# This file is the result of combining several RDB files, specifically # T0627.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0627.t2k.stride-ebghtl.rdb (weight 1.24869) # T0627.t2k.str.rdb (weight 1.53983) # 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 T0627.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0627 # 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 T0627.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 45 # # ============================================ # Comments from T0627.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0627 # 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 T0627.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 45 # # ============================================ # Comments from T0627.t2k.str.rdb # ============================================ # TARGET T0627 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0627.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 45 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0140 0.0281 0.9579 2 I 0.0832 0.1195 0.7973 3 D 0.1018 0.2160 0.6822 4 T 0.0964 0.3358 0.5678 5 F 0.1374 0.3984 0.4641 6 E 0.2145 0.3676 0.4179 7 R 0.1924 0.2829 0.5247 8 T 0.1304 0.1907 0.6789 9 G 0.0450 0.1344 0.8206 10 P 0.0484 0.2056 0.7460 11 L 0.1799 0.2755 0.5446 12 M 0.3197 0.1885 0.4918 13 E 0.3539 0.1357 0.5104 14 A 0.2553 0.1096 0.6350 15 S 0.1229 0.0660 0.8111 16 S 0.0817 0.0614 0.8569 17 Y 0.0285 0.0839 0.8876 18 P 0.0066 0.7697 0.2236 19 A 0.0038 0.9178 0.0783 20 W 0.0041 0.9420 0.0539 21 A 0.0037 0.9656 0.0307 22 Q 0.0037 0.9667 0.0296 23 Q 0.0038 0.9592 0.0371 24 L 0.0038 0.9555 0.0408 25 I 0.0039 0.9428 0.0533 26 N 0.0042 0.8842 0.1116 27 D 0.0050 0.7731 0.2219 28 C 0.0090 0.6540 0.3370 29 S 0.0095 0.5256 0.4649 30 P 0.0040 0.8943 0.1017 31 A 0.0039 0.9105 0.0856 32 K 0.0043 0.9258 0.0699 33 A 0.0048 0.9193 0.0758 34 R 0.0053 0.8751 0.1196 35 V 0.0079 0.8609 0.1312 36 V 0.0147 0.7345 0.2508 37 E 0.0149 0.5686 0.4165 38 H 0.0122 0.4119 0.5759 39 E 0.0049 0.8824 0.1127 40 L 0.0048 0.9384 0.0568 41 Y 0.0045 0.9557 0.0398 42 Q 0.0056 0.9468 0.0476 43 Q 0.0060 0.9324 0.0616 44 M 0.0063 0.9208 0.0729 45 R 0.0053 0.7779 0.2168 46 D 0.0086 0.2823 0.7091 47 A 0.0186 0.0677 0.9137 48 K 0.0679 0.0322 0.8999 49 L 0.1904 0.0262 0.7834 50 S 0.0234 0.0250 0.9515 51 P 0.0039 0.9349 0.0612 52 Q 0.0038 0.9609 0.0353 53 I 0.0038 0.9665 0.0297 54 M 0.0038 0.9712 0.0250 55 R 0.0037 0.9713 0.0250 56 Q 0.0037 0.9656 0.0307 57 Y 0.0037 0.9554 0.0409 58 L 0.0041 0.9419 0.0540 59 I 0.0038 0.9038 0.0924 60 G 0.0041 0.7472 0.2487 61 G 0.0046 0.7443 0.2510 62 W 0.0065 0.8300 0.1635 63 P 0.0063 0.9044 0.0892 64 V 0.0051 0.9470 0.0479 65 V 0.0041 0.9538 0.0421 66 E 0.0048 0.9355 0.0597 67 Q 0.0045 0.9022 0.0933 68 F 0.0066 0.9031 0.0903 69 A 0.0038 0.9545 0.0418 70 V 0.0038 0.9613 0.0349 71 Y 0.0038 0.9650 0.0312 72 M 0.0038 0.9602 0.0360 73 A 0.0040 0.9470 0.0490 74 K 0.0039 0.9367 0.0594 75 N 0.0043 0.9042 0.0915 76 L 0.0060 0.8535 0.1405 77 T 0.0160 0.6809 0.3031 78 K 0.0231 0.5224 0.4545 79 T 0.0224 0.2910 0.6866 80 R 0.0213 0.2799 0.6988 81 F 0.0219 0.3133 0.6648 82 G 0.0251 0.4065 0.5684 83 R 0.0317 0.3568 0.6115 84 H 0.0278 0.2967 0.6755 85 P 0.0157 0.4294 0.5549 86 G 0.0154 0.3735 0.6111 87 E 0.0100 0.7432 0.2468 88 D 0.0056 0.9124 0.0819 89 M 0.0045 0.9402 0.0552 90 A 0.0041 0.9479 0.0479 91 R 0.0041 0.9585 0.0374 92 R 0.0041 0.9564 0.0395 93 W 0.0037 0.9413 0.0549 94 L 0.0048 0.9273 0.0679 95 M 0.0056 0.9157 0.0787 96 R 0.0053 0.8577 0.1370 97 N 0.0061 0.7871 0.2068 98 I 0.0123 0.7496 0.2381 99 R 0.0302 0.6859 0.2839 100 V 0.0421 0.6490 0.3089 101 E 0.0468 0.6518 0.3013 102 L 0.0188 0.7900 0.1912 103 N 0.0174 0.7248 0.2578 104 H 0.0122 0.8200 0.1678 105 A 0.0063 0.9047 0.0889 106 D 0.0066 0.9396 0.0538 107 Y 0.0051 0.9591 0.0358 108 W 0.0046 0.9686 0.0268 109 V 0.0040 0.9731 0.0228 110 N 0.0037 0.9739 0.0224 111 W 0.0037 0.9751 0.0212 112 C 0.0037 0.9737 0.0226 113 A 0.0038 0.9674 0.0288 114 A 0.0038 0.9193 0.0769 115 H 0.0041 0.5117 0.4842 116 D 0.0106 0.0195 0.9699 117 V 0.0263 0.0077 0.9660 118 T 0.0372 0.0185 0.9443 119 L 0.0039 0.9390 0.0572 120 E 0.0038 0.9507 0.0455 121 D 0.0046 0.9489 0.0465 122 L 0.0041 0.9502 0.0457 123 H 0.0045 0.8722 0.1233 124 D 0.0065 0.5692 0.4242 125 Q 0.0133 0.1982 0.7885 126 R 0.0256 0.0824 0.8920 127 V 0.0194 0.0885 0.8921 128 A 0.0131 0.1151 0.8718 129 P 0.0040 0.9136 0.0824 130 E 0.0042 0.9353 0.0605 131 L 0.0041 0.9557 0.0402 132 H 0.0038 0.9618 0.0344 133 A 0.0041 0.9541 0.0417 134 L 0.0047 0.9574 0.0379 135 S 0.0048 0.9557 0.0396 136 H 0.0048 0.9544 0.0408 137 W 0.0060 0.9472 0.0468 138 C 0.0080 0.9472 0.0448 139 W 0.0110 0.9289 0.0601 140 Q 0.0139 0.8685 0.1176 141 T 0.0142 0.7424 0.2434 142 S 0.0293 0.4456 0.5251 143 S 0.0239 0.2724 0.7038 144 S 0.0173 0.3066 0.6761 145 D 0.0149 0.2680 0.7171 146 S 0.0204 0.4339 0.5457 147 L 0.0042 0.9395 0.0564 148 A 0.0038 0.9606 0.0355 149 V 0.0038 0.9620 0.0343 150 A 0.0044 0.9629 0.0326 151 M 0.0052 0.9661 0.0287 152 A 0.0045 0.9625 0.0331 153 A 0.0048 0.9453 0.0498 154 T 0.0055 0.9342 0.0603 155 N 0.0050 0.9176 0.0773 156 Y 0.0047 0.9210 0.0743 157 A 0.0074 0.9147 0.0779 158 I 0.0116 0.8856 0.1028 159 E 0.0081 0.7863 0.2056 160 G 0.0083 0.5907 0.4010 161 A 0.0264 0.6054 0.3682 162 T 0.0371 0.6050 0.3579 163 G 0.0228 0.8022 0.1750 164 E 0.0205 0.8911 0.0885 165 W 0.0336 0.9125 0.0538 166 S 0.0657 0.8779 0.0564 167 A 0.0724 0.8781 0.0495 168 V 0.0831 0.8547 0.0622 169 V 0.1293 0.7715 0.0992 170 C 0.1251 0.6586 0.2163 171 S 0.0988 0.5263 0.3749 172 T 0.0954 0.4139 0.4907 173 G 0.1095 0.4695 0.4210 174 V 0.2346 0.4554 0.3100 175 Y 0.2152 0.5203 0.2645 176 A 0.2056 0.4677 0.3267 177 E 0.1648 0.3218 0.5134 178 A 0.1224 0.1506 0.7270 179 F 0.0962 0.0628 0.8410 180 A 0.0779 0.1011 0.8211 181 E 0.0372 0.4014 0.5614 182 E 0.0405 0.3908 0.5687 183 T 0.0269 0.3503 0.6228 184 R 0.0180 0.2883 0.6938 185 K 0.0107 0.7293 0.2600 186 K 0.0042 0.9293 0.0666 187 S 0.0045 0.9610 0.0345 188 M 0.0037 0.9723 0.0240 189 K 0.0037 0.9727 0.0236 190 W 0.0041 0.9720 0.0240 191 L 0.0041 0.9705 0.0254 192 K 0.0066 0.9607 0.0328 193 M 0.0052 0.9475 0.0473 194 H 0.0077 0.8967 0.0956 195 A 0.0066 0.8156 0.1778 196 Q 0.0100 0.6659 0.3241 197 Y 0.0067 0.6370 0.3563 198 D 0.0112 0.4721 0.5167 199 D 0.0126 0.4417 0.5457 200 A 0.0135 0.4446 0.5419 201 H 0.0113 0.2707 0.7180 202 P 0.0060 0.7689 0.2251 203 W 0.0057 0.8969 0.0974 204 E 0.0046 0.9269 0.0685 205 A 0.0038 0.9580 0.0382 206 L 0.0038 0.9657 0.0305 207 E 0.0038 0.9693 0.0269 208 I 0.0037 0.9706 0.0257 209 I 0.0038 0.9711 0.0251 210 C 0.0038 0.9690 0.0272 211 T 0.0039 0.9475 0.0486 212 L 0.0041 0.9137 0.0822 213 V 0.0071 0.7636 0.2293 214 G 0.0085 0.3700 0.6215 215 N 0.0102 0.1933 0.7965 216 K 0.0139 0.0724 0.9137 217 P 0.0118 0.1131 0.8751 218 S 0.0101 0.1613 0.8286 219 L 0.0042 0.8392 0.1566 220 Q 0.0044 0.9023 0.0933 221 L 0.0042 0.9381 0.0577 222 Q 0.0038 0.9662 0.0300 223 A 0.0037 0.9731 0.0231 224 E 0.0037 0.9729 0.0234 225 L 0.0037 0.9738 0.0224 226 R 0.0037 0.9755 0.0207 227 Q 0.0037 0.9741 0.0222 228 A 0.0037 0.9731 0.0232 229 V 0.0037 0.9738 0.0225 230 T 0.0037 0.9688 0.0275 231 K 0.0037 0.9529 0.0433 232 S 0.0038 0.9614 0.0348 233 Y 0.0037 0.9698 0.0264 234 D 0.0038 0.9684 0.0278 235 Y 0.0037 0.9676 0.0286 236 M 0.0037 0.9707 0.0255 237 Y 0.0037 0.9699 0.0263 238 L 0.0037 0.9621 0.0342 239 F 0.0037 0.9470 0.0493 240 L 0.0038 0.9372 0.0591 241 E 0.0049 0.8973 0.0979 242 R 0.0053 0.7973 0.1975 243 C 0.0136 0.6879 0.2985 244 I 0.0409 0.4882 0.4708 245 Q 0.0537 0.2409 0.7054 246 L 0.0261 0.4842 0.4897 247 D 0.0352 0.4436 0.5212 248 K 0.0523 0.4229 0.5249 249 V 0.1067 0.2233 0.6700 250 K 0.1215 0.1340 0.7444 251 S 0.1366 0.1134 0.7500 252 P 0.1218 0.1505 0.7278 253 R 0.2099 0.1206 0.6695 254 G 0.4168 0.0973 0.4859 255 R 0.5635 0.0794 0.3571 256 V 0.6746 0.0864 0.2390 257 A 0.7028 0.0914 0.2058 258 A 0.6920 0.0816 0.2264 259 L 0.6144 0.0665 0.3191 260 E 0.3625 0.0458 0.5917 261 M 0.0156 0.0056 0.9788