# This file is the result of combining several RDB files, specifically # T0282.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0282.t2k.stride-ebghtl.rdb (weight 1.24869) # T0282.t2k.str2.rdb (weight 1.54758) # T0282.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 T0282.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0282 # 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 T0282.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 235 # # ============================================ # Comments from T0282.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0282 # 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 T0282.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 235 # # ============================================ # Comments from T0282.t2k.str2.rdb # ============================================ # TARGET T0282 # 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 T0282.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 235 # # ============================================ # Comments from T0282.t2k.alpha.rdb # ============================================ # TARGET T0282 # 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 T0282.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 235 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0829 0.0396 0.8775 2 N 0.1164 0.0390 0.8446 3 P 0.0826 0.1500 0.7674 4 N 0.0683 0.1489 0.7828 5 F 0.0943 0.1308 0.7749 6 T 0.1237 0.1110 0.7653 7 T 0.1191 0.0956 0.7853 8 E 0.0654 0.3234 0.6112 9 H 0.0949 0.3256 0.5794 10 T 0.0864 0.4364 0.4772 11 W 0.0830 0.4268 0.4902 12 Q 0.0764 0.3022 0.6214 13 G 0.0960 0.1733 0.7306 14 R 0.1554 0.1199 0.7246 15 H 0.2269 0.0810 0.6920 16 D 0.1152 0.0677 0.8171 17 P 0.0227 0.3774 0.6000 18 E 0.0223 0.3499 0.6278 19 D 0.0515 0.3408 0.6077 20 G 0.0421 0.3239 0.6339 21 Q 0.0587 0.3568 0.5844 22 A 0.0830 0.3837 0.5333 23 G 0.1226 0.3364 0.5411 24 R 0.1684 0.3478 0.4837 25 R 0.3064 0.3492 0.3443 26 V 0.3721 0.3428 0.2851 27 H 0.3869 0.2758 0.3373 28 H 0.3770 0.2004 0.4227 29 I 0.4058 0.1627 0.4316 30 A 0.3683 0.1116 0.5201 31 C 0.2320 0.0997 0.6683 32 P 0.1387 0.2978 0.5635 33 I 0.1360 0.3183 0.5457 34 Q 0.1300 0.3038 0.5662 35 V 0.1309 0.1609 0.7082 36 G 0.1089 0.1437 0.7474 37 E 0.1186 0.1367 0.7447 38 L 0.0838 0.1772 0.7390 39 A 0.0762 0.1973 0.7265 40 N 0.0411 0.3760 0.5830 41 Q 0.0460 0.3069 0.6471 42 E 0.0701 0.1556 0.7742 43 P 0.1422 0.0221 0.8358 44 G 0.2592 0.0345 0.7063 45 V 0.9092 0.0046 0.0862 46 A 0.9301 0.0033 0.0666 47 L 0.9266 0.0036 0.0698 48 I 0.8701 0.0199 0.1100 49 G 0.6997 0.0113 0.2891 50 F 0.4211 0.0151 0.5638 51 E 0.3393 0.0375 0.6232 52 C 0.2126 0.1016 0.6858 53 D 0.1418 0.1479 0.7103 54 A 0.0848 0.1864 0.7288 55 G 0.0981 0.1487 0.7532 56 V 0.1927 0.1419 0.6654 57 E 0.2004 0.1664 0.6332 58 R 0.1204 0.2243 0.6553 59 N 0.0915 0.1840 0.7245 60 K 0.0626 0.1378 0.7996 61 G 0.0567 0.1043 0.8390 62 R 0.0747 0.1015 0.8238 63 T 0.0775 0.2170 0.7055 64 G 0.0682 0.2792 0.6527 65 A 0.0709 0.4011 0.5280 66 K 0.0482 0.5447 0.4071 67 H 0.0714 0.4757 0.4529 68 A 0.0549 0.3662 0.5789 69 P 0.0083 0.8838 0.1079 70 S 0.0048 0.9460 0.0492 71 L 0.0048 0.9530 0.0422 72 I 0.0047 0.9550 0.0402 73 K 0.0048 0.9531 0.0421 74 Q 0.0057 0.9380 0.0564 75 A 0.0056 0.9040 0.0904 76 L 0.0091 0.8580 0.1329 77 A 0.0112 0.7496 0.2392 78 N 0.0263 0.5984 0.3753 79 L 0.0430 0.4459 0.5111 80 A 0.0501 0.3816 0.5683 81 W 0.0477 0.3204 0.6319 82 H 0.0620 0.1946 0.7434 83 H 0.0796 0.1039 0.8166 84 P 0.0849 0.0783 0.8368 85 I 0.1176 0.0346 0.8478 86 P 0.2813 0.0280 0.6908 87 I 0.4998 0.0341 0.4661 88 Y 0.6334 0.0338 0.3328 89 D 0.5683 0.0246 0.4071 90 L 0.2726 0.1582 0.5692 91 G 0.2062 0.1328 0.6610 92 N 0.1864 0.1331 0.6805 93 I 0.2865 0.0430 0.6705 94 R 0.2609 0.0369 0.7022 95 C 0.2003 0.0421 0.7576 96 E 0.1074 0.0453 0.8473 97 G 0.0507 0.1795 0.7698 98 D 0.0424 0.1724 0.7852 99 E 0.0782 0.1645 0.7573 100 L 0.0073 0.9001 0.0926 101 E 0.0052 0.9372 0.0575 102 Q 0.0052 0.9451 0.0496 103 A 0.0048 0.9513 0.0439 104 Q 0.0047 0.9569 0.0384 105 Q 0.0047 0.9573 0.0380 106 E 0.0047 0.9564 0.0389 107 C 0.0047 0.9561 0.0392 108 A 0.0047 0.9575 0.0378 109 Q 0.0048 0.9537 0.0415 110 V 0.0048 0.9522 0.0429 111 I 0.0049 0.9436 0.0514 112 Q 0.0050 0.9338 0.0612 113 Q 0.0059 0.9074 0.0867 114 A 0.0099 0.8372 0.1529 115 L 0.0305 0.6048 0.3647 116 P 0.0342 0.2258 0.7400 117 H 0.0277 0.0668 0.9055 118 A 0.0752 0.0254 0.8994 119 R 0.3238 0.0104 0.6658 120 A 0.7465 0.0064 0.2471 121 I 0.9014 0.0069 0.0917 122 V 0.9094 0.0063 0.0843 123 L 0.8202 0.0257 0.1541 124 G 0.3884 0.0291 0.5825 125 G 0.0809 0.0804 0.8387 126 G 0.0437 0.3087 0.6476 127 H 0.0481 0.5218 0.4301 128 E 0.0359 0.7287 0.2354 129 I 0.0340 0.7683 0.1977 130 A 0.0261 0.8224 0.1515 131 W 0.0073 0.9244 0.0682 132 A 0.0049 0.9496 0.0455 133 T 0.0048 0.9547 0.0405 134 F 0.0047 0.9581 0.0372 135 Q 0.0047 0.9586 0.0367 136 G 0.0047 0.9592 0.0361 137 L 0.0047 0.9574 0.0379 138 A 0.0048 0.9495 0.0457 139 Q 0.0050 0.9240 0.0710 140 H 0.0063 0.8673 0.1264 141 F 0.0115 0.7710 0.2174 142 L 0.0132 0.7416 0.2452 143 A 0.0169 0.6946 0.2885 144 T 0.0415 0.5484 0.4101 145 G 0.0471 0.4424 0.5104 146 V 0.0558 0.3267 0.6175 147 K 0.0498 0.2663 0.6840 148 Q 0.0602 0.0812 0.8586 149 P 0.0738 0.0319 0.8943 150 R 0.2192 0.0184 0.7624 151 I 0.6873 0.0071 0.3056 152 G 0.8888 0.0049 0.1063 153 I 0.9302 0.0033 0.0665 154 I 0.9292 0.0035 0.0673 155 N 0.9166 0.0037 0.0797 156 F 0.8143 0.0119 0.1738 157 D 0.5026 0.0228 0.4745 158 A 0.2293 0.0848 0.6859 159 H 0.1725 0.1450 0.6825 160 F 0.1756 0.1797 0.6446 161 D 0.1609 0.1818 0.6573 162 L 0.1046 0.2146 0.6807 163 R 0.0969 0.1358 0.7673 164 T 0.0803 0.0884 0.8313 165 F 0.0793 0.1638 0.7569 166 E 0.0718 0.2016 0.7266 167 S 0.0863 0.2026 0.7111 168 E 0.1009 0.1888 0.7103 169 L 0.1275 0.1936 0.6790 170 A 0.0945 0.1704 0.7350 171 P 0.0699 0.1752 0.7550 172 V 0.0819 0.1581 0.7600 173 R 0.0855 0.1502 0.7643 174 P 0.0956 0.1642 0.7401 175 S 0.1159 0.1723 0.7118 176 S 0.0939 0.2499 0.6562 177 G 0.0688 0.3766 0.5547 178 T 0.0368 0.7313 0.2319 179 P 0.0094 0.9175 0.0731 180 F 0.0051 0.9439 0.0510 181 N 0.0055 0.9453 0.0492 182 Q 0.0053 0.9484 0.0464 183 I 0.0058 0.9411 0.0531 184 H 0.0077 0.8991 0.0932 185 H 0.0093 0.7962 0.1945 186 F 0.0271 0.6666 0.3063 187 C 0.0360 0.4547 0.5092 188 Q 0.0391 0.4026 0.5583 189 Q 0.0487 0.4283 0.5230 190 Q 0.0515 0.3083 0.6403 191 G 0.0635 0.1313 0.8052 192 W 0.0734 0.0751 0.8515 193 D 0.0929 0.1207 0.7864 194 F 0.1032 0.1336 0.7633 195 H 0.2541 0.0798 0.6661 196 Y 0.7560 0.0119 0.2321 197 A 0.8906 0.0045 0.1049 198 C 0.9170 0.0038 0.0793 199 L 0.8759 0.0122 0.1119 200 G 0.8186 0.0104 0.1711 201 V 0.6788 0.0194 0.3018 202 S 0.3786 0.0352 0.5861 203 R 0.1673 0.0662 0.7665 204 A 0.0655 0.1201 0.8144 205 S 0.0787 0.0828 0.8385 206 N 0.0797 0.0461 0.8742 207 T 0.0603 0.0395 0.9002 208 P 0.0065 0.9030 0.0905 209 A 0.0051 0.9299 0.0650 210 L 0.0052 0.9378 0.0571 211 F 0.0051 0.9485 0.0464 212 E 0.0058 0.9455 0.0487 213 R 0.0052 0.9475 0.0473 214 A 0.0058 0.9462 0.0480 215 D 0.0055 0.9351 0.0594 216 K 0.0067 0.8632 0.1301 217 L 0.0452 0.3289 0.6259 218 G 0.0386 0.0225 0.9389 219 V 0.1250 0.0098 0.8652 220 W 0.6890 0.0078 0.3032 221 Y 0.8992 0.0040 0.0968 222 V 0.8774 0.0052 0.1173 223 E 0.5754 0.0096 0.4150 224 D 0.0203 0.8052 0.1745 225 K 0.0081 0.8338 0.1581 226 A 0.0083 0.8810 0.1107 227 F 0.0107 0.8847 0.1045 228 S 0.0120 0.8506 0.1373 229 P 0.0125 0.7593 0.2282 230 L 0.0417 0.4598 0.4986 231 S 0.0509 0.1898 0.7593 232 L 0.0218 0.4986 0.4796 233 K 0.0076 0.8602 0.1321 234 D 0.0061 0.9095 0.0843 235 H 0.0061 0.9389 0.0551 236 L 0.0058 0.9477 0.0466 237 T 0.0048 0.9502 0.0450 238 Q 0.0048 0.9494 0.0459 239 L 0.0048 0.9446 0.0507 240 Q 0.0053 0.9351 0.0597 241 H 0.0062 0.9053 0.0884 242 F 0.0115 0.8423 0.1462 243 I 0.0582 0.5553 0.3865 244 D 0.0368 0.2240 0.7392 245 D 0.0402 0.1351 0.8247 246 C 0.1024 0.0648 0.8328 247 D 0.1278 0.0243 0.8478 248 Y 0.4908 0.0065 0.5027 249 L 0.8836 0.0040 0.1125 250 Y 0.9227 0.0036 0.0738 251 L 0.9215 0.0035 0.0751 252 T 0.8984 0.0051 0.0965 253 I 0.8343 0.0080 0.1577 254 D 0.7379 0.0086 0.2536 255 L 0.4355 0.1030 0.4615 256 D 0.2205 0.1749 0.6047 257 V 0.2436 0.1697 0.5867 258 F 0.2309 0.1139 0.6553 259 P 0.1619 0.1009 0.7372 260 A 0.0201 0.5948 0.3851 261 A 0.0231 0.5509 0.4260 262 S 0.0677 0.5209 0.4114 263 A 0.1499 0.1242 0.7260 264 P 0.0883 0.0960 0.8157 265 G 0.1442 0.0720 0.7838 266 V 0.1896 0.0623 0.7481 267 S 0.1397 0.0410 0.8193 268 A 0.1723 0.0280 0.7997 269 P 0.2408 0.0500 0.7092 270 A 0.1822 0.0491 0.7687 271 A 0.1142 0.0982 0.7876 272 R 0.0549 0.0664 0.8787 273 G 0.0927 0.0543 0.8530 274 V 0.2040 0.0391 0.7569 275 S 0.1066 0.0335 0.8599 276 L 0.0061 0.9231 0.0708 277 E 0.0049 0.9455 0.0496 278 A 0.0048 0.9547 0.0405 279 L 0.0047 0.9585 0.0368 280 A 0.0047 0.9597 0.0356 281 P 0.0047 0.9595 0.0358 282 Y 0.0047 0.9595 0.0358 283 F 0.0047 0.9567 0.0385 284 D 0.0047 0.9523 0.0430 285 R 0.0049 0.9315 0.0636 286 I 0.0067 0.9047 0.0886 287 L 0.0119 0.8463 0.1418 288 H 0.0126 0.6929 0.2944 289 Y 0.0288 0.4294 0.5418 290 K 0.0533 0.1204 0.8264 291 N 0.0528 0.0892 0.8579 292 K 0.2140 0.0603 0.7257 293 L 0.6124 0.0121 0.3755 294 M 0.7355 0.0275 0.2370 295 I 0.8856 0.0071 0.1073 296 A 0.8558 0.0043 0.1399 297 D 0.8142 0.0081 0.1777 298 I 0.8815 0.0050 0.1135 299 A 0.8619 0.0104 0.1276 300 E 0.8570 0.0066 0.1364 301 Y 0.6485 0.0190 0.3325 302 N 0.2456 0.0217 0.7326 303 P 0.1302 0.0790 0.7908 304 S 0.1024 0.1306 0.7671 305 F 0.1342 0.0760 0.7898 306 D 0.0807 0.0448 0.8745 307 I 0.0147 0.2625 0.7228 308 D 0.0296 0.2889 0.6814 309 Q 0.0247 0.4980 0.4773 310 H 0.0240 0.7979 0.1781 311 T 0.0234 0.8793 0.0973 312 A 0.0055 0.9520 0.0425 313 R 0.0047 0.9594 0.0359 314 L 0.0047 0.9605 0.0348 315 A 0.0047 0.9599 0.0354 316 A 0.0047 0.9605 0.0348 317 R 0.0047 0.9606 0.0347 318 L 0.0047 0.9603 0.0350 319 C 0.0047 0.9598 0.0355 320 W 0.0047 0.9600 0.0353 321 D 0.0048 0.9584 0.0368 322 I 0.0048 0.9569 0.0383 323 A 0.0047 0.9554 0.0399 324 N 0.0048 0.9472 0.0480 325 A 0.0052 0.9271 0.0677 326 M 0.0063 0.9041 0.0896 327 A 0.0186 0.8026 0.1788 328 E 0.0241 0.5820 0.3939 329 Q 0.0427 0.4083 0.5490 330 V 0.0832 0.2865 0.6303 331 Q 0.0780 0.1409 0.7811 332 S 0.0484 0.0410 0.9106