# This file is the result of combining several RDB files, specifically # T0324.t06.dssp-ebghstl.rdb (weight 1.53986) # T0324.t06.stride-ebghtl.rdb (weight 1.24869) # T0324.t06.str2.rdb (weight 1.54758) # T0324.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 T0324.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0324 # 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 T0324.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 4841 # # ============================================ # Comments from T0324.t06.stride-ebghtl.rdb # ============================================ # TARGET T0324 # 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 T0324.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 4841 # # ============================================ # Comments from T0324.t06.str2.rdb # ============================================ # TARGET T0324 # 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 T0324.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 4841 # # ============================================ # Comments from T0324.t06.alpha.rdb # ============================================ # TARGET T0324 # 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 T0324.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 4841 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0735 0.0100 0.9165 2 T 0.1815 0.0108 0.8076 3 Y 0.2695 0.0085 0.7220 4 Q 0.4074 0.0391 0.5535 5 A 0.9102 0.0043 0.0855 6 L 0.9321 0.0032 0.0647 7 M 0.9321 0.0032 0.0648 8 F 0.9126 0.0046 0.0828 9 D 0.6723 0.0066 0.3211 10 I 0.2259 0.0780 0.6961 11 D 0.0828 0.0626 0.8546 12 G 0.0761 0.0806 0.8433 13 T 0.2458 0.1076 0.6465 14 L 0.4999 0.1046 0.3956 15 T 0.3816 0.1139 0.5045 16 N 0.2117 0.0877 0.7006 17 S 0.0690 0.1094 0.8216 18 Q 0.0515 0.2637 0.6849 19 P 0.0159 0.7623 0.2218 20 A 0.0126 0.8744 0.1131 21 Y 0.0072 0.9238 0.0690 22 T 0.0049 0.9498 0.0453 23 T 0.0047 0.9549 0.0403 24 V 0.0047 0.9565 0.0388 25 M 0.0047 0.9597 0.0356 26 R 0.0046 0.9609 0.0344 27 E 0.0047 0.9606 0.0347 28 V 0.0047 0.9595 0.0358 29 L 0.0047 0.9590 0.0363 30 A 0.0049 0.9523 0.0428 31 T 0.0078 0.9054 0.0868 32 Y 0.0462 0.5301 0.4236 33 G 0.0323 0.0364 0.9314 34 K 0.0506 0.0139 0.9355 35 P 0.0797 0.0242 0.8960 36 F 0.1007 0.0287 0.8706 37 S 0.0752 0.0323 0.8925 38 P 0.0180 0.7487 0.2334 39 A 0.0152 0.8648 0.1200 40 Q 0.0211 0.8527 0.1262 41 A 0.0348 0.8340 0.1312 42 Q 0.0445 0.7742 0.1812 43 K 0.0430 0.6575 0.2995 44 T 0.0502 0.4846 0.4652 45 F 0.0806 0.1545 0.7649 46 P 0.0527 0.2442 0.7031 47 M 0.0450 0.5375 0.4174 48 A 0.0375 0.6661 0.2964 49 A 0.0241 0.8086 0.1673 50 E 0.0159 0.8855 0.0986 51 Q 0.0143 0.9102 0.0755 52 A 0.0131 0.9184 0.0685 53 M 0.0147 0.9129 0.0725 54 T 0.0171 0.8892 0.0937 55 E 0.0148 0.8288 0.1564 56 L 0.0436 0.5919 0.3645 57 G 0.0426 0.1958 0.7616 58 I 0.0748 0.1890 0.7362 59 A 0.0804 0.2478 0.6718 60 A 0.0250 0.6583 0.3167 61 S 0.0229 0.6628 0.3143 62 E 0.0237 0.6977 0.2786 63 F 0.0217 0.7672 0.2111 64 D 0.0125 0.8442 0.1434 65 H 0.0110 0.8915 0.0975 66 F 0.0089 0.9080 0.0831 67 Q 0.0072 0.9274 0.0654 68 A 0.0062 0.9307 0.0630 69 Q 0.0065 0.9301 0.0634 70 Y 0.0065 0.9381 0.0554 71 E 0.0057 0.9455 0.0488 72 D 0.0057 0.9447 0.0496 73 V 0.0057 0.9424 0.0519 74 M 0.0075 0.9302 0.0623 75 A 0.0104 0.8853 0.1043 76 S 0.0127 0.8092 0.1782 77 H 0.0221 0.7023 0.2756 78 Y 0.0482 0.5399 0.4119 79 D 0.0313 0.4673 0.5014 80 Q 0.0524 0.3864 0.5611 81 I 0.1856 0.1709 0.6435 82 E 0.2809 0.1175 0.6017 83 L 0.2626 0.0977 0.6397 84 Y 0.0915 0.0550 0.8536 85 P 0.0165 0.4297 0.5538 86 G 0.0188 0.4260 0.5553 87 I 0.0100 0.8696 0.1203 88 T 0.0059 0.9422 0.0519 89 S 0.0054 0.9515 0.0430 90 L 0.0048 0.9519 0.0433 91 F 0.0050 0.9376 0.0574 92 E 0.0062 0.8342 0.1596 93 Q 0.0105 0.6127 0.3767 94 L 0.0475 0.1608 0.7917 95 P 0.0433 0.1889 0.7678 96 S 0.0272 0.2774 0.6954 97 E 0.0431 0.1249 0.8321 98 L 0.3536 0.0105 0.6359 99 R 0.6497 0.0199 0.3304 100 L 0.9274 0.0034 0.0691 101 G 0.9314 0.0034 0.0652 102 I 0.9311 0.0034 0.0655 103 V 0.8919 0.0060 0.1021 104 T 0.5076 0.0124 0.4800 105 S 0.0864 0.0509 0.8627 106 Q 0.0561 0.0864 0.8575 107 R 0.0627 0.2300 0.7073 108 R 0.0170 0.7398 0.2431 109 N 0.0114 0.8493 0.1393 110 E 0.0133 0.8889 0.0978 111 L 0.0144 0.9042 0.0813 112 E 0.0121 0.9113 0.0766 113 S 0.0089 0.9104 0.0807 114 G 0.0078 0.8972 0.0950 115 M 0.0150 0.8620 0.1230 116 R 0.0090 0.7567 0.2343 117 S 0.0130 0.6050 0.3820 118 Y 0.0626 0.1963 0.7411 119 P 0.0495 0.1230 0.8275 120 F 0.1069 0.2407 0.6524 121 M 0.1749 0.3004 0.5247 122 M 0.2404 0.3520 0.4076 123 R 0.3727 0.2260 0.4013 124 M 0.5270 0.1010 0.3720 125 A 0.5271 0.1117 0.3612 126 V 0.7796 0.0555 0.1650 127 T 0.8500 0.0409 0.1091 128 I 0.8384 0.0356 0.1260 129 S 0.6815 0.0265 0.2920 130 A 0.2832 0.1064 0.6104 131 D 0.1356 0.1116 0.7528 132 D 0.1072 0.1201 0.7728 133 T 0.1077 0.0701 0.8222 134 P 0.0754 0.1122 0.8124 135 K 0.0932 0.1065 0.8002 136 R 0.1126 0.0710 0.8163 137 K 0.0878 0.0334 0.8788 138 P 0.0778 0.0456 0.8766 139 D 0.0883 0.0409 0.8708 140 P 0.0138 0.7793 0.2068 141 L 0.0087 0.9271 0.0642 142 P 0.0051 0.9505 0.0444 143 L 0.0047 0.9586 0.0367 144 L 0.0047 0.9608 0.0345 145 T 0.0047 0.9605 0.0348 146 A 0.0047 0.9604 0.0350 147 L 0.0047 0.9595 0.0358 148 E 0.0049 0.9511 0.0441 149 K 0.0053 0.9134 0.0813 150 V 0.0461 0.4496 0.5043 151 N 0.0458 0.0175 0.9367 152 V 0.0672 0.0079 0.9249 153 A 0.0793 0.0110 0.9097 154 P 0.0387 0.5782 0.3831 155 Q 0.0579 0.5491 0.3930 156 N 0.1363 0.4166 0.4470 157 A 0.7982 0.0169 0.1850 158 L 0.8972 0.0066 0.0961 159 F 0.9099 0.0047 0.0854 160 I 0.8079 0.0440 0.1481 161 G 0.4822 0.0195 0.4983 162 D 0.1811 0.0326 0.7864 163 S 0.0949 0.0817 0.8234 164 V 0.0327 0.4011 0.5662 165 S 0.0394 0.4224 0.5381 166 D 0.0300 0.5047 0.4653 167 E 0.0061 0.9407 0.0532 168 Q 0.0049 0.9523 0.0429 169 T 0.0047 0.9577 0.0376 170 A 0.0047 0.9570 0.0383 171 Q 0.0049 0.9487 0.0464 172 A 0.0054 0.9115 0.0831 173 A 0.0457 0.4753 0.4789 174 N 0.0440 0.0235 0.9325 175 V 0.0925 0.0075 0.9000 176 D 0.2557 0.0323 0.7120 177 F 0.8385 0.0064 0.1551 178 G 0.9068 0.0056 0.0876 179 L 0.9166 0.0055 0.0779 180 A 0.8766 0.0095 0.1139 181 V 0.6776 0.0179 0.3045 182 W 0.3447 0.0418 0.6135 183 G 0.1249 0.0436 0.8315 184 M 0.1009 0.0433 0.8558 185 D 0.0857 0.0295 0.8848 186 P 0.0480 0.1306 0.8214 187 N 0.0480 0.2633 0.6887 188 A 0.0312 0.4223 0.5464 189 D 0.0475 0.4019 0.5506 190 H 0.0681 0.3584 0.5735 191 Q 0.1105 0.2396 0.6499 192 K 0.2039 0.1399 0.6562 193 V 0.3232 0.0655 0.6113 194 A 0.3947 0.1057 0.4997 195 H 0.7817 0.0460 0.1722 196 R 0.8191 0.0419 0.1389 197 F 0.6690 0.0259 0.3051 198 Q 0.2397 0.0559 0.7045 199 K 0.1059 0.0111 0.8830 200 P 0.0072 0.8509 0.1419 201 L 0.0055 0.9023 0.0921 202 D 0.0059 0.9246 0.0694 203 I 0.0052 0.9402 0.0546 204 L 0.0053 0.9446 0.0501 205 E 0.0056 0.9236 0.0708 206 L 0.0079 0.8201 0.1720 207 F 0.0456 0.5504 0.4040 208 K 0.0219 0.1027 0.8754