# This file is the result of combining several RDB files, specifically # T0284.t04.dssp-ebghstl.rdb (weight 1.53986) # T0284.t04.stride-ebghtl.rdb (weight 1.24869) # T0284.t04.str2.rdb (weight 1.54758) # T0284.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 T0284.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0284 # 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 T0284.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 682.55 # # ============================================ # Comments from T0284.t04.stride-ebghtl.rdb # ============================================ # TARGET T0284 # 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 T0284.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 682.55 # # ============================================ # Comments from T0284.t04.str2.rdb # ============================================ # TARGET T0284 # 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 T0284.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 682.55 # # ============================================ # Comments from T0284.t04.alpha.rdb # ============================================ # TARGET T0284 # 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 T0284.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 682.55 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0601 0.0417 0.8982 2 H 0.0663 0.0930 0.8408 3 R 0.0679 0.1415 0.7906 4 A 0.0589 0.1724 0.7686 5 S 0.0555 0.2182 0.7263 6 H 0.0140 0.6262 0.3598 7 H 0.0088 0.8059 0.1853 8 E 0.0120 0.8549 0.1331 9 L 0.0079 0.8969 0.0952 10 R 0.0050 0.9491 0.0459 11 A 0.0047 0.9570 0.0383 12 M 0.0047 0.9563 0.0390 13 F 0.0047 0.9567 0.0386 14 R 0.0047 0.9565 0.0388 15 A 0.0048 0.9510 0.0443 16 L 0.0054 0.9365 0.0581 17 L 0.0068 0.9044 0.0888 18 D 0.0082 0.7433 0.2485 19 S 0.0472 0.2523 0.7005 20 S 0.0313 0.0424 0.9264 21 R 0.0727 0.0203 0.9070 22 C 0.3489 0.0142 0.6369 23 Y 0.7488 0.0100 0.2412 24 H 0.8374 0.0128 0.1498 25 T 0.8093 0.0099 0.1808 26 A 0.6339 0.0317 0.3344 27 S 0.4155 0.0379 0.5466 28 V 0.2049 0.0690 0.7261 29 F 0.1240 0.0620 0.8140 30 D 0.0688 0.0451 0.8861 31 P 0.0060 0.9148 0.0793 32 M 0.0049 0.9428 0.0523 33 S 0.0050 0.9504 0.0446 34 A 0.0047 0.9603 0.0351 35 R 0.0046 0.9608 0.0346 36 I 0.0046 0.9599 0.0354 37 A 0.0047 0.9602 0.0351 38 A 0.0048 0.9546 0.0406 39 D 0.0052 0.9345 0.0603 40 L 0.0420 0.5137 0.4443 41 G 0.0549 0.0190 0.9261 42 F 0.1098 0.0070 0.8833 43 E 0.2516 0.0421 0.7063 44 C 0.9211 0.0038 0.0751 45 G 0.9308 0.0037 0.0656 46 I 0.9266 0.0045 0.0689 47 L 0.8169 0.0196 0.1635 48 G 0.2083 0.0262 0.7655 49 G 0.0544 0.0893 0.8563 50 S 0.0655 0.3552 0.5794 51 V 0.0547 0.7038 0.2415 52 A 0.0596 0.7719 0.1685 53 S 0.0762 0.7781 0.1458 54 L 0.0895 0.7446 0.1659 55 Q 0.1090 0.6937 0.1972 56 V 0.1253 0.6153 0.2594 57 L 0.0967 0.4438 0.4595 58 A 0.1033 0.1886 0.7080 59 A 0.0899 0.0496 0.8605 60 P 0.0557 0.1240 0.8203 61 D 0.0814 0.0961 0.8225 62 F 0.1156 0.1888 0.6956 63 A 0.1962 0.1267 0.6771 64 L 0.3468 0.0622 0.5910 65 I 0.3225 0.0165 0.6610 66 T 0.1398 0.0134 0.8468 67 L 0.0048 0.9442 0.0510 68 S 0.0047 0.9568 0.0385 69 E 0.0047 0.9595 0.0359 70 F 0.0047 0.9605 0.0348 71 V 0.0047 0.9603 0.0350 72 E 0.0047 0.9576 0.0377 73 Q 0.0050 0.9519 0.0431 74 A 0.0053 0.9466 0.0481 75 T 0.0063 0.9304 0.0634 76 R 0.0097 0.9089 0.0813 77 I 0.0189 0.8758 0.1053 78 G 0.0381 0.7695 0.1923 79 R 0.0489 0.5947 0.3563 80 V 0.0869 0.3990 0.5141 81 A 0.1276 0.1836 0.6888 82 R 0.1237 0.0865 0.7898 83 L 0.1707 0.0113 0.8180 84 P 0.3474 0.0091 0.6435 85 V 0.8749 0.0054 0.1197 86 I 0.9077 0.0067 0.0856 87 A 0.8799 0.0121 0.1079 88 D 0.6618 0.0105 0.3277 89 A 0.2047 0.0606 0.7347 90 D 0.0932 0.1239 0.7829 91 H 0.0758 0.1721 0.7521 92 G 0.0720 0.1053 0.8227 93 Y 0.1315 0.0820 0.7865 94 G 0.1031 0.0852 0.8117 95 N 0.0751 0.1053 0.8197 96 A 0.0054 0.9326 0.0620 97 L 0.0051 0.9524 0.0425 98 N 0.0048 0.9550 0.0402 99 V 0.0047 0.9574 0.0379 100 M 0.0047 0.9590 0.0363 101 R 0.0046 0.9598 0.0355 102 T 0.0046 0.9593 0.0361 103 V 0.0046 0.9615 0.0339 104 V 0.0046 0.9617 0.0337 105 E 0.0046 0.9618 0.0335 106 L 0.0046 0.9615 0.0339 107 E 0.0048 0.9545 0.0407 108 R 0.0049 0.8936 0.1015 109 A 0.0397 0.3943 0.5660 110 G 0.0411 0.0359 0.9231 111 I 0.1423 0.0288 0.8289 112 A 0.3531 0.0578 0.5891 113 A 0.8833 0.0107 0.1060 114 L 0.9122 0.0094 0.0784 115 T 0.9171 0.0078 0.0752 116 I 0.8404 0.0171 0.1425 117 E 0.5440 0.0406 0.4153 118 D 0.2364 0.0627 0.7008 119 T 0.1764 0.0815 0.7421 120 L 0.2471 0.0797 0.6732 121 L 0.1671 0.0625 0.7704 122 P 0.1249 0.1587 0.7164 123 A 0.0871 0.4071 0.5058 124 Q 0.1147 0.4135 0.4718 125 F 0.1591 0.2826 0.5583 126 G 0.1745 0.1216 0.7039 127 R 0.1510 0.1034 0.7456 128 K 0.1212 0.1034 0.7754 129 S 0.1506 0.0750 0.7744 130 T 0.2445 0.0548 0.7007 131 D 0.5345 0.0412 0.4243 132 L 0.7396 0.0325 0.2280 133 I 0.7608 0.0264 0.2128 134 C 0.6498 0.0274 0.3228 135 V 0.2497 0.2877 0.4626 136 E 0.1149 0.3959 0.4892 137 E 0.0869 0.4704 0.4427 138 G 0.0681 0.5367 0.3952 139 V 0.0604 0.7167 0.2229 140 G 0.0444 0.7989 0.1567 141 K 0.0522 0.8577 0.0901 142 I 0.0524 0.8763 0.0713 143 R 0.0496 0.8786 0.0718 144 A 0.0595 0.8594 0.0811 145 A 0.0388 0.8677 0.0935 146 L 0.0344 0.8720 0.0936 147 E 0.0354 0.8448 0.1198 148 A 0.0496 0.7369 0.2134 149 R 0.0575 0.5000 0.4425 150 V 0.0955 0.1988 0.7056 151 D 0.0631 0.0224 0.9146 152 P 0.0273 0.1218 0.8508 153 A 0.0644 0.0594 0.8762 154 L 0.5150 0.0212 0.4638 155 T 0.8565 0.0069 0.1367 156 I 0.9178 0.0051 0.0771 157 I 0.9050 0.0084 0.0866 158 A 0.8585 0.0086 0.1329 159 R 0.6211 0.0235 0.3554 160 T 0.3625 0.0764 0.5611 161 N 0.1172 0.2721 0.6108 162 A 0.0258 0.6511 0.3232 163 E 0.0268 0.6434 0.3298 164 L 0.0304 0.5844 0.3851 165 I 0.0459 0.3509 0.6031 166 D 0.0480 0.2491 0.7029 167 V 0.0069 0.8952 0.0979 168 D 0.0050 0.9483 0.0467 169 A 0.0047 0.9568 0.0385 170 V 0.0047 0.9591 0.0363 171 I 0.0047 0.9600 0.0354 172 Q 0.0047 0.9597 0.0357 173 R 0.0049 0.9532 0.0419 174 T 0.0047 0.9558 0.0395 175 L 0.0048 0.9550 0.0402 176 A 0.0047 0.9538 0.0415 177 Y 0.0048 0.9506 0.0446 178 Q 0.0052 0.9431 0.0517 179 E 0.0057 0.8985 0.0959 180 A 0.0394 0.4806 0.4800 181 G 0.0500 0.0313 0.9188 182 A 0.0905 0.0084 0.9011 183 D 0.1237 0.0432 0.8331 184 G 0.9015 0.0041 0.0944 185 I 0.9303 0.0033 0.0665 186 C 0.9269 0.0036 0.0696 187 L 0.8613 0.0051 0.1336 188 V 0.5251 0.0231 0.4519 189 G 0.2336 0.0282 0.7382 190 V 0.1309 0.0282 0.8409 191 R 0.0817 0.0435 0.8748 192 D 0.0766 0.0329 0.8905 193 F 0.0050 0.9430 0.0520 194 A 0.0047 0.9556 0.0397 195 H 0.0047 0.9578 0.0374 196 L 0.0047 0.9588 0.0365 197 E 0.0047 0.9590 0.0363 198 A 0.0050 0.9545 0.0406 199 I 0.0051 0.9481 0.0468 200 A 0.0065 0.9303 0.0633 201 E 0.0067 0.8745 0.1188 202 H 0.0129 0.6877 0.2994 203 L 0.0762 0.2795 0.6444 204 H 0.0621 0.1086 0.8292 205 I 0.1409 0.0422 0.8169 206 P 0.2842 0.0495 0.6663 207 L 0.7098 0.0402 0.2499 208 M 0.8032 0.0279 0.1690 209 L 0.8394 0.0314 0.1292 210 V 0.7757 0.0532 0.1710 211 T 0.6338 0.0471 0.3191 212 Y 0.4199 0.0635 0.5166 213 G 0.1580 0.0490 0.7930 214 N 0.1106 0.0511 0.8383 215 P 0.0858 0.1282 0.7860 216 Q 0.0559 0.1988 0.7453 217 L 0.0661 0.1572 0.7766 218 R 0.0971 0.0717 0.8311 219 D 0.0902 0.0802 0.8296 220 D 0.0063 0.9093 0.0844 221 A 0.0048 0.9489 0.0463 222 R 0.0047 0.9565 0.0388 223 L 0.0068 0.9556 0.0377 224 A 0.0079 0.9489 0.0432 225 R 0.0097 0.9227 0.0676 226 L 0.0442 0.4879 0.4679 227 G 0.0507 0.0513 0.8981 228 V 0.2408 0.0326 0.7266 229 R 0.6667 0.0506 0.2827 230 V 0.8621 0.0242 0.1137 231 V 0.8727 0.0206 0.1066 232 V 0.7859 0.0377 0.1764 233 N 0.3101 0.0625 0.6274 234 G 0.0721 0.0961 0.8318 235 H 0.0519 0.2588 0.6894 236 A 0.0338 0.7138 0.2524 237 A 0.0122 0.8912 0.0966 238 Y 0.0067 0.9415 0.0517 239 F 0.0055 0.9546 0.0399 240 A 0.0048 0.9568 0.0384 241 A 0.0048 0.9552 0.0401 242 I 0.0048 0.9576 0.0377 243 K 0.0048 0.9580 0.0372 244 A 0.0048 0.9557 0.0395 245 T 0.0048 0.9538 0.0413 246 Y 0.0048 0.9540 0.0411 247 D 0.0048 0.9504 0.0448 248 C 0.0050 0.9408 0.0542 249 L 0.0048 0.9446 0.0506 250 R 0.0049 0.9448 0.0503 251 E 0.0052 0.9347 0.0601 252 E 0.0064 0.9183 0.0753 253 R 0.0167 0.8577 0.1255 254 G 0.0078 0.7637 0.2285 255 A 0.0096 0.7693 0.2211 256 V 0.0180 0.7655 0.2165 257 A 0.0124 0.7859 0.2017 258 S 0.0132 0.7325 0.2543 259 D 0.0226 0.7030 0.2743 260 L 0.0462 0.6902 0.2635 261 T 0.0596 0.6508 0.2896 262 A 0.0467 0.7974 0.1558 263 S 0.0612 0.7919 0.1469 264 E 0.0982 0.7291 0.1727 265 L 0.0939 0.6714 0.2348 266 S 0.0914 0.4950 0.4135 267 K 0.1221 0.4280 0.4499 268 K 0.1360 0.2732 0.5909 269 Y 0.0942 0.1783 0.7275 270 T 0.0708 0.0990 0.8302 271 F 0.0682 0.1026 0.8291 272 P 0.0367 0.4661 0.4972 273 E 0.0394 0.5872 0.3734 274 E 0.0708 0.7067 0.2226 275 Y 0.0880 0.7429 0.1691 276 Q 0.1008 0.7570 0.1423 277 A 0.1017 0.7685 0.1298 278 W 0.0716 0.7914 0.1370 279 A 0.0502 0.8157 0.1341 280 R 0.0502 0.7694 0.1804 281 D 0.0683 0.7198 0.2119 282 Y 0.0900 0.6957 0.2143 283 M 0.1099 0.6370 0.2531 284 E 0.1280 0.5796 0.2924 285 V 0.1142 0.4415 0.4443 286 K 0.0818 0.2303 0.6879 287 E 0.0461 0.0680 0.8859