# This file is the result of combining several RDB files, specifically # T0441.t04.dssp-ebghstl.rdb (weight 1.53986) # T0441.t04.stride-ebghtl.rdb (weight 1.24869) # T0441.t04.str2.rdb (weight 1.54758) # T0441.t04.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 T0441.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0441 # 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 T0441.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 215.306 # # ============================================ # Comments from T0441.t04.stride-ebghtl.rdb # ============================================ # TARGET T0441 # 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 T0441.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 215.306 # # ============================================ # Comments from T0441.t04.str2.rdb # ============================================ # TARGET T0441 # 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 T0441.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 215.306 # # ============================================ # Comments from T0441.t04.alpha.rdb # ============================================ # TARGET T0441 # 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 T0441.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 215.306 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0648 0.0429 0.8924 2 S 0.0755 0.0538 0.8708 3 E 0.0759 0.0711 0.8530 4 P 0.0620 0.1425 0.7955 5 R 0.0820 0.2365 0.6816 6 K 0.1061 0.2339 0.6600 7 R 0.1160 0.2361 0.6479 8 R 0.0967 0.2085 0.6948 9 S 0.0687 0.1790 0.7523 10 T 0.0668 0.1190 0.8142 11 G 0.0588 0.0714 0.8698 12 N 0.1289 0.0372 0.8339 13 V 0.2370 0.0120 0.7510 14 T 0.1428 0.0172 0.8400 15 L 0.0048 0.9515 0.0437 16 A 0.0047 0.9593 0.0361 17 D 0.0047 0.9607 0.0347 18 V 0.0046 0.9613 0.0340 19 A 0.0047 0.9593 0.0360 20 K 0.0049 0.9504 0.0447 21 Q 0.0059 0.9176 0.0765 22 A 0.0464 0.4456 0.5079 23 G 0.0328 0.0484 0.9187 24 V 0.0689 0.0441 0.8870 25 G 0.1135 0.0762 0.8103 26 T 0.0949 0.4519 0.4532 27 M 0.1661 0.3948 0.4391 28 T 0.2013 0.4550 0.3437 29 V 0.0899 0.7476 0.1625 30 S 0.0740 0.7869 0.1391 31 R 0.0693 0.8128 0.1179 32 A 0.0779 0.7655 0.1566 33 L 0.1046 0.6079 0.2875 34 R 0.0651 0.3318 0.6030 35 T 0.0585 0.0435 0.8980 36 P 0.0205 0.2924 0.6871 37 E 0.0145 0.4181 0.5673 38 L 0.0438 0.3874 0.5688 39 V 0.0970 0.1110 0.7920 40 S 0.0556 0.0815 0.8628 41 D 0.0048 0.9502 0.0450 42 K 0.0047 0.9580 0.0373 43 L 0.0048 0.9572 0.0380 44 R 0.0047 0.9610 0.0344 45 E 0.0046 0.9617 0.0337 46 K 0.0046 0.9617 0.0337 47 I 0.0046 0.9612 0.0342 48 Q 0.0046 0.9615 0.0339 49 Q 0.0046 0.9612 0.0342 50 V 0.0046 0.9611 0.0343 51 V 0.0047 0.9601 0.0352 52 D 0.0049 0.9522 0.0429 53 E 0.0064 0.9061 0.0875 54 L 0.0450 0.4065 0.5485 55 G 0.0398 0.0272 0.9330 56 Y 0.0678 0.0222 0.9100 57 I 0.1064 0.0292 0.8645 58 P 0.1035 0.0920 0.8045 59 N 0.0739 0.2249 0.7012 60 K 0.0092 0.8803 0.1105 61 A 0.0064 0.9167 0.0769 62 A 0.0061 0.9293 0.0646 63 G 0.0055 0.9378 0.0567 64 A 0.0063 0.9166 0.0771 65 L 0.0071 0.8729 0.1199 66 A 0.0117 0.7958 0.1925 67 S 0.0412 0.4781 0.4807 68 A 0.0340 0.2193 0.7467 69 E 0.0714 0.1275 0.8011 70 S 0.1825 0.0537 0.7638 71 Y 0.3244 0.0459 0.6297 72 S 0.7721 0.0058 0.2221 73 I 0.9186 0.0034 0.0780 74 A 0.9314 0.0033 0.0653 75 L 0.9292 0.0034 0.0675 76 I 0.9033 0.0046 0.0921 77 I 0.7002 0.0090 0.2908 78 P 0.2947 0.0638 0.6415 79 S 0.1309 0.0820 0.7871 80 L 0.0618 0.2321 0.7061 81 F 0.0533 0.1757 0.7710 82 E 0.0597 0.1175 0.8227 83 K 0.0153 0.7005 0.2842 84 A 0.0205 0.7445 0.2350 85 C 0.0126 0.8710 0.1164 86 A 0.0068 0.8970 0.0963 87 H 0.0074 0.8751 0.1175 88 F 0.0079 0.8855 0.1067 89 L 0.0051 0.9402 0.0547 90 P 0.0047 0.9512 0.0441 91 S 0.0047 0.9571 0.0383 92 F 0.0047 0.9588 0.0365 93 Q 0.0047 0.9611 0.0342 94 Q 0.0046 0.9617 0.0337 95 A 0.0047 0.9615 0.0339 96 L 0.0047 0.9602 0.0352 97 N 0.0048 0.9473 0.0479 98 K 0.0056 0.8994 0.0951 99 A 0.0422 0.3172 0.6406 100 G 0.0412 0.0152 0.9436 101 Y 0.1252 0.0070 0.8678 102 Q 0.7385 0.0045 0.2570 103 L 0.9237 0.0032 0.0731 104 L 0.9307 0.0033 0.0660 105 L 0.9217 0.0041 0.0742 106 G 0.8169 0.0069 0.1763 107 Y 0.3878 0.0151 0.5971 108 S 0.1241 0.0463 0.8296 109 D 0.0606 0.0837 0.8558 110 Y 0.0535 0.0697 0.8768 111 S 0.0852 0.0519 0.8629 112 I 0.0056 0.9250 0.0694 113 E 0.0048 0.9540 0.0413 114 Q 0.0047 0.9566 0.0386 115 E 0.0047 0.9585 0.0368 116 E 0.0047 0.9604 0.0350 117 K 0.0047 0.9589 0.0363 118 L 0.0047 0.9580 0.0373 119 L 0.0047 0.9602 0.0352 120 S 0.0047 0.9599 0.0355 121 T 0.0047 0.9579 0.0374 122 F 0.0048 0.9534 0.0418 123 L 0.0051 0.9330 0.0620 124 E 0.0069 0.8459 0.1472 125 S 0.0282 0.5734 0.3984 126 R 0.0777 0.0225 0.8998 127 P 0.0701 0.0287 0.9012 128 A 0.1068 0.0450 0.8481 129 G 0.8787 0.0066 0.1147 130 V 0.9316 0.0033 0.0651 131 V 0.9325 0.0033 0.0643 132 L 0.9186 0.0040 0.0774 133 F 0.7000 0.0127 0.2873 134 G 0.2855 0.0246 0.6900 135 S 0.0970 0.0912 0.8118 136 E 0.0758 0.1381 0.7861 137 H 0.0705 0.0732 0.8563 138 S 0.0564 0.0853 0.8583 139 Q 0.0071 0.8716 0.1213 140 R 0.0057 0.9204 0.0739 141 T 0.0055 0.9352 0.0593 142 H 0.0047 0.9537 0.0416 143 Q 0.0047 0.9546 0.0407 144 L 0.0047 0.9562 0.0391 145 L 0.0048 0.9531 0.0421 146 E 0.0050 0.9406 0.0544 147 A 0.0064 0.8532 0.1404 148 S 0.0460 0.3541 0.5999 149 N 0.0422 0.0236 0.9341 150 T 0.0708 0.0083 0.9209 151 P 0.2439 0.0065 0.7496 152 V 0.9090 0.0037 0.0873 153 L 0.9272 0.0035 0.0693 154 E 0.9285 0.0035 0.0681 155 I 0.8751 0.0104 0.1145 156 A 0.5922 0.0179 0.3898 157 E 0.3239 0.0436 0.6326 158 L 0.2190 0.0997 0.6813 159 S 0.1364 0.1395 0.7241 160 S 0.0584 0.2321 0.7096 161 K 0.0709 0.2239 0.7051 162 A 0.1108 0.1824 0.7068 163 S 0.1717 0.1357 0.6926 164 Y 0.3343 0.1151 0.5506 165 L 0.3768 0.1160 0.5072 166 N 0.6027 0.0793 0.3180 167 I 0.6615 0.0622 0.2763 168 G 0.5520 0.0549 0.3931 169 V 0.3165 0.1180 0.5655 170 D 0.1587 0.0979 0.7434 171 H 0.0541 0.3767 0.5693 172 F 0.0066 0.8961 0.0973 173 E 0.0047 0.9500 0.0452 174 V 0.0047 0.9570 0.0383 175 G 0.0047 0.9596 0.0357 176 K 0.0046 0.9611 0.0342 177 A 0.0046 0.9612 0.0342 178 C 0.0047 0.9603 0.0351 179 T 0.0046 0.9612 0.0342 180 R 0.0046 0.9614 0.0340 181 H 0.0046 0.9611 0.0343 182 L 0.0047 0.9604 0.0349 183 I 0.0048 0.9532 0.0420 184 E 0.0062 0.9159 0.0779 185 Q 0.0382 0.4683 0.4934 186 G 0.0283 0.0586 0.9131 187 F 0.0763 0.0411 0.8826 188 K 0.2461 0.0833 0.6706 189 N 0.5952 0.0499 0.3549 190 V 0.8643 0.0251 0.1106 191 G 0.9077 0.0140 0.0783 192 F 0.9097 0.0142 0.0761 193 I 0.8523 0.0219 0.1258 194 G 0.4991 0.0258 0.4751 195 A 0.1794 0.0327 0.7879 196 R 0.0918 0.0873 0.8209 197 G 0.0479 0.1052 0.8469 198 N 0.0603 0.0923 0.8474 199 H 0.0612 0.2840 0.6548 200 S 0.0401 0.6207 0.3392 201 T 0.0274 0.7856 0.1871 202 L 0.0057 0.9375 0.0568 203 Q 0.0047 0.9561 0.0392 204 R 0.0048 0.9545 0.0407 205 Q 0.0048 0.9532 0.0420 206 L 0.0050 0.9484 0.0466 207 H 0.0056 0.9222 0.0722 208 G 0.0048 0.9367 0.0585 209 W 0.0047 0.9554 0.0399 210 Q 0.0047 0.9607 0.0346 211 S 0.0047 0.9615 0.0338 212 A 0.0046 0.9615 0.0339 213 M 0.0047 0.9603 0.0350 214 I 0.0049 0.9508 0.0443 215 E 0.0059 0.9138 0.0804 216 N 0.0443 0.4820 0.4737 217 Y 0.0338 0.0285 0.9377 218 L 0.0656 0.0098 0.9246 219 T 0.0812 0.0131 0.9057 220 P 0.1062 0.1659 0.7279 221 D 0.0854 0.2468 0.6678 222 H 0.0652 0.4804 0.4544 223 F 0.2009 0.2501 0.5490 224 L 0.5625 0.0958 0.3417 225 T 0.7396 0.0373 0.2231 226 T 0.6849 0.0324 0.2827 227 H 0.4319 0.0373 0.5309 228 E 0.1986 0.0451 0.7563 229 A 0.1158 0.0419 0.8423 230 P 0.0660 0.1367 0.7972 231 S 0.0795 0.1439 0.7766 232 S 0.0255 0.5720 0.4025 233 Q 0.0165 0.7522 0.2312 234 L 0.0257 0.7358 0.2385 235 G 0.0094 0.8701 0.1205 236 A 0.0055 0.9532 0.0413 237 E 0.0047 0.9607 0.0347 238 G 0.0047 0.9606 0.0348 239 L 0.0047 0.9609 0.0345 240 A 0.0047 0.9609 0.0345 241 K 0.0047 0.9578 0.0375 242 L 0.0049 0.9441 0.0510 243 L 0.0053 0.8483 0.1464 244 L 0.0078 0.5516 0.4405 245 R 0.0419 0.3068 0.6513 246 D 0.0584 0.0876 0.8541 247 S 0.0424 0.1231 0.8345 248 S 0.0986 0.0508 0.8506 249 L 0.1552 0.0205 0.8243 250 N 0.2458 0.0448 0.7094 251 A 0.9138 0.0047 0.0814 252 L 0.9311 0.0041 0.0648 253 V 0.9254 0.0059 0.0686 254 C 0.8208 0.0176 0.1616 255 S 0.2250 0.0863 0.6888 256 H 0.0447 0.2721 0.6832 257 E 0.0057 0.8865 0.1077 258 E 0.0049 0.9537 0.0415 259 I 0.0047 0.9587 0.0366 260 A 0.0047 0.9601 0.0352 261 I 0.0047 0.9606 0.0347 262 G 0.0046 0.9613 0.0340 263 A 0.0047 0.9602 0.0351 264 L 0.0047 0.9605 0.0348 265 F 0.0047 0.9611 0.0342 266 E 0.0047 0.9601 0.0352 267 C 0.0048 0.9578 0.0374 268 H 0.0051 0.9471 0.0478 269 R 0.0057 0.9128 0.0814 270 R 0.0401 0.4815 0.4784 271 V 0.0353 0.0722 0.8925 272 L 0.1058 0.0234 0.8708 273 K 0.2526 0.0185 0.7289 274 V 0.2247 0.0128 0.7625 275 P 0.1863 0.0431 0.7706 276 T 0.1601 0.1420 0.6979 277 D 0.3999 0.0866 0.5134 278 I 0.7860 0.0239 0.1901 279 A 0.9111 0.0082 0.0807 280 I 0.9197 0.0057 0.0746 281 I 0.8873 0.0099 0.1028 282 C 0.7200 0.0104 0.2696 283 L 0.4004 0.0355 0.5641 284 E 0.1438 0.0549 0.8013 285 G 0.0731 0.0775 0.8494 286 S 0.0908 0.1707 0.7385 287 S 0.0937 0.4382 0.4681 288 M 0.0400 0.7516 0.2084 289 G 0.0410 0.7643 0.1947 290 E 0.0362 0.7372 0.2266 291 H 0.0532 0.5817 0.3651 292 A 0.1147 0.3335 0.5518 293 Y 0.1090 0.0792 0.8118 294 P 0.0780 0.1289 0.7931 295 S 0.0927 0.2157 0.6916 296 L 0.1837 0.2340 0.5823 297 T 0.2782 0.1887 0.5331 298 S 0.3351 0.1680 0.4969 299 A 0.2823 0.1544 0.5633 300 E 0.2912 0.0961 0.6127 301 F 0.1755 0.0584 0.7660 302 D 0.1084 0.0835 0.8081 303 Y 0.0049 0.9226 0.0725 304 E 0.0047 0.9355 0.0598 305 R 0.0047 0.9453 0.0500 306 M 0.0053 0.9492 0.0455 307 G 0.0047 0.9554 0.0399 308 T 0.0046 0.9617 0.0337 309 K 0.0046 0.9612 0.0342 310 A 0.0046 0.9604 0.0350 311 A 0.0046 0.9613 0.0341 312 E 0.0046 0.9615 0.0339 313 K 0.0046 0.9562 0.0391 314 L 0.0047 0.9551 0.0403 315 L 0.0047 0.9576 0.0377 316 H 0.0049 0.9558 0.0393 317 A 0.0069 0.9317 0.0614 318 I 0.0126 0.8515 0.1359 319 K 0.0383 0.3693 0.5923 320 G 0.0216 0.0609 0.9174 321 E 0.0532 0.0246 0.9222 322 P 0.0671 0.0465 0.8864 323 E 0.0803 0.0579 0.8618 324 E 0.0905 0.0533 0.8563 325 R 0.1425 0.0150 0.8425 326 P 0.3174 0.0146 0.6680 327 T 0.7162 0.0129 0.2709 328 S 0.8287 0.0091 0.1622 329 M 0.7825 0.0155 0.2019 330 G 0.6757 0.0159 0.3083 331 F 0.6855 0.0091 0.3054 332 K 0.8308 0.0077 0.1615 333 L 0.8901 0.0055 0.1044 334 K 0.8885 0.0058 0.1058 335 R 0.8894 0.0067 0.1039 336 R 0.7044 0.0358 0.2598 337 A 0.5252 0.0375 0.4373 338 S 0.3928 0.0616 0.5457 339 T 0.3571 0.0620 0.5808 340 A 0.1957 0.0500 0.7542 341 I 0.0991 0.0441 0.8568 342 N 0.0599 0.0228 0.9173