0.1177 0.6118 126 L 0.5126 0.1694 0.3179 127 S 0.4663 0.2225 0.3112 128 L 0.4307 0.2616 0.3077 129 L 0.4001 0.2565 0.3434 130 F 0.3314 0.2581 0.4105 131 D 0.2218 0.2907 0.4875 132 Q 0.0462 0.7116 0.2422 133 A 0.0448 0.7366 0.2186 134 V 0.0470 0.7508 0.2022 135 V 0.0420 0.7249 0.2331 136 E 0.0357 0.5940 0.3703 137 N 0.0327 0.3124 0.6549 138 M 0.0778 0.0886 0.8337 139 Q 0.0629 0.0189 0.9182 140 P 0.0080 0.9166 0.0754 141 E 0.0049 0.9500 0.0451 142 D 0.0050 0.9513 0.0437 143 M 0.0048 0.9578 0.0374 144 Y 0.0047 0.9596 0.0357 145 Q 0.0047 0.9591 0.0362 146 L 0.0048 0.9552 0.0400 147 I 0.0049 0.9433 0.0518 148 H 0.0057 0.9046 0.0897 149 S 0.0071 0.8044 0.1885 150 Q 0.0120 0.7255 0.2625 151 S 0.0345 0.5620 0.4034 152 K 0.0332 0.5224 0.4444 153 G 0.1119 0.4375 0.4506 154 F 0.4218 0.2090 0.3692 155 R 0.4645 0.1321 0.4034 156 L 0.2087 0.0474 0.7439 157 P 0.0587 0.0910 0.8503 158 G 0.0424 0.0564 0.9011 159 W 0.1174 0.0874 0.7952 160 E 0.1433 0.1792 0.6775 161 E 0.0869 0.6878 0.2253 162 E 0.1142 0.6939 0.1919 163 R 0.1085 0.7574 0.1341 164 L 0.0620 0.8327 0.1054 165 Q 0.0380 0.8565 0.1056 166 Q 0.0305 0.8651 0.1044 167 F 0.0235 0.8823 0.0943 168 Q 0.0126 0.9120 0.0754 169 E 0.0151 0.8947 0.0902 170 L 0.0189 0.8773 0.1038 171 K 0.0161 0.8688 0.1151 172 A 0.0196 0.8263 0.1541 173 M 0.0274 0.7346 0.2380 174 Y 0.0592 0.4177 0.5231 175 A 0.0247 0.1808 0.7945 176 G 0.0287 0.0556 0.9157 177 V 0.1334 0.0164 0.8502 178 T 0.0743 0.0112 0.9145 179 E 0.0048 0.9469 0.0483 180 E 0.0047 0.9566 0.0388 181 D 0.0047 0.9575 0.0378 182 L 0.0047 0.9563 0.0390 183 V 0.0047 0.9574 0.0379 184 E 0.0047 0.9541 0.0412 185 N 0.0048 0.9441 0.0511 186 L 0.0048 0.9480 0.0472 187 R 0.0047 0.9549 0.0403 188 Y 0.0048 0.9450 0.0502 189 F 0.0049 0.9420 0.0532 190 L 0.0049 0.9468 0.0484 191 E 0.0052 0.9382 0.0566 192 R 0.0051 0.8985 0.0964 193 V 0.0059 0.8974 0.0968 194 I 0.0055 0.9137 0.0808 195 P 0.0055 0.9287 0.0658 196 V 0.0054 0.9445 0.0501 197 C 0.0081 0.9333 0.0585 198 E 0.0066 0.9287 0.0647 199 E 0.0091 0.8763 0.1146 200 E 0.0456 0.3446 0.6098 201 N 0.0502 0.0169 0.9329 202 I 0.2649 0.0071 0.7280 203 K 0.7599 0.0097 0.2304 204 M 0.9158 0.0054 0.0787 205 G 0.9228 0.0048 0.0724 206 I 0.8990 0.0060 0.0950 207 H 0.6662 0.0075 0.3263 208 P 0.1758 0.0545 0.7697 209 D 0.0686 0.0541 0.8773 210 D 0.0782 0.0414 0.8804 211 P 0.0592 0.0938 0.8470 212 P 0.0453 0.2298 0.7249 213 W 0.0593 0.3866 0.5542 214 E 0.0554 0.4767 0.4679 215 I 0.0773 0.4277 0.4950 216 F 0.1025 0.2263 0.6712 217 G 0.0807 0.1116 0.8077 218 L 0.0943 0.1794 0.7264 219 P 0.0721 0.3083 0.6196 220 R 0.1497 0.3596 0.4907 221 I 0.2811 0.3346 0.3842 222 T 0.3288 0.1743 0.4969 223 K 0.1805 0.1000 0.7195 224 N 0.0835 0.0251 0.8914 225 L 0.0054 0.9407 0.0539 226 A 0.0047 0.9563 0.0390 227 D 0.0049 0.9567 0.0384 228 L 0.0047 0.9591 0.0362 229 K 0.0047 0.9593 0.0360 230 R 0.0047 0.9539 0.0414 231 I 0.0052 0.9433 0.0516 232 L 0.0059 0.9262 0.0679 233 S 0.0070 0.8487 0.1444 234 L 0.0133 0.7144 0.2723 235 V 0.0810 0.2863 0.6326 236 D 0.0947 0.0825 0.8228 237 S 0.0880 0.0833 0.8286 238 P 0.0134 0.2805 0.7061 239 A 0.0344 0.3001 0.6656 240 N 0.1119 0.1579 0.7302 241 G 0.2596 0.0636 0.6767 242 I 0.6575 0.0207 0.3219 243 T 0.7943 0.0168 0.1889 244 F 0.6716 0.0249 0.3035 245 C 0.4545 0.0298 0.5157 246 T 0.2139 0.0674 0.7187 247 G 0.1460 0.0920 0.7620 248 S 0.1720 0.1519 0.6761 249 L 0.1592 0.2100 0.6308 250 G 0.1446 0.1441 0.7113 251 A 0.1655 0.1043 0.7301 252 D 0.1164 0.0494 0.8342 253 P 0.0341 0.1999 0.7660 254 T 0.0410 0.1878 0.7712 255 N 0.0488 0.2139 0.7374 256 D 0.0947 0.2468 0.6585 257 L 0.0167 0.8219 0.1614 258 P 0.0050 0.9530 0.0419 259 T 0.0047 0.9593 0.0360 260 M 0.0047 0.9588 0.0365 261 I 0.0048 0.9551 0.0402 262 R 0.0050 0.9386 0.0564 263 E 0.0063 0.8627 0.1311 264 I 0.0119 0.7032 0.2849 265 G 0.0219 0.4524 0.5258 266 H 0.0347 0.3772 0.5881 267 R 0.1473 0.2829 0.5699 268 I 0.3801 0.1412 0.4786 269 N 0.4429 0.1294 0.4277 270 F 0.8321 0.0455 0.1224 271 V 0.8644 0.0204 0.1153 272 H 0.8744 0.0152 0.1105 273 F 0.7972 0.0232 0.1797 274 R 0.5431 0.0556 0.4013 275 N 0.4160 0.0340 0.5500 276 V 0.3205 0.0709 0.6086 277 K 0.3828 0.0766 0.5406 278 Y 0.2858 0.1014 0.6129 279 L 0.1255 0.0803 0.7942 280 G 0.0719 0.0634 0.8647 281 E 0.0828 0.0679 0.8493 282 H 0.2007 0.0371 0.7622 283 R 0.2679 0.0380 0.6941 284 F 0.3315 0.1469 0.5216 285 E 0.3749 0.1684 0.4566 286 E 0.3815 0.1664 0.4522 287 T 0.3392 0.0990 0.5618 288 A 0.3125 0.0635 0.6240 289 H 0.2259 0.0270 0.7470 290 P 0.1601 0.0421 0.7978 291 S 0.1118 0.0727 0.8155 292 V 0.1107 0.1056 0.7837 293 A 0.0992 0.0891 0.8117 294 G 0.0959 0.0718 0.8323 295 S 0.2256 0.0751 0.6993 296 L 0.3467 0.0540 0.5993 297 D 0.2292 0.0388 0.7320 298 M 0.0102 0.8990 0.0908 299 A 0.0047 0.9589 0.0364 300 E 0.0046 0.9608 0.0345 301 L 0.0054 0.9583 0.0363 302 M 0.0047 0.9607 0.0346 303 Q 0.0046 0.9608 0.0346 304 A 0.0047 0.9601 0.0353 305 L 0.0047 0.9580 0.0373 306 V 0.0049 0.9458 0.0493 307 D 0.0055 0.8996 0.0948 308 V 0.0439 0.4278 0.5283 309 G 0.0498 0.0188 0.9314 310 Y 0.0899 0.0177 0.8924 311 E 0.1517 0.0491 0.7993 312 G 0.2800 0.0228 0.6972 313 V 0.4539 0.0181 0.5280 314 I 0.6774 0.0126 0.3100 315 R 0.5319 0.0136 0.4545 316 P 0.2535 0.1932 0.5533 317 D 0.1789 0.2218 0.5993 318 H 0.1333 0.3048 0.5619 319 G 0.1183 0.2195 0.6621 320 R 0.1862 0.2443 0.5695 321 A 0.3589 0.2202 0.4209 322 I 0.3074 0.1716 0.5210 323 W 0.2474 0.1459 0.6067 324 D 0.1424 0.1101 0.7475 325 E 0.0523 0.3120 0.6357 326 K 0.0788 0.2639 0.6572 327 A 0.1608 0.1709 0.6683 328 M 0.1231 0.0565 0.8205 329 P 0.0823 0.1408 0.7770 330 G 0.0836 0.1480 0.7685 331 Y 0.1244 0.2478 0.6278 332 G 0.1057 0.3093 0.5850 333 L 0.0245 0.8017 0.1738 334 Y 0.0166 0.8651 0.1183 335 D 0.0128 0.8731 0.1141 336 R 0.0096 0.9149 0.0755 337 A 0.0102 0.9332 0.0566 338 M 0.0070 0.9326 0.0604 339 G 0.0059 0.9373 0.0569 340 L 0.0049 0.9553 0.0398 341 T 0.0047 0.9586 0.0367 342 Y 0.0047 0.9571 0.0382 343 I 0.0048 0.9541 0.0411 344 Q 0.0047 0.9398 0.0555 345 G 0.0048 0.9194 0.0759 346 L 0.0047 0.9457 0.0496 347 Y 0.0047 0.9564 0.0389 348 E 0.0048 0.9566 0.0387 349 A 0.0049 0.9530 0.0422 350 T 0.0057 0.9386 0.0557 351 K 0.0077 0.9050 0.0873 352 A 0.0091 0.8397 0.1512 353 K 0.0163 0.7576 0.2262 354 Q 0.0345 0.5427 0.4228 355 N 0.0404 0.2896 0.6700 356 R 0.0416 0.0957 0.8627 357 K 0.0489 0.0340 0.9170