# This file is the result of combining several RDB files, specifically # T0298.t06.dssp-ebghstl.rdb (weight 1.53986) # T0298.t06.stride-ebghtl.rdb (weight 1.24869) # T0298.t06.str2.rdb (weight 1.54758) # T0298.t06.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 T0298.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0298 # 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 T0298.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 2376 # # ============================================ # Comments from T0298.t06.stride-ebghtl.rdb # ============================================ # TARGET T0298 # 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 T0298.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 2376 # # ============================================ # Comments from T0298.t06.str2.rdb # ============================================ # TARGET T0298 # 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 T0298.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 2376 # # ============================================ # Comments from T0298.t06.alpha.rdb # ============================================ # TARGET T0298 # 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 T0298.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 2376 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0585 0.0326 0.9089 2 S 0.0785 0.0428 0.8787 3 Q 0.1206 0.0325 0.8469 4 P 0.2019 0.0212 0.7769 5 L 0.5313 0.0090 0.4597 6 N 0.7908 0.0068 0.2024 7 V 0.9237 0.0035 0.0729 8 A 0.9294 0.0034 0.0672 9 V 0.9273 0.0037 0.0691 10 V 0.8263 0.0257 0.1480 11 G 0.3067 0.0372 0.6561 12 A 0.1045 0.0997 0.7958 13 T 0.0864 0.1510 0.7626 14 G 0.0417 0.3857 0.5727 15 S 0.0254 0.8261 0.1486 16 V 0.0079 0.9300 0.0621 17 G 0.0065 0.9450 0.0485 18 E 0.0049 0.9574 0.0377 19 A 0.0047 0.9590 0.0363 20 L 0.0047 0.9591 0.0362 21 V 0.0047 0.9583 0.0371 22 G 0.0048 0.9538 0.0414 23 L 0.0051 0.9383 0.0566 24 L 0.0057 0.9030 0.0913 25 D 0.0089 0.7766 0.2146 26 E 0.0129 0.6108 0.3763 27 R 0.0493 0.2686 0.6822 28 D 0.0383 0.0630 0.8986 29 F 0.0695 0.0192 0.9113 30 P 0.0808 0.0836 0.8356 31 L 0.3703 0.0660 0.5638 32 H 0.7273 0.0117 0.2610 33 R 0.8778 0.0053 0.1168 34 L 0.9085 0.0029 0.0886 35 H 0.8976 0.0085 0.0939 36 L 0.9135 0.0050 0.0815 37 L 0.8439 0.0099 0.1463 38 A 0.5782 0.0195 0.4023 39 S 0.2095 0.0153 0.7752 40 A 0.0271 0.4195 0.5533 41 E 0.0315 0.4482 0.5203 42 S 0.0498 0.4574 0.4928 43 A 0.0157 0.6727 0.3116 44 G 0.0263 0.4488 0.5249 45 Q 0.0758 0.5031 0.4211 46 R 0.1464 0.5322 0.3214 47 M 0.1117 0.5474 0.3409 48 G 0.1142 0.4404 0.4454 49 F 0.1363 0.4480 0.4157 50 A 0.2083 0.2682 0.5235 51 E 0.1594 0.2017 0.6388 52 S 0.1550 0.1816 0.6634 53 S 0.3038 0.1414 0.5548 54 L 0.5425 0.0579 0.3997 55 R 0.6300 0.0365 0.3335 56 V 0.5393 0.0609 0.3998 57 G 0.3036 0.0532 0.6432 58 D 0.2382 0.0209 0.7409 59 V 0.0365 0.5498 0.4138 60 D 0.0355 0.5145 0.4500 61 S 0.0495 0.5659 0.3847 62 F 0.1252 0.2120 0.6628 63 D 0.1448 0.1642 0.6910 64 F 0.0885 0.4651 0.4464 65 S 0.0501 0.3176 0.6323 66 S 0.1008 0.1895 0.7097 67 V 0.2960 0.0126 0.6914 68 G 0.2878 0.0351 0.6771 69 L 0.9280 0.0034 0.0686 70 A 0.9337 0.0032 0.0631 71 F 0.9314 0.0035 0.0650 72 F 0.8987 0.0070 0.0943 73 A 0.5350 0.0223 0.4427 74 A 0.1525 0.0406 0.8069 75 A 0.0857 0.1419 0.7725 76 A 0.0267 0.5207 0.4526 77 E 0.0250 0.6575 0.3175 78 V 0.0350 0.6463 0.3187 79 S 0.0245 0.6734 0.3021 80 R 0.0052 0.9194 0.0753 81 A 0.0049 0.9187 0.0764 82 H 0.0054 0.9231 0.0714 83 A 0.0048 0.9430 0.0522 84 E 0.0047 0.9553 0.0400 85 R 0.0047 0.9563 0.0390 86 A 0.0047 0.9555 0.0398 87 R 0.0048 0.9458 0.0494 88 A 0.0052 0.8991 0.0957 89 A 0.0407 0.3291 0.6302 90 G 0.0375 0.0156 0.9469 91 C 0.1299 0.0069 0.8632 92 S 0.7288 0.0071 0.2642 93 V 0.9259 0.0034 0.0707 94 I 0.9272 0.0035 0.0694 95 D 0.9022 0.0037 0.0941 96 L 0.6188 0.0150 0.3662 97 S 0.1790 0.0346 0.7864 98 G 0.0877 0.1089 0.8034 99 A 0.0875 0.1452 0.7673 100 L 0.1182 0.1323 0.7495 101 E 0.1033 0.0747 0.8220 102 P 0.0447 0.3108 0.6445 103 S 0.0290 0.3011 0.6698 104 V 0.0551 0.2344 0.7105 105 A 0.1036 0.0512 0.8452 106 P 0.1362 0.0577 0.8061 107 P 0.3286 0.1104 0.5611 108 V 0.5719 0.1151 0.3130 109 M 0.6102 0.1134 0.2764 110 V 0.4945 0.1705 0.3351 111 S 0.3680 0.1537 0.4782 112 V 0.2429 0.1217 0.6354 113 N 0.1361 0.0934 0.7705 114 A 0.0071 0.8466 0.1464 115 E 0.0059 0.8736 0.1205 116 R 0.0069 0.8758 0.1172 117 L 0.0122 0.8466 0.1413 118 A 0.0152 0.7461 0.2386 119 S 0.0160 0.6232 0.3609 120 Q 0.0244 0.4654 0.5101 121 A 0.0516 0.2861 0.6623 122 A 0.0732 0.0718 0.8550 123 P 0.1194 0.0963 0.7843 124 F 0.4843 0.0775 0.4382 125 L 0.8431 0.0171 0.1397 126 L 0.8536 0.0162 0.1301 127 S 0.7476 0.0257 0.2267 128 S 0.3168 0.0267 0.6565 129 P 0.1078 0.0775 0.8147 130 C 0.1216 0.1151 0.7633 131 A 0.1497 0.1686 0.6817 132 V 0.1212 0.2749 0.6039 133 A 0.0853 0.3819 0.5328 134 A 0.0446 0.5245 0.4310 135 E 0.0370 0.6177 0.3453 136 L 0.0220 0.7492 0.2288 137 C 0.0292 0.8197 0.1510 138 E 0.0157 0.8659 0.1183 139 V 0.0133 0.8615 0.1252 140 L 0.0147 0.8725 0.1129 141 A 0.0082 0.9218 0.0701 142 P 0.0079 0.9273 0.0648 143 L 0.0083 0.9323 0.0595 144 L 0.0117 0.9146 0.0737 145 A 0.0093 0.8447 0.1460 146 T 0.0119 0.6895 0.2986 147 L 0.0678 0.1882 0.7441 148 D 0.0983 0.0397 0.8619 149 C 0.2965 0.0288 0.6746 150 R 0.4593 0.0598 0.4808 151 Q 0.7877 0.0212 0.1911 152 L 0.8585 0.0104 0.1311 153 N 0.9119 0.0056 0.0824 154 L 0.8982 0.0078 0.0940 155 T 0.8630 0.0137 0.1233 156 A 0.8461 0.0243 0.1296 157 C 0.8007 0.0582 0.1411 158 L 0.7007 0.1167 0.1825 159 S 0.4787 0.1854 0.3359 160 V 0.2804 0.2206 0.4990 161 S 0.1627 0.2210 0.6163 162 S 0.0708 0.2590 0.6702 163 L 0.0481 0.3025 0.6494 164 G 0.0419 0.3079 0.6502 165 R 0.0168 0.7040 0.2792 166 E 0.0106 0.7913 0.1980 167 G 0.0095 0.8082 0.1823 168 V 0.0082 0.8997 0.0921 169 K 0.0057 0.9304 0.0639 170 E 0.0062 0.9226 0.0712 171 L 0.0060 0.9150 0.0790 172 A 0.0078 0.9057 0.0865 173 R 0.0080 0.8732 0.1188 174 Q 0.0127 0.8371 0.1502 175 T 0.0282 0.7726 0.1991 176 A 0.0219 0.7742 0.2039 177 E 0.0349 0.7537 0.2114 178 L 0.0592 0.7136 0.2272 179 L 0.1208 0.5323 0.3468 180 N 0.1260 0.2912 0.5829 181 A 0.0804 0.1554 0.7642 182 R 0.0762 0.0821 0.8417 183 P 0.0814 0.1013 0.8173 184 L 0.0694 0.1454 0.7852 185 E 0.0757 0.1493 0.7749 186 P 0.0312 0.5677 0.4011 187 R 0.0335 0.5927 0.3738 188 L 0.0530 0.5787 0.3683 189 F 0.0615 0.4321 0.5065 190 D 0.0492 0.4872 0.4636 191 R 0.0425 0.6527 0.3048 192 Q 0.0513 0.7132 0.2355 193 I 0.0637 0.6897 0.2466 194 A 0.0993 0.6391 0.2615 195 F 0.1254 0.5472 0.3274 196 N 0.1453 0.3959 0.4588 197 L 0.2392 0.3444 0.4164 198 L 0.3213 0.2905 0.3882 199 A 0.3114 0.2686 0.4200 200 Q 0.3149 0.2476 0.4375 201 V 0.2504 0.2287 0.5209 202 G 0.1825 0.1533 0.6643 203 A 0.2256 0.1767 0.5977 204 V 0.3357 0.1661 0.4982 205 D 0.1483 0.1708 0.6809 206 A 0.0600 0.2203 0.7197 207 E 0.0557 0.1328 0.8115 208 G 0.0537 0.0791 0.8673 209 H 0.1151 0.1227 0.7622 210 S 0.1057 0.4191 0.4751 211 A 0.0135 0.8912 0.0953 212 I 0.0103 0.9332 0.0565 213 E 0.0086 0.9385 0.0529 214 R 0.0078 0.9437 0.0485 215 R 0.0067 0.9347 0.0586 216 I 0.0066 0.9280 0.0655 217 F 0.0075 0.9379 0.0546 218 A 0.0064 0.9480 0.0456 219 E 0.0062 0.9467 0.0471 220 V 0.0071 0.9395 0.0534 221 Q 0.0105 0.9263 0.0632 222 A 0.0144 0.9041 0.0816 223 L 0.0155 0.8515 0.1330 224 L 0.0479 0.5961 0.3560 225 G 0.0417 0.4062 0.5521 226 E 0.0504 0.3674 0.5822 227 R 0.0788 0.2899 0.6313 228 I 0.1033 0.1107 0.7860 229 G 0.1472 0.0199 0.8329 230 P 0.2634 0.0166 0.7199 231 L 0.6346 0.0101 0.3553 232 N 0.6566 0.0226 0.3208 233 V 0.7758 0.0077 0.2165 234 T 0.7955 0.0088 0.1957 235 C 0.8155 0.0058 0.1786 236 I 0.8123 0.0081 0.1796 237 Q 0.7788 0.0113 0.2099 238 A 0.6058 0.0127 0.3815 239 P 0.5119 0.0162 0.4719 240 V 0.4891 0.0265 0.4845 241 F 0.3959 0.0580 0.5460 242 F 0.3723 0.0409 0.5868 243 G 0.4683 0.0316 0.5001 244 D 0.6091 0.0262 0.3646 245 S 0.8226 0.0165 0.1609 246 L 0.8778 0.0092 0.1130 247 S 0.9028 0.0058 0.0914 248 V 0.9007 0.0060 0.0932 249 T 0.9053 0.0050 0.0898 250 L 0.8988 0.0055 0.0957 251 Q 0.8550 0.0077 0.1373 252 C 0.6366 0.0144 0.3491 253 A 0.2489 0.0477 0.7034 254 E 0.1480 0.0313 0.8208 255 P 0.1339 0.0303 0.8358 256 V 0.1714 0.0111 0.8175 257 D 0.1006 0.0115 0.8879 258 L 0.0049 0.9478 0.0473 259 A 0.0047 0.9581 0.0372 260 A 0.0047 0.9592 0.0361 261 V 0.0047 0.9607 0.0347 262 T 0.0047 0.9604 0.0349 263 R 0.0047 0.9593 0.0360 264 V 0.0048 0.9549 0.0403 265 L 0.0050 0.9354 0.0596 266 D 0.0063 0.8235 0.1702 267 A 0.0107 0.5796 0.4096 268 T 0.0633 0.1110 0.8257 269 K 0.0326 0.1218 0.8456 270 G 0.0918 0.1052 0.8031 271 I 0.4958 0.0400 0.4642 272 E 0.7997 0.0221 0.1782 273 W 0.8236 0.0218 0.1546 274 V 0.6686 0.0330 0.2984 275 G 0.3665 0.0301 0.6034 276 E 0.1351 0.0750 0.7900 277 G 0.0858 0.0705 0.8436 278 D 0.0966 0.0676 0.8358 279 Y 0.1180 0.0297 0.8523 280 P 0.1513 0.0439 0.8048 281 T 0.3301 0.0465 0.6233 282 V 0.4728 0.0352 0.4920 283 V 0.4258 0.0673 0.5069 284 G 0.3810 0.1285 0.4905 285 D 0.3216 0.1489 0.5294 286 A 0.2883 0.1707 0.5410 287 L 0.1948 0.1158 0.6894 288 G 0.1012 0.0424 0.8564 289 Q 0.1189 0.0521 0.8290 290 D 0.1431 0.0752 0.7817 291 E 0.2162 0.1051 0.6787 292 T 0.4542 0.0849 0.4608 293 Y 0.6135 0.0624 0.3242 294 V 0.7035 0.0779 0.2186 295 G 0.6838 0.0677 0.2486 296 R 0.7066 0.0524 0.2410 297 V 0.6472 0.0775 0.2753 298 R 0.6059 0.0733 0.3209 299 A 0.4286 0.1076 0.4638 300 G 0.2418 0.0690 0.6892 301 Q 0.2171 0.0700 0.7129 302 A 0.2187 0.0674 0.7139 303 D 0.1163 0.0361 0.8477 304 P 0.0262 0.1556 0.8182 305 C 0.1020 0.1013 0.7967 306 Q 0.6828 0.0325 0.2847 307 V 0.8699 0.0058 0.1243 308 N 0.9075 0.0062 0.0863 309 L 0.9212 0.0079 0.0709 310 W 0.9188 0.0111 0.0701 311 I 0.9134 0.0135 0.0730 312 V 0.8269 0.0657 0.1074 313 S 0.6214 0.1425 0.2361 314 D 0.2512 0.3534 0.3954 315 N 0.1090 0.5455 0.3455 316 V 0.0461 0.7457 0.2082 317 R 0.0267 0.8113 0.1620 318 K 0.0244 0.8016 0.1740 319 G 0.0135 0.7552 0.2313 320 A 0.0091 0.8225 0.1684 321 A 0.0058 0.8918 0.1024 322 L 0.0050 0.9235 0.0714 323 N 0.0051 0.9280 0.0670 324 A 0.0050 0.9508 0.0442 325 V 0.0050 0.9579 0.0371 326 L 0.0047 0.9585 0.0368 327 L 0.0047 0.9591 0.0362 328 G 0.0047 0.9600 0.0354 329 E 0.0047 0.9600 0.0353 330 L 0.0047 0.9578 0.0375 331 L 0.0049 0.9497 0.0453 332 I 0.0067 0.9109 0.0824 333 K 0.0098 0.8175 0.1727 334 H 0.0357 0.5966 0.3678 335 Y 0.0406 0.3048 0.6546 336 L 0.0350 0.0801 0.8849