# This file is the result of combining several RDB files, specifically # T0225.t04.dssp-ebghstl.rdb (weight 1.53986) # T0225.t04.stride-ebghtl.rdb (weight 1.24869) # T0225.t04.str2.rdb (weight 1.54758) # T0225.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 T0225.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0225 # 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 T0225.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 2174 # # ============================================ # Comments from T0225.t04.stride-ebghtl.rdb # ============================================ # TARGET T0225 # 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 T0225.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 2174 # # ============================================ # Comments from T0225.t04.str2.rdb # ============================================ # TARGET T0225 # 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 T0225.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 2174 # # ============================================ # Comments from T0225.t04.alpha.rdb # ============================================ # TARGET T0225 # 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 T0225.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 2174 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1740 0.0097 0.8163 2 K 0.7073 0.0070 0.2857 3 I 0.8982 0.0042 0.0975 4 L 0.9228 0.0041 0.0731 5 I 0.9012 0.0049 0.0939 6 T 0.6954 0.0311 0.2736 7 G 0.1813 0.0289 0.7898 8 A 0.0915 0.0863 0.8222 9 N 0.0967 0.1562 0.7472 10 G 0.0795 0.2371 0.6833 11 Q 0.0715 0.5577 0.3707 12 L 0.0319 0.7691 0.1990 13 G 0.0084 0.9006 0.0910 14 R 0.0053 0.9532 0.0415 15 E 0.0054 0.9557 0.0389 16 I 0.0055 0.9562 0.0384 17 Q 0.0052 0.9584 0.0364 18 K 0.0047 0.9594 0.0360 19 Q 0.0047 0.9564 0.0388 20 L 0.0048 0.9459 0.0492 21 K 0.0054 0.8742 0.1204 22 G 0.0076 0.6227 0.3697 23 K 0.0401 0.2368 0.7232 24 N 0.0424 0.0202 0.9374 25 V 0.1225 0.0086 0.8689 26 E 0.7282 0.0060 0.2658 27 V 0.8879 0.0034 0.1087 28 I 0.8939 0.0049 0.1012 29 P 0.8300 0.0058 0.1642 30 T 0.6104 0.0121 0.3775 31 D 0.4640 0.0110 0.5250 32 V 0.3396 0.0490 0.6114 33 Q 0.4686 0.0509 0.4804 34 D 0.5573 0.0480 0.3947 35 L 0.3935 0.0446 0.5618 36 D 0.3323 0.0372 0.6305 37 I 0.1116 0.3506 0.5378 38 T 0.1031 0.2447 0.6522 39 N 0.1085 0.1747 0.7168 40 V 0.0062 0.9313 0.0625 41 L 0.0050 0.9510 0.0440 42 A 0.0050 0.9509 0.0441 43 V 0.0051 0.9529 0.0420 44 N 0.0055 0.9542 0.0403 45 K 0.0054 0.9477 0.0469 46 F 0.0058 0.9436 0.0506 47 F 0.0077 0.9113 0.0809 48 N 0.0107 0.8073 0.1820 49 E 0.0128 0.6104 0.3768 50 K 0.0559 0.3935 0.5506 51 K 0.0942 0.0360 0.8699 52 P 0.0993 0.0531 0.8476 53 N 0.1139 0.0722 0.8139 54 V 0.8777 0.0146 0.1076 55 V 0.9246 0.0101 0.0653 56 I 0.9229 0.0101 0.0670 57 N 0.8639 0.0284 0.1077 58 C 0.5241 0.1048 0.3711 59 A 0.3201 0.2042 0.4757 60 A 0.2581 0.3031 0.4389 61 H 0.1775 0.3861 0.4364 62 T 0.1062 0.4130 0.4808 63 A 0.0906 0.3347 0.5747 64 V 0.0585 0.5127 0.4288 65 D 0.0290 0.7165 0.2546 66 K 0.0212 0.7792 0.1996 67 C 0.0253 0.7465 0.2282 68 E 0.0157 0.8150 0.1693 69 E 0.0210 0.7812 0.1977 70 Q 0.0479 0.6418 0.3103 71 Y 0.0123 0.8858 0.1019 72 D 0.0115 0.8962 0.0923 73 L 0.0189 0.8976 0.0835 74 A 0.0261 0.8887 0.0853 75 Y 0.0401 0.8615 0.0984 76 K 0.0509 0.8300 0.1191 77 I 0.0429 0.7945 0.1626 78 N 0.0460 0.5854 0.3686 79 A 0.0800 0.5259 0.3941 80 I 0.0701 0.6070 0.3229 81 G 0.0208 0.6682 0.3110 82 P 0.0051 0.9240 0.0709 83 K 0.0047 0.9585 0.0368 84 N 0.0046 0.9611 0.0343 85 L 0.0047 0.9608 0.0345 86 A 0.0046 0.9614 0.0340 87 A 0.0046 0.9614 0.0340 88 A 0.0046 0.9615 0.0339 89 A 0.0047 0.9601 0.0352 90 Y 0.0048 0.9542 0.0410 91 S 0.0054 0.9204 0.0741 92 V 0.0417 0.3940 0.5644 93 G 0.0426 0.0138 0.9436 94 A 0.0749 0.0078 0.9173 95 E 0.4411 0.0093 0.5497 96 I 0.9145 0.0033 0.0822 97 V 0.9299 0.0033 0.0668 98 Q 0.9280 0.0033 0.0686 99 I 0.8476 0.0099 0.1425 100 S 0.4855 0.0132 0.5013 101 T 0.1744 0.0860 0.7396 102 D 0.0893 0.3058 0.6049 103 Y 0.1271 0.4445 0.4284 104 V 0.2282 0.3301 0.4417 105 F 0.2862 0.1640 0.5498 106 D 0.1601 0.0744 0.7655 107 G 0.0696 0.0763 0.8541 108 E 0.0661 0.1230 0.8109 109 A 0.0735 0.1130 0.8135 110 K 0.0972 0.0777 0.8251 111 E 0.1366 0.0176 0.8458 112 P 0.1970 0.0217 0.7813 113 I 0.2901 0.0262 0.6837 114 T 0.2685 0.0237 0.7079 115 E 0.1520 0.1569 0.6910 116 F 0.1188 0.1137 0.7674 117 D 0.0949 0.0449 0.8601 118 E 0.0839 0.0756 0.8405 119 V 0.1180 0.0606 0.8214 120 N 0.1173 0.0277 0.8550 121 P 0.0473 0.1513 0.8014 122 Q 0.0693 0.1324 0.7983 123 S 0.0786 0.1274 0.7941 124 A 0.0223 0.6467 0.3311 125 Y 0.0251 0.6988 0.2760 126 G 0.0152 0.7879 0.1969 127 K 0.0170 0.8275 0.1555 128 T 0.0229 0.8348 0.1422 129 K 0.0112 0.8930 0.0958 130 L 0.0088 0.9263 0.0649 131 E 0.0068 0.9354 0.0578 132 G 0.0051 0.9539 0.0410 133 E 0.0049 0.9583 0.0368 134 N 0.0047 0.9604 0.0349 135 F 0.0047 0.9599 0.0353 136 V 0.0050 0.9569 0.0381 137 K 0.0052 0.9455 0.0493 138 A 0.0068 0.8851 0.1082 139 L 0.0494 0.5550 0.3956 140 N 0.0508 0.0265 0.9227 141 P 0.0620 0.0218 0.9162 142 K 0.1529 0.0497 0.7974 143 Y 0.8657 0.0078 0.1265 144 Y 0.9248 0.0041 0.0711 145 I 0.9315 0.0033 0.0652 146 V 0.9154 0.0056 0.0790 147 R 0.8384 0.0069 0.1547 148 T 0.5733 0.0223 0.4044 149 A 0.4028 0.0530 0.5441 150 W 0.4016 0.1036 0.4948 151 L 0.3799 0.1152 0.5049 152 Y 0.3292 0.0825 0.5883 153 G 0.1338 0.0385 0.8277 154 D 0.0548 0.0885 0.8567 155 G 0.0330 0.1161 0.8509 156 N 0.0388 0.2337 0.7275 157 N 0.0402 0.4118 0.5480 158 F 0.0307 0.7144 0.2549 159 V 0.0068 0.9219 0.0714 160 K 0.0048 0.9552 0.0400 161 T 0.0050 0.9580 0.0370 162 M 0.0047 0.9585 0.0369 163 I 0.0048 0.9569 0.0384 164 N 0.0048 0.9543 0.0409 165 L 0.0058 0.9343 0.0599 166 G 0.0079 0.8627 0.1294 167 K 0.0145 0.6904 0.2951 168 T 0.0401 0.3430 0.6169 169 H 0.0401 0.0544 0.9056 170 D 0.0645 0.0297 0.9059 171 E 0.2214 0.0251 0.7535 172 L 0.5052 0.0111 0.4838 173 K 0.7067 0.0081 0.2853 174 V 0.7946 0.0094 0.1961 175 V 0.6315 0.0215 0.3470 176 H 0.3249 0.0389 0.6362 177 D 0.1253 0.0667 0.8079 178 Q 0.1237 0.0732 0.8031 179 V 0.2661 0.0424 0.6915 180 G 0.2169 0.0288 0.7543 181 T 0.1780 0.0365 0.7855 182 P 0.3441 0.0757 0.5802 183 T 0.5381 0.0823 0.3796 184 S 0.4758 0.1352 0.3890 185 T 0.0450 0.8625 0.0925 186 V 0.0087 0.9254 0.0659 187 D 0.0060 0.9460 0.0481 188 L 0.0047 0.9600 0.0353 189 A 0.0047 0.9599 0.0355 190 R 0.0046 0.9614 0.0339 191 V 0.0046 0.9615 0.0339 192 V 0.0046 0.9614 0.0339 193 L 0.0046 0.9613 0.0340 194 K 0.0047 0.9595 0.0358 195 V 0.0048 0.9500 0.0452 196 I 0.0060 0.9052 0.0889 197 D 0.0137 0.7402 0.2462 198 E 0.0537 0.4246 0.5217 199 K 0.0342 0.2283 0.7374 200 N 0.0540 0.1303 0.8157 201 Y 0.0891 0.0524 0.8585 202 G 0.1620 0.0294 0.8085 203 T 0.6558 0.0137 0.3305 204 F 0.8734 0.0062 0.1204 205 H 0.8772 0.0062 0.1167 206 C 0.6858 0.0114 0.3029 207 T 0.3417 0.0245 0.6338 208 C 0.1478 0.0304 0.8218 209 K 0.0481 0.0791 0.8728 210 G 0.0631 0.0540 0.8828 211 I 0.2143 0.0603 0.7255 212 C 0.3530 0.0319 0.6151 213 S 0.2423 0.0469 0.7108 214 W 0.0048 0.9520 0.0432 215 Y 0.0047 0.9600 0.0353 216 D 0.0047 0.9610 0.0343 217 F 0.0047 0.9607 0.0346 218 A 0.0047 0.9610 0.0344 219 V 0.0046 0.9617 0.0337 220 E 0.0046 0.9612 0.0342 221 I 0.0047 0.9599 0.0354 222 F 0.0048 0.9575 0.0377 223 R 0.0055 0.9472 0.0473 224 L 0.0116 0.8891 0.0993 225 T 0.0472 0.5597 0.3930 226 G 0.0340 0.0314 0.9346 227 I 0.0646 0.0116 0.9238 228 D 0.1159 0.0138 0.8703 229 V 0.2369 0.0237 0.7394 230 K 0.4393 0.0186 0.5421 231 V 0.6620 0.0173 0.3208 232 T 0.6019 0.0105 0.3876 233 P 0.4294 0.0163 0.5542 234 C 0.2232 0.0148 0.7620 235 T 0.1744 0.0282 0.7974 236 T 0.0818 0.1554 0.7629 237 E 0.0563 0.2589 0.6848 238 E 0.0741 0.2576 0.6683 239 F 0.1138 0.0650 0.8212 240 P 0.0946 0.0457 0.8596 241 R 0.0981 0.0243 0.8776 242 P 0.0722 0.0518 0.8760 243 A 0.0538 0.1805 0.7657 244 K 0.0603 0.1395 0.8002 245 R 0.0936 0.0316 0.8747 246 P 0.0781 0.1250 0.7969 247 K 0.1245 0.2101 0.6654 248 Y 0.2396 0.2403 0.5202 249 S 0.4267 0.1909 0.3823 250 V 0.4906 0.1942 0.3152 251 L 0.3900 0.1602 0.4498 252 R 0.1644 0.1635 0.6721 253 N 0.0227 0.7794 0.1979 254 Y 0.0127 0.8980 0.0892 255 M 0.0137 0.9048 0.0814 256 L 0.0230 0.8976 0.0794 257 E 0.0331 0.8714 0.0954 258 L 0.0148 0.8732 0.1119 259 T 0.0175 0.7413 0.2412 260 T 0.0595 0.4154 0.5251 261 G 0.0373 0.0802 0.8825 262 D 0.0850 0.0698 0.8453 263 I 0.1236 0.0573 0.8191 264 T 0.1327 0.0530 0.8143 265 R 0.0920 0.0804 0.8276 266 E 0.1088 0.0872 0.8041 267 W 0.0051 0.9350 0.0599 268 K 0.0048 0.9575 0.0377 269 E 0.0047 0.9601 0.0352 270 S 0.0047 0.9595 0.0358 271 L 0.0047 0.9600 0.0353 272 K 0.0047 0.9607 0.0347 273 E 0.0047 0.9587 0.0366 274 Y 0.0047 0.9560 0.0393 275 I 0.0047 0.9569 0.0384 276 D 0.0047 0.9493 0.0459 277 L 0.0050 0.9184 0.0766 278 L 0.0067 0.8327 0.1607 279 Q 0.0129 0.5952 0.3919 280 M 0.0199 0.1953 0.7848