# This file is the result of combining several RDB files, specifically # T0372.t04.dssp-ebghstl.rdb (weight 1.53986) # T0372.t04.stride-ebghtl.rdb (weight 1.24869) # T0372.t04.str2.rdb (weight 1.54758) # T0372.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 T0372.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0372 # 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 T0372.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 108 # # ============================================ # Comments from T0372.t04.stride-ebghtl.rdb # ============================================ # TARGET T0372 # 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 T0372.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 108 # # ============================================ # Comments from T0372.t04.str2.rdb # ============================================ # TARGET T0372 # 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 T0372.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 108 # # ============================================ # Comments from T0372.t04.alpha.rdb # ============================================ # TARGET T0372 # 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 T0372.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 108 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0902 0.0349 0.8748 2 I 0.1261 0.0225 0.8514 3 P 0.1553 0.0383 0.8064 4 F 0.1333 0.0613 0.8055 5 K 0.1435 0.0740 0.7825 6 D 0.1545 0.0533 0.7921 7 I 0.1834 0.0204 0.7962 8 T 0.1674 0.0194 0.8132 9 L 0.0516 0.4661 0.4822 10 A 0.0345 0.3759 0.5896 11 D 0.0415 0.3476 0.6109 12 R 0.0093 0.8952 0.0954 13 D 0.0066 0.9204 0.0730 14 T 0.0079 0.9272 0.0650 15 I 0.0108 0.9354 0.0538 16 T 0.0091 0.9408 0.0501 17 A 0.0106 0.9361 0.0533 18 F 0.0131 0.9212 0.0657 19 T 0.0269 0.8762 0.0969 20 M 0.0306 0.8118 0.1575 21 K 0.0346 0.6951 0.2703 22 S 0.0579 0.4252 0.5169 23 D 0.0486 0.2327 0.7188 24 R 0.0663 0.2278 0.7060 25 R 0.1073 0.2522 0.6405 26 N 0.1208 0.2538 0.6253 27 C 0.1152 0.2514 0.6334 28 D 0.1013 0.3501 0.5487 29 L 0.0818 0.5368 0.3814 30 S 0.0678 0.6264 0.3058 31 F 0.0336 0.8212 0.1453 32 S 0.0265 0.8491 0.1244 33 N 0.0252 0.8565 0.1183 34 L 0.0276 0.8645 0.1078 35 C 0.0422 0.8250 0.1328 36 S 0.0552 0.7645 0.1802 37 W 0.0781 0.6903 0.2316 38 R 0.0882 0.5624 0.3495 39 F 0.0994 0.3983 0.5023 40 L 0.1391 0.2113 0.6497 41 Y 0.1294 0.1172 0.7533 42 D 0.1647 0.0987 0.7367 43 T 0.5369 0.0462 0.4170 44 Q 0.7940 0.0190 0.1870 45 F 0.8911 0.0092 0.0997 46 A 0.8928 0.0083 0.0989 47 V 0.8662 0.0086 0.1252 48 I 0.6681 0.0374 0.2945 49 D 0.1109 0.0473 0.8418 50 D 0.0751 0.0468 0.8781 51 F 0.7110 0.0163 0.2728 52 L 0.9184 0.0033 0.0782 53 V 0.9249 0.0038 0.0713 54 F 0.9269 0.0033 0.0698 55 K 0.9124 0.0074 0.0802 56 F 0.9089 0.0064 0.0847 57 W 0.8777 0.0114 0.1109 58 A 0.7447 0.0277 0.2276 59 G 0.2832 0.0422 0.6746 60 E 0.0798 0.0660 0.8542 61 Q 0.2421 0.0431 0.7148 62 L 0.7450 0.0105 0.2446 63 A 0.8941 0.0048 0.1010 64 Y 0.9156 0.0048 0.0796 65 M 0.8937 0.0063 0.1000 66 M 0.7499 0.0087 0.2414 67 P 0.4942 0.0177 0.4881 68 V 0.2011 0.0463 0.7525 69 G 0.0826 0.0364 0.8810 70 N 0.0530 0.1157 0.8313 71 G 0.0301 0.1993 0.7706 72 D 0.0440 0.3341 0.6219 73 L 0.0085 0.8040 0.1875 74 K 0.0048 0.9487 0.0466 75 A 0.0047 0.9564 0.0389 76 V 0.0047 0.9555 0.0398 77 L 0.0047 0.9593 0.0360 78 R 0.0047 0.9605 0.0348 79 K 0.0047 0.9599 0.0354 80 L 0.0048 0.9555 0.0397 81 I 0.0048 0.9542 0.0411 82 E 0.0050 0.9432 0.0519 83 D 0.0061 0.9130 0.0809 84 A 0.0148 0.8825 0.1027 85 D 0.0114 0.8372 0.1513 86 K 0.0089 0.7177 0.2734 87 E 0.0306 0.4033 0.5661 88 K 0.0345 0.1355 0.8300 89 H 0.0545 0.0722 0.8733 90 N 0.1231 0.0487 0.8282 91 F 0.4109 0.0430 0.5461 92 C 0.6821 0.0339 0.2840 93 M 0.8568 0.0251 0.1181 94 L 0.7692 0.0550 0.1758 95 G 0.6132 0.0365 0.3503 96 V 0.3441 0.0322 0.6237 97 C 0.1180 0.0334 0.8486 98 S 0.0073 0.7298 0.2629 99 N 0.0075 0.7432 0.2493 100 M 0.0102 0.8098 0.1800 101 R 0.0111 0.8621 0.1268 102 A 0.0081 0.9069 0.0850 103 D 0.0063 0.9188 0.0750 104 L 0.0070 0.9103 0.0827 105 E 0.0076 0.8861 0.1063 106 A 0.0088 0.8306 0.1606 107 I 0.0185 0.6767 0.3048 108 L 0.0718 0.1860 0.7421 109 P 0.0273 0.3135 0.6593 110 E 0.0241 0.4094 0.5665 111 R 0.0784 0.4166 0.5050 112 F 0.3177 0.3260 0.3563 113 I 0.4398 0.2572 0.3030 114 F 0.5040 0.1981 0.2979 115 T 0.3225 0.2770 0.4004 116 E 0.1736 0.3075 0.5189 117 D 0.1430 0.4247 0.4324 118 R 0.1049 0.5410 0.3541 119 A 0.1183 0.5638 0.3179 120 Y 0.1000 0.6464 0.2536 121 A 0.1098 0.6473 0.2429 122 D 0.0621 0.7242 0.2137 123 Y 0.1087 0.7197 0.1716 124 I 0.1210 0.7020 0.1771 125 Y 0.1289 0.5965 0.2746 126 L 0.0974 0.4669 0.4357 127 R 0.0409 0.5928 0.3663 128 S 0.0178 0.6435 0.3387 129 D 0.0269 0.6567 0.3164 130 L 0.0324 0.7166 0.2510 131 A 0.0272 0.6379 0.3349 132 T 0.0497 0.5384 0.4119 133 L 0.0890 0.1983 0.7127 134 K 0.0511 0.2015 0.7475 135 G 0.0341 0.4086 0.5573 136 K 0.0261 0.7346 0.2393 137 K 0.0223 0.8322 0.1455 138 F 0.0127 0.8903 0.0971 139 Q 0.0097 0.9217 0.0686 140 A 0.0112 0.9161 0.0727 141 K 0.0071 0.9373 0.0556 142 R 0.0088 0.9425 0.0486 143 N 0.0077 0.9389 0.0534 144 H 0.0070 0.9422 0.0507 145 I 0.0067 0.9487 0.0446 146 N 0.0067 0.9455 0.0477 147 R 0.0072 0.9356 0.0572 148 F 0.0084 0.9244 0.0672 149 R 0.0192 0.8735 0.1074 150 N 0.0212 0.7367 0.2421 151 T 0.0369 0.4037 0.5594 152 Y 0.0705 0.0276 0.9019 153 P 0.0552 0.0843 0.8604 154 D 0.2741 0.0528 0.6731 155 Y 0.7303 0.0150 0.2547 156 E 0.8476 0.0056 0.1468 157 Y 0.8733 0.0045 0.1222 158 T 0.7424 0.0080 0.2496 159 P 0.4653 0.0088 0.5259 160 I 0.1255 0.0229 0.8516 161 T 0.0612 0.0104 0.9284 162 P 0.0080 0.6934 0.2986 163 D 0.0071 0.7777 0.2151 164 R 0.0074 0.8439 0.1487 165 I 0.0067 0.9023 0.0910 166 Q 0.0060 0.9263 0.0677 167 E 0.0059 0.9313 0.0628 168 C 0.0083 0.9264 0.0653 169 L 0.0080 0.9144 0.0776 170 D 0.0124 0.8574 0.1301 171 L 0.0127 0.8456 0.1417 172 E 0.0232 0.7951 0.1817 173 A 0.0075 0.9105 0.0820 174 E 0.0093 0.9064 0.0843 175 W 0.0136 0.8783 0.1081 176 C 0.0407 0.7878 0.1716 177 K 0.0544 0.6482 0.2974 178 V 0.0584 0.5295 0.4121 179 N 0.0498 0.2329 0.7174 180 N 0.0634 0.1203 0.8162 181 C 0.1071 0.1704 0.7225 182 D 0.1324 0.2066 0.6610 183 Q 0.1088 0.2206 0.6706 184 Q 0.1170 0.1887 0.6943 185 E 0.1420 0.1898 0.6681 186 G 0.1683 0.1778 0.6539 187 T 0.1249 0.2719 0.6032 188 G 0.0574 0.5341 0.4085 189 N 0.0442 0.6308 0.3250 190 E 0.0369 0.7414 0.2217 191 R 0.0413 0.7955 0.1633 192 R 0.0455 0.8048 0.1497 193 A 0.0571 0.7807 0.1622 194 L 0.0648 0.7988 0.1364 195 I 0.0576 0.8327 0.1097 196 Y 0.0395 0.8405 0.1200 197 A 0.0279 0.8359 0.1362 198 L 0.0241 0.8220 0.1539 199 H 0.0203 0.7481 0.2316 200 N 0.0369 0.6571 0.3059 201 F 0.0187 0.7056 0.2757 202 E 0.0125 0.7060 0.2814 203 A 0.0203 0.6596 0.3201 204 L 0.0818 0.3443 0.5739 205 G 0.0944 0.0936 0.8120 206 L 0.2719 0.1003 0.6278 207 T 0.4346 0.0771 0.4883 208 G 0.6312 0.0420 0.3268 209 G 0.8402 0.0131 0.1467 210 I 0.9061 0.0071 0.0868 211 L 0.8990 0.0057 0.0953 212 H 0.7777 0.0113 0.2110 213 V 0.4780 0.0520 0.4701 214 N 0.0467 0.0184 0.9350 215 G 0.0528 0.0304 0.9168 216 K 0.7402 0.0068 0.2530 217 I 0.9228 0.0029 0.0743 218 V 0.8772 0.0178 0.1050 219 A 0.9306 0.0033 0.0661 220 F 0.9278 0.0032 0.0691 221 T 0.9103 0.0042 0.0856 222 F 0.8246 0.0069 0.1685 223 G 0.6658 0.0167 0.3175 224 M 0.5590 0.0168 0.4242 225 P 0.4996 0.0207 0.4796 226 I 0.3513 0.0501 0.5986 227 N 0.1733 0.0441 0.7826 228 H 0.0432 0.1076 0.8492 229 E 0.1000 0.0701 0.8299 230 T 0.7026 0.0166 0.2808 231 F 0.8788 0.0047 0.1165 232 G 0.9268 0.0034 0.0698 233 V 0.9205 0.0040 0.0755 234 H 0.8832 0.0065 0.1103 235 V 0.7398 0.0304 0.2298 236 E 0.6161 0.0694 0.3145 237 K 0.4504 0.1255 0.4240 238 A 0.2180 0.1279 0.6542 239 D 0.1021 0.0327 0.8652 240 T 0.0229 0.1513 0.8258 241 S 0.0459 0.1176 0.8364 242 I 0.0519 0.2062 0.7420 243 D 0.0288 0.3902 0.5810 244 G 0.0396 0.6420 0.3184 245 A 0.0146 0.9019 0.0835 246 Y 0.0075 0.9453 0.0471 247 A 0.0057 0.9561 0.0382 248 M 0.0055 0.9569 0.0376 249 I 0.0048 0.9558 0.0393 250 N 0.0050 0.9545 0.0406 251 Y 0.0047 0.9545 0.0408 252 E 0.0050 0.9542 0.0409 253 F 0.0051 0.9431 0.0518 254 A 0.0056 0.9204 0.0741 255 N 0.0075 0.8299 0.1626 256 R 0.0148 0.6190 0.3662 257 I 0.0663 0.0854 0.8483 258 P 0.0387 0.1830 0.7782 259 E 0.0233 0.2442 0.7325 260 Q 0.0663 0.1623 0.7714 261 Y 0.4382 0.0370 0.5249 262 I 0.6916 0.0340 0.2744 263 Y 0.8792 0.0096 0.1113 264 I 0.7739 0.0175 0.2086 265 N 0.4217 0.0119 0.5663 266 R 0.0864 0.4457 0.4678 267 E 0.0231 0.5800 0.3969 268 E 0.0215 0.6253 0.3532 269 D 0.0499 0.5743 0.3757 270 L 0.0633 0.5230 0.4137 271 G 0.0511 0.3601 0.5889 272 I 0.0520 0.4633 0.4847 273 E 0.0282 0.6286 0.3432 274 G 0.0251 0.6413 0.3336 275 L 0.0254 0.6993 0.2753 276 R 0.0163 0.6666 0.3171 277 K 0.0183 0.4423 0.5394 278 A 0.0882 0.2387 0.6731 279 K 0.1053 0.1899 0.7048 280 L 0.1311 0.1672 0.7017 281 S 0.1302 0.1465 0.7233 282 Y 0.1267 0.1191 0.7542 283 Q 0.0941 0.0732 0.8327 284 P 0.0792 0.1757 0.7450 285 V 0.0639 0.4998 0.4363 286 T 0.0570 0.7008 0.2422 287 I 0.0229 0.9008 0.0763 288 L 0.0187 0.9263 0.0551 289 E 0.0216 0.9304 0.0480 290 K 0.0316 0.9227 0.0458 291 Y 0.0378 0.9084 0.0538 292 M 0.0629 0.8743 0.0628 293 A 0.0602 0.8645 0.0753 294 C 0.0564 0.8502 0.0935 295 L 0.0849 0.7610 0.1541 296 K 0.0989 0.5906 0.3106 297 D 0.0900 0.3720 0.5380 298 H 0.1030 0.1046 0.7925 299 P 0.0593 0.3923 0.5485 300 M 0.0543 0.4500 0.4957 301 D 0.1235 0.4244 0.4521 302 M 0.3174 0.3319 0.3507 303 V 0.4244 0.1947 0.3809 304 R 0.3000 0.1320 0.5680 305 W 0.1272 0.0422 0.8306