# This file is the result of combining several RDB files, specifically # T0294.t04.dssp-ebghstl.rdb (weight 1.53986) # T0294.t04.stride-ebghtl.rdb (weight 1.24869) # T0294.t04.str2.rdb (weight 1.54758) # T0294.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 T0294.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0294 # 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 T0294.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 2028 # # ============================================ # Comments from T0294.t04.stride-ebghtl.rdb # ============================================ # TARGET T0294 # 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 T0294.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 2028 # # ============================================ # Comments from T0294.t04.str2.rdb # ============================================ # TARGET T0294 # 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 T0294.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 2028 # # ============================================ # Comments from T0294.t04.alpha.rdb # ============================================ # TARGET T0294 # 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 T0294.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 2028 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0811 0.0800 0.8388 2 R 0.1433 0.0331 0.8237 3 P 0.1562 0.0704 0.7734 4 V 0.1536 0.2063 0.6401 5 R 0.1586 0.2062 0.6351 6 L 0.3177 0.0784 0.6039 7 M 0.5140 0.0117 0.4743 8 K 0.8456 0.0076 0.1468 9 V 0.9237 0.0037 0.0725 10 F 0.9264 0.0040 0.0695 11 V 0.9104 0.0053 0.0844 12 T 0.7384 0.0167 0.2449 13 R 0.3083 0.0305 0.6612 14 R 0.1450 0.0410 0.8140 15 I 0.0996 0.0196 0.8808 16 P 0.0612 0.0265 0.9123 17 A 0.0175 0.7049 0.2777 18 E 0.0087 0.8707 0.1205 19 G 0.0080 0.9166 0.0754 20 R 0.0089 0.9337 0.0574 21 V 0.0085 0.9505 0.0410 22 A 0.0081 0.9525 0.0394 23 L 0.0101 0.9469 0.0430 24 A 0.0181 0.9282 0.0537 25 R 0.0090 0.9115 0.0795 26 A 0.0140 0.8114 0.1747 27 A 0.0486 0.2992 0.6521 28 D 0.0501 0.0319 0.9180 29 C 0.1774 0.0162 0.8063 30 E 0.6744 0.0100 0.3156 31 V 0.8588 0.0054 0.1358 32 E 0.8632 0.0076 0.1293 33 Q 0.8285 0.0082 0.1632 34 W 0.5525 0.0181 0.4294 35 D 0.2481 0.0326 0.7193 36 S 0.0942 0.0557 0.8501 37 D 0.0532 0.0587 0.8881 38 E 0.0717 0.0264 0.9019 39 P 0.0906 0.0209 0.8884 40 I 0.1241 0.0132 0.8626 41 P 0.0649 0.0194 0.9157 42 A 0.0049 0.9275 0.0676 43 K 0.0047 0.9522 0.0432 44 E 0.0048 0.9543 0.0409 45 L 0.0047 0.9550 0.0402 46 E 0.0048 0.9440 0.0511 47 R 0.0055 0.8907 0.1038 48 G 0.0075 0.8049 0.1875 49 V 0.0317 0.5028 0.4655 50 A 0.0159 0.3295 0.6546 51 G 0.0290 0.1215 0.8495 52 A 0.1891 0.0280 0.7828 53 H 0.3140 0.0409 0.6450 54 G 0.8857 0.0052 0.1090 55 L 0.9300 0.0033 0.0667 56 L 0.9298 0.0034 0.0668 57 C 0.9019 0.0053 0.0928 58 L 0.7442 0.0095 0.2463 59 L 0.3677 0.0250 0.6074 60 S 0.1140 0.0659 0.8201 61 D 0.0952 0.0655 0.8393 62 H 0.1446 0.1134 0.7420 63 V 0.1408 0.0855 0.7736 64 D 0.0780 0.0946 0.8274 65 K 0.0048 0.9464 0.0488 66 R 0.0047 0.9547 0.0406 67 I 0.0047 0.9559 0.0394 68 L 0.0048 0.9524 0.0429 69 D 0.0051 0.9005 0.0945 70 A 0.0076 0.7961 0.1963 71 A 0.0429 0.5848 0.3723 72 G 0.0323 0.2337 0.7340 73 A 0.0397 0.1749 0.7854 74 N 0.0814 0.0988 0.8198 75 L 0.4697 0.0290 0.5012 76 K 0.7929 0.0215 0.1856 77 V 0.9208 0.0094 0.0699 78 I 0.9081 0.0160 0.0759 79 S 0.9062 0.0107 0.0831 80 T 0.8205 0.0194 0.1601 81 M 0.5897 0.0452 0.3652 82 S 0.3719 0.0616 0.5664 83 V 0.1871 0.1074 0.7055 84 G 0.1535 0.0898 0.7567 85 I 0.1790 0.2110 0.6100 86 D 0.1287 0.2634 0.6078 87 H 0.1910 0.3312 0.4778 88 L 0.3052 0.2223 0.4724 89 A 0.2782 0.1803 0.5415 90 L 0.0140 0.8920 0.0940 91 D 0.0062 0.9430 0.0509 92 E 0.0053 0.9519 0.0429 93 I 0.0051 0.9542 0.0407 94 K 0.0053 0.9390 0.0558 95 K 0.0063 0.8885 0.1053 96 R 0.0417 0.3621 0.5962 97 G 0.0403 0.0188 0.9409 98 I 0.1686 0.0080 0.8234 99 R 0.7403 0.0054 0.2543 100 V 0.8636 0.0074 0.1289 101 G 0.7654 0.0171 0.2175 102 Y 0.5400 0.0149 0.4451 103 T 0.1919 0.0248 0.7833 104 P 0.0795 0.1072 0.8133 105 D 0.0680 0.1600 0.7720 106 V 0.1017 0.2472 0.6512 107 L 0.0965 0.2665 0.6370 108 T 0.0329 0.5858 0.3814 109 D 0.0096 0.8517 0.1387 110 T 0.0069 0.9332 0.0600 111 T 0.0048 0.9567 0.0385 112 A 0.0047 0.9599 0.0354 113 E 0.0047 0.9612 0.0342 114 L 0.0046 0.9612 0.0341 115 A 0.0046 0.9613 0.0341 116 V 0.0046 0.9614 0.0340 117 S 0.0046 0.9615 0.0338 118 L 0.0046 0.9616 0.0338 119 L 0.0047 0.9610 0.0343 120 L 0.0047 0.9607 0.0346 121 T 0.0047 0.9573 0.0380 122 T 0.0049 0.9398 0.0552 123 C 0.0060 0.8601 0.1340 124 R 0.0092 0.6511 0.3397 125 R 0.0170 0.4061 0.5769 126 L 0.0300 0.3250 0.6450 127 P 0.0126 0.7169 0.2705 128 E 0.0061 0.8611 0.1329 129 A 0.0066 0.8513 0.1421 130 I 0.0075 0.8985 0.0940 131 E 0.0049 0.9461 0.0490 132 E 0.0053 0.9415 0.0532 133 V 0.0101 0.9242 0.0657 134 K 0.0105 0.8831 0.1064 135 N 0.0326 0.5518 0.4156 136 G 0.0383 0.1765 0.7852 137 G 0.0590 0.1166 0.8244 138 W 0.1414 0.1635 0.6951 139 T 0.1052 0.2435 0.6513 140 S 0.1189 0.2526 0.6285 141 W 0.1410 0.1855 0.6735 142 K 0.1465 0.1342 0.7193 143 P 0.1723 0.3356 0.4921 144 L 0.2370 0.3683 0.3947 145 W 0.2710 0.3420 0.3871 146 L 0.2711 0.2415 0.4874 147 C 0.1975 0.1672 0.6352 148 G 0.1655 0.1021 0.7325 149 Y 0.3151 0.0810 0.6038 150 G 0.3936 0.0720 0.5344 151 L 0.2844 0.1524 0.5632 152 T 0.1414 0.1311 0.7275 153 Q 0.1264 0.0611 0.8125 154 S 0.4175 0.0146 0.5680 155 T 0.8078 0.0045 0.1877 156 V 0.9185 0.0039 0.0776 157 G 0.9288 0.0037 0.0676 158 I 0.9292 0.0035 0.0673 159 I 0.8499 0.0312 0.1189 160 G 0.5630 0.0233 0.4137 161 L 0.1716 0.0957 0.7327 162 G 0.0689 0.2026 0.7285 163 R 0.0406 0.7346 0.2247 164 I 0.0087 0.9215 0.0698 165 G 0.0062 0.9452 0.0486 166 Q 0.0049 0.9595 0.0356 167 A 0.0046 0.9606 0.0348 168 I 0.0047 0.9587 0.0366 169 A 0.0047 0.9555 0.0397 170 R 0.0050 0.9460 0.0490 171 R 0.0057 0.9147 0.0795 172 L 0.0135 0.8057 0.1808 173 K 0.0095 0.6778 0.3127 174 P 0.0136 0.6853 0.3011 175 F 0.0525 0.3792 0.5683 176 G 0.0709 0.1197 0.8095 177 V 0.1526 0.0277 0.8197 178 Q 0.3742 0.0584 0.5674 179 R 0.8082 0.0111 0.1808 180 F 0.9039 0.0046 0.0915 181 L 0.9187 0.0043 0.0769 182 Y 0.8963 0.0055 0.0982 183 T 0.7320 0.0200 0.2480 184 G 0.2542 0.0263 0.7195 185 R 0.1108 0.0409 0.8482 186 Q 0.1010 0.0202 0.8787 187 P 0.0756 0.0280 0.8964 188 R 0.0641 0.0218 0.9142 189 P 0.0343 0.5504 0.4153 190 E 0.0081 0.8858 0.1061 191 E 0.0127 0.8908 0.0965 192 A 0.0194 0.8675 0.1131 193 A 0.0275 0.8245 0.1480 194 E 0.0338 0.6863 0.2799 195 F 0.0802 0.3750 0.5448 196 Q 0.1029 0.1218 0.7753 197 A 0.2622 0.0639 0.6739 198 E 0.5693 0.0523 0.3784 199 F 0.6949 0.0185 0.2866 200 V 0.4726 0.0157 0.5117 201 S 0.1919 0.0126 0.7955 202 T 0.0064 0.9098 0.0837 203 P 0.0048 0.9519 0.0434 204 E 0.0048 0.9537 0.0415 205 L 0.0052 0.9486 0.0463 206 A 0.0050 0.9099 0.0851 207 A 0.0068 0.6603 0.3329 208 Q 0.0172 0.4288 0.5540 209 S 0.1073 0.0856 0.8071 210 D 0.0891 0.0740 0.8369 211 F 0.7837 0.0320 0.1843 212 I 0.9161 0.0134 0.0704 213 V 0.9279 0.0069 0.0652 214 V 0.8870 0.0166 0.0964 215 A 0.6271 0.0241 0.3488 216 C 0.2507 0.0257 0.7236 217 S 0.1620 0.0351 0.8029 218 L 0.1085 0.0581 0.8333 219 T 0.0596 0.0295 0.9109 220 P 0.0095 0.2945 0.6960 221 A 0.0160 0.2700 0.7140 222 T 0.0492 0.2720 0.6788 223 E 0.0291 0.4041 0.5668 224 G 0.0306 0.3263 0.6431 225 L 0.0925 0.3498 0.5577 226 C 0.1895 0.1679 0.6426 227 N 0.0822 0.0901 0.8276 228 K 0.0051 0.9321 0.0628 229 D 0.0048 0.9484 0.0468 230 F 0.0051 0.9436 0.0513 231 F 0.0053 0.9352 0.0595 232 Q 0.0056 0.8665 0.1279 233 K 0.0109 0.6228 0.3663 234 M 0.0645 0.3642 0.5713 235 K 0.0496 0.1471 0.8033 236 E 0.0198 0.1626 0.8176 237 T 0.1195 0.0637 0.8168 238 A 0.8022 0.0094 0.1884 239 V 0.9254 0.0033 0.0713 240 F 0.9334 0.0031 0.0634 241 I 0.9253 0.0044 0.0703 242 N 0.8572 0.0070 0.1358 243 I 0.4706 0.0359 0.4935 244 S 0.2098 0.0447 0.7455 245 R 0.1132 0.0844 0.8023 246 G 0.0785 0.0724 0.8491 247 D 0.1242 0.1392 0.7366 248 V 0.3261 0.0946 0.5793 249 V 0.3443 0.0416 0.6141 250 N 0.1464 0.0425 0.8111 251 Q 0.0049 0.9383 0.0568 252 D 0.0047 0.9564 0.0389 253 D 0.0048 0.9569 0.0384 254 L 0.0047 0.9597 0.0356 255 Y 0.0047 0.9595 0.0359 256 Q 0.0047 0.9607 0.0346 257 A 0.0047 0.9599 0.0354 258 L 0.0047 0.9526 0.0426 259 A 0.0059 0.9056 0.0885 260 S 0.0432 0.4377 0.5191 261 G 0.0298 0.0728 0.8975 262 K 0.0692 0.0865 0.8443 263 I 0.4724 0.0637 0.4639 264 A 0.5852 0.0748 0.3401 265 A 0.7532 0.0530 0.1938 266 A 0.7972 0.0446 0.1582 267 G 0.8101 0.0404 0.1495 268 L 0.8083 0.0309 0.1608 269 D 0.7382 0.0300 0.2318 270 V 0.5457 0.0533 0.4010 271 T 0.3560 0.0539 0.5901 272 S 0.2195 0.0446 0.7359 273 P 0.1201 0.0571 0.8228 274 E 0.1038 0.0216 0.8746 275 P 0.1330 0.0239 0.8431 276 L 0.1269 0.0160 0.8571 277 P 0.0758 0.0351 0.8891 278 T 0.0346 0.1338 0.8316 279 N 0.0362 0.1114 0.8523 280 H 0.0794 0.0550 0.8656 281 P 0.0618 0.2475 0.6907 282 L 0.0802 0.4117 0.5081 283 L 0.1320 0.3613 0.5067 284 T 0.1643 0.1917 0.6439 285 L 0.1089 0.0651 0.8260 286 K 0.0341 0.1588 0.8071 287 N 0.1096 0.0746 0.8158 288 C 0.6127 0.0202 0.3671 289 V 0.8274 0.0084 0.1641 290 I 0.8378 0.0101 0.1521 291 L 0.6386 0.0218 0.3396 292 P 0.3566 0.0551 0.5883 293 H 0.2172 0.0844 0.6984 294 I 0.1009 0.2794 0.6197 295 G 0.0724 0.3586 0.5690 296 S 0.0570 0.4583 0.4847 297 A 0.0586 0.4655 0.4759 298 T 0.0461 0.5441 0.4098 299 H 0.0059 0.9306 0.0635 300 R 0.0048 0.9524 0.0429 301 T 0.0047 0.9549 0.0403 302 R 0.0047 0.9587 0.0366 303 N 0.0047 0.9594 0.0359 304 T 0.0047 0.9593 0.0360 305 M 0.0047 0.9602 0.0351 306 S 0.0047 0.9612 0.0342 307 L 0.0046 0.9618 0.0336 308 L 0.0046 0.9618 0.0336 309 A 0.0046 0.9609 0.0345 310 A 0.0046 0.9600 0.0354 311 N 0.0047 0.9566 0.0388 312 N 0.0047 0.9375 0.0578 313 L 0.0047 0.9403 0.0550 314 L 0.0047 0.9458 0.0495 315 A 0.0053 0.9305 0.0642 316 G 0.0060 0.8841 0.1098 317 L 0.0152 0.7147 0.2701 318 R 0.0339 0.2890 0.6771 319 G 0.0233 0.0632 0.9136 320 E 0.0693 0.0244 0.9063 321 P 0.1156 0.0230 0.8613 322 M 0.0909 0.0418 0.8673 323 P 0.0642 0.1681 0.7678 324 S 0.0658 0.1359 0.7983 325 E 0.1625 0.1089 0.7286 326 L 0.2059 0.0805 0.7136 327 K 0.1652 0.0916 0.7432 328 L 0.0884 0.0550 0.8566