# This file is the result of combining several RDB files, specifically # T0338.t06.dssp-ebghstl.rdb (weight 1.53986) # T0338.t06.stride-ebghtl.rdb (weight 1.24869) # T0338.t06.str2.rdb (weight 1.54758) # T0338.t06.alpha.rdb (weight 0.659012) # T0338.t04.dssp-ebghstl.rdb (weight 1.53986) # T0338.t04.stride-ebghtl.rdb (weight 1.24869) # T0338.t04.str2.rdb (weight 1.54758) # T0338.t04.alpha.rdb (weight 0.659012) # T0338.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0338.t2k.stride-ebghtl.rdb (weight 1.24869) # T0338.t2k.str2.rdb (weight 1.54758) # T0338.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 T0338.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0338 # 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 T0338.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 986 # # ============================================ # Comments from T0338.t06.stride-ebghtl.rdb # ============================================ # TARGET T0338 # 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 T0338.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 986 # # ============================================ # Comments from T0338.t06.str2.rdb # ============================================ # TARGET T0338 # 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 T0338.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 986 # # ============================================ # Comments from T0338.t06.alpha.rdb # ============================================ # TARGET T0338 # 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 T0338.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 986 # # ============================================ # Comments from T0338.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0338 # 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 T0338.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 989 # # ============================================ # Comments from T0338.t04.stride-ebghtl.rdb # ============================================ # TARGET T0338 # 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 T0338.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 989 # # ============================================ # Comments from T0338.t04.str2.rdb # ============================================ # TARGET T0338 # 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 T0338.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 989 # # ============================================ # Comments from T0338.t04.alpha.rdb # ============================================ # TARGET T0338 # 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 T0338.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 989 # # ============================================ # Comments from T0338.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0338 # 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 T0338.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 328 # # ============================================ # Comments from T0338.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0338 # 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 T0338.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 328 # # ============================================ # Comments from T0338.t2k.str2.rdb # ============================================ # TARGET T0338 # 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 T0338.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 328 # # ============================================ # Comments from T0338.t2k.alpha.rdb # ============================================ # TARGET T0338 # 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 T0338.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 328 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0377 0.1223 0.8400 2 S 0.0863 0.3735 0.5402 3 S 0.0822 0.4916 0.4262 4 R 0.0987 0.5413 0.3599 5 W 0.1579 0.5166 0.3255 6 F 0.1600 0.4715 0.3685 7 F 0.1335 0.3768 0.4897 8 T 0.0598 0.6320 0.3081 9 R 0.0240 0.8245 0.1514 10 E 0.0180 0.8533 0.1287 11 Q 0.0151 0.8529 0.1320 12 L 0.0186 0.8050 0.1763 13 E 0.0276 0.6414 0.3310 14 N 0.0511 0.2921 0.6567 15 T 0.0582 0.1086 0.8332 16 P 0.0491 0.2275 0.7234 17 S 0.0344 0.3842 0.5814 18 R 0.0388 0.4370 0.5242 19 R 0.0486 0.4137 0.5377 20 C 0.0444 0.2736 0.6820 21 G 0.0546 0.1409 0.8045 22 V 0.0818 0.0823 0.8358 23 E 0.0702 0.0847 0.8450 24 A 0.0165 0.8305 0.1529 25 D 0.0106 0.8773 0.1121 26 K 0.0075 0.9071 0.0854 27 E 0.0066 0.9331 0.0603 28 L 0.0051 0.9442 0.0507 29 S 0.0050 0.9452 0.0498 30 C 0.0048 0.9491 0.0461 31 R 0.0047 0.9570 0.0382 32 Q 0.0048 0.9581 0.0371 33 Q 0.0047 0.9566 0.0387 34 A 0.0047 0.9576 0.0377 35 A 0.0047 0.9601 0.0352 36 N 0.0047 0.9600 0.0353 37 L 0.0047 0.9599 0.0355 38 I 0.0047 0.9604 0.0350 39 Q 0.0047 0.9598 0.0355 40 E 0.0048 0.9572 0.0380 41 M 0.0048 0.9540 0.0413 42 G 0.0049 0.9441 0.0510 43 Q 0.0057 0.9226 0.0717 44 R 0.0077 0.8414 0.1509 45 L 0.0480 0.5541 0.3979 46 N 0.0450 0.1296 0.8254 47 V 0.0544 0.0478 0.8977 48 S 0.0473 0.1055 0.8472 49 Q 0.0084 0.8547 0.1369 50 L 0.0069 0.9202 0.0729 51 T 0.0071 0.9404 0.0524 52 I 0.0050 0.9572 0.0378 53 N 0.0047 0.9603 0.0350 54 T 0.0047 0.9600 0.0353 55 A 0.0047 0.9605 0.0348 56 I 0.0047 0.9601 0.0352 57 V 0.0047 0.9589 0.0364 58 Y 0.0047 0.9567 0.0386 59 M 0.0048 0.9554 0.0398 60 H 0.0053 0.9515 0.0432 61 R 0.0063 0.9378 0.0559 62 F 0.0104 0.9189 0.0707 63 Y 0.0209 0.8621 0.1169 64 M 0.0394 0.7131 0.2476 65 H 0.0631 0.5207 0.4162 66 H 0.1180 0.3146 0.5675 67 S 0.1373 0.2157 0.6471 68 F 0.0907 0.3948 0.5145 69 T 0.0752 0.4140 0.5108 70 K 0.0785 0.3617 0.5597 71 F 0.0831 0.2183 0.6986 72 N 0.1025 0.1025 0.7950 73 K 0.0151 0.8257 0.1592 74 N 0.0139 0.8986 0.0875 75 I 0.0106 0.9397 0.0497 76 I 0.0072 0.9526 0.0403 77 S 0.0078 0.9556 0.0366 78 S 0.0066 0.9572 0.0362 79 T 0.0060 0.9578 0.0362 80 A 0.0050 0.9583 0.0367 81 L 0.0048 0.9567 0.0385 82 F 0.0060 0.9444 0.0496 83 L 0.0051 0.9200 0.0749 84 A 0.0071 0.8682 0.1247 85 A 0.0171 0.7962 0.1866 86 K 0.0270 0.6845 0.2885 87 V 0.0458 0.6779 0.2763 88 E 0.0451 0.6162 0.3386 89 E 0.0515 0.4593 0.4892 90 Q 0.0657 0.2434 0.6909 91 A 0.0653 0.1190 0.8158 92 R 0.0639 0.1268 0.8092 93 K 0.0696 0.1688 0.7616 94 L 0.0381 0.7422 0.2197 95 E 0.0166 0.8872 0.0962 96 H 0.0201 0.9077 0.0722 97 V 0.0193 0.9280 0.0527 98 I 0.0285 0.9212 0.0503 99 K 0.0325 0.9091 0.0583 100 V 0.0350 0.8933 0.0716 101 A 0.0465 0.8694 0.0842 102 H 0.0386 0.8496 0.1118 103 A 0.0463 0.7719 0.1818 104 C 0.0627 0.6655 0.2717 105 L 0.0857 0.5037 0.4107 106 H 0.0834 0.3369 0.5797 107 P 0.0611 0.2714 0.6675 108 L 0.0549 0.2377 0.7074 109 E 0.0685 0.2112 0.7203 110 P 0.0817 0.2339 0.6844 111 L 0.1059 0.2367 0.6573 112 L 0.1068 0.2513 0.6419 113 D 0.1090 0.2607 0.6303 114 T 0.0838 0.3172 0.5990 115 K 0.0665 0.3657 0.5678 116 C 0.0385 0.4840 0.4775 117 D 0.0362 0.5403 0.4235 118 A 0.0539 0.5057 0.4404 119 Y 0.0679 0.4835 0.4486 120 L 0.0450 0.6047 0.3502 121 Q 0.0500 0.5898 0.3602 122 Q 0.0375 0.6807 0.2818 123 T 0.0056 0.9389 0.0555 124 R 0.0051 0.9471 0.0479 125 E 0.0049 0.9510 0.0441 126 L 0.0048 0.9570 0.0382 127 V 0.0048 0.9545 0.0407 128 I 0.0048 0.9516 0.0436 129 L 0.0047 0.9511 0.0442 130 E 0.0047 0.9585 0.0368 131 T 0.0047 0.9600 0.0353 132 I 0.0048 0.9591 0.0361 133 M 0.0047 0.9586 0.0367 134 L 0.0048 0.9538 0.0413 135 Q 0.0052 0.9400 0.0548 136 T 0.0068 0.8692 0.1240 137 L 0.0552 0.5426 0.4022 138 G 0.0654 0.1058 0.8288 139 F 0.1617 0.0465 0.7918 140 E 0.4199 0.0540 0.5261 141 I 0.6532 0.0460 0.3008 142 T 0.6658 0.0519 0.2823 143 I 0.4957 0.0462 0.4581 144 E 0.2125 0.0666 0.7210 145 H 0.1070 0.0496 0.8433 146 P 0.0444 0.2956 0.6600 147 H 0.0240 0.5624 0.4136 148 T 0.0220 0.8046 0.1735 149 D 0.0096 0.9101 0.0803 150 V 0.0058 0.9435 0.0507 151 V 0.0055 0.9520 0.0425 152 K 0.0055 0.9541 0.0404 153 C 0.0055 0.9528 0.0417 154 T 0.0054 0.9426 0.0520 155 Q 0.0055 0.9136 0.0809 156 L 0.0071 0.8362 0.1567 157 V 0.0328 0.6469 0.3203 158 R 0.0249 0.3321 0.6430 159 A 0.0314 0.2699 0.6987 160 S 0.0447 0.2920 0.6633 161 K 0.0122 0.7137 0.2741 162 D 0.0111 0.7900 0.1989 163 L 0.0081 0.9004 0.0915 164 A 0.0061 0.9365 0.0573 165 Q 0.0050 0.9523 0.0427 166 T 0.0048 0.9562 0.0390 167 S 0.0047 0.9579 0.0374 168 Y 0.0047 0.9587 0.0366 169 F 0.0048 0.9569 0.0383 170 M 0.0048 0.9492 0.0460 171 A 0.0052 0.9412 0.0535 172 T 0.0064 0.9149 0.0787 173 N 0.0083 0.8279 0.1638 174 S 0.0158 0.6742 0.3100 175 L 0.0430 0.4310 0.5259 176 H 0.0797 0.2906 0.6297 177 L 0.0875 0.2475 0.6650 178 T 0.1024 0.1734 0.7242 179 T 0.1269 0.2447 0.6284 180 F 0.2573 0.2531 0.4895 181 C 0.3713 0.2611 0.3676 182 L 0.3926 0.2253 0.3821 183 Q 0.3154 0.1647 0.5200 184 Y 0.1425 0.1192 0.7383 185 K 0.0688 0.0670 0.8642 186 P 0.0106 0.8090 0.1805 187 T 0.0050 0.8944 0.1006 188 V 0.0048 0.9499 0.0453 189 I 0.0047 0.9594 0.0359 190 A 0.0047 0.9597 0.0356 191 C 0.0047 0.9604 0.0350 192 V 0.0047 0.9603 0.0350 193 C 0.0047 0.9610 0.0344 194 I 0.0047 0.9606 0.0347 195 H 0.0047 0.9598 0.0355 196 L 0.0047 0.9596 0.0357 197 A 0.0047 0.9573 0.0380 198 C 0.0051 0.9465 0.0484 199 K 0.0057 0.9057 0.0886 200 W 0.0080 0.8380 0.1541 201 S 0.0457 0.4832 0.4711 202 N 0.0468 0.1049 0.8483 203 W 0.0830 0.0592 0.8578 204 E 0.1308 0.0774 0.7918 205 I 0.1475 0.0854 0.7672 206 P 0.1414 0.0944 0.7642 207 V 0.1288 0.1522 0.7190 208 S 0.0858 0.2085 0.7056 209 T 0.0860 0.1785 0.7355 210 D 0.0654 0.1979 0.7367 211 G 0.0779 0.1778 0.7443 212 K 0.1456 0.1684 0.6860 213 H 0.2015 0.2105 0.5880 214 W 0.2594 0.3410 0.3996 215 W 0.3336 0.3621 0.3043 216 E 0.3871 0.3691 0.2438 217 Y 0.4194 0.3411 0.2396 218 V 0.4067 0.2973 0.2960 219 D 0.3148 0.2262 0.4590 220 P 0.0988 0.1491 0.7521 221 T 0.0708 0.0460 0.8832 222 V 0.1596 0.0186 0.8218 223 T 0.1016 0.0148 0.8837 224 L 0.0054 0.8997 0.0949 225 E 0.0049 0.9155 0.0796 226 L 0.0054 0.9282 0.0664 227 L 0.0049 0.9466 0.0485 228 D 0.0048 0.9555 0.0397 229 E 0.0047 0.9570 0.0383 230 L 0.0047 0.9583 0.0370 231 T 0.0047 0.9594 0.0359 232 H 0.0047 0.9595 0.0359 233 E 0.0047 0.9578 0.0375 234 F 0.0047 0.9564 0.0389 235 L 0.0048 0.9520 0.0432 236 Q 0.0049 0.9391 0.0560 237 I 0.0056 0.9186 0.0758 238 L 0.0095 0.8818 0.1087 239 E 0.0104 0.7605 0.2291 240 K 0.0202 0.5784 0.4013 241 T 0.0484 0.2905 0.6612 242 P 0.0256 0.4096 0.5648 243 N 0.0203 0.4953 0.4844 244 R 0.0427 0.4741 0.4831 245 L 0.0426 0.4558 0.5016 246 K 0.0537 0.4852 0.4610 247 K 0.0695 0.4910 0.4395 248 I 0.0784 0.4094 0.5122 249 R 0.0655 0.4003 0.5342 250 N 0.0780 0.3598 0.5622 251 W 0.0968 0.3266 0.5766 252 R 0.0953 0.3325 0.5722 253 A 0.0738 0.3399 0.5863 254 N 0.0666 0.2516 0.6818 255 Q 0.0569 0.0977 0.8454 256 A 0.0382 0.0468 0.9151