# This file is the result of combining several RDB files, specifically # T0330.t06.dssp-ebghstl.rdb (weight 1.53986) # T0330.t06.stride-ebghtl.rdb (weight 1.24869) # T0330.t06.str2.rdb (weight 1.54758) # T0330.t06.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 T0330.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 4532 # # ============================================ # Comments from T0330.t06.stride-ebghtl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 4532 # # ============================================ # Comments from T0330.t06.str2.rdb # ============================================ # TARGET T0330 # 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 T0330.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 4532 # # ============================================ # Comments from T0330.t06.alpha.rdb # ============================================ # TARGET T0330 # 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 T0330.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 4532 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0641 0.0107 0.9251 2 S 0.1307 0.0112 0.8581 3 R 0.2390 0.0134 0.7477 4 T 0.4908 0.0460 0.4632 5 L 0.9150 0.0041 0.0809 6 V 0.9323 0.0032 0.0645 7 L 0.9317 0.0032 0.0651 8 F 0.9118 0.0047 0.0835 9 D 0.6638 0.0066 0.3296 10 I 0.2181 0.0746 0.7072 11 D 0.0754 0.0568 0.8678 12 G 0.0693 0.0745 0.8562 13 T 0.2813 0.0957 0.6231 14 L 0.6213 0.0911 0.2876 15 L 0.5442 0.1039 0.3520 16 K 0.4208 0.0981 0.4812 17 V 0.1270 0.3347 0.5383 18 E 0.0605 0.5524 0.3871 19 S 0.0265 0.7317 0.2419 20 M 0.0213 0.8027 0.1760 21 N 0.0179 0.8275 0.1546 22 R 0.0057 0.9256 0.0687 23 R 0.0048 0.9437 0.0515 24 V 0.0048 0.9495 0.0457 25 L 0.0048 0.9541 0.0412 26 A 0.0047 0.9591 0.0362 27 D 0.0047 0.9587 0.0365 28 A 0.0047 0.9582 0.0370 29 L 0.0047 0.9572 0.0381 30 I 0.0050 0.9507 0.0443 31 E 0.0063 0.9153 0.0784 32 V 0.0226 0.7244 0.2530 33 Y 0.0354 0.3011 0.6634 34 G 0.0389 0.1281 0.8331 35 T 0.0566 0.1187 0.8247 36 E 0.0689 0.1457 0.7854 37 G 0.0757 0.1203 0.8040 38 S 0.1094 0.1687 0.7219 39 T 0.1472 0.2555 0.5973 40 G 0.2209 0.2301 0.5490 41 S 0.3017 0.2388 0.4595 42 H 0.3348 0.2212 0.4440 43 D 0.2835 0.2116 0.5049 44 F 0.2219 0.2250 0.5531 45 S 0.1625 0.1910 0.6465 46 G 0.1128 0.1613 0.7259 47 K 0.1126 0.1909 0.6965 48 M 0.1113 0.2143 0.6744 49 D 0.0583 0.2667 0.6750 50 G 0.0384 0.4640 0.4976 51 A 0.0321 0.7615 0.2064 52 I 0.0332 0.8642 0.1026 53 I 0.0119 0.9339 0.0542 54 Y 0.0072 0.9506 0.0422 55 E 0.0061 0.9548 0.0391 56 V 0.0054 0.9544 0.0402 57 L 0.0059 0.9463 0.0478 58 S 0.0059 0.9148 0.0793 59 N 0.0065 0.8331 0.1604 60 V 0.0439 0.5385 0.4176 61 G 0.0389 0.1654 0.7957 62 L 0.0570 0.1658 0.7772 63 E 0.0557 0.2506 0.6937 64 R 0.0304 0.6793 0.2902 65 A 0.0181 0.8000 0.1819 66 E 0.0158 0.8438 0.1404 67 I 0.0132 0.8712 0.1156 68 A 0.0108 0.8833 0.1060 69 D 0.0066 0.8960 0.0974 70 K 0.0065 0.9064 0.0871 71 F 0.0074 0.9090 0.0836 72 D 0.0059 0.9185 0.0756 73 K 0.0059 0.9244 0.0697 74 A 0.0059 0.9235 0.0705 75 K 0.0053 0.9424 0.0523 76 E 0.0051 0.9481 0.0468 77 T 0.0053 0.9501 0.0446 78 Y 0.0055 0.9519 0.0426 79 I 0.0055 0.9544 0.0401 80 A 0.0058 0.9525 0.0417 81 L 0.0056 0.9494 0.0450 82 F 0.0066 0.9359 0.0575 83 R 0.0079 0.9158 0.0763 84 E 0.0102 0.8783 0.1115 85 R 0.0140 0.8055 0.1805 86 A 0.0333 0.7057 0.2610 87 R 0.0504 0.4820 0.4676 88 R 0.0436 0.5987 0.3577 89 E 0.0423 0.5273 0.4304 90 D 0.0684 0.3760 0.5556 91 I 0.1920 0.2084 0.5996 92 T 0.2584 0.1950 0.5466 93 L 0.2300 0.2268 0.5432 94 L 0.0703 0.2213 0.7084 95 E 0.0101 0.6977 0.2922 96 G 0.0097 0.6363 0.3540 97 V 0.0050 0.9176 0.0774 98 R 0.0047 0.9547 0.0406 99 E 0.0047 0.9560 0.0393 100 L 0.0047 0.9583 0.0370 101 L 0.0047 0.9589 0.0364 102 D 0.0047 0.9578 0.0375 103 A 0.0048 0.9506 0.0447 104 L 0.0049 0.9301 0.0650 105 S 0.0052 0.8520 0.1428 106 S 0.0069 0.6175 0.3756 107 R 0.0332 0.2518 0.7149 108 S 0.0566 0.0413 0.9021 109 D 0.0704 0.0373 0.8923 110 V 0.4111 0.0078 0.5811 111 L 0.7300 0.0038 0.2662 112 L 0.9245 0.0041 0.0713 113 G 0.9322 0.0033 0.0645 114 L 0.9306 0.0035 0.0659 115 L 0.8959 0.0056 0.0984 116 T 0.5299 0.0124 0.4577 117 G 0.0961 0.0382 0.8657 118 N 0.0843 0.0488 0.8670 119 F 0.0633 0.2532 0.6835 120 E 0.0360 0.6542 0.3098 121 A 0.0280 0.7566 0.2154 122 S 0.0322 0.7712 0.1966 123 G 0.0349 0.8038 0.1613 124 R 0.0334 0.8251 0.1415 125 H 0.0348 0.8512 0.1140 126 K 0.0252 0.8585 0.1162 127 L 0.0383 0.7812 0.1806 128 K 0.0337 0.5821 0.3842 129 L 0.0489 0.2726 0.6785 130 P 0.0421 0.1573 0.8006 131 G 0.0418 0.0835 0.8747 132 I 0.0822 0.1353 0.7825 133 D 0.0640 0.3144 0.6216 134 H 0.0828 0.3825 0.5347 135 Y 0.1654 0.2695 0.5652 136 F 0.2816 0.0837 0.6347 137 P 0.2084 0.1331 0.6585 138 F 0.4858 0.1288 0.3854 139 G 0.7002 0.0842 0.2156 140 A 0.7386 0.0715 0.1899 141 F 0.5607 0.0685 0.3708 142 A 0.2342 0.1811 0.5846 143 D 0.0765 0.4010 0.5226 144 D 0.0634 0.5176 0.4190 145 A 0.0620 0.5534 0.3846 146 L 0.0617 0.5000 0.4383 147 D 0.0462 0.4004 0.5534 148 R 0.0393 0.2571 0.7036 149 N 0.0561 0.1312 0.8127 150 E 0.0530 0.1708 0.7762 151 L 0.0721 0.1635 0.7644 152 P 0.0090 0.8525 0.1386 153 H 0.0054 0.9316 0.0630 154 I 0.0047 0.9515 0.0437 155 A 0.0047 0.9571 0.0382 156 L 0.0047 0.9605 0.0348 157 E 0.0047 0.9600 0.0353 158 R 0.0047 0.9587 0.0366 159 A 0.0047 0.9526 0.0427 160 R 0.0049 0.9211 0.0740 161 R 0.0057 0.8450 0.1494 162 M 0.0133 0.7156 0.2710 163 T 0.0256 0.4877 0.4867 164 G 0.0203 0.3066 0.6731 165 A 0.0437 0.1734 0.7829 166 N 0.0530 0.0445 0.9025 167 Y 0.1249 0.0130 0.8621 168 S 0.1026 0.0095 0.8879 169 P 0.0305 0.5564 0.4131 170 S 0.0552 0.4865 0.4583 171 Q 0.2268 0.3566 0.4166 172 I 0.8414 0.0143 0.1443 173 V 0.9059 0.0077 0.0864 174 I 0.9170 0.0057 0.0772 175 I 0.8179 0.0367 0.1454 176 G 0.4863 0.0185 0.4953 177 D 0.1908 0.0257 0.7835 178 T 0.0744 0.0831 0.8426 179 E 0.0095 0.7288 0.2617 180 H 0.0171 0.7522 0.2307 181 D 0.0189 0.7836 0.1975 182 I 0.0074 0.9375 0.0551 183 R 0.0059 0.9455 0.0486 184 C 0.0049 0.9527 0.0424 185 A 0.0053 0.9513 0.0434 186 R 0.0050 0.9415 0.0535 187 E 0.0058 0.8834 0.1108 188 L 0.0471 0.3467 0.6063 189 D 0.0456 0.0145 0.9399 190 A 0.0941 0.0072 0.8987 191 R 0.4045 0.0166 0.5789 192 S 0.9072 0.0034 0.0893 193 I 0.9249 0.0037 0.0715 194 A 0.9247 0.0036 0.0717 195 V 0.8717 0.0077 0.1206 196 A 0.5690 0.0166 0.4143 197 T 0.1915 0.0440 0.7646 198 G 0.0711 0.0671 0.8618 199 N 0.0957 0.0765 0.8277 200 F 0.1353 0.0563 0.8083 201 T 0.1232 0.0676 0.8092 202 M 0.0104 0.9014 0.0882 203 E 0.0058 0.9410 0.0532 204 E 0.0052 0.9441 0.0507 205 L 0.0058 0.9341 0.0601 206 A 0.0084 0.8922 0.0994 207 R 0.0115 0.7388 0.2497 208 H 0.0478 0.3930 0.5592 209 K 0.0742 0.0376 0.8881 210 P 0.0553 0.0881 0.8566 211 G 0.1393 0.0909 0.7697 212 T 0.7745 0.0313 0.1942 213 L 0.8679 0.0239 0.1082 214 F 0.7847 0.0223 0.1930 215 K 0.4046 0.0705 0.5249 216 N 0.1594 0.0369 0.8037 217 F 0.0135 0.7594 0.2271 218 A 0.0068 0.8424 0.1509 219 E 0.0099 0.8578 0.1323 220 T 0.0068 0.8955 0.0977 221 D 0.0050 0.9451 0.0499 222 E 0.0048 0.9501 0.0451 223 V 0.0048 0.9511 0.0441 224 L 0.0050 0.9435 0.0515 225 A 0.0053 0.9284 0.0663 226 S 0.0069 0.8574 0.1357 227 I 0.0132 0.7153 0.2715 228 L 0.0469 0.4358 0.5173 229 T 0.0536 0.0891 0.8573 230 P 0.0343 0.1566 0.8091 231 K 0.0454 0.1593 0.7952 232 H 0.0601 0.0933 0.8466 233 S 0.0533 0.0307 0.9160