# This file is the result of combining several RDB files, specifically # T0457.t04.dssp-ebghstl.rdb (weight 1.53986) # T0457.t04.stride-ebghtl.rdb (weight 1.24869) # T0457.t04.str2.rdb (weight 1.54758) # T0457.t04.alpha.rdb (weight 0.659012) # T0457.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0457.t2k.stride-ebghtl.rdb (weight 1.24869) # T0457.t2k.str2.rdb (weight 1.54758) # T0457.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 T0457.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0457 # 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 T0457.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 1674 # # ============================================ # Comments from T0457.t04.stride-ebghtl.rdb # ============================================ # TARGET T0457 # 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 T0457.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 1674 # # ============================================ # Comments from T0457.t04.str2.rdb # ============================================ # TARGET T0457 # 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 T0457.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 1674 # # ============================================ # Comments from T0457.t04.alpha.rdb # ============================================ # TARGET T0457 # 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 T0457.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 1674 # # ============================================ # Comments from T0457.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0457 # 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 T0457.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 563 # # ============================================ # Comments from T0457.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0457 # 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 T0457.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 563 # # ============================================ # Comments from T0457.t2k.str2.rdb # ============================================ # TARGET T0457 # 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 T0457.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 563 # # ============================================ # Comments from T0457.t2k.alpha.rdb # ============================================ # TARGET T0457 # 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 T0457.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 563 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0527 0.2478 0.6995 2 V 0.1051 0.5811 0.3138 3 E 0.1214 0.6524 0.2262 4 I 0.0778 0.7067 0.2155 5 F 0.0205 0.8614 0.1181 6 N 0.0098 0.9107 0.0795 7 E 0.0079 0.9315 0.0607 8 I 0.0068 0.9418 0.0513 9 M 0.0065 0.9444 0.0491 10 Q 0.0061 0.9414 0.0526 11 R 0.0060 0.9303 0.0638 12 V 0.0112 0.9044 0.0844 13 K 0.0106 0.7922 0.1972 14 E 0.0231 0.5125 0.4644 15 A 0.0787 0.1044 0.8169 16 E 0.0305 0.0588 0.9107 17 T 0.2720 0.0197 0.7084 18 I 0.9164 0.0034 0.0803 19 I 0.9317 0.0032 0.0651 20 I 0.9270 0.0034 0.0696 21 H 0.8843 0.0106 0.1051 22 R 0.6904 0.0086 0.3010 23 H 0.4196 0.0205 0.5599 24 V 0.1933 0.0512 0.7555 25 R 0.1230 0.0350 0.8419 26 P 0.0908 0.0827 0.8265 27 D 0.0941 0.0784 0.8275 28 P 0.0175 0.4206 0.5620 29 D 0.0156 0.5330 0.4513 30 A 0.0125 0.8482 0.1393 31 Y 0.0063 0.9249 0.0689 32 G 0.0050 0.9449 0.0501 33 S 0.0047 0.9528 0.0425 34 Q 0.0047 0.9589 0.0364 35 L 0.0047 0.9604 0.0349 36 G 0.0047 0.9602 0.0351 37 L 0.0047 0.9588 0.0366 38 K 0.0047 0.9566 0.0387 39 L 0.0049 0.9503 0.0448 40 Y 0.0051 0.9405 0.0545 41 L 0.0056 0.9204 0.0739 42 E 0.0063 0.8503 0.1434 43 R 0.0107 0.7111 0.2782 44 K 0.0463 0.3505 0.6031 45 F 0.0532 0.0556 0.8913 46 P 0.1107 0.0526 0.8367 47 E 0.4189 0.0429 0.5382 48 K 0.6970 0.0210 0.2820 49 N 0.8323 0.0106 0.1571 50 I 0.8651 0.0072 0.1277 51 Y 0.8352 0.0091 0.1557 52 A 0.6458 0.0172 0.3370 53 T 0.2256 0.0560 0.7184 54 G 0.0721 0.0716 0.8563 55 E 0.0727 0.1030 0.8243 56 A 0.0931 0.1209 0.7860 57 E 0.0729 0.3037 0.6234 58 P 0.0518 0.4712 0.4770 59 S 0.0348 0.6354 0.3298 60 L 0.0296 0.7070 0.2634 61 S 0.0313 0.6655 0.3032 62 F 0.0404 0.5961 0.3635 63 I 0.0840 0.3575 0.5585 64 G 0.0611 0.3249 0.6139 65 D 0.0734 0.3061 0.6205 66 L 0.0665 0.4373 0.4963 67 D 0.0788 0.4698 0.4514 68 E 0.1156 0.4966 0.3878 69 I 0.1672 0.4077 0.4252 70 D 0.1713 0.3465 0.4822 71 D 0.1343 0.2735 0.5922 72 S 0.1172 0.1970 0.6858 73 V 0.0961 0.2124 0.6914 74 Y 0.0976 0.1776 0.7248 75 S 0.1117 0.1526 0.7357 76 D 0.1365 0.0625 0.8010 77 A 0.2603 0.0378 0.7020 78 L 0.8851 0.0037 0.1112 79 V 0.9262 0.0036 0.0702 80 I 0.9317 0.0033 0.0650 81 V 0.9267 0.0032 0.0702 82 C 0.8666 0.0078 0.1255 83 D 0.5352 0.0103 0.4545 84 T 0.0914 0.0940 0.8146 85 A 0.0512 0.1262 0.8226 86 N 0.0721 0.1355 0.7924 87 A 0.0221 0.5220 0.4559 88 P 0.0290 0.5694 0.4017 89 R 0.0409 0.5761 0.3830 90 I 0.0608 0.4832 0.4560 91 D 0.0496 0.4678 0.4826 92 D 0.0378 0.5758 0.3865 93 Q 0.0393 0.6031 0.3576 94 R 0.0556 0.5246 0.4198 95 Y 0.0575 0.4656 0.4768 96 L 0.0515 0.3872 0.5613 97 N 0.0597 0.2700 0.6703 98 G 0.1149 0.0984 0.7867 99 Q 0.2207 0.0365 0.7428 100 S 0.6123 0.0099 0.3778 101 L 0.8853 0.0051 0.1096 102 I 0.9247 0.0034 0.0720 103 K 0.9242 0.0033 0.0725 104 I 0.8982 0.0050 0.0968 105 D 0.7280 0.0096 0.2625 106 H 0.2839 0.0329 0.6832 107 H 0.1389 0.0307 0.8304 108 P 0.0699 0.1295 0.8006 109 A 0.0626 0.1478 0.7896 110 T 0.0572 0.2390 0.7038 111 D 0.0455 0.2734 0.6810 112 Q 0.0578 0.2723 0.6699 113 Y 0.1142 0.2086 0.6773 114 G 0.1355 0.1574 0.7071 115 D 0.2141 0.1317 0.6542 116 V 0.4022 0.0949 0.5030 117 N 0.5389 0.0622 0.3989 118 F 0.6616 0.0419 0.2966 119 V 0.5781 0.0423 0.3796 120 N 0.2808 0.0422 0.6770 121 T 0.0776 0.1436 0.7788 122 E 0.0478 0.1364 0.8158 123 A 0.0698 0.3027 0.6275 124 S 0.0358 0.5637 0.4005 125 S 0.0189 0.8315 0.1496 126 T 0.0063 0.9323 0.0614 127 S 0.0047 0.9568 0.0384 128 E 0.0047 0.9597 0.0356 129 I 0.0047 0.9608 0.0345 130 I 0.0047 0.9601 0.0352 131 F 0.0047 0.9605 0.0348 132 D 0.0047 0.9584 0.0369 133 F 0.0048 0.9540 0.0413 134 I 0.0049 0.9405 0.0545 135 S 0.0051 0.9107 0.0842 136 H 0.0055 0.8533 0.1412 137 F 0.0078 0.7703 0.2219 138 N 0.0114 0.6629 0.3257 139 D 0.0355 0.4043 0.5602 140 L 0.0309 0.1277 0.8414 141 S 0.0665 0.0575 0.8760 142 I 0.1031 0.0349 0.8621 143 I 0.0773 0.0356 0.8871 144 D 0.0582 0.0264 0.9154 145 E 0.0067 0.8661 0.1272 146 H 0.0055 0.9154 0.0790 147 V 0.0049 0.9465 0.0486 148 A 0.0048 0.9537 0.0415 149 R 0.0060 0.9503 0.0437 150 V 0.0111 0.9414 0.0475 151 L 0.0145 0.9373 0.0482 152 Y 0.0221 0.9248 0.0531 153 L 0.0373 0.8881 0.0746 154 G 0.0794 0.8076 0.1130 155 I 0.2518 0.6093 0.1388 156 V 0.3212 0.4344 0.2444 157 G 0.3524 0.2382 0.4094 158 D 0.2964 0.1176 0.5860 159 T 0.1579 0.1491 0.6930 160 G 0.1025 0.1240 0.7735 161 R 0.2247 0.1283 0.6470 162 F 0.4453 0.0568 0.4979 163 L 0.4502 0.0515 0.4982 164 F 0.2821 0.0478 0.6701 165 S 0.0555 0.1204 0.8241 166 N 0.0488 0.0700 0.8812 167 T 0.1040 0.0480 0.8480 168 S 0.0623 0.0436 0.8941 169 P 0.0074 0.9128 0.0799 170 H 0.0061 0.9350 0.0589 171 T 0.0049 0.9524 0.0428 172 M 0.0047 0.9591 0.0362 173 E 0.0050 0.9593 0.0357 174 V 0.0047 0.9597 0.0356 175 A 0.0047 0.9586 0.0367 176 S 0.0047 0.9563 0.0391 177 Q 0.0047 0.9508 0.0445 178 L 0.0050 0.9424 0.0526 179 L 0.0065 0.9191 0.0743 180 A 0.0085 0.8175 0.1739 181 Y 0.0412 0.3448 0.6140 182 P 0.0401 0.0470 0.9130 183 F 0.0653 0.0329 0.9018 184 N 0.0846 0.0281 0.8873 185 H 0.0068 0.8977 0.0955 186 N 0.0058 0.9357 0.0585 187 A 0.0053 0.9483 0.0464 188 E 0.0058 0.9465 0.0478 189 L 0.0064 0.9302 0.0634 190 N 0.0079 0.8855 0.1066 191 K 0.0119 0.8010 0.1871 192 M 0.0353 0.6009 0.3638 193 S 0.0263 0.4114 0.5623 194 E 0.0291 0.2407 0.7302 195 K 0.0599 0.0979 0.8423 196 D 0.0559 0.0782 0.8659 197 P 0.0076 0.8774 0.1149 198 K 0.0060 0.9005 0.0935 199 L 0.0057 0.9270 0.0674 200 M 0.0057 0.9370 0.0573 201 P 0.0060 0.9360 0.0580 202 F 0.0057 0.9371 0.0572 203 Q 0.0056 0.9446 0.0499 204 G 0.0051 0.9436 0.0513 205 Y 0.0058 0.9389 0.0553 206 V 0.0067 0.9265 0.0668 207 L 0.0098 0.9032 0.0870 208 Q 0.0136 0.8190 0.1674 209 N 0.0232 0.6155 0.3613 210 F 0.1513 0.4073 0.4414 211 E 0.4050 0.2943 0.3007 212 L 0.5428 0.2089 0.2482 213 S 0.3944 0.1654 0.4402 214 D 0.2006 0.2052 0.5942 215 S 0.1288 0.1146 0.7566 216 H 0.3367 0.0593 0.6040 217 E 0.7007 0.0268 0.2725 218 Y 0.8782 0.0116 0.1103 219 C 0.8908 0.0133 0.0959 220 Q 0.9055 0.0107 0.0838 221 I 0.8903 0.0134 0.0963 222 K 0.8809 0.0144 0.1048 223 I 0.8086 0.0232 0.1682 224 T 0.5342 0.0555 0.4103 225 N 0.0593 0.7389 0.2018 226 D 0.0263 0.8149 0.1589 227 V 0.0199 0.8399 0.1402 228 L 0.0206 0.8494 0.1300 229 K 0.0242 0.8050 0.1709 230 Q 0.0302 0.6950 0.2748 231 F 0.0744 0.4238 0.5018 232 D 0.0840 0.1842 0.7318 233 I 0.0892 0.1302 0.7806 234 Q 0.0768 0.1093 0.8139 235 P 0.0261 0.6806 0.2932 236 N 0.0124 0.7763 0.2113 237 E 0.0144 0.8265 0.1590 238 A 0.0052 0.9272 0.0676 239 S 0.0049 0.9409 0.0542 240 Q 0.0049 0.9429 0.0523 241 F 0.0048 0.9481 0.0471 242 V 0.0048 0.9474 0.0478 243 N 0.0050 0.9364 0.0585 244 T 0.0056 0.9219 0.0725 245 V 0.0086 0.8981 0.0933 246 A 0.0113 0.8275 0.1611 247 D 0.0223 0.6402 0.3375 248 I 0.0560 0.4729 0.4711 249 S 0.0354 0.2262 0.7384 250 G 0.0390 0.0526 0.9084 251 L 0.2369 0.0101 0.7531 252 K 0.5719 0.0083 0.4198 253 I 0.8987 0.0034 0.0979 254 W 0.9260 0.0032 0.0708 255 M 0.9294 0.0032 0.0674 256 F 0.9294 0.0032 0.0674 257 G 0.9244 0.0033 0.0723 258 V 0.9087 0.0052 0.0861 259 D 0.8954 0.0072 0.0974 260 E 0.7534 0.0162 0.2304 261 G 0.0710 0.0267 0.9024 262 D 0.0373 0.0644 0.8984 263 Q 0.7469 0.0104 0.2427 264 I 0.9222 0.0033 0.0746 265 R 0.9277 0.0036 0.0687 266 C 0.9257 0.0036 0.0707 267 R 0.9094 0.0051 0.0854 268 I 0.8775 0.0070 0.1154 269 R 0.7367 0.0174 0.2459 270 S 0.4297 0.0282 0.5420 271 K 0.1186 0.0790 0.8024 272 G 0.0900 0.0313 0.8786 273 I 0.1726 0.0275 0.7999 274 T 0.2435 0.0299 0.7265 275 I 0.0079 0.8874 0.1047 276 N 0.0050 0.9404 0.0546 277 D 0.0047 0.9544 0.0409 278 V 0.0053 0.9532 0.0415 279 A 0.0054 0.9392 0.0553 280 N 0.0064 0.8735 0.1201 281 Q 0.0103 0.8048 0.1850 282 F 0.0680 0.4182 0.5138 283 G 0.0596 0.0835 0.8569 284 G 0.0572 0.0661 0.8767 285 G 0.0751 0.1280 0.7968 286 G 0.1099 0.1690 0.7211 287 H 0.1438 0.2374 0.6188 288 P 0.1096 0.4320 0.4583 289 N 0.1161 0.3320 0.5518 290 A 0.1556 0.3027 0.5418 291 S 0.1646 0.1693 0.6662 292 G 0.2261 0.0937 0.6802 293 V 0.4841 0.0482 0.4677 294 S 0.6493 0.0278 0.3229 295 V 0.5061 0.0320 0.4619 296 Y 0.1396 0.0813 0.7791 297 S 0.0672 0.0878 0.8450 298 W 0.0898 0.1802 0.7300 299 D 0.0847 0.3001 0.6152 300 E 0.0087 0.8614 0.1300 301 F 0.0058 0.9150 0.0793 302 E 0.0053 0.9363 0.0583 303 E 0.0054 0.9399 0.0547 304 L 0.0054 0.9482 0.0464 305 A 0.0053 0.9479 0.0468 306 Q 0.0054 0.9473 0.0473 307 A 0.0049 0.9483 0.0468 308 L 0.0048 0.9515 0.0436 309 R 0.0049 0.9474 0.0477 310 Q 0.0049 0.9463 0.0488 311 K 0.0050 0.9405 0.0545 312 L 0.0058 0.9216 0.0726 313 L 0.0079 0.8761 0.1160 314 E 0.0148 0.7859 0.1993 315 H 0.0502 0.5372 0.4126 316 H 0.0447 0.3390 0.6163 317 H 0.0408 0.3106 0.6486 318 H 0.0512 0.2186 0.7302 319 H 0.0572 0.1258 0.8170 320 H 0.0471 0.0425 0.9105