# This file is the result of combining several RDB files, specifically # T0627.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0627.t2k.stride-ebghtl.rdb (weight 1.24869) # T0627.t2k.str2.rdb (weight 1.54758) # T0627.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 T0627.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0627 # 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 T0627.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 45 # # ============================================ # Comments from T0627.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0627 # 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 T0627.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 45 # # ============================================ # Comments from T0627.t2k.str2.rdb # ============================================ # TARGET T0627 # 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 T0627.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 45 # # ============================================ # Comments from T0627.t2k.alpha.rdb # ============================================ # TARGET T0627 # 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 T0627.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 45 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0613 0.0721 0.8666 2 I 0.0988 0.1374 0.7638 3 D 0.1105 0.2533 0.6362 4 T 0.0912 0.4111 0.4978 5 F 0.1215 0.4760 0.4026 6 E 0.1836 0.4395 0.3769 7 R 0.1668 0.3627 0.4705 8 T 0.1343 0.2637 0.6020 9 G 0.0557 0.1862 0.7581 10 P 0.0527 0.2633 0.6840 11 L 0.1551 0.3764 0.4685 12 M 0.2818 0.3053 0.4129 13 E 0.3444 0.2207 0.4349 14 A 0.2682 0.1340 0.5978 15 S 0.1523 0.0736 0.7741 16 S 0.1051 0.1006 0.7942 17 Y 0.0616 0.1006 0.8377 18 P 0.0185 0.7928 0.1887 19 A 0.0063 0.9237 0.0701 20 W 0.0054 0.9449 0.0498 21 A 0.0049 0.9547 0.0405 22 Q 0.0051 0.9541 0.0408 23 Q 0.0051 0.9479 0.0469 24 L 0.0050 0.9450 0.0500 25 I 0.0056 0.9342 0.0602 26 N 0.0068 0.8797 0.1135 27 D 0.0112 0.7063 0.2825 28 C 0.0219 0.6216 0.3565 29 S 0.0175 0.4998 0.4827 30 P 0.0067 0.8844 0.1089 31 A 0.0059 0.9152 0.0789 32 K 0.0059 0.9205 0.0735 33 A 0.0073 0.9130 0.0798 34 R 0.0088 0.8750 0.1162 35 V 0.0141 0.8166 0.1693 36 V 0.0315 0.6429 0.3256 37 E 0.0327 0.4288 0.5385 38 H 0.0493 0.2785 0.6722 39 E 0.0081 0.8867 0.1053 40 L 0.0060 0.9281 0.0659 41 Y 0.0065 0.9387 0.0548 42 Q 0.0082 0.9300 0.0617 43 Q 0.0088 0.9153 0.0759 44 M 0.0150 0.8724 0.1126 45 R 0.0121 0.7535 0.2344 46 D 0.0453 0.2832 0.6715 47 A 0.0325 0.0752 0.8923 48 K 0.0804 0.0404 0.8793 49 L 0.1929 0.0231 0.7840 50 S 0.0607 0.0228 0.9166 51 P 0.0056 0.9225 0.0719 52 Q 0.0048 0.9473 0.0479 53 I 0.0050 0.9492 0.0459 54 M 0.0048 0.9543 0.0409 55 R 0.0047 0.9549 0.0404 56 Q 0.0048 0.9495 0.0456 57 Y 0.0052 0.9387 0.0560 58 L 0.0069 0.9225 0.0706 59 I 0.0082 0.9046 0.0872 60 G 0.0092 0.8273 0.1635 61 G 0.0088 0.7761 0.2151 62 W 0.0137 0.8641 0.1223 63 P 0.0074 0.8960 0.0966 64 V 0.0073 0.9222 0.0705 65 V 0.0065 0.9344 0.0591 66 E 0.0065 0.9108 0.0827 67 Q 0.0097 0.8314 0.1589 68 F 0.0167 0.8295 0.1538 69 A 0.0053 0.9240 0.0707 70 V 0.0052 0.9465 0.0483 71 Y 0.0049 0.9488 0.0462 72 M 0.0050 0.9450 0.0499 73 A 0.0052 0.9349 0.0599 74 K 0.0056 0.9286 0.0658 75 N 0.0066 0.9095 0.0839 76 L 0.0098 0.8709 0.1192 77 T 0.0205 0.6664 0.3132 78 K 0.0315 0.4495 0.5190 79 T 0.0613 0.1948 0.7439 80 R 0.0362 0.2769 0.6869 81 F 0.0404 0.3015 0.6581 82 G 0.0482 0.3734 0.5784 83 R 0.0556 0.2966 0.6478 84 H 0.0652 0.2663 0.6686 85 P 0.0301 0.4946 0.4753 86 G 0.0319 0.4356 0.5324 87 E 0.0267 0.7393 0.2340 88 D 0.0091 0.9025 0.0884 89 M 0.0068 0.9291 0.0641 90 A 0.0058 0.9375 0.0567 91 R 0.0053 0.9458 0.0489 92 R 0.0060 0.9445 0.0495 93 W 0.0056 0.9334 0.0611 94 L 0.0062 0.9164 0.0774 95 M 0.0070 0.9031 0.0899 96 R 0.0079 0.8522 0.1400 97 N 0.0133 0.7338 0.2529 98 I 0.0220 0.6817 0.2964 99 R 0.0517 0.6259 0.3224 100 V 0.0782 0.5851 0.3367 101 E 0.0872 0.5663 0.3465 102 L 0.0695 0.6691 0.2614 103 N 0.0574 0.6005 0.3421 104 H 0.0450 0.7063 0.2487 105 A 0.0094 0.9197 0.0709 106 D 0.0066 0.9389 0.0544 107 Y 0.0055 0.9470 0.0474 108 W 0.0059 0.9507 0.0434 109 V 0.0052 0.9551 0.0397 110 N 0.0049 0.9576 0.0375 111 W 0.0048 0.9568 0.0384 112 C 0.0049 0.9532 0.0419 113 A 0.0058 0.9397 0.0545 114 A 0.0086 0.8669 0.1244 115 H 0.0441 0.4556 0.5002 116 D 0.0495 0.0337 0.9168 117 V 0.0834 0.0126 0.9040 118 T 0.0632 0.0133 0.9234 119 L 0.0053 0.9123 0.0824 120 E 0.0048 0.9305 0.0647 121 D 0.0050 0.9366 0.0583 122 L 0.0057 0.9317 0.0625 123 H 0.0093 0.8491 0.1416 124 D 0.0151 0.5317 0.4532 125 Q 0.0543 0.1739 0.7718 126 R 0.0583 0.0828 0.8589 127 V 0.0510 0.0795 0.8694 128 A 0.0521 0.1020 0.8460 129 P 0.0063 0.9027 0.0909 130 E 0.0055 0.9315 0.0630 131 L 0.0054 0.9429 0.0518 132 H 0.0049 0.9504 0.0447 133 A 0.0053 0.9488 0.0459 134 L 0.0054 0.9456 0.0490 135 S 0.0059 0.9460 0.0481 136 H 0.0056 0.9443 0.0501 137 W 0.0063 0.9337 0.0600 138 C 0.0084 0.9236 0.0680 139 W 0.0136 0.9034 0.0830 140 Q 0.0156 0.8580 0.1263 141 T 0.0233 0.7122 0.2645 142 S 0.0604 0.3723 0.5672 143 S 0.0472 0.2462 0.7067 144 S 0.0464 0.2613 0.6923 145 D 0.0298 0.2189 0.7512 146 S 0.0415 0.3773 0.5811 147 L 0.0067 0.9268 0.0664 148 A 0.0049 0.9479 0.0472 149 V 0.0049 0.9484 0.0467 150 A 0.0054 0.9477 0.0469 151 M 0.0060 0.9511 0.0429 152 A 0.0054 0.9456 0.0490 153 A 0.0058 0.9318 0.0624 154 T 0.0073 0.9234 0.0694 155 N 0.0078 0.9130 0.0792 156 Y 0.0069 0.9173 0.0758 157 A 0.0103 0.9035 0.0862 158 I 0.0115 0.8883 0.1001 159 E 0.0153 0.8235 0.1612 160 G 0.0174 0.6528 0.3298 161 A 0.0291 0.5782 0.3928 162 T 0.0467 0.6097 0.3436 163 G 0.0251 0.7941 0.1808 164 E 0.0174 0.8930 0.0896 165 W 0.0286 0.8994 0.0720 166 S 0.0372 0.8966 0.0663 167 A 0.0608 0.8624 0.0768 168 V 0.0838 0.8207 0.0955 169 V 0.1128 0.7674 0.1198 170 C 0.1042 0.7029 0.1929 171 S 0.0795 0.6163 0.3042 172 T 0.0832 0.4708 0.4460 173 G 0.0918 0.5280 0.3802 174 V 0.1986 0.5114 0.2901 175 Y 0.2255 0.5061 0.2684 176 A 0.2282 0.4429 0.3289 177 E 0.1930 0.3111 0.4959 178 A 0.1431 0.1706 0.6863 179 F 0.1284 0.0828 0.7888 180 A 0.1220 0.1175 0.7605 181 E 0.0536 0.4303 0.5161 182 E 0.0604 0.3991 0.5405 183 T 0.0539 0.3494 0.5967 184 R 0.0459 0.2709 0.6832 185 K 0.0279 0.7194 0.2527 186 K 0.0077 0.8965 0.0958 187 S 0.0057 0.9336 0.0607 188 M 0.0048 0.9497 0.0455 189 K 0.0047 0.9562 0.0391 190 W 0.0048 0.9540 0.0413 191 L 0.0047 0.9544 0.0409 192 K 0.0048 0.9512 0.0440 193 M 0.0050 0.9274 0.0676 194 H 0.0070 0.8595 0.1335 195 A 0.0144 0.7533 0.2323 196 Q 0.0168 0.6098 0.3734 197 Y 0.0160 0.6058 0.3782 198 D 0.0254 0.4397 0.5349 199 D 0.0213 0.4708 0.5080 200 A 0.0277 0.4697 0.5026 201 H 0.0483 0.2821 0.6697 202 P 0.0115 0.7740 0.2144 203 W 0.0073 0.8829 0.1098 204 E 0.0065 0.9110 0.0825 205 A 0.0048 0.9429 0.0523 206 L 0.0047 0.9519 0.0434 207 E 0.0047 0.9548 0.0405 208 I 0.0047 0.9574 0.0380 209 I 0.0047 0.9563 0.0389 210 C 0.0048 0.9531 0.0421 211 T 0.0051 0.9352 0.0596 212 L 0.0065 0.8915 0.1019 213 V 0.0300 0.6998 0.2703 214 G 0.0256 0.3541 0.6203 215 N 0.0327 0.1978 0.7695 216 K 0.0645 0.0794 0.8560 217 P 0.0354 0.2061 0.7585 218 S 0.0460 0.2604 0.6936 219 L 0.0076 0.8727 0.1197 220 Q 0.0062 0.9126 0.0812 221 L 0.0054 0.9320 0.0626 222 Q 0.0047 0.9550 0.0403 223 A 0.0047 0.9581 0.0372 224 E 0.0047 0.9574 0.0379 225 L 0.0047 0.9574 0.0379 226 R 0.0047 0.9597 0.0356 227 Q 0.0047 0.9586 0.0367 228 A 0.0047 0.9572 0.0381 229 V 0.0047 0.9580 0.0373 230 T 0.0048 0.9544 0.0408 231 K 0.0048 0.9412 0.0539 232 S 0.0048 0.9477 0.0475 233 Y 0.0048 0.9543 0.0410 234 D 0.0048 0.9533 0.0419 235 Y 0.0048 0.9528 0.0424 236 M 0.0048 0.9548 0.0404 237 Y 0.0048 0.9532 0.0420 238 L 0.0051 0.9439 0.0510 239 F 0.0054 0.9333 0.0613 240 L 0.0054 0.9254 0.0692 241 E 0.0063 0.8953 0.0984 242 R 0.0080 0.7976 0.1944 243 C 0.0181 0.6211 0.3608 244 I 0.0675 0.4135 0.5190 245 Q 0.0853 0.1926 0.7221 246 L 0.0436 0.4308 0.5257 247 D 0.0429 0.4172 0.5399 248 K 0.0679 0.3998 0.5323 249 V 0.1413 0.2266 0.6321 250 K 0.1659 0.1545 0.6795 251 S 0.1781 0.1089 0.7130 252 P 0.1334 0.2160 0.6505 253 R 0.2325 0.1592 0.6083 254 G 0.3904 0.1392 0.4704 255 R 0.4841 0.1003 0.4156 256 V 0.5674 0.1297 0.3028 257 A 0.5840 0.1574 0.2586 258 A 0.6026 0.1332 0.2642 259 L 0.5336 0.1021 0.3643 260 E 0.3313 0.0726 0.5960 261 M 0.0598 0.0291 0.9111