# This file is the result of combining several RDB files, specifically # T0297.t06.dssp-ebghstl.rdb (weight 1.53986) # T0297.t06.stride-ebghtl.rdb (weight 1.24869) # T0297.t06.str2.rdb (weight 1.54758) # T0297.t06.alpha.rdb (weight 0.659012) # T0297.t04.dssp-ebghstl.rdb (weight 1.53986) # T0297.t04.stride-ebghtl.rdb (weight 1.24869) # T0297.t04.str2.rdb (weight 1.54758) # T0297.t04.alpha.rdb (weight 0.659012) # T0297.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0297.t2k.stride-ebghtl.rdb (weight 1.24869) # T0297.t2k.str2.rdb (weight 1.54758) # T0297.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 T0297.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0297 # Using neural net t06-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 T0297.t06-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 1705 # # ============================================ # Comments from T0297.t06.stride-ebghtl.rdb # ============================================ # TARGET T0297 # Using neural net t06-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 T0297.t06-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 1705 # # ============================================ # Comments from T0297.t06.str2.rdb # ============================================ # TARGET T0297 # Using neural net t06-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 T0297.t06-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 1705 # # ============================================ # Comments from T0297.t06.alpha.rdb # ============================================ # TARGET T0297 # Using neural net t06-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 T0297.t06-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 1705 # # ============================================ # Comments from T0297.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0297 # Using neural net t06-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 T0297.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 1496 # # ============================================ # Comments from T0297.t04.stride-ebghtl.rdb # ============================================ # TARGET T0297 # 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 T0297.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 1496 # # ============================================ # Comments from T0297.t04.str2.rdb # ============================================ # TARGET T0297 # Using neural net t06-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 T0297.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 1496 # # ============================================ # Comments from T0297.t04.alpha.rdb # ============================================ # TARGET T0297 # 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 T0297.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 1496 # # ============================================ # Comments from T0297.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0297 # 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 T0297.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 309 # # ============================================ # Comments from T0297.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0297 # 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 T0297.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 309 # # ============================================ # Comments from T0297.t2k.str2.rdb # ============================================ # TARGET T0297 # 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 T0297.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 309 # # ============================================ # Comments from T0297.t2k.alpha.rdb # ============================================ # TARGET T0297 # 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 T0297.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 309 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1127 0.0499 0.8374 2 A 0.2605 0.0361 0.7034 3 V 0.3339 0.0262 0.6400 4 Q 0.2528 0.0296 0.7176 5 L 0.2527 0.0537 0.6935 6 L 0.2222 0.1141 0.6637 7 E 0.1746 0.1514 0.6740 8 N 0.0978 0.2826 0.6196 9 W 0.0676 0.3479 0.5845 10 L 0.0592 0.3612 0.5796 11 L 0.0555 0.3116 0.6329 12 K 0.0491 0.3036 0.6474 13 E 0.0512 0.4088 0.5400 14 Q 0.0313 0.6984 0.2703 15 E 0.0346 0.7573 0.2081 16 K 0.0399 0.7924 0.1677 17 I 0.0407 0.8151 0.1442 18 Q 0.0463 0.7998 0.1539 19 T 0.0370 0.8198 0.1432 20 K 0.0333 0.8277 0.1389 21 Y 0.0374 0.8233 0.1393 22 R 0.0421 0.8012 0.1566 23 H 0.0526 0.7369 0.2105 24 L 0.0592 0.6708 0.2701 25 N 0.0575 0.5805 0.3620 26 H 0.0527 0.4768 0.4705 27 I 0.0694 0.3596 0.5710 28 S 0.0783 0.3043 0.6174 29 V 0.0794 0.2138 0.7068 30 V 0.0941 0.1190 0.7868 31 E 0.1120 0.0377 0.8503 32 P 0.1709 0.0202 0.8090 33 N 0.6504 0.0089 0.3407 34 I 0.9182 0.0034 0.0785 35 L 0.9280 0.0036 0.0684 36 F 0.9250 0.0034 0.0716 37 I 0.8226 0.0220 0.1554 38 G 0.4995 0.0303 0.4702 39 D 0.2110 0.0824 0.7066 40 S 0.1641 0.2150 0.6209 41 I 0.1221 0.4321 0.4458 42 V 0.1371 0.4671 0.3958 43 E 0.1452 0.3867 0.4681 44 Y 0.1287 0.2455 0.6258 45 Y 0.1525 0.1660 0.6815 46 P 0.1650 0.1400 0.6949 47 L 0.1203 0.2498 0.6299 48 Q 0.0756 0.3682 0.5562 49 E 0.0599 0.3947 0.5453 50 L 0.0631 0.3636 0.5732 51 F 0.0804 0.2350 0.6845 52 G 0.0891 0.1397 0.7712 53 T 0.0993 0.0909 0.8099 54 S 0.1367 0.0637 0.7996 55 K 0.2960 0.0301 0.6739 56 T 0.6296 0.0209 0.3495 57 I 0.8527 0.0160 0.1314 58 V 0.8458 0.0239 0.1303 59 N 0.8012 0.0226 0.1762 60 R 0.6255 0.0369 0.3376 61 G 0.4046 0.0428 0.5526 62 I 0.2527 0.0540 0.6933 63 R 0.1385 0.0563 0.8053 64 G 0.0815 0.1167 0.8019 65 Y 0.0795 0.2510 0.6695 66 Q 0.1019 0.3362 0.5618 67 T 0.0400 0.6568 0.3032 68 G 0.0091 0.8803 0.1107 69 L 0.0091 0.8980 0.0928 70 L 0.0067 0.9273 0.0660 71 L 0.0079 0.9231 0.0690 72 E 0.0108 0.8798 0.1094 73 N 0.0140 0.8139 0.1721 74 L 0.0310 0.6603 0.3086 75 D 0.0209 0.7133 0.2657 76 A 0.0181 0.7450 0.2369 77 H 0.0241 0.7596 0.2163 78 L 0.0418 0.6314 0.3268 79 Y 0.0321 0.4992 0.4687 80 G 0.0327 0.3071 0.6603 81 G 0.0858 0.1189 0.7953 82 A 0.1347 0.0262 0.8391 83 V 0.1580 0.0162 0.8258 84 D 0.2697 0.0492 0.6811 85 K 0.8513 0.0064 0.1423 86 I 0.9306 0.0032 0.0662 87 F 0.9326 0.0032 0.0641 88 L 0.9222 0.0039 0.0738 89 L 0.8414 0.0094 0.1491 90 I 0.4577 0.0326 0.5097 91 G 0.2084 0.0323 0.7594 92 T 0.1380 0.1925 0.6695 93 N 0.1100 0.2832 0.6068 94 D 0.1129 0.3929 0.4942 95 I 0.0578 0.4944 0.4478 96 G 0.0420 0.3465 0.6115 97 K 0.0350 0.1744 0.7907 98 D 0.0466 0.0684 0.8850 99 V 0.1031 0.0256 0.8713 100 P 0.0752 0.0238 0.9010 101 V 0.0053 0.9293 0.0654 102 N 0.0048 0.9431 0.0521 103 E 0.0050 0.9458 0.0491 104 A 0.0051 0.9507 0.0441 105 L 0.0048 0.9446 0.0506 106 N 0.0050 0.9062 0.0888 107 N 0.0052 0.9090 0.0858 108 L 0.0047 0.9549 0.0404 109 E 0.0047 0.9606 0.0347 110 A 0.0047 0.9608 0.0346 111 I 0.0047 0.9607 0.0346 112 I 0.0047 0.9600 0.0353 113 Q 0.0047 0.9593 0.0361 114 S 0.0047 0.9584 0.0369 115 V 0.0049 0.9531 0.0421 116 A 0.0053 0.9369 0.0578 117 R 0.0068 0.8363 0.1568 118 D 0.0283 0.5765 0.3952 119 Y 0.0637 0.0802 0.8561 120 P 0.0561 0.0711 0.8728 121 L 0.0795 0.0726 0.8479 122 T 0.4089 0.0137 0.5774 123 E 0.8304 0.0045 0.1652 124 I 0.9261 0.0032 0.0707 125 K 0.9241 0.0037 0.0722 126 L 0.9094 0.0040 0.0865 127 L 0.8187 0.0087 0.1726 128 S 0.5182 0.0109 0.4709 129 I 0.2496 0.0175 0.7329 130 L 0.1605 0.0294 0.8101 131 P 0.1087 0.0619 0.8293 132 V 0.0690 0.1616 0.7694 133 N 0.0555 0.1817 0.7628 134 E 0.0578 0.1900 0.7522 135 R 0.0546 0.1841 0.7613 136 E 0.0465 0.4905 0.4630 137 E 0.0430 0.5484 0.4086 138 Y 0.0425 0.5620 0.3955 139 Q 0.0501 0.5662 0.3837 140 Q 0.0465 0.6057 0.3478 141 A 0.0345 0.6370 0.3285 142 V 0.0392 0.5939 0.3669 143 Y 0.0401 0.5569 0.4031 144 I 0.0409 0.5752 0.3839 145 R 0.0388 0.5893 0.3719 146 S 0.0247 0.6931 0.2822 147 N 0.0111 0.7958 0.1931 148 E 0.0076 0.8791 0.1133 149 K 0.0065 0.9040 0.0895 150 I 0.0051 0.9253 0.0696 151 Q 0.0048 0.9458 0.0494 152 N 0.0048 0.9437 0.0515 153 W 0.0048 0.9521 0.0431 154 N 0.0048 0.9553 0.0399 155 Q 0.0048 0.9557 0.0395 156 A 0.0048 0.9561 0.0391 157 Y 0.0048 0.9547 0.0406 158 Q 0.0048 0.9508 0.0443 159 E 0.0050 0.9445 0.0505 160 L 0.0058 0.9283 0.0659 161 A 0.0086 0.8988 0.0927 162 S 0.0062 0.8622 0.1316 163 A 0.0106 0.6975 0.2920 164 Y 0.0487 0.3171 0.6341 165 M 0.0244 0.1388 0.8368 166 Q 0.0283 0.0789 0.8929 167 V 0.2097 0.0280 0.7623 168 E 0.5321 0.0323 0.4356 169 F 0.7638 0.0219 0.2142 170 V 0.7624 0.0188 0.2187 171 P 0.5743 0.0235 0.4021 172 V 0.1717 0.3342 0.4942 173 F 0.1043 0.4460 0.4498 174 D 0.0538 0.6044 0.3418 175 C 0.0562 0.6693 0.2745 176 L 0.0761 0.6130 0.3109 177 T 0.0886 0.5611 0.3503 178 D 0.0603 0.4933 0.4464 179 Q 0.0410 0.4715 0.4874 180 A 0.0456 0.3712 0.5832 181 G 0.0528 0.2950 0.6522 182 Q 0.0728 0.2940 0.6332 183 L 0.0840 0.3561 0.5599 184 K 0.0601 0.4650 0.4749 185 K 0.0646 0.5282 0.4072 186 E 0.1174 0.4865 0.3961 187 Y 0.1868 0.3292 0.4840 188 T 0.1595 0.2301 0.6104 189 T 0.1098 0.2335 0.6566 190 D 0.0765 0.1235 0.8000 191 G 0.1188 0.1001 0.7811 192 L 0.3170 0.0627 0.6204 193 H 0.3575 0.0521 0.5904 194 L 0.1980 0.0686 0.7334 195 S 0.0669 0.0639 0.8692 196 I 0.0071 0.8946 0.0983 197 A 0.0148 0.8782 0.1070 198 G 0.0078 0.9251 0.0672 199 Y 0.0050 0.9562 0.0388 200 Q 0.0047 0.9572 0.0381 201 A 0.0048 0.9554 0.0398 202 L 0.0048 0.9539 0.0413 203 S 0.0049 0.9506 0.0445 204 K 0.0055 0.9211 0.0734 205 S 0.0057 0.8687 0.1256 206 L 0.0098 0.8333 0.1569 207 K 0.0093 0.8472 0.1435 208 D 0.0096 0.7964 0.1940 209 Y 0.0118 0.6791 0.3092 210 L 0.0619 0.3958 0.5423 211 Y 0.0266 0.1935 0.7799