# This file is the result of combining several RDB files, specifically # T0440.t04.dssp-ebghstl.rdb (weight 1.53986) # T0440.t04.stride-ebghtl.rdb (weight 1.24869) # T0440.t04.str2.rdb (weight 1.54758) # T0440.t04.alpha.rdb (weight 0.659012) # T0440.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0440.t2k.stride-ebghtl.rdb (weight 1.24869) # T0440.t2k.str2.rdb (weight 1.54758) # T0440.t2k.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 T0440.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1471 # # ============================================ # Comments from T0440.t04.stride-ebghtl.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1471 # # ============================================ # Comments from T0440.t04.str2.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1471 # # ============================================ # Comments from T0440.t04.alpha.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1471 # # ============================================ # Comments from T0440.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0440 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0440.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 217 # # ============================================ # Comments from T0440.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0440 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0440.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 217 # # ============================================ # Comments from T0440.t2k.str2.rdb # ============================================ # TARGET T0440 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0440.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 217 # # ============================================ # Comments from T0440.t2k.alpha.rdb # ============================================ # TARGET T0440 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0440.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 217 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0868 0.0349 0.8783 2 K 0.1565 0.0434 0.8001 3 R 0.2582 0.0618 0.6800 4 D 0.2487 0.0859 0.6655 5 G 0.3253 0.1087 0.5660 6 H 0.4286 0.1008 0.4706 7 T 0.4584 0.1003 0.4413 8 H 0.3133 0.0844 0.6023 9 T 0.1362 0.0888 0.7749 10 E 0.0861 0.1414 0.7726 11 F 0.0891 0.1608 0.7501 12 C 0.1114 0.0821 0.8065 13 P 0.0377 0.2828 0.6794 14 H 0.0329 0.2782 0.6889 15 G 0.0484 0.3011 0.6505 16 T 0.0611 0.2122 0.7267 17 H 0.0580 0.1555 0.7864 18 D 0.0662 0.0967 0.8371 19 D 0.0804 0.1083 0.8114 20 V 0.0064 0.9358 0.0578 21 E 0.0049 0.9549 0.0402 22 E 0.0048 0.9586 0.0365 23 M 0.0048 0.9586 0.0366 24 V 0.0047 0.9583 0.0369 25 L 0.0047 0.9578 0.0374 26 K 0.0048 0.9583 0.0369 27 A 0.0049 0.9547 0.0404 28 I 0.0050 0.9445 0.0505 29 E 0.0066 0.8897 0.1037 30 L 0.0379 0.3437 0.6184 31 D 0.0455 0.0251 0.9294 32 F 0.1009 0.0078 0.8913 33 D 0.4000 0.0387 0.5613 34 E 0.8786 0.0086 0.1128 35 Y 0.9166 0.0048 0.0786 36 S 0.9159 0.0040 0.0801 37 I 0.8547 0.0097 0.1356 38 V 0.5557 0.0356 0.4087 39 E 0.2354 0.0823 0.6823 40 H 0.1482 0.1079 0.7439 41 A 0.1442 0.0765 0.7793 42 P 0.1336 0.0988 0.7676 43 L 0.1300 0.1124 0.7576 44 S 0.0974 0.1559 0.7467 45 S 0.0817 0.2651 0.6531 46 E 0.0699 0.3233 0.6068 47 F 0.0869 0.3148 0.5983 48 M 0.0964 0.2401 0.6635 49 K 0.1034 0.1823 0.7143 50 N 0.0917 0.1551 0.7532 51 T 0.0768 0.2074 0.7157 52 A 0.0347 0.5099 0.4554 53 G 0.0391 0.5057 0.4553 54 D 0.0550 0.5301 0.4149 55 K 0.0516 0.5351 0.4132 56 E 0.0639 0.4847 0.4514 57 A 0.0493 0.5009 0.4498 58 V 0.0546 0.4495 0.4958 59 T 0.0394 0.4737 0.4869 60 T 0.0481 0.4885 0.4634 61 A 0.0267 0.6157 0.3576 62 S 0.0279 0.5897 0.3824 63 M 0.0386 0.5448 0.4166 64 A 0.0454 0.4401 0.5145 65 M 0.0126 0.7661 0.2213 66 S 0.0093 0.7696 0.2211 67 D 0.0136 0.7343 0.2521 68 L 0.0095 0.8636 0.1268 69 P 0.0052 0.9315 0.0633 70 Y 0.0052 0.9395 0.0553 71 Y 0.0051 0.9460 0.0489 72 F 0.0047 0.9556 0.0397 73 K 0.0047 0.9558 0.0394 74 K 0.0048 0.9541 0.0411 75 M 0.0047 0.9576 0.0377 76 N 0.0047 0.9556 0.0396 77 H 0.0048 0.9502 0.0451 78 I 0.0048 0.9474 0.0478 79 K 0.0052 0.9377 0.0571 80 K 0.0060 0.9189 0.0751 81 K 0.0108 0.8580 0.1312 82 Y 0.0312 0.6969 0.2719 83 A 0.0271 0.4708 0.5021 84 S 0.0241 0.2301 0.7458 85 D 0.0510 0.1266 0.8225 86 L 0.3131 0.0199 0.6670 87 L 0.6213 0.0083 0.3705 88 I 0.8807 0.0055 0.1137 89 H 0.8737 0.0092 0.1171 90 I 0.8532 0.0137 0.1331 91 G 0.8265 0.0125 0.1610 92 F 0.8434 0.0120 0.1446 93 E 0.8298 0.0141 0.1561 94 V 0.7427 0.0294 0.2279 95 D 0.6587 0.0468 0.2945 96 Y 0.4358 0.0643 0.4999 97 L 0.1979 0.0693 0.7328 98 I 0.0555 0.2005 0.7441 99 G 0.0338 0.2427 0.7235 100 Y 0.0446 0.4048 0.5506 101 E 0.0274 0.7443 0.2283 102 D 0.0190 0.8353 0.1457 103 F 0.0157 0.8702 0.1141 104 T 0.0124 0.8958 0.0917 105 R 0.0102 0.9094 0.0804 106 D 0.0091 0.9096 0.0813 107 F 0.0072 0.8982 0.0945 108 L 0.0098 0.8604 0.1298 109 N 0.0084 0.7968 0.1948 110 E 0.0126 0.6635 0.3239 111 Y 0.0384 0.3853 0.5763 112 G 0.0374 0.1354 0.8272 113 P 0.0616 0.1068 0.8316 114 Q 0.0849 0.1306 0.7845 115 T 0.1893 0.0220 0.7887 116 D 0.2316 0.0440 0.7244 117 D 0.8981 0.0059 0.0960 118 G 0.9287 0.0040 0.0673 119 V 0.9176 0.0057 0.0767 120 L 0.8748 0.0084 0.1168 121 S 0.6345 0.0164 0.3491 122 L 0.5101 0.0514 0.4384 123 H 0.5211 0.0787 0.4003 124 F 0.5643 0.0766 0.3591 125 L 0.4199 0.0887 0.4914 126 E 0.2039 0.0923 0.7038 127 G 0.1191 0.1054 0.7755 128 Q 0.1216 0.1398 0.7385 129 G 0.1290 0.1755 0.6955 130 G 0.1301 0.2391 0.6308 131 F 0.1271 0.2390 0.6340 132 R 0.1094 0.2792 0.6114 133 S 0.0820 0.4060 0.5119 134 I 0.0563 0.5824 0.3613 135 D 0.0551 0.6220 0.3229 136 F 0.0551 0.5933 0.3516 137 S 0.0468 0.5955 0.3577 138 A 0.0279 0.7237 0.2483 139 E 0.0218 0.7847 0.1935 140 D 0.0219 0.7974 0.1808 141 Y 0.0167 0.8240 0.1594 142 N 0.0180 0.8158 0.1662 143 E 0.0274 0.7433 0.2293 144 G 0.0335 0.6408 0.3256 145 I 0.0609 0.6589 0.2802 146 V 0.0652 0.6908 0.2440 147 Q 0.0574 0.6614 0.2813 148 F 0.0491 0.6889 0.2620 149 Y 0.0468 0.6297 0.3234 150 G 0.0431 0.5521 0.4048 151 G 0.0642 0.3916 0.5442 152 F 0.0564 0.3559 0.5877 153 E 0.0407 0.3744 0.5850 154 Q 0.0395 0.4094 0.5510 155 A 0.0518 0.5289 0.4193 156 Q 0.0071 0.9039 0.0890 157 L 0.0057 0.9386 0.0557 158 A 0.0051 0.9491 0.0458 159 Y 0.0051 0.9498 0.0451 160 L 0.0051 0.9497 0.0452 161 E 0.0049 0.9478 0.0473 162 G 0.0050 0.9447 0.0503 163 V 0.0050 0.9442 0.0508 164 K 0.0048 0.9510 0.0441 165 Q 0.0048 0.9541 0.0411 166 S 0.0048 0.9555 0.0397 167 I 0.0047 0.9574 0.0379 168 E 0.0047 0.9566 0.0387 169 A 0.0048 0.9533 0.0419 170 D 0.0049 0.9453 0.0498 171 L 0.0062 0.9227 0.0711 172 G 0.0078 0.8456 0.1466 173 L 0.0382 0.5358 0.4260 174 F 0.0342 0.1430 0.8227 175 K 0.0601 0.0479 0.8920 176 P 0.1860 0.0319 0.7820 177 R 0.4454 0.0578 0.4969 178 R 0.8547 0.0218 0.1235 179 M 0.8413 0.0269 0.1318 180 G 0.7815 0.0285 0.1900 181 H 0.5161 0.0481 0.4358 182 I 0.2029 0.2687 0.5284 183 S 0.1468 0.4614 0.3918 184 L 0.1452 0.6049 0.2499 185 C 0.1818 0.6133 0.2049 186 Q 0.1884 0.5839 0.2277 187 K 0.1508 0.5414 0.3078 188 F 0.1108 0.4110 0.4782 189 Q 0.1013 0.1916 0.7071 190 Q 0.0799 0.2130 0.7071 191 F 0.0883 0.1840 0.7276 192 F 0.0561 0.2288 0.7152 193 G 0.0568 0.2620 0.6812 194 E 0.0431 0.4086 0.5483 195 D 0.0560 0.4190 0.5250 196 T 0.0641 0.4754 0.4605 197 S 0.0603 0.4520 0.4877 198 D 0.0362 0.4625 0.5012 199 F 0.0422 0.3500 0.6079 200 S 0.0401 0.6441 0.3158 201 E 0.0119 0.8169 0.1712 202 E 0.0107 0.8468 0.1425 203 V 0.0076 0.9018 0.0906 204 M 0.0051 0.9389 0.0560 205 E 0.0049 0.9502 0.0449 206 K 0.0049 0.9535 0.0417 207 F 0.0048 0.9557 0.0395 208 R 0.0047 0.9590 0.0363 209 V 0.0047 0.9590 0.0363 210 I 0.0047 0.9577 0.0376 211 L 0.0047 0.9585 0.0368 212 A 0.0047 0.9593 0.0360 213 L 0.0047 0.9591 0.0362 214 V 0.0047 0.9565 0.0388 215 K 0.0049 0.9429 0.0522 216 K 0.0054 0.8859 0.1087 217 R 0.0429 0.3411 0.6160 218 D 0.0346 0.0211 0.9443 219 Y 0.1436 0.0127 0.8437 220 E 0.7772 0.0052 0.2176 221 L 0.8793 0.0050 0.1157 222 D 0.9122 0.0036 0.0842 223 F 0.8763 0.0088 0.1148 224 N 0.6893 0.0158 0.2950 225 T 0.3059 0.0888 0.6053 226 A 0.1256 0.1879 0.6865 227 G 0.0985 0.3112 0.5903 228 L 0.1278 0.3658 0.5065 229 F 0.1379 0.2698 0.5923 230 K 0.0908 0.2648 0.6444 231 P 0.0496 0.2853 0.6651 232 L 0.0544 0.2734 0.6722 233 C 0.0958 0.2020 0.7023 234 G 0.0657 0.1339 0.8004 235 E 0.1155 0.0775 0.8070 236 T 0.1982 0.0723 0.7294 237 Y 0.1422 0.0400 0.8178 238 P 0.0796 0.0405 0.8799 239 P 0.0543 0.0963 0.8494 240 K 0.0062 0.9162 0.0777 241 K 0.0052 0.9435 0.0514 242 I 0.0049 0.9536 0.0416 243 V 0.0047 0.9580 0.0373 244 T 0.0048 0.9573 0.0379 245 L 0.0047 0.9583 0.0370 246 A 0.0048 0.9579 0.0373 247 S 0.0050 0.9469 0.0481 248 E 0.0054 0.8997 0.0949 249 L 0.0449 0.3296 0.6255 250 Q 0.0438 0.0159 0.9403 251 I 0.0740 0.0086 0.9174 252 P 0.4434 0.0072 0.5493 253 F 0.8478 0.0047 0.1475 254 V 0.8873 0.0049 0.1079 255 Y 0.8206 0.0126 0.1668 256 G 0.5172 0.0207 0.4621 257 S 0.1564 0.0743 0.7693 258 D 0.0645 0.1560 0.7795 259 S 0.0625 0.2073 0.7302 260 H 0.0601 0.1694 0.7705 261 G 0.0738 0.1260 0.8002 262 V 0.0266 0.6637 0.3097 263 Q 0.0179 0.7315 0.2506 264 D 0.0290 0.7594 0.2116 265 I 0.0321 0.7384 0.2295 266 G 0.0355 0.6429 0.3216 267 R 0.0310 0.6181 0.3509 268 G 0.0427 0.5761 0.3812 269 Y 0.0130 0.8584 0.1286 270 S 0.0106 0.8961 0.0933 271 T 0.0117 0.8959 0.0924 272 Y 0.0183 0.8576 0.1240 273 C 0.0347 0.6836 0.2817 274 Q 0.0364 0.4861 0.4775 275 K 0.0314 0.0838 0.8848