# This file is the result of combining several RDB files, specifically # T0393.t04.dssp-ebghstl.rdb (weight 1.53986) # T0393.t04.stride-ebghtl.rdb (weight 1.24869) # T0393.t04.str2.rdb (weight 1.54758) # T0393.t04.alpha.rdb (weight 0.659012) # T0393.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0393.t2k.stride-ebghtl.rdb (weight 1.24869) # T0393.t2k.str2.rdb (weight 1.54758) # T0393.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 T0393.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0393 # Using neural net t04-2621-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 T0393.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 2001 # # ============================================ # Comments from T0393.t04.stride-ebghtl.rdb # ============================================ # TARGET T0393 # 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 T0393.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 2001 # # ============================================ # Comments from T0393.t04.str2.rdb # ============================================ # TARGET T0393 # Using neural net t04-2621-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 T0393.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 2001 # # ============================================ # Comments from T0393.t04.alpha.rdb # ============================================ # TARGET T0393 # 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 T0393.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 2001 # # ============================================ # Comments from T0393.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0393 # 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 T0393.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 667 # # ============================================ # Comments from T0393.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0393 # 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 T0393.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 667 # # ============================================ # Comments from T0393.t2k.str2.rdb # ============================================ # TARGET T0393 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0393.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 667 # # ============================================ # Comments from T0393.t2k.alpha.rdb # ============================================ # TARGET T0393 # 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 T0393.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 667 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1084 0.0623 0.8293 2 K 0.1731 0.0819 0.7450 3 R 0.1103 0.1260 0.7637 4 S 0.1051 0.1148 0.7801 5 I 0.0365 0.3526 0.6109 6 E 0.0273 0.2987 0.6740 7 D 0.0342 0.1725 0.7933 8 T 0.1389 0.0164 0.8447 9 P 0.4110 0.0116 0.5774 10 I 0.9102 0.0049 0.0849 11 V 0.9269 0.0041 0.0690 12 L 0.9279 0.0042 0.0679 13 I 0.8607 0.0322 0.1071 14 G 0.4769 0.0216 0.5015 15 A 0.1048 0.1038 0.7913 16 G 0.0486 0.3447 0.6067 17 N 0.0060 0.9060 0.0880 18 L 0.0049 0.9326 0.0625 19 A 0.0048 0.9511 0.0441 20 T 0.0048 0.9563 0.0389 21 N 0.0047 0.9587 0.0366 22 L 0.0047 0.9594 0.0360 23 A 0.0047 0.9586 0.0367 24 K 0.0047 0.9589 0.0364 25 A 0.0047 0.9590 0.0363 26 L 0.0048 0.9570 0.0382 27 Y 0.0050 0.9443 0.0507 28 R 0.0061 0.8792 0.1147 29 K 0.0399 0.2877 0.6724 30 G 0.0420 0.0152 0.9428 31 F 0.0908 0.0083 0.9008 32 R 0.4801 0.0082 0.5117 33 I 0.8976 0.0033 0.0991 34 V 0.9239 0.0036 0.0726 35 Q 0.9248 0.0035 0.0717 36 V 0.9047 0.0038 0.0915 37 Y 0.7285 0.0166 0.2549 38 S 0.3163 0.0128 0.6709 39 R 0.0773 0.0427 0.8800 40 T 0.0764 0.0164 0.9072 41 E 0.0056 0.8718 0.1226 42 E 0.0050 0.9129 0.0821 43 S 0.0050 0.9303 0.0647 44 A 0.0047 0.9481 0.0471 45 R 0.0051 0.9475 0.0474 46 E 0.0047 0.9458 0.0495 47 L 0.0047 0.9449 0.0504 48 A 0.0048 0.9367 0.0585 49 Q 0.0053 0.8988 0.0959 50 K 0.0071 0.8275 0.1654 51 V 0.0507 0.4640 0.4853 52 E 0.0443 0.0678 0.8879 53 A 0.1135 0.0447 0.8418 54 E 0.2746 0.0481 0.6773 55 Y 0.4125 0.0593 0.5282 56 T 0.2723 0.0911 0.6366 57 T 0.1272 0.1267 0.7461 58 D 0.1073 0.1024 0.7903 59 L 0.0111 0.8062 0.1826 60 A 0.0058 0.8849 0.1093 61 E 0.0056 0.8930 0.1014 62 V 0.0074 0.8760 0.1166 63 N 0.0152 0.7847 0.2001 64 P 0.0107 0.5451 0.4442 65 Y 0.0260 0.2420 0.7319 66 A 0.0993 0.0200 0.8807 67 K 0.0803 0.0530 0.8667 68 L 0.9134 0.0037 0.0829 69 Y 0.9335 0.0032 0.0633 70 I 0.9307 0.0033 0.0659 71 V 0.9105 0.0066 0.0828 72 S 0.6294 0.0123 0.3583 73 L 0.2051 0.0103 0.7845 74 K 0.1076 0.0250 0.8674 75 D 0.0440 0.2805 0.6754 76 S 0.0225 0.4447 0.5328 77 A 0.0273 0.6289 0.3438 78 F 0.0176 0.8207 0.1618 79 A 0.0107 0.8963 0.0930 80 E 0.0097 0.9123 0.0780 81 L 0.0087 0.9156 0.0757 82 L 0.0076 0.9188 0.0736 83 Q 0.0083 0.8887 0.1030 84 G 0.0102 0.8259 0.1639 85 I 0.0193 0.7754 0.2054 86 V 0.0204 0.7570 0.2226 87 E 0.0165 0.7294 0.2541 88 G 0.0276 0.6425 0.3299 89 K 0.0877 0.4087 0.5037 90 R 0.0776 0.2223 0.7002 91 E 0.0325 0.1382 0.8293 92 E 0.0305 0.0540 0.9155 93 A 0.2562 0.0137 0.7301 94 L 0.8304 0.0037 0.1659 95 M 0.9056 0.0074 0.0870 96 V 0.9149 0.0053 0.0798 97 H 0.8808 0.0063 0.1129 98 T 0.5986 0.0346 0.3668 99 A 0.2602 0.0816 0.6582 100 G 0.1399 0.1201 0.7400 101 S 0.1353 0.1117 0.7530 102 I 0.1597 0.0698 0.7706 103 P 0.1252 0.1282 0.7466 104 M 0.0277 0.6182 0.3540 105 N 0.0256 0.6595 0.3149 106 V 0.0235 0.7103 0.2662 107 W 0.0187 0.7528 0.2285 108 E 0.0138 0.7886 0.1976 109 G 0.0145 0.7997 0.1858 110 H 0.0190 0.7802 0.2008 111 V 0.0320 0.7025 0.2656 112 P 0.0305 0.5557 0.4138 113 H 0.0535 0.3507 0.5958 114 Y 0.0528 0.1317 0.8155 115 G 0.1287 0.0798 0.7914 116 V 0.4850 0.0452 0.4698 117 F 0.7291 0.0315 0.2394 118 Y 0.7377 0.0317 0.2307 119 P 0.6655 0.0461 0.2884 120 M 0.4570 0.0640 0.4790 121 Q 0.2370 0.0507 0.7124 122 T 0.1475 0.1041 0.7484 123 F 0.1242 0.1297 0.7461 124 S 0.0943 0.1384 0.7674 125 K 0.0482 0.3466 0.6052 126 Q 0.0544 0.5102 0.4354 127 R 0.0816 0.6402 0.2782 128 E 0.0830 0.6882 0.2287 129 V 0.0935 0.6524 0.2540 130 D 0.0790 0.5554 0.3655 131 F 0.0921 0.3705 0.5374 132 K 0.1291 0.2382 0.6327 133 E 0.1511 0.1927 0.6562 134 I 0.2748 0.1561 0.5691 135 P 0.4248 0.1402 0.4350 136 F 0.6284 0.1154 0.2562 137 F 0.6224 0.1144 0.2632 138 I 0.4655 0.1202 0.4143 139 E 0.2497 0.1618 0.5885 140 A 0.1127 0.1121 0.7752 141 S 0.0637 0.0636 0.8727 142 S 0.0600 0.0566 0.8834 143 T 0.0058 0.9072 0.0870 144 E 0.0054 0.9292 0.0653 145 D 0.0052 0.9398 0.0551 146 A 0.0048 0.9523 0.0429 147 A 0.0049 0.9471 0.0479 148 F 0.0048 0.9438 0.0514 149 L 0.0050 0.9448 0.0502 150 K 0.0048 0.9538 0.0414 151 A 0.0048 0.9527 0.0425 152 I 0.0049 0.9516 0.0435 153 A 0.0053 0.9416 0.0531 154 S 0.0053 0.9130 0.0817 155 T 0.0079 0.8082 0.1840 156 L 0.0346 0.5013 0.4641 157 S 0.0382 0.1108 0.8509 158 N 0.0780 0.0972 0.8248 159 R 0.3611 0.0491 0.5898 160 V 0.6965 0.0154 0.2882 161 Y 0.8242 0.0109 0.1649 162 D 0.8253 0.0079 0.1668 163 A 0.5444 0.0111 0.4445 164 D 0.1808 0.0212 0.7980 165 S 0.0154 0.3889 0.5957 166 E 0.0166 0.4327 0.5507 167 Q 0.0299 0.5937 0.3764 168 R 0.0449 0.6530 0.3021 169 K 0.0786 0.7118 0.2096 170 S 0.1385 0.7394 0.1221 171 L 0.1618 0.7549 0.0833 172 H 0.1545 0.7732 0.0723 173 L 0.1177 0.8143 0.0680 174 A 0.0775 0.8515 0.0710 175 A 0.0595 0.8482 0.0923 176 V 0.0407 0.7975 0.1618 177 F 0.0300 0.7295 0.2405 178 T 0.0150 0.8291 0.1559 179 C 0.0059 0.9188 0.0754 180 N 0.0049 0.9438 0.0514 181 F 0.0047 0.9542 0.0410 182 T 0.0047 0.9588 0.0365 183 N 0.0047 0.9604 0.0349 184 H 0.0047 0.9600 0.0353 185 M 0.0047 0.9596 0.0358 186 Y 0.0047 0.9603 0.0350 187 A 0.0047 0.9592 0.0361 188 L 0.0047 0.9570 0.0383 189 A 0.0047 0.9567 0.0386 190 A 0.0048 0.9565 0.0387 191 E 0.0048 0.9541 0.0411 192 L 0.0048 0.9544 0.0408 193 L 0.0049 0.9510 0.0441 194 K 0.0053 0.9370 0.0577 195 K 0.0069 0.8518 0.1413 196 Y 0.0440 0.3563 0.5997 197 N 0.0396 0.0257 0.9348 198 L 0.0574 0.0110 0.9316 199 P 0.0642 0.0123 0.9236 200 F 0.0084 0.8373 0.1543 201 D 0.0055 0.8757 0.1188 202 V 0.0063 0.8999 0.0938 203 M 0.0063 0.9101 0.0835 204 L 0.0055 0.9361 0.0583 205 P 0.0048 0.9448 0.0504 206 L 0.0050 0.9452 0.0498 207 I 0.0048 0.9476 0.0476 208 D 0.0049 0.9423 0.0528 209 E 0.0057 0.9256 0.0687 210 T 0.0060 0.9158 0.0782 211 A 0.0065 0.8952 0.0983 212 R 0.0081 0.8648 0.1271 213 K 0.0086 0.7518 0.2396 214 V 0.0102 0.7863 0.2035 215 H 0.0132 0.8207 0.1662 216 E 0.0137 0.7728 0.2135 217 L 0.0334 0.6412 0.3254 218 E 0.0510 0.4001 0.5489 219 P 0.0431 0.4281 0.5288 220 K 0.0426 0.4627 0.4947 221 T 0.0521 0.4030 0.5449 222 A 0.0533 0.3315 0.6152 223 Q 0.0745 0.2357 0.6898 224 T 0.0811 0.1629 0.7560 225 G 0.0564 0.2883 0.6554 226 P 0.0698 0.4149 0.5153 227 A 0.1271 0.5004 0.3725 228 I 0.1166 0.5428 0.3406 229 R 0.0581 0.5132 0.4286 230 Y 0.0341 0.3106 0.6553 231 D 0.0420 0.3433 0.6147 232 E 0.0078 0.8876 0.1046 233 N 0.0055 0.9354 0.0592 234 V 0.0048 0.9489 0.0463 235 I 0.0047 0.9571 0.0382 236 G 0.0047 0.9598 0.0355 237 N 0.0047 0.9588 0.0365 238 H 0.0047 0.9578 0.0375 239 L 0.0047 0.9546 0.0406 240 R 0.0050 0.9404 0.0546 241 M 0.0057 0.8983 0.0960 242 L 0.0128 0.7935 0.1937 243 A 0.0142 0.6310 0.3548 244 D 0.0222 0.4544 0.5233 245 D 0.0382 0.3265 0.6353 246 P 0.0516 0.2764 0.6720 247 A 0.0093 0.7177 0.2730 248 M 0.0093 0.7960 0.1948 249 Q 0.0128 0.8519 0.1354 250 R 0.0218 0.8832 0.0950 251 L 0.0269 0.8982 0.0749 252 Y 0.0334 0.8957 0.0708 253 E 0.0393 0.8886 0.0721 254 L 0.0312 0.8898 0.0790 255 L 0.0363 0.8368 0.1269 256 S 0.0549 0.6741 0.2710 257 R 0.0733 0.5460 0.3807 258 S 0.1035 0.3967 0.4998 259 I 0.0889 0.3328 0.5783 260 H 0.0867 0.2203 0.6930 261 E 0.1187 0.1987 0.6826 262 R 0.1267 0.1326 0.7407 263 Q 0.0499 0.0586 0.8915