# This file is the result of combining several RDB files, specifically # T0376.t06.dssp-ebghstl.rdb (weight 1.53986) # T0376.t06.stride-ebghtl.rdb (weight 1.24869) # T0376.t06.str2.rdb (weight 1.54758) # T0376.t06.alpha.rdb (weight 0.659012) # T0376.t04.dssp-ebghstl.rdb (weight 1.53986) # T0376.t04.stride-ebghtl.rdb (weight 1.24869) # T0376.t04.str2.rdb (weight 1.54758) # T0376.t04.alpha.rdb (weight 0.659012) # T0376.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0376.t2k.stride-ebghtl.rdb (weight 1.24869) # T0376.t2k.str2.rdb (weight 1.54758) # T0376.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 T0376.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0376 # 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 T0376.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 922 # # ============================================ # Comments from T0376.t06.stride-ebghtl.rdb # ============================================ # TARGET T0376 # 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 T0376.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 922 # # ============================================ # Comments from T0376.t06.str2.rdb # ============================================ # TARGET T0376 # 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 T0376.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 922 # # ============================================ # Comments from T0376.t06.alpha.rdb # ============================================ # TARGET T0376 # 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 T0376.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 922 # # ============================================ # Comments from T0376.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0376 # 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 T0376.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 938 # # ============================================ # Comments from T0376.t04.stride-ebghtl.rdb # ============================================ # TARGET T0376 # 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 T0376.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 938 # # ============================================ # Comments from T0376.t04.str2.rdb # ============================================ # TARGET T0376 # 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 T0376.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 938 # # ============================================ # Comments from T0376.t04.alpha.rdb # ============================================ # TARGET T0376 # 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 T0376.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 938 # # ============================================ # Comments from T0376.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0376 # 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 T0376.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 729 # # ============================================ # Comments from T0376.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0376 # 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 T0376.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 729 # # ============================================ # Comments from T0376.t2k.str2.rdb # ============================================ # TARGET T0376 # 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 T0376.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 729 # # ============================================ # Comments from T0376.t2k.alpha.rdb # ============================================ # TARGET T0376 # 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 T0376.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 729 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0716 0.0467 0.8817 2 T 0.1044 0.0704 0.8252 3 A 0.0995 0.1327 0.7677 4 S 0.0914 0.1515 0.7571 5 I 0.1540 0.1276 0.7183 6 F 0.2488 0.0658 0.6854 7 S 0.2079 0.0742 0.7180 8 G 0.4378 0.0396 0.5226 9 V 0.7061 0.0261 0.2679 10 I 0.7375 0.0205 0.2420 11 P 0.6741 0.0195 0.3063 12 A 0.5124 0.0365 0.4511 13 L 0.4708 0.0464 0.4828 14 M 0.4560 0.0449 0.4990 15 T 0.3782 0.0175 0.6043 16 P 0.3607 0.0213 0.6180 17 C 0.4315 0.0255 0.5430 18 R 0.0987 0.0263 0.8750 19 Q 0.0187 0.1175 0.8638 20 D 0.0484 0.0346 0.9169 21 R 0.0372 0.0373 0.9255 22 T 0.1630 0.0181 0.8189 23 P 0.6552 0.0105 0.3343 24 D 0.1896 0.0149 0.7955 25 F 0.0080 0.8949 0.0971 26 D 0.0050 0.9425 0.0524 27 A 0.0051 0.9493 0.0455 28 L 0.0048 0.9559 0.0394 29 V 0.0047 0.9580 0.0373 30 R 0.0047 0.9569 0.0384 31 K 0.0047 0.9571 0.0381 32 G 0.0047 0.9586 0.0367 33 K 0.0047 0.9593 0.0360 34 E 0.0047 0.9583 0.0370 35 L 0.0048 0.9574 0.0378 36 I 0.0049 0.9468 0.0483 37 A 0.0058 0.8756 0.1186 38 D 0.0387 0.3090 0.6524 39 G 0.0451 0.0200 0.9349 40 M 0.0935 0.0076 0.8989 41 S 0.2011 0.0386 0.7603 42 A 0.8997 0.0055 0.0948 43 V 0.9294 0.0035 0.0671 44 V 0.9245 0.0045 0.0710 45 Y 0.8958 0.0065 0.0977 46 C 0.5477 0.0226 0.4297 47 G 0.1318 0.0323 0.8360 48 S 0.1087 0.1339 0.7574 49 M 0.0757 0.1828 0.7415 50 G 0.0681 0.1971 0.7348 51 D 0.0921 0.2641 0.6438 52 W 0.1028 0.3173 0.5800 53 P 0.0829 0.3491 0.5680 54 L 0.1087 0.2052 0.6861 55 L 0.1024 0.0598 0.8378 56 T 0.0541 0.0380 0.9079 57 D 0.0050 0.9418 0.0532 58 E 0.0047 0.9548 0.0404 59 Q 0.0048 0.9560 0.0392 60 R 0.0047 0.9604 0.0349 61 M 0.0047 0.9599 0.0355 62 E 0.0047 0.9595 0.0358 63 G 0.0047 0.9591 0.0363 64 V 0.0047 0.9581 0.0371 65 E 0.0051 0.9540 0.0409 66 R 0.0053 0.9416 0.0532 67 L 0.0074 0.9241 0.0685 68 V 0.0136 0.8353 0.1511 69 K 0.0291 0.5232 0.4477 70 A 0.0304 0.1178 0.8518 71 G 0.0337 0.0588 0.9075 72 I 0.1694 0.0089 0.8217 73 P 0.5954 0.0054 0.3992 74 V 0.9022 0.0060 0.0919 75 I 0.9207 0.0044 0.0749 76 V 0.8729 0.0183 0.1088 77 G 0.7399 0.0175 0.2426 78 T 0.3613 0.0390 0.5997 79 G 0.1394 0.0581 0.8024 80 A 0.0800 0.1635 0.7565 81 V 0.0390 0.2859 0.6750 82 N 0.0456 0.2853 0.6691 83 T 0.0063 0.8385 0.1552 84 A 0.0048 0.9537 0.0416 85 S 0.0047 0.9556 0.0396 86 A 0.0047 0.9590 0.0363 87 V 0.0047 0.9604 0.0350 88 A 0.0047 0.9594 0.0359 89 H 0.0047 0.9564 0.0389 90 A 0.0048 0.9574 0.0378 91 V 0.0048 0.9551 0.0401 92 H 0.0048 0.9531 0.0421 93 A 0.0049 0.9496 0.0455 94 Q 0.0054 0.9402 0.0545 95 K 0.0063 0.8657 0.1280 96 V 0.0402 0.3756 0.5843 97 G 0.0533 0.0207 0.9260 98 A 0.0852 0.0100 0.9048 99 K 0.1663 0.0364 0.7973 100 G 0.9104 0.0046 0.0850 101 L 0.9269 0.0038 0.0693 102 M 0.9296 0.0035 0.0669 103 V 0.8937 0.0060 0.1003 104 I 0.5404 0.0086 0.4510 105 P 0.2355 0.0189 0.7456 106 R 0.1435 0.1650 0.6915 107 V 0.1901 0.2168 0.5931 108 L 0.1542 0.2073 0.6385 109 S 0.1023 0.1076 0.7901 110 R 0.0720 0.0989 0.8291 111 G 0.0842 0.0761 0.8397 112 S 0.1110 0.0463 0.8427 113 V 0.0854 0.0342 0.8804 114 I 0.0067 0.9145 0.0788 115 A 0.0049 0.9460 0.0491 116 A 0.0048 0.9507 0.0445 117 Q 0.0047 0.9566 0.0386 118 K 0.0047 0.9593 0.0360 119 A 0.0047 0.9575 0.0378 120 H 0.0047 0.9568 0.0385 121 F 0.0047 0.9592 0.0361 122 K 0.0047 0.9592 0.0361 123 A 0.0048 0.9552 0.0400 124 I 0.0050 0.9474 0.0477 125 L 0.0058 0.9235 0.0708 126 S 0.0070 0.8409 0.1522 127 A 0.0134 0.6594 0.3272 128 A 0.0525 0.3038 0.6437 129 P 0.0260 0.1685 0.8055 130 E 0.0473 0.1063 0.8464 131 I 0.1463 0.0197 0.8339 132 P 0.3824 0.0103 0.6073 133 A 0.9032 0.0039 0.0929 134 V 0.9283 0.0033 0.0685 135 I 0.9206 0.0041 0.0753 136 Y 0.8692 0.0107 0.1201 137 N 0.6100 0.0195 0.3705 138 S 0.2048 0.0221 0.7731 139 P 0.1075 0.1524 0.7401 140 Y 0.0760 0.2647 0.6593 141 Y 0.0796 0.3089 0.6115 142 G 0.1006 0.2109 0.6884 143 F 0.0891 0.1161 0.7948 144 A 0.1687 0.0597 0.7716 145 T 0.1971 0.0427 0.7602 146 R 0.1700 0.0531 0.7769 147 A 0.0660 0.0386 0.8954 148 D 0.0056 0.9327 0.0617 149 L 0.0049 0.9496 0.0456 150 F 0.0050 0.9529 0.0421 151 F 0.0048 0.9544 0.0408 152 A 0.0051 0.9488 0.0460 153 L 0.0056 0.9359 0.0585 154 R 0.0066 0.9077 0.0857 155 A 0.0171 0.7625 0.2204 156 E 0.0189 0.4563 0.5248 157 H 0.0739 0.0929 0.8333 158 K 0.0246 0.1374 0.8380 159 N 0.0706 0.0738 0.8556 160 L 0.6668 0.0247 0.3085 161 V 0.7952 0.0325 0.1723 162 G 0.8634 0.0148 0.1218 163 F 0.8590 0.0227 0.1183 164 K 0.7258 0.0507 0.2235 165 E 0.4733 0.0821 0.4446 166 F 0.1872 0.1039 0.7089 167 G 0.0832 0.0646 0.8521 168 G 0.0600 0.0531 0.8868 169 P 0.0750 0.0823 0.8427 170 A 0.0081 0.8864 0.1054 171 D 0.0064 0.9262 0.0673 172 M 0.0053 0.9406 0.0541 173 R 0.0047 0.9544 0.0408 174 Y 0.0056 0.9532 0.0412 175 A 0.0053 0.9509 0.0438 176 A 0.0059 0.9496 0.0445 177 E 0.0071 0.9419 0.0510 178 N 0.0070 0.9137 0.0793 179 I 0.0100 0.8377 0.1523 180 T 0.0344 0.6751 0.2905 181 S 0.0304 0.4291 0.5405 182 R 0.0291 0.2878 0.6831 183 D 0.0589 0.1913 0.7498 184 D 0.0613 0.1617 0.7770 185 E 0.0677 0.1647 0.7676 186 V 0.2167 0.1071 0.6762 187 T 0.6352 0.0264 0.3384 188 L 0.8184 0.0154 0.1663 189 M 0.8699 0.0119 0.1182 190 I 0.8017 0.0167 0.1816 191 G 0.5012 0.0302 0.4685 192 V 0.1253 0.0897 0.7850 193 D 0.0636 0.2013 0.7351 194 T 0.0321 0.5916 0.3763 195 A 0.0116 0.8227 0.1657 196 V 0.0162 0.8285 0.1553 197 V 0.0139 0.8596 0.1266 198 H 0.0081 0.9174 0.0744 199 G 0.0063 0.9376 0.0561 200 F 0.0060 0.9416 0.0524 201 V 0.0060 0.9383 0.0556 202 N 0.0083 0.8915 0.1002 203 C 0.0371 0.5826 0.3803 204 G 0.0436 0.1418 0.8146 205 A 0.0819 0.0642 0.8539 206 T 0.1287 0.0970 0.7743 207 G 0.5629 0.1448 0.2923 208 A 0.7216 0.1500 0.1284 209 I 0.7510 0.1358 0.1132 210 T 0.6649 0.1589 0.1762 211 G 0.3639 0.2385 0.3976 212 I 0.1655 0.4130 0.4215 213 G 0.0881 0.5245 0.3875 214 N 0.0731 0.4630 0.4639 215 V 0.0852 0.3453 0.5695 216 L 0.0679 0.2101 0.7220 217 P 0.0104 0.8041 0.1855 218 K 0.0052 0.9301 0.0647 219 E 0.0049 0.9448 0.0503 220 V 0.0048 0.9550 0.0402 221 I 0.0047 0.9590 0.0364 222 H 0.0049 0.9575 0.0376 223 L 0.0047 0.9569 0.0384 224 C 0.0047 0.9571 0.0382 225 K 0.0047 0.9554 0.0399 226 L 0.0048 0.9501 0.0451 227 S 0.0053 0.9219 0.0728 228 Q 0.0072 0.8183 0.1746 229 A 0.0448 0.3327 0.6226 230 A 0.0407 0.0907 0.8686 231 A 0.0572 0.0928 0.8500 232 K 0.0130 0.6878 0.2992 233 G 0.0077 0.8710 0.1213 234 D 0.0055 0.9165 0.0780 235 A 0.0052 0.9350 0.0598 236 D 0.0060 0.9416 0.0524 237 A 0.0053 0.9399 0.0548 238 R 0.0057 0.9299 0.0644 239 A 0.0063 0.9214 0.0723 240 R 0.0066 0.8818 0.1115 241 A 0.0089 0.8181 0.1730 242 L 0.0118 0.7846 0.2036 243 E 0.0209 0.7856 0.1935 244 L 0.0090 0.8683 0.1228 245 E 0.0074 0.9045 0.0881 246 Q 0.0087 0.9079 0.0834 247 A 0.0093 0.9013 0.0894 248 L 0.0110 0.8847 0.1044 249 A 0.0167 0.8268 0.1565 250 V 0.0316 0.7074 0.2610 251 L 0.0385 0.5882 0.3733 252 S 0.0413 0.3866 0.5721 253 S 0.0356 0.2216 0.7428 254 F 0.0484 0.2049 0.7466 255 D 0.0300 0.5947 0.3754 256 E 0.0154 0.8418 0.1428 257 G 0.0066 0.9324 0.0611 258 P 0.0050 0.9537 0.0413 259 D 0.0047 0.9578 0.0374 260 L 0.0047 0.9600 0.0353 261 V 0.0047 0.9599 0.0354 262 L 0.0048 0.9572 0.0380 263 Y 0.0051 0.9418 0.0532 264 F 0.0077 0.9030 0.0893 265 K 0.0421 0.5585 0.3995 266 Y 0.0396 0.1191 0.8413 267 M 0.0850 0.0887 0.8263 268 M 0.1652 0.1126 0.7222 269 V 0.1123 0.1166 0.7711 270 L 0.0872 0.1116 0.8013 271 K 0.0986 0.0882 0.8132 272 G 0.1440 0.0799 0.7761 273 D 0.1390 0.0697 0.7913 274 K 0.1056 0.0754 0.8190 275 E 0.0940 0.1065 0.7995 276 Y 0.1281 0.1357 0.7362 277 T 0.1060 0.1108 0.7832 278 L 0.0969 0.0604 0.8427 279 H 0.0700 0.0327 0.8973 280 F 0.0493 0.0366 0.9140 281 N 0.0067 0.8888 0.1044 282 E 0.0052 0.9214 0.0734 283 T 0.0061 0.9294 0.0645 284 D 0.0048 0.9489 0.0463 285 A 0.0050 0.9469 0.0480 286 L 0.0049 0.9476 0.0475 287 T 0.0048 0.9517 0.0435 288 D 0.0047 0.9565 0.0387 289 S 0.0047 0.9548 0.0404 290 Q 0.0048 0.9509 0.0443 291 R 0.0049 0.9423 0.0529 292 G 0.0050 0.9139 0.0811 293 Y 0.0055 0.8758 0.1187 294 V 0.0060 0.8950 0.0990 295 E 0.0052 0.9202 0.0746 296 A 0.0049 0.9360 0.0591 297 Q 0.0050 0.9431 0.0519 298 F 0.0053 0.9491 0.0457 299 K 0.0055 0.9421 0.0524 300 L 0.0067 0.9224 0.0709 301 F 0.0086 0.9188 0.0726 302 N 0.0093 0.9102 0.0805 303 S 0.0118 0.9008 0.0874 304 W 0.0240 0.8692 0.1068 305 Y 0.0187 0.8594 0.1219 306 A 0.0153 0.8187 0.1660 307 D 0.0269 0.6439 0.3292 308 W 0.0142 0.6534 0.3324 309 S 0.0196 0.6045 0.3759 310 K 0.0232 0.4796 0.4972 311 L 0.0780 0.2002 0.7218 312 P 0.0358 0.2140 0.7502 313 G 0.0631 0.1917 0.7453 314 A 0.2460 0.3846 0.3693 315 V 0.4296 0.3522 0.2183 316 Q 0.4603 0.3424 0.1973 317 T 0.3940 0.3738 0.2322 318 C 0.2352 0.5029 0.2619 319 K 0.1728 0.4933 0.3339 320 A 0.1107 0.4334 0.4558 321 A 0.0320 0.2275 0.7405