# This file is the result of combining several RDB files, specifically # T0147.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0147.t2k.stride-ebghtl.rdb (weight 1.24869) # T0147.t2k.str.rdb (weight 1.53983) # T0147.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 T0147.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0147 # 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 T0147.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 80 # # ============================================ # Comments from T0147.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0147 # 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 T0147.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 80 # # ============================================ # Comments from T0147.t2k.str.rdb # ============================================ # TARGET T0147 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0147.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 80 # # ============================================ # Comments from T0147.t2k.alpha.rdb # ============================================ # TARGET T0147 # 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 T0147.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 80 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0731 0.0233 0.9036 2 Y 0.2487 0.0237 0.7275 3 P 0.3815 0.0229 0.5957 4 V 0.4214 0.0215 0.5571 5 D 0.4785 0.0219 0.4996 6 L 0.6877 0.0380 0.2743 7 H 0.7347 0.0320 0.2333 8 M 0.7396 0.0345 0.2260 9 H 0.6532 0.0331 0.3137 10 T 0.4324 0.0387 0.5289 11 V 0.3968 0.0596 0.5436 12 A 0.2151 0.0731 0.7118 13 S 0.1168 0.0680 0.8152 14 T 0.0350 0.1500 0.8150 15 H 0.0362 0.1405 0.8233 16 A 0.0805 0.1672 0.7523 17 Y 0.1530 0.1040 0.7430 18 S 0.1203 0.0805 0.7992 19 T 0.0920 0.0635 0.8445 20 L 0.0054 0.9277 0.0668 21 S 0.0045 0.9512 0.0443 22 D 0.0046 0.9578 0.0376 23 Y 0.0045 0.9574 0.0381 24 I 0.0046 0.9576 0.0378 25 A 0.0045 0.9560 0.0394 26 Q 0.0045 0.9572 0.0384 27 A 0.0046 0.9531 0.0423 28 K 0.0046 0.9454 0.0499 29 Q 0.0073 0.9005 0.0922 30 K 0.0377 0.3515 0.6108 31 G 0.0398 0.0216 0.9387 32 I 0.1144 0.0087 0.8769 33 K 0.4469 0.0330 0.5201 34 L 0.9241 0.0048 0.0711 35 F 0.9290 0.0041 0.0669 36 A 0.9286 0.0037 0.0677 37 I 0.8910 0.0074 0.1015 38 T 0.5974 0.0210 0.3816 39 D 0.2187 0.0404 0.7409 40 H 0.0908 0.1000 0.8092 41 G 0.0517 0.1810 0.7673 42 P 0.0437 0.2625 0.6938 43 D 0.0510 0.3034 0.6456 44 M 0.0486 0.2757 0.6757 45 E 0.0455 0.2788 0.6757 46 D 0.0459 0.4227 0.5315 47 A 0.0324 0.5578 0.4099 48 P 0.0316 0.5664 0.4020 49 H 0.0201 0.6790 0.3009 50 H 0.0155 0.7634 0.2210 51 W 0.0152 0.7759 0.2089 52 H 0.0116 0.8376 0.1507 53 F 0.0104 0.8707 0.1189 54 I 0.0098 0.8666 0.1236 55 N 0.0086 0.8774 0.1140 56 M 0.0116 0.8703 0.1181 57 R 0.0120 0.8600 0.1279 58 I 0.0115 0.8360 0.1525 59 W 0.0156 0.7890 0.1954 60 P 0.0113 0.8125 0.1762 61 R 0.0167 0.7671 0.2162 62 V 0.0339 0.6617 0.3044 63 V 0.0634 0.4553 0.4813 64 D 0.0368 0.2275 0.7357 65 G 0.0497 0.0663 0.8840 66 V 0.2809 0.0151 0.7040 67 G 0.6345 0.0104 0.3551 68 I 0.7257 0.0165 0.2578 69 L 0.5767 0.0195 0.4038 70 R 0.4498 0.0395 0.5107 71 G 0.5696 0.0210 0.4094 72 I 0.8086 0.0088 0.1826 73 E 0.8860 0.0059 0.1081 74 A 0.8722 0.0062 0.1216 75 N 0.8777 0.0071 0.1151 76 I 0.8622 0.0089 0.1288 77 K 0.7877 0.0106 0.2017 78 N 0.3899 0.0402 0.5700 79 V 0.0620 0.0779 0.8601 80 D 0.0632 0.0553 0.8815 81 G 0.2590 0.0465 0.6944 82 E 0.5574 0.0314 0.4112 83 I 0.7347 0.0319 0.2334 84 D 0.6204 0.0395 0.3402 85 C 0.4817 0.0793 0.4390 86 S 0.2434 0.1330 0.6236 87 G 0.1086 0.4129 0.4786 88 K 0.0803 0.5324 0.3873 89 M 0.0877 0.4901 0.4222 90 F 0.0802 0.4669 0.4529 91 D 0.0814 0.3473 0.5714 92 S 0.0511 0.4168 0.5321 93 L 0.0937 0.2822 0.6241 94 D 0.1715 0.1892 0.6392 95 L 0.5316 0.1450 0.3234 96 I 0.7252 0.1341 0.1407 97 I 0.8288 0.0791 0.0921 98 A 0.8131 0.0830 0.1040 99 G 0.7832 0.0875 0.1293 100 F 0.6779 0.1193 0.2028 101 H 0.5610 0.1263 0.3127 102 E 0.3722 0.1746 0.4532 103 P 0.3026 0.1934 0.5040 104 V 0.2137 0.1901 0.5963 105 F 0.1515 0.1527 0.6958 106 A 0.0765 0.2193 0.7042 107 P 0.0588 0.2183 0.7230 108 H 0.0673 0.3095 0.6231 109 D 0.0698 0.3579 0.5723 110 K 0.0436 0.5956 0.3608 111 A 0.0341 0.6533 0.3126 112 T 0.0374 0.6778 0.2848 113 N 0.0252 0.8198 0.1550 114 T 0.0095 0.9220 0.0685 115 Q 0.0071 0.9479 0.0450 116 A 0.0071 0.9510 0.0420 117 M 0.0060 0.9560 0.0380 118 I 0.0063 0.9561 0.0376 119 A 0.0059 0.9536 0.0405 120 T 0.0055 0.9452 0.0492 121 I 0.0076 0.9242 0.0682 122 A 0.0114 0.8358 0.1528 123 S 0.0578 0.5326 0.4097 124 G 0.0350 0.1637 0.8013 125 N 0.0470 0.0707 0.8823 126 V 0.2369 0.0381 0.7250 127 H 0.4451 0.0420 0.5129 128 I 0.7202 0.0432 0.2366 129 I 0.6625 0.0428 0.2947 130 S 0.5023 0.0451 0.4526 131 H 0.2527 0.0427 0.7046 132 P 0.1086 0.1362 0.7551 133 G 0.0873 0.1526 0.7601 134 N 0.1157 0.2407 0.6437 135 P 0.1275 0.4099 0.4626 136 K 0.1394 0.4663 0.3943 137 Y 0.1556 0.4449 0.3995 138 E 0.1487 0.3786 0.4727 139 I 0.1346 0.3236 0.5418 140 D 0.0965 0.3123 0.5912 141 V 0.0498 0.3840 0.5661 142 K 0.0450 0.3025 0.6525 143 A 0.1057 0.3710 0.5232 144 V 0.1702 0.4117 0.4181 145 A 0.1107 0.5165 0.3728 146 E 0.0821 0.5050 0.4129 147 A 0.0076 0.9089 0.0834 148 A 0.0057 0.9294 0.0649 149 A 0.0057 0.9371 0.0573 150 K 0.0056 0.9327 0.0617 151 H 0.0073 0.9283 0.0644 152 Q 0.0078 0.9168 0.0754 153 V 0.0083 0.9173 0.0745 154 A 0.0114 0.9107 0.0779 155 L 0.0136 0.8901 0.0963 156 E 0.0155 0.8197 0.1647 157 I 0.0406 0.5103 0.4492 158 N 0.0481 0.1156 0.8363 159 N 0.1153 0.1059 0.7788 160 S 0.2653 0.1493 0.5854 161 S 0.3400 0.1931 0.4670 162 F 0.4135 0.1939 0.3927 163 L 0.3795 0.1819 0.4387 164 H 0.2597 0.1400 0.6003 165 S 0.0975 0.1432 0.7593 166 R 0.0753 0.1068 0.8179 167 K 0.0560 0.2275 0.7165 168 G 0.0599 0.2406 0.6995 169 S 0.1037 0.2436 0.6527 170 E 0.1254 0.2001 0.6745 171 D 0.1103 0.1615 0.7282 172 N 0.0686 0.2025 0.7290 173 C 0.0284 0.5613 0.4103 174 R 0.0049 0.9418 0.0533 175 E 0.0048 0.9538 0.0413 176 V 0.0050 0.9560 0.0390 177 A 0.0046 0.9582 0.0371 178 A 0.0047 0.9570 0.0383 179 A 0.0044 0.9574 0.0381 180 V 0.0045 0.9559 0.0396 181 R 0.0047 0.9489 0.0464 182 D 0.0056 0.9185 0.0758 183 A 0.0457 0.3932 0.5610 184 G 0.0407 0.0176 0.9417 185 G 0.0973 0.0100 0.8928 186 W 0.6283 0.0073 0.3644 187 V 0.8743 0.0054 0.1203 188 A 0.8959 0.0072 0.0969 189 L 0.8485 0.0147 0.1368 190 G 0.5754 0.0184 0.4063 191 S 0.1851 0.0308 0.7841 192 D 0.0667 0.1642 0.7691 193 S 0.0457 0.2446 0.7096 194 H 0.0498 0.1985 0.7517 195 T 0.0662 0.1254 0.8083 196 A 0.0343 0.4082 0.5575 197 F 0.0226 0.4317 0.5457 198 T 0.0347 0.4470 0.5184 199 M 0.0386 0.5505 0.4109 200 G 0.0215 0.5787 0.3998 201 E 0.0310 0.6794 0.2896 202 F 0.0078 0.9119 0.0803 203 E 0.0058 0.9487 0.0456 204 E 0.0050 0.9551 0.0399 205 C 0.0046 0.9590 0.0364 206 L 0.0044 0.9604 0.0353 207 K 0.0044 0.9603 0.0354 208 I 0.0044 0.9604 0.0352 209 L 0.0044 0.9580 0.0376 210 D 0.0048 0.9498 0.0454 211 A 0.0064 0.9041 0.0895 212 V 0.0438 0.4530 0.5032 213 D 0.0411 0.0318 0.9271 214 F 0.0571 0.0124 0.9305 215 P 0.0662 0.0201 0.9137 216 P 0.0392 0.6760 0.2848 217 E 0.0365 0.7541 0.2095 218 R 0.0663 0.7489 0.1847 219 I 0.1654 0.6474 0.1872 220 L 0.1611 0.5968 0.2421 221 N 0.1744 0.4970 0.3286 222 V 0.1008 0.3709 0.5283 223 S 0.0850 0.2566 0.6583 224 P 0.0475 0.5309 0.4216 225 R 0.0140 0.7908 0.1951 226 R 0.0138 0.8503 0.1359 227 L 0.0082 0.8979 0.0939 228 L 0.0069 0.9251 0.0681 229 N 0.0074 0.9317 0.0609 230 F 0.0058 0.9390 0.0552 231 L 0.0054 0.9343 0.0603 232 E 0.0051 0.9221 0.0727 233 S 0.0069 0.8478 0.1454 234 R 0.0419 0.5107 0.4474 235 G 0.0454 0.1221 0.8325 236 M 0.0731 0.0877 0.8392 237 A 0.0842 0.1346 0.7812 238 P 0.0973 0.2236 0.6791 239 I 0.0688 0.5371 0.3941 240 A 0.0466 0.6624 0.2910 241 E 0.0426 0.6549 0.3026 242 F 0.0545 0.4460 0.4995 243 A 0.0748 0.2454 0.6799 244 D 0.0525 0.1357 0.8118 245 L 0.0403 0.0440 0.9157