# This file is the result of combining several RDB files, specifically # T0347.t06.dssp-ebghstl.rdb (weight 1.53986) # T0347.t06.stride-ebghtl.rdb (weight 1.24869) # T0347.t06.str2.rdb (weight 1.54758) # T0347.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 T0347.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0347 # 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 T0347.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 13.6915 # # ============================================ # Comments from T0347.t06.stride-ebghtl.rdb # ============================================ # TARGET T0347 # 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 T0347.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 13.6915 # # ============================================ # Comments from T0347.t06.str2.rdb # ============================================ # TARGET T0347 # 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 T0347.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 13.6915 # # ============================================ # Comments from T0347.t06.alpha.rdb # ============================================ # TARGET T0347 # 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 T0347.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 13.6915 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0636 0.0249 0.9115 2 T 0.0792 0.0711 0.8497 3 H 0.0997 0.0899 0.8104 4 I 0.0953 0.1365 0.7682 5 Y 0.0916 0.1286 0.7798 6 E 0.0905 0.1026 0.8069 7 P 0.0701 0.1975 0.7324 8 R 0.1631 0.2113 0.6256 9 L 0.4340 0.1324 0.4336 10 S 0.6204 0.0830 0.2966 11 R 0.7810 0.0369 0.1820 12 I 0.7300 0.0155 0.2545 13 A 0.5849 0.0206 0.3945 14 I 0.0677 0.7338 0.1985 15 D 0.0281 0.7743 0.1976 16 K 0.0176 0.7630 0.2194 17 L 0.1139 0.3304 0.5557 18 R 0.0946 0.1259 0.7794 19 P 0.0776 0.3323 0.5900 20 T 0.1332 0.2672 0.5996 21 Q 0.2148 0.3876 0.3976 22 I 0.3096 0.4090 0.2814 23 A 0.3329 0.4497 0.2174 24 V 0.2484 0.4890 0.2626 25 G 0.2055 0.3950 0.3994 26 F 0.0330 0.8446 0.1224 27 R 0.0234 0.8814 0.0952 28 E 0.0265 0.8992 0.0743 29 V 0.0153 0.9279 0.0568 30 E 0.0096 0.9345 0.0559 31 L 0.0108 0.9179 0.0713 32 K 0.0089 0.8988 0.0924 33 R 0.0085 0.9028 0.0887 34 K 0.0073 0.9070 0.0856 35 E 0.0085 0.8951 0.0963 36 W 0.0102 0.8848 0.1051 37 R 0.0111 0.8446 0.1443 38 E 0.0155 0.7354 0.2491 39 T 0.0356 0.5233 0.4411 40 R 0.0470 0.3231 0.6299 41 K 0.0274 0.5464 0.4261 42 K 0.0287 0.5059 0.4655 43 D 0.0414 0.4947 0.4639 44 G 0.0187 0.6390 0.3423 45 D 0.0152 0.7528 0.2320 46 D 0.0160 0.7732 0.2109 47 F 0.0210 0.7544 0.2246 48 L 0.0524 0.5679 0.3797 49 G 0.0402 0.3064 0.6534 50 N 0.0414 0.1625 0.7961 51 H 0.1590 0.0468 0.7942 52 I 0.3045 0.0168 0.6787 53 V 0.5680 0.0092 0.4228 54 P 0.6172 0.0099 0.3729 55 V 0.8170 0.0110 0.1720 56 V 0.8475 0.0097 0.1427 57 A 0.7866 0.0197 0.1937 58 G 0.2989 0.0141 0.6870 59 P 0.0688 0.0717 0.8596 60 K 0.0419 0.0491 0.9090 61 D 0.0386 0.0469 0.9145 62 R 0.2167 0.0235 0.7598 63 A 0.7609 0.0069 0.2322 64 Y 0.8901 0.0062 0.1037 65 L 0.9000 0.0089 0.0912 66 I 0.8131 0.0316 0.1553 67 D 0.4597 0.0975 0.4428 68 H 0.1030 0.3302 0.5667 69 H 0.0562 0.5289 0.4148 70 H 0.0390 0.7801 0.1808 71 L 0.0179 0.9073 0.0749 72 V 0.0080 0.9407 0.0513 73 L 0.0063 0.9420 0.0517 74 A 0.0061 0.9408 0.0531 75 L 0.0084 0.9256 0.0660 76 S 0.0119 0.8952 0.0930 77 K 0.0117 0.8283 0.1600 78 E 0.0425 0.4121 0.5454 79 G 0.0413 0.0429 0.9158 80 V 0.1007 0.0580 0.8412 81 E 0.2513 0.1082 0.6406 82 H 0.6192 0.0512 0.3296 83 V 0.7079 0.0229 0.2691 84 L 0.8106 0.0210 0.1684 85 T 0.8473 0.0263 0.1263 86 S 0.8494 0.0312 0.1194 87 E 0.8538 0.0320 0.1142 88 V 0.7432 0.0817 0.1752 89 A 0.5925 0.1216 0.2859 90 K 0.4267 0.1282 0.4451 91 F 0.1694 0.2735 0.5571 92 S 0.0848 0.3430 0.5723 93 H 0.0572 0.2815 0.6613 94 L 0.0856 0.1172 0.7972 95 G 0.0604 0.0492 0.8905 96 K 0.0202 0.5809 0.3990 97 D 0.0094 0.8203 0.1703 98 E 0.0099 0.8773 0.1128 99 F 0.0080 0.9263 0.0657 100 W 0.0065 0.9348 0.0587 101 S 0.0073 0.9333 0.0595 102 V 0.0111 0.9220 0.0669 103 M 0.0230 0.8700 0.1070 104 D 0.0160 0.7461 0.2379 105 H 0.0154 0.4700 0.5147 106 R 0.0535 0.1396 0.8069 107 N 0.0550 0.0347 0.9103 108 L 0.3295 0.0175 0.6530 109 I 0.6916 0.0092 0.2992 110 Y 0.7389 0.0080 0.2532 111 P 0.6086 0.0363 0.3551 112 F 0.5195 0.0386 0.4419 113 D 0.1921 0.0244 0.7835 114 A 0.0182 0.1708 0.8110 115 Q 0.0502 0.0573 0.8926 116 G 0.0624 0.0500 0.8876 117 L 0.1727 0.0202 0.8072 118 R 0.4705 0.0166 0.5129 119 R 0.2248 0.0264 0.7488 120 Q 0.1642 0.0384 0.7974 121 S 0.0334 0.5734 0.3932 122 G 0.0196 0.5329 0.4474 123 D 0.0289 0.5372 0.4339 124 I 0.0833 0.1383 0.7784 125 P 0.0794 0.1601 0.7604 126 K 0.0492 0.4808 0.4701 127 N 0.0697 0.4134 0.5169 128 I 0.0638 0.5820 0.3541 129 H 0.0491 0.4858 0.4651 130 D 0.0632 0.3884 0.5484 131 L 0.0551 0.4221 0.5229 132 E 0.0511 0.2686 0.6804 133 D 0.0518 0.1684 0.7798 134 D 0.0923 0.0502 0.8575 135 P 0.0118 0.6116 0.3766 136 F 0.0144 0.7490 0.2366 137 R 0.0152 0.8472 0.1376 138 S 0.0165 0.9016 0.0820 139 L 0.0093 0.9352 0.0555 140 A 0.0092 0.9429 0.0478 141 G 0.0083 0.9495 0.0422 142 A 0.0080 0.9528 0.0393 143 L 0.0110 0.9469 0.0420 144 R 0.0170 0.9260 0.0571 145 M 0.0172 0.8820 0.1008 146 A 0.0404 0.4908 0.4687 147 G 0.0339 0.0619 0.9043 148 G 0.0666 0.0741 0.8593 149 Y 0.1808 0.0857 0.7335 150 A 0.1908 0.1096 0.6996 151 K 0.1836 0.0912 0.7252 152 V 0.2019 0.0633 0.7349 153 I 0.2613 0.0481 0.6906 154 I 0.2252 0.0310 0.7438 155 P 0.1807 0.0698 0.7495 156 F 0.0847 0.4833 0.4320 157 S 0.0496 0.6231 0.3273 158 E 0.0580 0.6709 0.2711 159 F 0.0752 0.6303 0.2944 160 G 0.0691 0.6832 0.2477 161 W 0.0221 0.8617 0.1162 162 A 0.0100 0.9221 0.0679 163 D 0.0071 0.9418 0.0511 164 F 0.0067 0.9378 0.0555 165 L 0.0062 0.9224 0.0714 166 R 0.0074 0.8788 0.1138 167 R 0.0100 0.7882 0.2018 168 R 0.0184 0.6069 0.3747 169 I 0.0570 0.3299 0.6131 170 D 0.0617 0.1812 0.7571 171 R 0.0159 0.6329 0.3512 172 D 0.0146 0.6488 0.3366 173 L 0.0157 0.7008 0.2836 174 L 0.0446 0.4653 0.4901 175 S 0.0391 0.3576 0.6034 176 D 0.0175 0.3972 0.5853 177 S 0.0310 0.3487 0.6203 178 F 0.0231 0.5706 0.4063 179 D 0.0091 0.8842 0.1067 180 D 0.0053 0.9236 0.0711 181 A 0.0050 0.9368 0.0582 182 L 0.0048 0.9487 0.0464 183 A 0.0047 0.9553 0.0400 184 E 0.0048 0.9492 0.0460 185 A 0.0049 0.9472 0.0479 186 M 0.0048 0.9457 0.0495 187 K 0.0049 0.9262 0.0689 188 L 0.0059 0.8541 0.1401 189 A 0.0112 0.7223 0.2665 190 K 0.0221 0.5135 0.4644 191 S 0.0517 0.2955 0.6528 192 R 0.0072 0.6262 0.3667 193 E 0.0111 0.6052 0.3837 194 A 0.0219 0.6782 0.2999 195 R 0.0244 0.5087 0.4668 196 H 0.0407 0.3239 0.6354 197 L 0.1023 0.0602 0.8375 198 P 0.0769 0.1568 0.7663 199 G 0.1281 0.1571 0.7148 200 W 0.2192 0.1716 0.6091 201 C 0.2325 0.1367 0.6308 202 G 0.1301 0.0758 0.7940 203 V 0.1209 0.0662 0.8128 204 E 0.0901 0.0612 0.8487 205 E 0.0464 0.0322 0.9215