# This file is the result of combining several RDB files, specifically # T0296.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0296.t2k.stride-ebghtl.rdb (weight 1.24869) # T0296.t2k.str2.rdb (weight 1.54758) # T0296.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 T0296.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0296 # 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 T0296.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 57 # # ============================================ # Comments from T0296.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0296 # 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 T0296.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 57 # # ============================================ # Comments from T0296.t2k.str2.rdb # ============================================ # TARGET T0296 # 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 T0296.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 57 # # ============================================ # Comments from T0296.t2k.alpha.rdb # ============================================ # TARGET T0296 # 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 T0296.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 57 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.0991 0.1780 0.7229 2 P 0.0948 0.5859 0.3193 3 I 0.0379 0.8696 0.0925 4 S 0.0296 0.8976 0.0728 5 L 0.0269 0.9025 0.0707 6 I 0.0273 0.8739 0.0988 7 G 0.0265 0.7763 0.1972 8 A 0.0239 0.6105 0.3656 9 A 0.0305 0.4418 0.5277 10 T 0.0794 0.2128 0.7078 11 D 0.0568 0.0877 0.8555 12 A 0.0247 0.6006 0.3748 13 T 0.0132 0.7061 0.2807 14 D 0.0230 0.7772 0.1998 15 Y 0.0108 0.9146 0.0746 16 V 0.0080 0.9418 0.0502 17 V 0.0069 0.9445 0.0486 18 L 0.0056 0.9451 0.0493 19 A 0.0059 0.9413 0.0528 20 K 0.0061 0.9190 0.0749 21 A 0.0097 0.8327 0.1576 22 L 0.0166 0.7841 0.1993 23 D 0.0148 0.6921 0.2931 24 K 0.0060 0.8933 0.1007 25 A 0.0055 0.9236 0.0709 26 A 0.0058 0.9220 0.0722 27 K 0.0086 0.9025 0.0889 28 E 0.0095 0.8345 0.1559 29 I 0.0541 0.4852 0.4607 30 G 0.0755 0.0658 0.8586 31 V 0.1680 0.0308 0.8012 32 D 0.3503 0.0523 0.5974 33 F 0.6591 0.0783 0.2626 34 I 0.6756 0.0741 0.2502 35 G 0.5307 0.0746 0.3946 36 G 0.3160 0.1279 0.5561 37 F 0.3446 0.1438 0.5116 38 S 0.3632 0.1867 0.4501 39 A 0.4301 0.2986 0.2713 40 L 0.4871 0.2604 0.2526 41 V 0.3779 0.2559 0.3662 42 Q 0.2779 0.2171 0.5051 43 K 0.0767 0.1667 0.7567 44 G 0.0562 0.0837 0.8601 45 Y 0.1236 0.0462 0.8302 46 Q 0.1394 0.0382 0.8224 47 K 0.0316 0.3724 0.5959 48 G 0.0286 0.3458 0.6255 49 D 0.0412 0.6177 0.3411 50 E 0.0202 0.8600 0.1197 51 I 0.0306 0.8593 0.1101 52 L 0.0201 0.8872 0.0928 53 I 0.0110 0.9126 0.0764 54 N 0.0098 0.8822 0.1080 55 S 0.0107 0.8596 0.1298 56 I 0.0122 0.8607 0.1270 57 P 0.0064 0.9289 0.0647 58 R 0.0061 0.9222 0.0717 59 A 0.0067 0.9030 0.0904 60 L 0.0127 0.8457 0.1417 61 A 0.0146 0.7322 0.2532 62 E 0.0243 0.4989 0.4768 63 T 0.0646 0.1709 0.7644 64 D 0.1164 0.1351 0.7485 65 K 0.4859 0.1051 0.4090 66 V 0.7095 0.0637 0.2269 67 C 0.7619 0.0633 0.1748 68 S 0.7811 0.0470 0.1718 69 S 0.7847 0.0541 0.1612 70 V 0.7349 0.0591 0.2060 71 N 0.6500 0.0730 0.2770 72 I 0.4405 0.1499 0.4096 73 G 0.3816 0.1350 0.4834 74 S 0.3329 0.1347 0.5324 75 T 0.2123 0.1591 0.6287 76 K 0.1130 0.2396 0.6475 77 S 0.0508 0.1504 0.7988 78 G 0.0689 0.0893 0.8418 79 I 0.2538 0.0609 0.6853 80 N 0.1640 0.0523 0.7838 81 M 0.0079 0.9108 0.0813 82 T 0.0053 0.9382 0.0565 83 A 0.0049 0.9498 0.0453 84 V 0.0053 0.9509 0.0438 85 A 0.0056 0.9437 0.0507 86 D 0.0056 0.9275 0.0669 87 M 0.0068 0.9017 0.0916 88 G 0.0058 0.9133 0.0809 89 R 0.0053 0.9255 0.0692 90 I 0.0050 0.9264 0.0686 91 I 0.0059 0.9352 0.0589 92 K 0.0068 0.9327 0.0605 93 E 0.0071 0.9316 0.0613 94 T 0.0065 0.9193 0.0742 95 A 0.0123 0.8571 0.1306 96 N 0.0128 0.7339 0.2533 97 L 0.0413 0.4992 0.4595 98 S 0.0525 0.2007 0.7468 99 D 0.0340 0.1826 0.7834 100 M 0.0437 0.2013 0.7550 101 G 0.0570 0.1662 0.7768 102 V 0.1282 0.1934 0.6784 103 A 0.2813 0.3021 0.4166 104 K 0.4742 0.2564 0.2694 105 L 0.6896 0.1837 0.1267 106 V 0.7618 0.1326 0.1056 107 V 0.7464 0.1505 0.1030 108 F 0.7420 0.1488 0.1092 109 A 0.6469 0.1546 0.1985 110 N 0.5150 0.1235 0.3615 111 A 0.2929 0.0616 0.6456 112 V 0.1558 0.0485 0.7957 113 E 0.0450 0.0957 0.8593 114 D 0.0473 0.0605 0.8923 115 N 0.0836 0.0336 0.8828 116 P 0.1536 0.1303 0.7162 117 F 0.2676 0.1318 0.6006 118 M 0.3646 0.1303 0.5051 119 A 0.3090 0.1374 0.5536 120 G 0.2065 0.1204 0.6731 121 A 0.1631 0.1860 0.6508 122 F 0.1788 0.1688 0.6524 123 H 0.2093 0.1088 0.6818 124 G 0.1770 0.0939 0.7290 125 V 0.1454 0.1139 0.7407 126 G 0.1284 0.0854 0.7862 127 E 0.1490 0.0742 0.7768 128 A 0.1852 0.0841 0.7307 129 D 0.2357 0.0728 0.6915 130 V 0.6447 0.0322 0.3231 131 I 0.8402 0.0152 0.1446 132 I 0.8539 0.0218 0.1242 133 N 0.8015 0.0221 0.1765 134 V 0.6350 0.0636 0.3014 135 G 0.5243 0.0763 0.3994 136 V 0.4269 0.1031 0.4700 137 S 0.2821 0.1072 0.6107 138 G 0.1389 0.1255 0.7356 139 P 0.0352 0.4969 0.4679 140 G 0.0291 0.6485 0.3224 141 V 0.0221 0.8742 0.1037 142 V 0.0091 0.9289 0.0620 143 K 0.0061 0.9427 0.0512 144 R 0.0058 0.9439 0.0503 145 A 0.0051 0.9421 0.0527 146 L 0.0055 0.9114 0.0831 147 E 0.0060 0.7699 0.2241 148 K 0.0125 0.6367 0.3508 149 V 0.0574 0.2379 0.7047 150 R 0.0227 0.2082 0.7692 151 G 0.0308 0.1641 0.8051 152 Q 0.0537 0.1829 0.7634 153 S 0.0882 0.2085 0.7033 154 F 0.0361 0.7632 0.2007 155 D 0.0110 0.8954 0.0937 156 V 0.0079 0.9253 0.0668 157 V 0.0059 0.9427 0.0514 158 A 0.0053 0.9467 0.0480 159 E 0.0049 0.9464 0.0488 160 T 0.0049 0.9483 0.0468 161 V 0.0051 0.9453 0.0496 162 K 0.0050 0.9430 0.0520 163 K 0.0052 0.9372 0.0577 164 T 0.0051 0.9371 0.0578 165 A 0.0049 0.9395 0.0556 166 F 0.0049 0.9374 0.0578 167 K 0.0049 0.9308 0.0643 168 I 0.0050 0.9256 0.0694 169 T 0.0051 0.9152 0.0797 170 R 0.0051 0.9103 0.0846 171 I 0.0050 0.9126 0.0824 172 G 0.0053 0.9131 0.0817 173 Q 0.0050 0.9410 0.0541 174 L 0.0052 0.9504 0.0445 175 V 0.0047 0.9544 0.0409 176 G 0.0047 0.9564 0.0389 177 Q 0.0047 0.9604 0.0349 178 M 0.0047 0.9594 0.0359 179 A 0.0047 0.9578 0.0375 180 S 0.0048 0.9522 0.0431 181 E 0.0057 0.9280 0.0663 182 R 0.0084 0.8677 0.1239 183 L 0.0498 0.4815 0.4688 184 G 0.0409 0.0446 0.9145 185 V 0.0810 0.0174 0.9017 186 E 0.1875 0.0244 0.7880 187 F 0.5733 0.0323 0.3944 188 G 0.7149 0.0285 0.2566 189 I 0.8604 0.0123 0.1274 190 V 0.8431 0.0124 0.1445 191 D 0.7083 0.0208 0.2708 192 L 0.4074 0.0999 0.4927 193 S 0.3223 0.1209 0.5569 194 L 0.2298 0.1495 0.6208 195 A 0.2099 0.0703 0.7198 196 P 0.1853 0.0734 0.7412 197 T 0.1149 0.0689 0.8161 198 P 0.0378 0.2990 0.6632 199 A 0.0329 0.2608 0.7063 200 V 0.0496 0.2864 0.6640 201 G 0.0489 0.2023 0.7488 202 D 0.0691 0.3770 0.5539 203 S 0.1169 0.5519 0.3312 204 V 0.0062 0.9419 0.0518 205 A 0.0050 0.9551 0.0399 206 R 0.0047 0.9585 0.0369 207 V 0.0047 0.9587 0.0366 208 L 0.0047 0.9560 0.0393 209 E 0.0049 0.9485 0.0466 210 E 0.0071 0.9157 0.0772 211 M 0.0285 0.7251 0.2464 212 G 0.0485 0.3004 0.6511 213 L 0.0483 0.2719 0.6797 214 E 0.0691 0.3536 0.5774 215 T 0.0820 0.3597 0.5583 216 V 0.0866 0.2061 0.7073 217 G 0.0597 0.0857 0.8546 218 T 0.0563 0.1618 0.7819 219 H 0.0435 0.5236 0.4329 220 G 0.0286 0.7465 0.2249 221 T 0.0071 0.9201 0.0728 222 T 0.0047 0.9576 0.0377 223 A 0.0047 0.9607 0.0346 224 A 0.0047 0.9606 0.0347 225 L 0.0047 0.9600 0.0353 226 A 0.0047 0.9589 0.0364 227 L 0.0048 0.9552 0.0400 228 L 0.0053 0.9509 0.0438 229 N 0.0108 0.9387 0.0505 230 D 0.0055 0.9483 0.0462 231 Q 0.0052 0.9519 0.0429 232 V 0.0058 0.9473 0.0470 233 K 0.0084 0.9337 0.0579 234 K 0.0127 0.8869 0.1004 235 G 0.0312 0.8085 0.1604 236 G 0.0191 0.8027 0.1781 237 V 0.0295 0.8311 0.1394 238 M 0.0225 0.8348 0.1427 239 A 0.0447 0.7226 0.2327 240 C 0.0784 0.4462 0.4755 241 N 0.1039 0.2083 0.6877 242 Q 0.1556 0.1130 0.7313 243 V 0.2788 0.0969 0.6243 244 G 0.2739 0.0931 0.6331 245 G 0.2484 0.1021 0.6495 246 L 0.3064 0.1201 0.5735 247 S 0.2578 0.1038 0.6384 248 G 0.3173 0.1195 0.5632 249 A 0.4525 0.0760 0.4716 250 F 0.5453 0.0513 0.4034 251 I 0.5665 0.0289 0.4046 252 P 0.3923 0.0728 0.5348 253 V 0.0827 0.5673 0.3500 254 S 0.0539 0.6048 0.3413 255 E 0.0332 0.6626 0.3042 256 D 0.0166 0.7607 0.2227 257 E 0.0073 0.9333 0.0594 258 G 0.0061 0.9398 0.0541 259 M 0.0048 0.9520 0.0433 260 I 0.0049 0.9567 0.0384 261 A 0.0049 0.9584 0.0367 262 A 0.0051 0.9542 0.0407 263 V 0.0052 0.9480 0.0468 264 Q 0.0054 0.9284 0.0663 265 N 0.0421 0.5521 0.4057 266 G 0.0253 0.1199 0.8548 267 S 0.0811 0.0595 0.8594 268 L 0.3774 0.0372 0.5854 269 N 0.2876 0.0422 0.6702 270 L 0.0105 0.8775 0.1120 271 E 0.0071 0.9045 0.0884 272 K 0.0090 0.8952 0.0958 273 L 0.0151 0.9046 0.0803 274 E 0.0292 0.8737 0.0971 275 A 0.0368 0.8347 0.1286 276 M 0.0498 0.7250 0.2252 277 T 0.1085 0.5675 0.3240 278 A 0.1712 0.3988 0.4300 279 I 0.2691 0.3537 0.3772 280 C 0.3731 0.2759 0.3510 281 S 0.3431 0.2167 0.4401 282 V 0.3139 0.1790 0.5071 283 G 0.3110 0.1167 0.5724 284 L 0.3588 0.1123 0.5289 285 D 0.3402 0.1176 0.5421 286 M 0.5337 0.0522 0.4141 287 I 0.6118 0.0252 0.3630 288 A 0.5857 0.0202 0.3942 289 I 0.4227 0.0175 0.5598 290 P 0.1707 0.0447 0.7847 291 E 0.0664 0.0854 0.8482 292 D 0.0596 0.0956 0.8448 293 T 0.0899 0.0433 0.8668 294 P 0.0728 0.0838 0.8434 295 A 0.0051 0.9105 0.0845 296 E 0.0048 0.9384 0.0568 297 T 0.0048 0.9453 0.0499 298 I 0.0047 0.9557 0.0396 299 A 0.0047 0.9563 0.0390 300 A 0.0047 0.9564 0.0389 301 M 0.0047 0.9572 0.0380 302 I 0.0048 0.9560 0.0392 303 A 0.0047 0.9583 0.0370 304 D 0.0048 0.9547 0.0405 305 E 0.0049 0.9559 0.0392 306 A 0.0050 0.9556 0.0394 307 A 0.0055 0.9511 0.0433 308 I 0.0083 0.9451 0.0466 309 G 0.0112 0.9365 0.0523 310 V 0.0120 0.9120 0.0760 311 I 0.0364 0.7377 0.2259 312 N 0.0308 0.3567 0.6125 313 M 0.0326 0.0867 0.8807 314 K 0.0920 0.0199 0.8880 315 T 0.2654 0.0104 0.7242 316 T 0.4890 0.0288 0.4822 317 A 0.8397 0.0070 0.1534 318 V 0.9092 0.0038 0.0871 319 R 0.9150 0.0037 0.0813 320 I 0.9000 0.0049 0.0950 321 I 0.8477 0.0057 0.1466 322 P 0.6700 0.0089 0.3210 323 K 0.2879 0.0224 0.6897 324 G 0.0735 0.0444 0.8822 325 K 0.0432 0.0465 0.9103 326 E 0.0786 0.0540 0.8674 327 G 0.1243 0.0720 0.8037 328 D 0.2835 0.1168 0.5996 329 M 0.5678 0.1084 0.3239 330 I 0.6763 0.0905 0.2332 331 E 0.6258 0.1105 0.2638 332 F 0.4021 0.1317 0.4661 333 G 0.1939 0.1216 0.6845 334 G 0.1934 0.1504 0.6562 335 L 0.2981 0.2075 0.4943 336 L 0.2949 0.1546 0.5506 337 G 0.2385 0.0880 0.6735 338 T 0.3104 0.0439 0.6457 339 A 0.3560 0.0141 0.6299 340 P 0.3846 0.0115 0.6040 341 V 0.7114 0.0151 0.2735 342 M 0.7272 0.0128 0.2600 343 K 0.6714 0.0078 0.3208 344 V 0.4784 0.0278 0.4938 345 N 0.2088 0.0480 0.7432 346 G 0.0756 0.1063 0.8181 347 A 0.0845 0.0831 0.8324 348 S 0.1015 0.0663 0.8321 349 S 0.0221 0.7329 0.2451 350 V 0.0088 0.9099 0.0813 351 D 0.0088 0.9262 0.0651 352 F 0.0157 0.9147 0.0696 353 I 0.0257 0.8753 0.0990 354 S 0.0286 0.8126 0.1588 355 R 0.0439 0.5586 0.3976 356 G 0.0508 0.1522 0.7970 357 G 0.0751 0.0828 0.8421 358 Q 0.1479 0.0607 0.7914 359 I 0.1252 0.0302 0.8446 360 P 0.0564 0.0194 0.9241