# This file is the result of combining several RDB files, specifically # T0339.t04.dssp-ebghstl.rdb (weight 1.53986) # T0339.t04.stride-ebghtl.rdb (weight 1.24869) # T0339.t04.str2.rdb (weight 1.54758) # T0339.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 T0339.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0339 # 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 T0339.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 2101 # # ============================================ # Comments from T0339.t04.stride-ebghtl.rdb # ============================================ # TARGET T0339 # 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 T0339.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 2101 # # ============================================ # Comments from T0339.t04.str2.rdb # ============================================ # TARGET T0339 # 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 T0339.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 2101 # # ============================================ # Comments from T0339.t04.alpha.rdb # ============================================ # TARGET T0339 # 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 T0339.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 2101 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 E 0.0722 0.0308 0.8970 2 R 0.2567 0.0198 0.7235 3 K 0.6675 0.0132 0.3194 4 V 0.8822 0.0074 0.1104 5 Y 0.8948 0.0071 0.0981 6 M 0.7845 0.0114 0.2040 7 D 0.4435 0.0188 0.5376 8 Y 0.1666 0.0839 0.7495 9 N 0.0928 0.1436 0.7636 10 A 0.1088 0.1405 0.7508 11 T 0.1040 0.1110 0.7850 12 T 0.1002 0.0541 0.8457 13 P 0.0982 0.0581 0.8438 14 L 0.0992 0.0295 0.8712 15 E 0.0639 0.0231 0.9130 16 P 0.0071 0.9286 0.0643 17 E 0.0048 0.9525 0.0427 18 V 0.0047 0.9574 0.0378 19 I 0.0047 0.9596 0.0357 20 Q 0.0047 0.9591 0.0362 21 A 0.0048 0.9563 0.0390 22 M 0.0048 0.9531 0.0421 23 T 0.0050 0.9529 0.0422 24 K 0.0048 0.9510 0.0442 25 A 0.0051 0.9393 0.0556 26 M 0.0052 0.9247 0.0701 27 W 0.0069 0.8978 0.0954 28 E 0.0094 0.8491 0.1414 29 A 0.0177 0.7274 0.2550 30 W 0.0503 0.3998 0.5499 31 G 0.0697 0.1260 0.8043 32 N 0.0892 0.0409 0.8699 33 P 0.0354 0.1121 0.8525 34 S 0.0405 0.1010 0.8586 35 S 0.0734 0.0874 0.8392 36 P 0.0511 0.2926 0.6563 37 Y 0.0757 0.3968 0.5275 38 S 0.0654 0.5738 0.3608 39 A 0.0559 0.6057 0.3384 40 G 0.0415 0.6458 0.3127 41 R 0.0253 0.8012 0.1735 42 K 0.0299 0.7996 0.1705 43 A 0.0140 0.8658 0.1202 44 K 0.0075 0.9221 0.0704 45 D 0.0047 0.9498 0.0455 46 I 0.0047 0.9584 0.0370 47 I 0.0047 0.9612 0.0342 48 N 0.0046 0.9616 0.0337 49 A 0.0046 0.9610 0.0343 50 A 0.0047 0.9600 0.0353 51 R 0.0047 0.9612 0.0342 52 E 0.0046 0.9615 0.0339 53 S 0.0047 0.9607 0.0346 54 L 0.0047 0.9601 0.0352 55 A 0.0047 0.9594 0.0359 56 K 0.0052 0.9514 0.0435 57 M 0.0078 0.9102 0.0821 58 I 0.0463 0.5940 0.3597 59 G 0.0317 0.0490 0.9193 60 G 0.0676 0.0136 0.9188 61 K 0.0743 0.0106 0.9152 62 P 0.0380 0.4996 0.4624 63 Q 0.0742 0.4689 0.4569 64 D 0.3477 0.3237 0.3286 65 I 0.8551 0.0308 0.1140 66 I 0.8658 0.0328 0.1015 67 F 0.8401 0.0298 0.1300 68 T 0.4464 0.0538 0.4998 69 S 0.1057 0.1159 0.7784 70 G 0.0570 0.1707 0.7724 71 G 0.0230 0.6763 0.3008 72 T 0.0074 0.8976 0.0949 73 E 0.0051 0.9495 0.0454 74 S 0.0048 0.9561 0.0391 75 N 0.0048 0.9552 0.0400 76 N 0.0047 0.9589 0.0364 77 L 0.0047 0.9594 0.0359 78 V 0.0047 0.9596 0.0357 79 I 0.0047 0.9598 0.0355 80 H 0.0047 0.9578 0.0376 81 S 0.0047 0.9515 0.0438 82 V 0.0048 0.9454 0.0498 83 V 0.0052 0.9427 0.0521 84 K 0.0056 0.9300 0.0645 85 H 0.0076 0.8930 0.0994 86 F 0.0169 0.7994 0.1837 87 H 0.0257 0.6661 0.3082 88 A 0.0289 0.5805 0.3907 89 N 0.0485 0.4151 0.5364 90 Q 0.0666 0.3018 0.6316 91 T 0.0924 0.2475 0.6601 92 S 0.0892 0.1915 0.7193 93 K 0.0868 0.1404 0.7728 94 G 0.1090 0.1002 0.7908 95 H 0.1628 0.0815 0.7557 96 T 0.1751 0.0768 0.7481 97 G 0.1233 0.0870 0.7897 98 G 0.1079 0.0940 0.7981 99 H 0.1473 0.0956 0.7570 100 H 0.1509 0.0939 0.7552 101 S 0.1196 0.0794 0.8010 102 P 0.1150 0.1575 0.7275 103 V 0.1482 0.1879 0.6639 104 K 0.1169 0.1208 0.7623 105 G 0.0906 0.0562 0.8531 106 A 0.1063 0.0674 0.8263 107 K 0.1447 0.0344 0.8209 108 P 0.2094 0.0488 0.7418 109 H 0.7974 0.0105 0.1920 110 F 0.9211 0.0037 0.0751 111 I 0.9230 0.0036 0.0735 112 T 0.8606 0.0065 0.1329 113 S 0.4704 0.0192 0.5105 114 S 0.1921 0.0784 0.7294 115 V 0.1172 0.2116 0.6712 116 E 0.1193 0.2762 0.6044 117 H 0.1127 0.2769 0.6104 118 D 0.0522 0.3080 0.6398 119 S 0.0591 0.3933 0.5477 120 I 0.0941 0.4213 0.4846 121 R 0.0891 0.5834 0.3274 122 L 0.0421 0.7475 0.2103 123 P 0.0189 0.8854 0.0957 124 L 0.0074 0.9437 0.0489 125 E 0.0061 0.9487 0.0452 126 H 0.0056 0.9498 0.0446 127 L 0.0067 0.9442 0.0491 128 V 0.0077 0.9342 0.0581 129 E 0.0089 0.9022 0.0889 130 E 0.0141 0.7439 0.2420 131 Q 0.0504 0.2873 0.6622 132 V 0.0909 0.0229 0.8862 133 A 0.3199 0.0080 0.6721 134 A 0.8530 0.0049 0.1421 135 V 0.9159 0.0033 0.0808 136 T 0.9123 0.0050 0.0827 137 F 0.8991 0.0037 0.0972 138 V 0.7941 0.0062 0.1998 139 P 0.6560 0.0051 0.3389 140 V 0.3021 0.0664 0.6315 141 S 0.1522 0.0986 0.7492 142 K 0.0454 0.2698 0.6848 143 V 0.0514 0.2066 0.7420 144 S 0.0688 0.0981 0.8331 145 G 0.0686 0.0562 0.8752 146 Q 0.2428 0.0282 0.7290 147 T 0.3751 0.0101 0.6148 148 E 0.1409 0.0102 0.8489 149 V 0.0054 0.9433 0.0513 150 D 0.0049 0.9572 0.0378 151 D 0.0047 0.9583 0.0370 152 I 0.0050 0.9542 0.0407 153 L 0.0051 0.9457 0.0492 154 A 0.0057 0.8830 0.1113 155 A 0.0093 0.7505 0.2402 156 V 0.0539 0.4109 0.5352 157 R 0.0472 0.0447 0.9081 158 P 0.0104 0.1391 0.8505 159 T 0.0231 0.0598 0.9170 160 T 0.2704 0.0152 0.7145 161 R 0.7388 0.0150 0.2462 162 L 0.9319 0.0030 0.0651 163 V 0.9309 0.0034 0.0657 164 T 0.9332 0.0032 0.0636 165 I 0.9204 0.0035 0.0761 166 M 0.7693 0.0052 0.2255 167 L 0.4652 0.0119 0.5230 168 A 0.2082 0.0567 0.7351 169 N 0.1702 0.0478 0.7821 170 N 0.0856 0.0422 0.8722 171 E 0.0349 0.1448 0.8204 172 T 0.0935 0.1162 0.7904 173 G 0.2203 0.0722 0.7075 174 I 0.4953 0.0382 0.4665 175 V 0.7407 0.0142 0.2451 176 M 0.5298 0.0164 0.4538 177 P 0.2848 0.0220 0.6932 178 V 0.0088 0.8929 0.0983 179 P 0.0048 0.9536 0.0416 180 E 0.0047 0.9560 0.0393 181 I 0.0048 0.9563 0.0389 182 S 0.0047 0.9601 0.0352 183 Q 0.0046 0.9604 0.0349 184 R 0.0047 0.9607 0.0346 185 I 0.0047 0.9592 0.0361 186 K 0.0047 0.9536 0.0417 187 A 0.0050 0.9129 0.0821 188 L 0.0256 0.6740 0.3005 189 N 0.0267 0.2203 0.7530 190 Q 0.0299 0.4517 0.5184 191 E 0.0951 0.5112 0.3937 192 R 0.1364 0.5210 0.3426 193 V 0.1629 0.4421 0.3949 194 A 0.1271 0.4188 0.4541 195 A 0.0946 0.3137 0.5916 196 G 0.0811 0.1400 0.7789 197 L 0.1170 0.0430 0.8401 198 P 0.1127 0.0492 0.8381 199 P 0.1961 0.0449 0.7590 200 I 0.5687 0.0098 0.4215 201 L 0.8695 0.0053 0.1252 202 V 0.9285 0.0051 0.0664 203 H 0.9204 0.0105 0.0692 204 T 0.8801 0.0188 0.1010 205 D 0.5396 0.0644 0.3960 206 A 0.2092 0.1856 0.6052 207 A 0.1257 0.5030 0.3713 208 Q 0.1127 0.5578 0.3295 209 A 0.1606 0.4805 0.3589 210 L 0.1256 0.3434 0.5310 211 G 0.1026 0.1771 0.7203 212 K 0.1429 0.2017 0.6553 213 Q 0.2689 0.0816 0.6495 214 R 0.3534 0.0516 0.5950 215 V 0.3857 0.0262 0.5881 216 D 0.2543 0.0180 0.7277 217 V 0.0101 0.8426 0.1473 218 E 0.0113 0.8298 0.1589 219 D 0.0092 0.8616 0.1292 220 L 0.0953 0.4270 0.4777 221 G 0.1021 0.0350 0.8628 222 V 0.1625 0.0092 0.8283 223 D 0.2948 0.0450 0.6602 224 F 0.9043 0.0048 0.0910 225 L 0.9276 0.0041 0.0683 226 T 0.9278 0.0045 0.0677 227 I 0.8634 0.0150 0.1216 228 V 0.5034 0.0326 0.4640 229 G 0.3051 0.1149 0.5800 230 H 0.2632 0.2487 0.4882 231 K 0.2795 0.3669 0.3536 232 F 0.2466 0.2854 0.4680 233 Y 0.2200 0.1526 0.6274 234 G 0.1403 0.0444 0.8153 235 P 0.0753 0.0797 0.8450 236 R 0.1377 0.0502 0.8121 237 I 0.4277 0.0263 0.5460 238 G 0.6881 0.0102 0.3017 239 A 0.9121 0.0039 0.0840 240 L 0.9258 0.0034 0.0708 241 Y 0.9212 0.0045 0.0744 242 I 0.8831 0.0067 0.1101 243 R 0.4641 0.0375 0.4984 244 G 0.1660 0.0394 0.7946 245 L 0.0584 0.1837 0.7578 246 G 0.0628 0.2059 0.7312 247 E 0.0973 0.2211 0.6817 248 F 0.1617 0.1603 0.6780 249 T 0.1483 0.1404 0.7113 250 P 0.1834 0.1505 0.6662 251 L 0.2125 0.1378 0.6496 252 Y 0.2001 0.1151 0.6848 253 P 0.1551 0.2699 0.5750 254 M 0.2244 0.2927 0.4829 255 L 0.3042 0.2327 0.4631 256 F 0.2241 0.1630 0.6129 257 G 0.1270 0.1075 0.7655 258 G 0.1038 0.0910 0.8051 259 G 0.0954 0.0862 0.8184 260 Q 0.1160 0.0856 0.7984 261 E 0.1272 0.1493 0.7234 262 R 0.1042 0.1708 0.7251 263 N 0.1219 0.1139 0.7642 264 F 0.1223 0.0969 0.7808 265 R 0.1244 0.0872 0.7884 266 P 0.0869 0.1574 0.7557 267 G 0.0712 0.1508 0.7780 268 T 0.0909 0.1302 0.7788 269 E 0.0582 0.1973 0.7445 270 N 0.0359 0.2947 0.6694 271 T 0.0189 0.7324 0.2488 272 P 0.0080 0.9017 0.0904 273 M 0.0060 0.9400 0.0540 274 I 0.0054 0.9477 0.0469 275 A 0.0050 0.9478 0.0472 276 G 0.0051 0.9439 0.0511 277 L 0.0048 0.9540 0.0412 278 G 0.0047 0.9594 0.0360 279 K 0.0047 0.9598 0.0355 280 A 0.0047 0.9595 0.0358 281 A 0.0047 0.9593 0.0360 282 E 0.0047 0.9551 0.0402 283 L 0.0048 0.9423 0.0529 284 V 0.0052 0.9094 0.0855 285 T 0.0054 0.8448 0.1498 286 Q 0.0062 0.7326 0.2612 287 N 0.0089 0.6190 0.3721 288 C 0.0055 0.8887 0.1058 289 E 0.0053 0.9405 0.0542 290 A 0.0050 0.9464 0.0486 291 Y 0.0054 0.9455 0.0492 292 E 0.0051 0.9378 0.0570 293 A 0.0054 0.8768 0.1178 294 H 0.0066 0.8080 0.1855 295 M 0.0075 0.8462 0.1463 296 R 0.0052 0.9341 0.0607 297 D 0.0053 0.9349 0.0598 298 V 0.0050 0.9479 0.0471 299 R 0.0048 0.9556 0.0397 300 D 0.0047 0.9533 0.0420 301 Y 0.0048 0.9495 0.0457 302 L 0.0050 0.9398 0.0551 303 E 0.0048 0.9489 0.0464 304 E 0.0049 0.9433 0.0518 305 R 0.0051 0.9272 0.0677 306 L 0.0065 0.9038 0.0897 307 E 0.0088 0.8475 0.1437 308 A 0.0106 0.7582 0.2312 309 E 0.0349 0.4437 0.5214 310 F 0.0438 0.1881 0.7681 311 G 0.0356 0.0529 0.9115 312 Q 0.1492 0.0403 0.8104 313 K 0.3714 0.0242 0.6044 314 R 0.6873 0.0194 0.2933 315 I 0.8241 0.0080 0.1679 316 H 0.8816 0.0097 0.1088 317 L 0.8070 0.0192 0.1738 318 N 0.5238 0.0351 0.4411 319 S 0.2421 0.0461 0.7117 320 Q 0.1411 0.0521 0.8068 321 F 0.1202 0.0559 0.8239 322 P 0.0737 0.0980 0.8283 323 G 0.0534 0.1681 0.7785 324 T 0.0874 0.2986 0.6140 325 Q 0.0993 0.2751 0.6256 326 R 0.1669 0.1574 0.6758 327 L 0.1976 0.0469 0.7555 328 P 0.1538 0.0782 0.7680 329 N 0.3132 0.0473 0.6395 330 T 0.6833 0.0173 0.2994 331 C 0.7945 0.0106 0.1948 332 N 0.8683 0.0072 0.1245 333 F 0.8784 0.0072 0.1144 334 S 0.8665 0.0067 0.1268 335 I 0.6933 0.0145 0.2922 336 R 0.2892 0.0350 0.6758 337 G 0.0867 0.0512 0.8621 338 P 0.0786 0.1652 0.7562 339 R 0.1005 0.2529 0.6467 340 L 0.1303 0.3110 0.5588 341 Q 0.0900 0.3776 0.5324 342 G 0.0108 0.8940 0.0952 343 H 0.0067 0.9503 0.0429 344 V 0.0055 0.9584 0.0361 345 V 0.0049 0.9588 0.0363 346 L 0.0055 0.9562 0.0383 347 A 0.0057 0.9472 0.0471 348 Q 0.0064 0.9201 0.0735 349 C 0.0080 0.8950 0.0969 350 R 0.0181 0.8115 0.1704 351 V 0.0663 0.8119 0.1217 352 L 0.1246 0.7714 0.1040 353 M 0.1996 0.6506 0.1498 354 A 0.2436 0.5186 0.2378 355 S 0.2644 0.3644 0.3713 356 V 0.1752 0.3361 0.4887 357 G 0.1518 0.2119 0.6364 358 A 0.2325 0.2635 0.5040 359 A 0.2624 0.3090 0.4286 360 C 0.2847 0.2195 0.4958 361 H 0.2455 0.1365 0.6180 362 S 0.1300 0.0670 0.8030 363 D 0.0682 0.1234 0.8084 364 H 0.0717 0.1221 0.8062 365 G 0.0869 0.0851 0.8279 366 D 0.0835 0.0676 0.8490 367 Q 0.1105 0.0450 0.8445 368 P 0.1030 0.0943 0.8027 369 S 0.0882 0.2227 0.6890 370 P 0.0786 0.4320 0.4894 371 V 0.0989 0.5564 0.3447 372 L 0.0987 0.6158 0.2855 373 L 0.0408 0.7166 0.2426 374 S 0.0365 0.6618 0.3017 375 Y 0.0661 0.3111 0.6228 376 G 0.0528 0.0782 0.8690 377 V 0.0755 0.0239 0.9006 378 P 0.1067 0.0465 0.8468 379 F 0.0607 0.3871 0.5521 380 D 0.0660 0.3909 0.5432 381 V 0.1240 0.3490 0.5270 382 A 0.1652 0.1821 0.6527 383 R 0.1274 0.2357 0.6369 384 N 0.2208 0.1020 0.6772 385 A 0.7545 0.0246 0.2209 386 L 0.8935 0.0084 0.0982 387 R 0.9156 0.0071 0.0773 388 L 0.8741 0.0192 0.1067 389 S 0.7438 0.0253 0.2309 390 V 0.4568 0.0616 0.4816 391 G 0.2621 0.0871 0.6508 392 R 0.1633 0.1755 0.6612 393 S 0.1193 0.1459 0.7348 394 T 0.1219 0.0516 0.8265 395 T 0.0700 0.0417 0.8883 396 R 0.0048 0.9427 0.0525 397 A 0.0048 0.9561 0.0392 398 E 0.0047 0.9584 0.0369 399 V 0.0047 0.9608 0.0346 400 D 0.0046 0.9608 0.0346 401 L 0.0046 0.9588 0.0366 402 V 0.0047 0.9578 0.0375 403 V 0.0047 0.9606 0.0347 404 Q 0.0047 0.9603 0.0350 405 D 0.0047 0.9573 0.0381 406 L 0.0047 0.9596 0.0357 407 K 0.0047 0.9609 0.0344 408 Q 0.0047 0.9612 0.0341 409 A 0.0047 0.9586 0.0366 410 V 0.0047 0.9562 0.0391 411 A 0.0048 0.9409 0.0543 412 Q 0.0056 0.8904 0.1040 413 L 0.0078 0.7605 0.2317 414 E 0.0101 0.5666 0.4233 415 D 0.0165 0.3411 0.6425 416 Q 0.0290 0.0872 0.8838