# This file is the result of combining several RDB files, specifically # 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) # 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.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 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1127 0.1175 0.7699 2 A 0.1831 0.2383 0.5786 3 V 0.2392 0.4574 0.3034 4 Q 0.2588 0.5191 0.2222 5 L 0.2413 0.5588 0.1999 6 L 0.2300 0.4744 0.2956 7 E 0.1389 0.5211 0.3401 8 N 0.0918 0.5291 0.3791 9 W 0.1398 0.4841 0.3761 10 L 0.2122 0.3824 0.4053 11 L 0.2517 0.3078 0.4405 12 K 0.2141 0.2407 0.5451 13 E 0.1799 0.2929 0.5273 14 Q 0.1307 0.3444 0.5249 15 E 0.1325 0.4064 0.4611 16 K 0.1775 0.3507 0.4719 17 I 0.2082 0.2732 0.5186 18 Q 0.1700 0.2002 0.6298 19 T 0.1413 0.1904 0.6683 20 K 0.1384 0.1561 0.7055 21 Y 0.2262 0.1195 0.6543 22 R 0.3419 0.1033 0.5549 23 H 0.4436 0.0898 0.4665 24 L 0.2999 0.1902 0.5099 25 N 0.2348 0.1705 0.5947 26 H 0.2026 0.1748 0.6226 27 I 0.2373 0.0796 0.6831 28 S 0.2061 0.0659 0.7280 29 V 0.1616 0.1012 0.7372 30 V 0.1348 0.0594 0.8058 31 E 0.1130 0.0298 0.8571 32 P 0.1307 0.0347 0.8346 33 N 0.3902 0.0359 0.5739 34 I 0.9054 0.0047 0.0899 35 L 0.9258 0.0039 0.0703 36 F 0.9216 0.0046 0.0738 37 I 0.8051 0.0219 0.1729 38 G 0.2873 0.0380 0.6747 39 D 0.1188 0.1276 0.7536 40 S 0.1137 0.3407 0.5456 41 I 0.0575 0.6583 0.2842 42 V 0.0584 0.6880 0.2536 43 E 0.0590 0.5615 0.3795 44 Y 0.0655 0.3722 0.5623 45 Y 0.0796 0.1375 0.7829 46 P 0.0758 0.1689 0.7553 47 L 0.0219 0.7548 0.2233 48 Q 0.0172 0.8331 0.1497 49 E 0.0144 0.8420 0.1436 50 L 0.0245 0.7708 0.2047 51 F 0.0698 0.4722 0.4580 52 G 0.0424 0.2095 0.7481 53 T 0.0555 0.1202 0.8243 54 S 0.0875 0.0745 0.8381 55 K 0.2189 0.0678 0.7133 56 T 0.6062 0.0583 0.3355 57 I 0.8317 0.0385 0.1298 58 V 0.8279 0.0355 0.1366 59 N 0.7886 0.0430 0.1685 60 R 0.5764 0.0748 0.3489 61 G 0.3829 0.0765 0.5407 62 I 0.3237 0.1001 0.5762 63 R 0.1784 0.1265 0.6950 64 G 0.0810 0.1805 0.7385 65 Y 0.0873 0.3497 0.5629 66 Q 0.1026 0.4540 0.4435 67 T 0.0376 0.7321 0.2304 68 G 0.0124 0.8408 0.1468 69 L 0.0143 0.8655 0.1201 70 L 0.0116 0.8954 0.0930 71 L 0.0087 0.9157 0.0756 72 E 0.0066 0.9138 0.0797 73 N 0.0072 0.8931 0.0997 74 L 0.0109 0.8798 0.1093 75 D 0.0078 0.8890 0.1031 76 A 0.0080 0.8822 0.1098 77 H 0.0113 0.8649 0.1238 78 L 0.0280 0.7599 0.2121 79 Y 0.0291 0.5144 0.4564 80 G 0.0301 0.2158 0.7541 81 G 0.0492 0.0813 0.8695 82 A 0.0875 0.0391 0.8734 83 V 0.1327 0.0321 0.8352 84 D 0.1487 0.0553 0.7960 85 K 0.8877 0.0052 0.1071 86 I 0.9301 0.0032 0.0667 87 F 0.9337 0.0032 0.0631 88 L 0.9268 0.0038 0.0694 89 L 0.8993 0.0041 0.0966 90 I 0.6785 0.0278 0.2937 91 G 0.3837 0.0291 0.5872 92 T 0.2645 0.1206 0.6149 93 N 0.1534 0.2452 0.6013 94 D 0.1215 0.3204 0.5580 95 I 0.0700 0.2745 0.6554 96 G 0.0568 0.1743 0.7688 97 K 0.0523 0.1023 0.8454 98 D 0.0618 0.0639 0.8743 99 V 0.0950 0.0147 0.8902 100 P 0.0889 0.0169 0.8942 101 V 0.0049 0.9396 0.0554 102 N 0.0047 0.9590 0.0363 103 E 0.0047 0.9587 0.0366 104 A 0.0047 0.9574 0.0379 105 L 0.0047 0.9535 0.0418 106 N 0.0049 0.9378 0.0572 107 N 0.0049 0.9344 0.0608 108 L 0.0047 0.9574 0.0379 109 E 0.0046 0.9615 0.0339 110 A 0.0046 0.9615 0.0339 111 I 0.0046 0.9613 0.0341 112 I 0.0047 0.9610 0.0344 113 Q 0.0047 0.9603 0.0350 114 S 0.0047 0.9579 0.0374 115 V 0.0049 0.9494 0.0457 116 A 0.0054 0.9289 0.0657 117 R 0.0074 0.8258 0.1668 118 D 0.0148 0.6077 0.3774 119 Y 0.0809 0.0535 0.8656 120 P 0.0166 0.1330 0.8504 121 L 0.0403 0.0759 0.8838 122 T 0.2516 0.0180 0.7305 123 E 0.6144 0.0055 0.3802 124 I 0.9156 0.0033 0.0811 125 K 0.9253 0.0035 0.0712 126 L 0.9265 0.0033 0.0702 127 L 0.8724 0.0102 0.1175 128 S 0.7373 0.0078 0.2549 129 I 0.4050 0.0230 0.5720 130 L 0.2176 0.0284 0.7540 131 P 0.1365 0.0501 0.8134 132 V 0.0439 0.3679 0.5882 133 N 0.0504 0.3507 0.5989 134 E 0.0607 0.3819 0.5574 135 R 0.0775 0.3385 0.5840 136 E 0.0429 0.6823 0.2748 137 E 0.0435 0.7353 0.2213 138 Y 0.0571 0.7212 0.2217 139 Q 0.0613 0.6841 0.2546 140 Q 0.0450 0.7405 0.2145 141 A 0.0343 0.7931 0.1726 142 V 0.0467 0.7889 0.1644 143 Y 0.0679 0.7445 0.1876 144 I 0.0649 0.7057 0.2294 145 R 0.0659 0.6125 0.3216 146 S 0.0413 0.6324 0.3262 147 N 0.0153 0.7742 0.2104 148 E 0.0060 0.9109 0.0831 149 K 0.0060 0.9280 0.0661 150 I 0.0050 0.9442 0.0508 151 Q 0.0047 0.9554 0.0399 152 N 0.0047 0.9526 0.0427 153 W 0.0047 0.9541 0.0412 154 N 0.0047 0.9574 0.0379 155 Q 0.0047 0.9588 0.0365 156 A 0.0047 0.9590 0.0364 157 Y 0.0047 0.9596 0.0357 158 Q 0.0047 0.9608 0.0346 159 E 0.0047 0.9601 0.0352 160 L 0.0048 0.9541 0.0412 161 A 0.0049 0.9443 0.0508 162 S 0.0055 0.8747 0.1198 163 A 0.0101 0.6924 0.2975 164 Y 0.0653 0.3042 0.6305 165 M 0.0246 0.1463 0.8292 166 Q 0.0655 0.0516 0.8829 167 V 0.4699 0.0112 0.5190 168 E 0.8338 0.0086 0.1576 169 F 0.9090 0.0047 0.0863 170 V 0.8437 0.0079 0.1484 171 P 0.7103 0.0122 0.2775 172 V 0.3011 0.1675 0.5314 173 F 0.0907 0.3872 0.5221 174 D 0.0455 0.5793 0.3751 175 C 0.0493 0.6596 0.2911 176 L 0.0753 0.6277 0.2969 177 T 0.0785 0.5679 0.3536 178 D 0.0524 0.5241 0.4235 179 Q 0.0299 0.5701 0.4000 180 A 0.0495 0.4683 0.4822 181 G 0.0478 0.3378 0.6143 182 Q 0.0677 0.2959 0.6364 183 L 0.0994 0.2973 0.6032 184 K 0.0773 0.3521 0.5706 185 K 0.0851 0.4330 0.4819 186 E 0.1277 0.4127 0.4596 187 Y 0.2080 0.2525 0.5395 188 T 0.1901 0.1312 0.6787 189 T 0.1226 0.1464 0.7309 190 D 0.1064 0.0989 0.7948 191 G 0.1115 0.0907 0.7978 192 L 0.2066 0.0755 0.7179 193 H 0.2493 0.0615 0.6892 194 L 0.1173 0.0718 0.8109 195 S 0.0633 0.0638 0.8729 196 I 0.0050 0.9414 0.0537 197 A 0.0047 0.9524 0.0429 198 G 0.0047 0.9571 0.0382 199 Y 0.0047 0.9604 0.0349 200 Q 0.0046 0.9610 0.0343 201 A 0.0047 0.9594 0.0359 202 L 0.0047 0.9552 0.0401 203 S 0.0047 0.9565 0.0388 204 K 0.0048 0.9519 0.0433 205 S 0.0049 0.9343 0.0608 206 L 0.0051 0.9242 0.0707 207 K 0.0052 0.9233 0.0715 208 D 0.0055 0.8964 0.0982 209 Y 0.0078 0.7862 0.2060 210 L 0.0232 0.5669 0.4098 211 Y 0.0206 0.1259 0.8536