# This file is the result of combining several RDB files, specifically # T0325.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0325.t2k.stride-ebghtl.rdb (weight 1.24869) # T0325.t2k.str2.rdb (weight 1.54758) # T0325.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 T0325.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0325 # 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 T0325.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 128 # # ============================================ # Comments from T0325.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0325 # 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 T0325.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 128 # # ============================================ # Comments from T0325.t2k.str2.rdb # ============================================ # TARGET T0325 # 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 T0325.t2k-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 128 # # ============================================ # Comments from T0325.t2k.alpha.rdb # ============================================ # TARGET T0325 # 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 T0325.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 128 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0584 0.0603 0.8813 2 S 0.1261 0.0451 0.8288 3 N 0.1852 0.0339 0.7808 4 K 0.3311 0.0352 0.6336 5 K 0.7261 0.0141 0.2598 6 L 0.8723 0.0097 0.1180 7 I 0.9034 0.0071 0.0894 8 I 0.8677 0.0146 0.1177 9 N 0.6932 0.0184 0.2884 10 A 0.3406 0.1402 0.5192 11 D 0.1309 0.1965 0.6726 12 D 0.0801 0.2525 0.6674 13 F 0.0850 0.1743 0.7407 14 G 0.0607 0.0916 0.8477 15 Y 0.0936 0.0482 0.8582 16 T 0.0651 0.0370 0.8979 17 P 0.0104 0.6596 0.3300 18 A 0.0103 0.6890 0.3006 19 V 0.0130 0.8815 0.1055 20 T 0.0076 0.9342 0.0582 21 Q 0.0054 0.9546 0.0400 22 G 0.0051 0.9578 0.0371 23 I 0.0047 0.9606 0.0347 24 I 0.0047 0.9605 0.0348 25 E 0.0047 0.9607 0.0346 26 A 0.0047 0.9572 0.0380 27 H 0.0053 0.9393 0.0554 28 K 0.0069 0.8766 0.1165 29 R 0.0457 0.3132 0.6411 30 G 0.0392 0.0643 0.8964 31 V 0.1391 0.0721 0.7888 32 V 0.4735 0.0514 0.4751 33 T 0.4515 0.0792 0.4694 34 S 0.5462 0.1448 0.3089 35 T 0.5118 0.2060 0.2821 36 T 0.4797 0.2590 0.2613 37 A 0.4113 0.3162 0.2725 38 L 0.3423 0.2631 0.3946 39 P 0.2281 0.2371 0.5348 40 T 0.1125 0.1573 0.7302 41 S 0.0614 0.1830 0.7556 42 P 0.0274 0.7118 0.2608 43 Y 0.0166 0.7696 0.2138 44 F 0.0060 0.8976 0.0964 45 L 0.0051 0.9340 0.0609 46 E 0.0051 0.9390 0.0559 47 A 0.0048 0.9447 0.0505 48 M 0.0049 0.9455 0.0495 49 E 0.0049 0.9446 0.0505 50 S 0.0050 0.9387 0.0563 51 A 0.0058 0.9049 0.0894 52 R 0.0070 0.8293 0.1637 53 I 0.0101 0.6695 0.3204 54 S 0.0339 0.4619 0.5041 55 A 0.0629 0.0956 0.8415 56 P 0.0360 0.1357 0.8283 57 T 0.0408 0.1004 0.8588 58 L 0.1473 0.0418 0.8110 59 A 0.3469 0.0335 0.6195 60 I 0.7676 0.0097 0.2227 61 G 0.8518 0.0072 0.1409 62 V 0.9013 0.0038 0.0948 63 H 0.9174 0.0044 0.0782 64 L 0.9116 0.0045 0.0839 65 T 0.8955 0.0051 0.0995 66 L 0.8022 0.0138 0.1840 67 T 0.6231 0.0328 0.3440 68 L 0.2501 0.0659 0.6840 69 N 0.0994 0.0475 0.8531 70 Q 0.1594 0.0314 0.8092 71 A 0.2071 0.0372 0.7557 72 K 0.1536 0.0577 0.7887 73 P 0.1042 0.0607 0.8352 74 I 0.0860 0.0791 0.8350 75 L 0.0453 0.2717 0.6830 76 P 0.0381 0.3527 0.6093 77 R 0.0709 0.3172 0.6119 78 E 0.1277 0.1760 0.6964 79 M 0.1321 0.1887 0.6793 80 V 0.0953 0.1793 0.7254 81 P 0.0962 0.2641 0.6397 82 S 0.1443 0.1786 0.6771 83 L 0.0803 0.1256 0.7941 84 V 0.0310 0.2535 0.7155 85 D 0.0473 0.1491 0.8036 86 E 0.0432 0.1870 0.7698 87 A 0.0670 0.2700 0.6630 88 G 0.0993 0.3958 0.5049 89 Y 0.0675 0.4910 0.4416 90 F 0.0718 0.5814 0.3468 91 W 0.0519 0.7570 0.1911 92 H 0.0556 0.7829 0.1616 93 Q 0.0632 0.7998 0.1370 94 S 0.0460 0.8152 0.1388 95 I 0.0335 0.7911 0.1754 96 F 0.0333 0.7160 0.2506 97 E 0.0328 0.6075 0.3598 98 E 0.0379 0.3920 0.5701 99 K 0.0542 0.2184 0.7274 100 V 0.0849 0.0654 0.8497 101 N 0.0693 0.0314 0.8993 102 L 0.0051 0.9213 0.0736 103 E 0.0048 0.9441 0.0511 104 E 0.0048 0.9525 0.0427 105 V 0.0047 0.9589 0.0364 106 Y 0.0047 0.9588 0.0365 107 N 0.0047 0.9599 0.0354 108 E 0.0047 0.9593 0.0360 109 W 0.0047 0.9604 0.0349 110 D 0.0047 0.9599 0.0354 111 A 0.0047 0.9602 0.0351 112 Q 0.0047 0.9601 0.0353 113 I 0.0047 0.9600 0.0353 114 I 0.0047 0.9605 0.0348 115 S 0.0048 0.9599 0.0354 116 F 0.0048 0.9587 0.0365 117 M 0.0050 0.9457 0.0493 118 K 0.0055 0.9059 0.0886 119 S 0.0424 0.4835 0.4741 120 G 0.0346 0.0520 0.9134 121 R 0.0714 0.0177 0.9109 122 R 0.1186 0.0141 0.8673 123 P 0.1308 0.1304 0.7388 124 D 0.1994 0.2220 0.5786 125 H 0.4393 0.1871 0.3736 126 I 0.5136 0.1110 0.3755 127 D 0.3924 0.0864 0.5212 128 S 0.2169 0.1672 0.6159 129 H 0.1981 0.1879 0.6140 130 H 0.2002 0.2658 0.5340 131 N 0.3370 0.2797 0.3833 132 V 0.3460 0.3095 0.3445 133 H 0.3239 0.2864 0.3897 134 G 0.2616 0.2578 0.4806 135 K 0.1444 0.2102 0.6454 136 N 0.0781 0.1759 0.7460 137 K 0.0288 0.3257 0.6455 138 K 0.0839 0.3956 0.5206 139 L 0.0546 0.6344 0.3110 140 L 0.0080 0.8541 0.1379 141 G 0.0048 0.9509 0.0444 142 V 0.0047 0.9597 0.0356 143 A 0.0047 0.9590 0.0363 144 L 0.0047 0.9580 0.0373 145 A 0.0047 0.9574 0.0379 146 L 0.0047 0.9576 0.0377 147 A 0.0049 0.9519 0.0432 148 R 0.0053 0.9420 0.0527 149 K 0.0081 0.8958 0.0960 150 Y 0.0466 0.5539 0.3995 151 Q 0.0472 0.0383 0.9145 152 L 0.0690 0.0173 0.9137 153 P 0.1585 0.0430 0.7985 154 L 0.4173 0.0882 0.4945 155 R 0.5924 0.0586 0.3489 156 N 0.5066 0.0466 0.4467 157 A 0.2662 0.0544 0.6794 158 S 0.1270 0.1166 0.7564 159 R 0.0863 0.1806 0.7331 160 S 0.0734 0.1869 0.7397 161 I 0.0588 0.2969 0.6442 162 E 0.0539 0.2882 0.6579 163 T 0.0566 0.3178 0.6256 164 K 0.0514 0.4006 0.5479 165 D 0.0523 0.4219 0.5258 166 Y 0.0611 0.4750 0.4639 167 L 0.0805 0.4368 0.4827 168 E 0.0975 0.4381 0.4644 169 L 0.0958 0.4939 0.4103 170 Y 0.1097 0.5161 0.3741 171 Q 0.0954 0.5422 0.3623 172 D 0.0727 0.5670 0.3603 173 V 0.0683 0.5217 0.4100 174 R 0.0928 0.3967 0.5104 175 T 0.0972 0.2995 0.6033 176 P 0.0998 0.3384 0.5618 177 D 0.0849 0.3519 0.5632 178 E 0.0970 0.3413 0.5617 179 M 0.1070 0.4064 0.4867 180 L 0.1160 0.4735 0.4105 181 Y 0.1352 0.4960 0.3689 182 Q 0.1557 0.5245 0.3198 183 F 0.1694 0.4784 0.3522 184 Y 0.1692 0.4531 0.3778 185 D 0.1257 0.5394 0.3350 186 K 0.0955 0.5660 0.3386 187 A 0.0782 0.5040 0.4178 188 I 0.0748 0.4131 0.5120 189 S 0.0577 0.3865 0.5559 190 T 0.0593 0.4774 0.4633 191 E 0.0471 0.5803 0.3727 192 T 0.0451 0.6359 0.3190 193 I 0.0093 0.8935 0.0971 194 L 0.0078 0.9219 0.0703 195 Q 0.0065 0.9298 0.0636 196 L 0.0062 0.9308 0.0630 197 L 0.0075 0.9209 0.0716 198 D 0.0078 0.8988 0.0934 199 M 0.0101 0.8588 0.1311 200 V 0.0220 0.7724 0.2056 201 V 0.0266 0.6316 0.3418 202 C 0.0471 0.4277 0.5252 203 S 0.0609 0.1722 0.7670 204 E 0.0518 0.1316 0.8166 205 G 0.0549 0.1036 0.8415 206 E 0.1345 0.0636 0.8019 207 V 0.5432 0.0205 0.4363 208 F 0.8104 0.0118 0.1777 209 E 0.8934 0.0077 0.0988 210 I 0.9084 0.0060 0.0856 211 N 0.8710 0.0111 0.1179 212 C 0.7849 0.0135 0.2017 213 H 0.4046 0.0221 0.5733 214 P 0.1680 0.1415 0.6905 215 A 0.1620 0.1587 0.6793 216 F 0.1943 0.1619 0.6438 217 I 0.1173 0.1635 0.7192 218 D 0.0821 0.1533 0.7646 219 T 0.0255 0.5426 0.4319 220 I 0.0275 0.6599 0.3126 221 L 0.0314 0.7023 0.2662 222 Q 0.0272 0.6671 0.3057 223 N 0.0360 0.5301 0.4339 224 Q 0.0422 0.4025 0.5553 225 S 0.0583 0.2279 0.7138 226 G 0.0234 0.3546 0.6220 227 Y 0.0244 0.4221 0.5534 228 C 0.0370 0.4722 0.4908 229 M 0.0359 0.6145 0.3496 230 P 0.0311 0.7479 0.2210 231 R 0.0206 0.8745 0.1049 232 I 0.0084 0.9415 0.0501 233 R 0.0083 0.9442 0.0475 234 E 0.0065 0.9488 0.0447 235 V 0.0067 0.9478 0.0455 236 E 0.0059 0.9430 0.0511 237 I 0.0068 0.9049 0.0883 238 L 0.0148 0.7798 0.2054 239 T 0.0362 0.5437 0.4200 240 S 0.0565 0.1282 0.8153 241 Q 0.0063 0.8897 0.1040 242 E 0.0050 0.9241 0.0709 243 V 0.0056 0.9440 0.0504 244 K 0.0048 0.9589 0.0363 245 E 0.0050 0.9591 0.0359 246 A 0.0048 0.9597 0.0355 247 I 0.0049 0.9582 0.0369 248 E 0.0050 0.9481 0.0469 249 E 0.0061 0.8901 0.1039 250 R 0.0446 0.3011 0.6543 251 G 0.0310 0.0218 0.9472 252 I 0.1203 0.0079 0.8718 253 L 0.6622 0.0060 0.3318 254 L 0.8557 0.0050 0.1393 255 A 0.7759 0.0113 0.2127 256 N 0.5473 0.0107 0.4420 257 Y 0.1629 0.3221 0.5150 258 E 0.0556 0.4982 0.4462 259 S 0.0575 0.5936 0.3489 260 L 0.1248 0.3612 0.5141 261 A 0.1174 0.1858 0.6968 262 M 0.0626 0.0895 0.8479