# This file is the result of combining several RDB files, specifically # T0305.t06.dssp-ebghstl.rdb (weight 1.53986) # T0305.t06.stride-ebghtl.rdb (weight 1.24869) # T0305.t06.str2.rdb (weight 1.54758) # T0305.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 T0305.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1149 # # ============================================ # Comments from T0305.t06.stride-ebghtl.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1149 # # ============================================ # Comments from T0305.t06.str2.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1149 # # ============================================ # Comments from T0305.t06.alpha.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1149 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Y 0.0723 0.0879 0.8397 2 F 0.1158 0.0924 0.7918 3 Q 0.1566 0.1271 0.7162 4 S 0.1475 0.1047 0.7477 5 M 0.0089 0.8928 0.0983 6 K 0.0055 0.9377 0.0568 7 Q 0.0051 0.9446 0.0503 8 F 0.0048 0.9523 0.0429 9 V 0.0050 0.9542 0.0407 10 K 0.0051 0.9505 0.0444 11 H 0.0061 0.9374 0.0566 12 I 0.0086 0.9142 0.0772 13 G 0.0136 0.8647 0.1218 14 E 0.0169 0.8500 0.1332 15 L 0.0274 0.7949 0.1777 16 Y 0.0673 0.5829 0.3499 17 S 0.0273 0.4830 0.4898 18 N 0.0287 0.2723 0.6989 19 N 0.0451 0.1588 0.7961 20 Q 0.0296 0.2834 0.6870 21 H 0.0505 0.3049 0.6445 22 G 0.0739 0.3091 0.6170 23 F 0.0664 0.6285 0.3051 24 S 0.0244 0.8504 0.1253 25 E 0.0168 0.9103 0.0730 26 D 0.0145 0.9135 0.0720 27 F 0.0084 0.9286 0.0630 28 E 0.0070 0.9332 0.0598 29 E 0.0081 0.9124 0.0795 30 V 0.0124 0.8644 0.1233 31 Q 0.0173 0.8211 0.1616 32 R 0.0355 0.6658 0.2986 33 C 0.0846 0.4083 0.5071 34 T 0.1185 0.1126 0.7688 35 A 0.0637 0.2407 0.6956 36 D 0.0861 0.2117 0.7022 37 M 0.1303 0.2015 0.6682 38 N 0.1540 0.1107 0.7353 39 I 0.3038 0.0841 0.6121 40 T 0.3685 0.0977 0.5338 41 A 0.2294 0.3001 0.4705 42 E 0.2053 0.3349 0.4598 43 H 0.1645 0.3697 0.4658 44 S 0.1103 0.2218 0.6679 45 N 0.0821 0.1477 0.7702 46 H 0.0724 0.0381 0.8895 47 P 0.0154 0.4277 0.5569 48 E 0.0245 0.4464 0.5291 49 N 0.0618 0.4660 0.4722 50 K 0.0403 0.5054 0.4543 51 H 0.0520 0.4859 0.4621 52 K 0.0740 0.4127 0.5133 53 N 0.1389 0.2221 0.6390 54 R 0.1786 0.1604 0.6610 55 Y 0.2657 0.1329 0.6014 56 I 0.2074 0.1230 0.6696 57 N 0.2252 0.0668 0.7080 58 I 0.3868 0.0519 0.5613 59 L 0.3965 0.0501 0.5534 60 A 0.3389 0.0811 0.5800 61 Y 0.2161 0.1247 0.6592 62 D 0.1396 0.1737 0.6867 63 H 0.1191 0.1399 0.7410 64 S 0.2855 0.0633 0.6512 65 R 0.5331 0.0287 0.4383 66 V 0.8110 0.0086 0.1804 67 K 0.8174 0.0079 0.1747 68 L 0.6804 0.0103 0.3092 69 R 0.4959 0.0120 0.4921 70 P 0.3858 0.0160 0.5982 71 L 0.1855 0.0234 0.7911 72 P 0.0697 0.0626 0.8677 73 G 0.0454 0.0515 0.9031 74 K 0.1064 0.0519 0.8417 75 D 0.1243 0.0545 0.8211 76 S 0.0836 0.0611 0.8553 77 K 0.0775 0.0816 0.8409 78 H 0.1083 0.1089 0.7829 79 S 0.1299 0.0865 0.7836 80 D 0.2506 0.0701 0.6792 81 Y 0.6848 0.0316 0.2836 82 I 0.7822 0.0210 0.1968 83 N 0.7111 0.0197 0.2692 84 A 0.5243 0.0692 0.4065 85 N 0.4534 0.1023 0.4443 86 Y 0.4877 0.0967 0.4156 87 V 0.4977 0.0354 0.4670 88 D 0.3394 0.0560 0.6045 89 G 0.1686 0.0957 0.7357 90 Y 0.1147 0.1401 0.7452 91 N 0.0782 0.1241 0.7977 92 K 0.1147 0.1232 0.7621 93 A 0.1519 0.1056 0.7425 94 K 0.2346 0.0683 0.6971 95 A 0.6553 0.0240 0.3208 96 Y 0.9069 0.0054 0.0877 97 I 0.9154 0.0068 0.0778 98 A 0.8817 0.0111 0.1072 99 T 0.7070 0.0189 0.2741 100 Q 0.3594 0.0365 0.6040 101 G 0.1281 0.0389 0.8330 102 P 0.0964 0.0539 0.8497 103 L 0.0692 0.1331 0.7977 104 K 0.0172 0.5507 0.4321 105 S 0.0214 0.5250 0.4536 106 T 0.0424 0.6373 0.3204 107 F 0.0098 0.8871 0.1031 108 E 0.0070 0.9107 0.0822 109 D 0.0071 0.9140 0.0789 110 F 0.0088 0.9273 0.0639 111 W 0.0121 0.9198 0.0682 112 R 0.0236 0.9087 0.0677 113 M 0.0280 0.9054 0.0666 114 I 0.0318 0.8968 0.0714 115 W 0.0402 0.8598 0.0999 116 E 0.0554 0.7999 0.1447 117 Q 0.0552 0.4755 0.4693 118 N 0.0553 0.1163 0.8284 119 T 0.1418 0.0202 0.8380 120 G 0.2185 0.0256 0.7559 121 I 0.9047 0.0039 0.0913 122 I 0.9305 0.0033 0.0662 123 V 0.9311 0.0035 0.0654 124 M 0.9048 0.0057 0.0895 125 I 0.6699 0.0168 0.3133 126 T 0.3126 0.0509 0.6365 127 N 0.1756 0.0830 0.7415 128 L 0.2547 0.2784 0.4668 129 V 0.2316 0.4111 0.3573 130 E 0.1732 0.4314 0.3954 131 K 0.0573 0.1680 0.7747 132 G 0.0408 0.0589 0.9003 133 R 0.1717 0.0556 0.7726 134 R 0.4506 0.0649 0.4845 135 K 0.4965 0.0571 0.4464 136 C 0.4337 0.0917 0.4746 137 D 0.3631 0.1591 0.4777 138 Q 0.4707 0.1454 0.3839 139 Y 0.4426 0.1297 0.4277 140 W 0.3097 0.0399 0.6505 141 P 0.1349 0.0506 0.8144 142 T 0.0750 0.0813 0.8437 143 E 0.0589 0.0910 0.8502 144 N 0.1353 0.0661 0.7986 145 S 0.3413 0.1062 0.5525 146 E 0.4967 0.1404 0.3629 147 E 0.6136 0.1053 0.2811 148 Y 0.4991 0.0666 0.4343 149 G 0.2799 0.0251 0.6950 150 N 0.4093 0.0193 0.5714 151 I 0.8135 0.0048 0.1816 152 I 0.9158 0.0037 0.0805 153 V 0.9232 0.0033 0.0735 154 T 0.8983 0.0045 0.0972 155 L 0.8785 0.0038 0.1176 156 K 0.7416 0.0273 0.2311 157 S 0.7316 0.0129 0.2555 158 T 0.7510 0.0157 0.2333 159 K 0.8108 0.0120 0.1772 160 I 0.7468 0.0317 0.2216 161 H 0.5951 0.0389 0.3660 162 A 0.4300 0.0843 0.4857 163 C 0.4521 0.0438 0.5041 164 Y 0.7241 0.0099 0.2660 165 T 0.8768 0.0054 0.1178 166 V 0.9068 0.0033 0.0899 167 R 0.8934 0.0076 0.0990 168 R 0.9158 0.0037 0.0805 169 F 0.9155 0.0040 0.0805 170 S 0.9176 0.0042 0.0782 171 I 0.9061 0.0048 0.0891 172 R 0.7943 0.0181 0.1876 173 N 0.5784 0.0261 0.3955 174 T 0.3525 0.0863 0.5612 175 K 0.5080 0.0840 0.4080 176 V 0.5877 0.0995 0.3128 177 K 0.5365 0.1287 0.3349 178 K 0.4010 0.2005 0.3985 179 G 0.2685 0.2203 0.5111 180 Q 0.2556 0.2109 0.5334 181 K 0.1943 0.1737 0.6320 182 G 0.1223 0.1235 0.7543 183 N 0.0995 0.0376 0.8628 184 P 0.0497 0.1522 0.7981 185 K 0.0567 0.1504 0.7930 186 G 0.0807 0.1404 0.7789 187 R 0.0985 0.1246 0.7770 188 Q 0.1286 0.0966 0.7748 189 N 0.2377 0.0582 0.7040 190 E 0.5310 0.0255 0.4435 191 R 0.7548 0.0077 0.2375 192 V 0.8867 0.0046 0.1087 193 V 0.8969 0.0039 0.0992 194 I 0.8893 0.0073 0.1033 195 Q 0.9094 0.0056 0.0850 196 Y 0.9045 0.0077 0.0877 197 H 0.8798 0.0079 0.1124 198 Y 0.7432 0.0145 0.2422 199 T 0.4555 0.0597 0.4848 200 Q 0.2589 0.0521 0.6891 201 W 0.1524 0.0379 0.8097 202 P 0.0874 0.0990 0.8136 203 D 0.0709 0.1848 0.7443 204 M 0.0607 0.1631 0.7762 205 G 0.0567 0.0464 0.8969 206 V 0.1060 0.0201 0.8739 207 P 0.1101 0.0344 0.8555 208 E 0.0535 0.3026 0.6439 209 Y 0.0449 0.3047 0.6504 210 A 0.0196 0.6517 0.3287 211 L 0.0089 0.8763 0.1148 212 P 0.0086 0.9228 0.0686 213 V 0.0047 0.9571 0.0382 214 L 0.0047 0.9603 0.0350 215 T 0.0047 0.9602 0.0352 216 F 0.0046 0.9604 0.0349 217 V 0.0047 0.9596 0.0357 218 R 0.0047 0.9568 0.0386 219 R 0.0048 0.9471 0.0481 220 S 0.0051 0.9157 0.0792 221 S 0.0088 0.8480 0.1432 222 A 0.0121 0.7788 0.2091 223 A 0.0305 0.6228 0.3466 224 R 0.0652 0.3496 0.5852 225 M 0.0780 0.0444 0.8777 226 P 0.0555 0.0761 0.8684 227 E 0.0387 0.1097 0.8517 228 T 0.0615 0.0625 0.8760 229 G 0.1045 0.0172 0.8783 230 P 0.3382 0.0071 0.6548 231 V 0.8820 0.0040 0.1140 232 L 0.9278 0.0034 0.0688 233 V 0.9253 0.0036 0.0712 234 H 0.8779 0.0050 0.1171 235 C 0.5086 0.0178 0.4736 236 S 0.1577 0.0701 0.7723 237 A 0.0829 0.1094 0.8077 238 G 0.0706 0.1276 0.8018 239 V 0.1106 0.1786 0.7108 240 G 0.0978 0.2531 0.6491 241 R 0.0550 0.6063 0.3388 242 T 0.0274 0.8364 0.1362 243 G 0.0098 0.9259 0.0642 244 T 0.0062 0.9537 0.0401 245 Y 0.0047 0.9586 0.0366 246 I 0.0049 0.9594 0.0357 247 V 0.0049 0.9601 0.0350 248 I 0.0047 0.9605 0.0348 249 D 0.0047 0.9606 0.0348 250 S 0.0049 0.9588 0.0363 251 M 0.0049 0.9562 0.0389 252 L 0.0047 0.9562 0.0391 253 Q 0.0048 0.9495 0.0457 254 Q 0.0051 0.9351 0.0598 255 I 0.0064 0.9081 0.0855 256 K 0.0072 0.8583 0.1345 257 D 0.0137 0.6785 0.3078 258 K 0.0430 0.2878 0.6692 259 S 0.0308 0.0897 0.8795 260 T 0.1653 0.0454 0.7893 261 V 0.4013 0.0205 0.5782 262 N 0.2262 0.0197 0.7541 263 V 0.0050 0.9437 0.0514 264 L 0.0048 0.9560 0.0392 265 G 0.0048 0.9565 0.0388 266 F 0.0047 0.9589 0.0364 267 L 0.0047 0.9602 0.0352 268 K 0.0046 0.9601 0.0352 269 H 0.0047 0.9575 0.0378 270 I 0.0047 0.9524 0.0428 271 R 0.0050 0.9360 0.0591 272 T 0.0069 0.8692 0.1239 273 Q 0.0149 0.7535 0.2316 274 R 0.0534 0.4947 0.4519 275 N 0.0215 0.4145 0.5640 276 Y 0.0408 0.2570 0.7022 277 L 0.1397 0.1779 0.6824 278 V 0.2305 0.0810 0.6885 279 Q 0.1537 0.0521 0.7942 280 T 0.0657 0.0401 0.8942 281 E 0.0048 0.9470 0.0482 282 E 0.0048 0.9551 0.0402 283 Q 0.0047 0.9597 0.0356 284 Y 0.0047 0.9602 0.0352 285 I 0.0047 0.9607 0.0346 286 F 0.0046 0.9611 0.0342 287 I 0.0046 0.9614 0.0340 288 H 0.0046 0.9612 0.0341 289 D 0.0046 0.9614 0.0340 290 A 0.0046 0.9612 0.0342 291 L 0.0047 0.9597 0.0356 292 L 0.0047 0.9586 0.0367 293 E 0.0049 0.9509 0.0442 294 A 0.0054 0.9254 0.0692 295 I 0.0085 0.8606 0.1309 296 L 0.0190 0.6481 0.3330 297 G 0.0293 0.0855 0.8852