# This file is the result of combining several RDB files, specifically # T0398.t04.dssp-ebghstl.rdb (weight 1.53986) # T0398.t04.stride-ebghtl.rdb (weight 1.24869) # T0398.t04.str2.rdb (weight 1.54758) # T0398.t04.alpha.rdb (weight 0.659012) # T0398.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0398.t2k.stride-ebghtl.rdb (weight 1.24869) # T0398.t2k.str2.rdb (weight 1.54758) # T0398.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 T0398.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0398 # Using neural net t04-2621-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 T0398.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 1138.46 # # ============================================ # Comments from T0398.t04.stride-ebghtl.rdb # ============================================ # TARGET T0398 # 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 T0398.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 1138.46 # # ============================================ # Comments from T0398.t04.str2.rdb # ============================================ # TARGET T0398 # 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 T0398.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 1138.46 # # ============================================ # Comments from T0398.t04.alpha.rdb # ============================================ # TARGET T0398 # 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 T0398.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 1138.46 # # ============================================ # Comments from T0398.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0398 # 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 T0398.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 1610 # # ============================================ # Comments from T0398.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0398 # 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 T0398.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 1610 # # ============================================ # Comments from T0398.t2k.str2.rdb # ============================================ # TARGET T0398 # 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 T0398.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 1610 # # ============================================ # Comments from T0398.t2k.alpha.rdb # ============================================ # TARGET T0398 # 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 T0398.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 1610 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0887 0.0646 0.8466 2 L 0.1124 0.0898 0.7978 3 T 0.1966 0.0651 0.7383 4 G 0.4371 0.0262 0.5367 5 K 0.7131 0.0115 0.2754 6 H 0.8395 0.0082 0.1523 7 V 0.8724 0.0072 0.1204 8 V 0.8751 0.0071 0.1178 9 I 0.8230 0.0123 0.1647 10 I 0.4646 0.0198 0.5156 11 G 0.1333 0.0640 0.8027 12 G 0.0324 0.2474 0.7202 13 D 0.0386 0.3959 0.5655 14 A 0.0173 0.8267 0.1560 15 R 0.0078 0.9014 0.0907 16 Q 0.0076 0.9346 0.0579 17 L 0.0068 0.9412 0.0520 18 E 0.0091 0.9364 0.0545 19 I 0.0080 0.9384 0.0536 20 I 0.0126 0.8867 0.1007 21 R 0.0144 0.7719 0.2138 22 K 0.0340 0.7942 0.1718 23 L 0.1246 0.7435 0.1319 24 S 0.1830 0.6857 0.1313 25 T 0.2719 0.5923 0.1358 26 F 0.2403 0.5162 0.2435 27 D 0.2214 0.3498 0.4288 28 A 0.2421 0.2534 0.5046 29 K 0.3344 0.1783 0.4874 30 I 0.5018 0.1438 0.3543 31 S 0.5309 0.1327 0.3364 32 L 0.4760 0.1650 0.3590 33 V 0.3043 0.1619 0.5337 34 G 0.1657 0.1253 0.7090 35 F 0.1285 0.0831 0.7884 36 D 0.1087 0.0936 0.7977 37 Q 0.0775 0.1121 0.8103 38 L 0.0240 0.7478 0.2283 39 D 0.0091 0.8874 0.1035 40 D 0.0097 0.8872 0.1031 41 G 0.0140 0.8980 0.0880 42 F 0.0188 0.9032 0.0780 43 I 0.0242 0.8804 0.0954 44 G 0.0247 0.8565 0.1187 45 V 0.0392 0.7942 0.1666 46 T 0.0545 0.7548 0.1907 47 K 0.0764 0.6998 0.2238 48 M 0.1231 0.5915 0.2855 49 R 0.1109 0.5471 0.3420 50 I 0.1068 0.4794 0.4138 51 D 0.0493 0.6653 0.2854 52 E 0.0315 0.7500 0.2185 53 V 0.0444 0.7574 0.1981 54 D 0.0602 0.7276 0.2122 55 W 0.0925 0.6109 0.2966 56 N 0.0955 0.4806 0.4238 57 T 0.0953 0.3201 0.5846 58 V 0.1242 0.1924 0.6833 59 D 0.1871 0.1369 0.6760 60 A 0.4563 0.0983 0.4454 61 I 0.6471 0.0561 0.2968 62 L 0.7393 0.0345 0.2262 63 L 0.7214 0.0227 0.2559 64 P 0.5382 0.0337 0.4281 65 I 0.3058 0.0416 0.6526 66 S 0.1998 0.0557 0.7445 67 G 0.1290 0.0782 0.7927 68 T 0.0852 0.1040 0.8108 69 N 0.0596 0.3198 0.6205 70 E 0.0277 0.4448 0.5275 71 A 0.0498 0.4482 0.5020 72 G 0.1326 0.4638 0.4036 73 K 0.2537 0.4527 0.2936 74 V 0.3636 0.4302 0.2063 75 D 0.4163 0.3691 0.2146 76 T 0.3669 0.3439 0.2892 77 I 0.2410 0.3942 0.3648 78 F 0.2212 0.2815 0.4974 79 S 0.2859 0.2096 0.5045 80 N 0.3791 0.1891 0.4318 81 E 0.3878 0.1668 0.4454 82 S 0.3536 0.1486 0.4978 83 I 0.2551 0.1748 0.5701 84 V 0.2529 0.2411 0.5060 85 L 0.2808 0.2177 0.5015 86 T 0.1625 0.2255 0.6120 87 E 0.0168 0.8037 0.1795 88 E 0.0147 0.8018 0.1835 89 M 0.0177 0.7928 0.1895 90 I 0.0310 0.7253 0.2438 91 E 0.0343 0.6074 0.3583 92 K 0.0488 0.5122 0.4390 93 T 0.0948 0.3504 0.5548 94 P 0.0962 0.2631 0.6407 95 N 0.1548 0.2375 0.6077 96 H 0.2967 0.1761 0.5271 97 C 0.5143 0.0937 0.3920 98 V 0.6489 0.0739 0.2772 99 V 0.7784 0.0459 0.1757 100 Y 0.8022 0.0451 0.1527 101 S 0.7553 0.0565 0.1882 102 G 0.6091 0.0734 0.3176 103 I 0.4502 0.0804 0.4695 104 S 0.3296 0.0738 0.5966 105 N 0.2034 0.2343 0.5623 106 T 0.1400 0.3796 0.4804 107 Y 0.1298 0.4702 0.4000 108 L 0.1232 0.4753 0.4015 109 N 0.0920 0.5623 0.3457 110 Q 0.0802 0.6333 0.2866 111 C 0.0791 0.6901 0.2308 112 M 0.0891 0.7250 0.1860 113 K 0.0605 0.7849 0.1546 114 K 0.0597 0.7840 0.1563 115 T 0.0314 0.8594 0.1092 116 N 0.0383 0.8570 0.1046 117 R 0.0382 0.8388 0.1230 118 T 0.0394 0.7971 0.1634 119 L 0.0309 0.8299 0.1392 120 V 0.0262 0.8220 0.1519 121 K 0.0217 0.7994 0.1789 122 L 0.0241 0.7559 0.2200 123 M 0.0349 0.6644 0.3007 124 E 0.0304 0.6195 0.3501 125 R 0.0210 0.6756 0.3034 126 D 0.0238 0.6685 0.3077 127 D 0.0192 0.7510 0.2297 128 I 0.0168 0.8385 0.1447 129 A 0.0131 0.8537 0.1332 130 I 0.0129 0.8660 0.1211 131 Y 0.0147 0.8560 0.1293 132 N 0.0208 0.8304 0.1487 133 S 0.0265 0.8204 0.1531 134 I 0.0356 0.8244 0.1400 135 P 0.0364 0.8177 0.1458 136 T 0.0406 0.7822 0.1772 137 A 0.0448 0.7360 0.2192 138 E 0.0574 0.7292 0.2133 139 G 0.0708 0.7191 0.2102 140 T 0.0703 0.7181 0.2116 141 I 0.0775 0.6516 0.2709 142 M 0.0681 0.5937 0.3382 143 M 0.0786 0.5122 0.4092 144 A 0.0914 0.4827 0.4258 145 I 0.1164 0.4064 0.4772 146 Q 0.1068 0.3353 0.5580 147 H 0.1233 0.2768 0.6000 148 T 0.1775 0.1659 0.6566 149 D 0.2128 0.1022 0.6850 150 F 0.4288 0.0796 0.4915 151 T 0.5035 0.0692 0.4273 152 I 0.3439 0.0599 0.5961 153 H 0.0998 0.0605 0.8398 154 G 0.0531 0.0472 0.8996 155 A 0.2669 0.0150 0.7181 156 N 0.7690 0.0045 0.2264 157 V 0.9231 0.0055 0.0715 158 A 0.9302 0.0033 0.0665 159 V 0.9297 0.0034 0.0670 160 L 0.8460 0.0332 0.1208 161 G 0.4537 0.0234 0.5229 162 L 0.1164 0.0841 0.7996 163 G 0.0563 0.2737 0.6700 164 R 0.0096 0.9204 0.0701 165 V 0.0056 0.9376 0.0568 166 G 0.0048 0.9517 0.0435 167 M 0.0048 0.9589 0.0363 168 S 0.0047 0.9600 0.0354 169 V 0.0047 0.9596 0.0357 170 A 0.0047 0.9599 0.0354 171 R 0.0047 0.9596 0.0357 172 K 0.0047 0.9583 0.0371 173 F 0.0048 0.9552 0.0400 174 A 0.0051 0.9327 0.0622 175 A 0.0054 0.8371 0.1574 176 L 0.0420 0.2986 0.6594 177 G 0.0501 0.0134 0.9365 178 A 0.0888 0.0071 0.9041 179 K 0.5740 0.0049 0.4211 180 V 0.9149 0.0030 0.0821 181 K 0.9276 0.0036 0.0688 182 V 0.9251 0.0035 0.0715 183 G 0.8422 0.0159 0.1419 184 A 0.4768 0.0076 0.5157 185 R 0.0680 0.0430 0.8890 186 E 0.0997 0.0223 0.8780 187 S 0.0155 0.5322 0.4522 188 D 0.0185 0.6385 0.3429 189 L 0.0140 0.7752 0.2108 190 L 0.0076 0.8643 0.1281 191 A 0.0107 0.8746 0.1147 192 R 0.0094 0.9046 0.0860 193 I 0.0089 0.9110 0.0801 194 A 0.0076 0.9124 0.0801 195 E 0.0081 0.8575 0.1343 196 M 0.0405 0.4989 0.4607 197 G 0.0365 0.1281 0.8354 198 M 0.0808 0.0795 0.8397 199 E 0.2239 0.1133 0.6628 200 P 0.3851 0.1677 0.4472 201 F 0.3927 0.1559 0.4514 202 H 0.3468 0.1557 0.4975 203 I 0.1402 0.3600 0.4998 204 S 0.0617 0.4612 0.4771 205 K 0.0491 0.5269 0.4240 206 A 0.0629 0.5362 0.4009 207 A 0.0961 0.4898 0.4141 208 Q 0.1181 0.3787 0.5033 209 E 0.2765 0.2560 0.4674 210 L 0.5279 0.1145 0.3576 211 R 0.6946 0.0639 0.2415 212 D 0.8117 0.0444 0.1439 213 V 0.8382 0.0284 0.1334 214 D 0.8195 0.0226 0.1579 215 V 0.6875 0.0172 0.2953 216 C 0.4591 0.0196 0.5213 217 I 0.2124 0.0490 0.7386 218 N 0.1042 0.0461 0.8497 219 T 0.0555 0.1086 0.8360 220 I 0.0546 0.1206 0.8248 221 P 0.0724 0.1422 0.7855 222 A 0.0543 0.3209 0.6247 223 L 0.0967 0.2992 0.6041 224 V 0.2694 0.1902 0.5404 225 V 0.3466 0.0765 0.5769 226 T 0.1190 0.0786 0.8024 227 A 0.0057 0.9306 0.0636 228 N 0.0049 0.9421 0.0529 229 V 0.0051 0.9445 0.0504 230 L 0.0060 0.9359 0.0581 231 A 0.0086 0.8459 0.1455 232 E 0.0157 0.5843 0.4000 233 M 0.0752 0.1676 0.7571 234 P 0.0704 0.0387 0.8909 235 S 0.0387 0.0992 0.8621 236 H 0.0704 0.0451 0.8845 237 T 0.6947 0.0081 0.2972 238 F 0.9224 0.0033 0.0743 239 V 0.9316 0.0034 0.0650 240 I 0.9181 0.0046 0.0774 241 D 0.8638 0.0058 0.1304 242 L 0.5470 0.0411 0.4119 243 A 0.3049 0.0628 0.6323 244 S 0.1337 0.1053 0.7610 245 K 0.0700 0.1150 0.8150 246 P 0.0689 0.1629 0.7682 247 G 0.1040 0.1937 0.7023 248 G 0.1384 0.2093 0.6523 249 T 0.1636 0.1983 0.6381 250 D 0.0264 0.6732 0.3004 251 F 0.0090 0.9201 0.0709 252 R 0.0072 0.9397 0.0531 253 Y 0.0060 0.9460 0.0479 254 A 0.0063 0.9450 0.0488 255 E 0.0076 0.9246 0.0677 256 K 0.0088 0.8762 0.1149 257 R 0.0370 0.5920 0.3710 258 G 0.0348 0.1635 0.8017 259 I 0.1112 0.1051 0.7836 260 K 0.2400 0.0726 0.6874 261 A 0.5726 0.0465 0.3809 262 L 0.7105 0.0358 0.2537 263 L 0.6428 0.0431 0.3141 264 V 0.4604 0.0599 0.4797 265 P 0.1818 0.1094 0.7088 266 G 0.1551 0.0752 0.7697 267 L 0.2059 0.0467 0.7474 268 P 0.2706 0.0638 0.6656 269 G 0.3793 0.1167 0.5040 270 I 0.4555 0.1105 0.4340 271 V 0.3578 0.0862 0.5559 272 A 0.1890 0.0677 0.7433 273 P 0.0934 0.0680 0.8386 274 K 0.0774 0.1039 0.8187 275 T 0.0832 0.1705 0.7464 276 A 0.0470 0.3521 0.6010 277 G 0.0240 0.5998 0.3762 278 R 0.0174 0.8279 0.1548 279 I 0.0169 0.8585 0.1246 280 L 0.0205 0.8503 0.1292 281 A 0.0247 0.7842 0.1910 282 D 0.0346 0.6255 0.3399 283 V 0.0632 0.5110 0.4258 284 L 0.1163 0.3712 0.5126 285 V 0.1253 0.4165 0.4582 286 K 0.1545 0.4704 0.3751 287 L 0.2560 0.4651 0.2790 288 L 0.3518 0.3607 0.2875 289 A 0.2932 0.2584 0.4484 290 E 0.2465 0.0830 0.6705 291 P 0.1423 0.0400 0.8177 292 S 0.0551 0.0334 0.9115