# This file is the result of combining several RDB files, specifically # T0506.t04.dssp-ebghstl.rdb (weight 1.53986) # T0506.t04.stride-ebghtl.rdb (weight 1.24869) # T0506.t04.str2.rdb (weight 1.54758) # T0506.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 T0506.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0506 # 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 T0506.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 1355 # # ============================================ # Comments from T0506.t04.stride-ebghtl.rdb # ============================================ # TARGET T0506 # 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 T0506.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 1355 # # ============================================ # Comments from T0506.t04.str2.rdb # ============================================ # TARGET T0506 # 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 T0506.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 1355 # # ============================================ # Comments from T0506.t04.alpha.rdb # ============================================ # TARGET T0506 # 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 T0506.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 1355 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1375 0.1500 0.7124 2 L 0.1767 0.1807 0.6425 3 D 0.1694 0.1515 0.6791 4 V 0.1511 0.1275 0.7214 5 A 0.1226 0.0422 0.8352 6 P 0.0774 0.0625 0.8601 7 P 0.0682 0.1337 0.7980 8 V 0.1136 0.1289 0.7576 9 I 0.1866 0.0687 0.7448 10 T 0.0946 0.0260 0.8793 11 P 0.0212 0.4720 0.5069 12 R 0.0200 0.4082 0.5718 13 G 0.0270 0.3419 0.6310 14 T 0.0994 0.1040 0.7966 15 K 0.1293 0.0762 0.7945 16 I 0.1592 0.0752 0.7656 17 E 0.1171 0.0314 0.8515 18 P 0.0427 0.2173 0.7401 19 S 0.0519 0.1982 0.7499 20 A 0.0594 0.1447 0.7959 21 G 0.0524 0.0683 0.8792 22 A 0.0792 0.0325 0.8883 23 P 0.0668 0.0697 0.8636 24 F 0.0205 0.6930 0.2865 25 E 0.0153 0.8034 0.1813 26 A 0.0086 0.8900 0.1014 27 V 0.0054 0.9431 0.0515 28 R 0.0050 0.9564 0.0386 29 V 0.0050 0.9568 0.0382 30 A 0.0047 0.9565 0.0388 31 R 0.0047 0.9568 0.0384 32 D 0.0049 0.9511 0.0440 33 V 0.0052 0.9356 0.0592 34 L 0.0063 0.8750 0.1188 35 H 0.0089 0.7156 0.2755 36 T 0.0221 0.3936 0.5843 37 S 0.0622 0.1093 0.8285 38 R 0.0630 0.0952 0.8418 39 T 0.6901 0.0358 0.2740 40 A 0.9005 0.0078 0.0917 41 A 0.9243 0.0057 0.0700 42 L 0.9152 0.0068 0.0780 43 A 0.8573 0.0087 0.1340 44 T 0.7335 0.0130 0.2534 45 L 0.5328 0.0171 0.4501 46 D 0.2919 0.0102 0.6979 47 P 0.0446 0.1639 0.7915 48 V 0.0273 0.1487 0.8240 49 S 0.0520 0.0922 0.8558 50 G 0.0601 0.0386 0.9013 51 Y 0.2094 0.0149 0.7757 52 P 0.5367 0.0224 0.4409 53 Y 0.5932 0.0259 0.3809 54 T 0.6527 0.0185 0.3288 55 T 0.6370 0.0145 0.3485 56 A 0.6976 0.0241 0.2784 57 T 0.7345 0.0214 0.2441 58 N 0.7543 0.0194 0.2263 59 I 0.7550 0.0173 0.2277 60 G 0.8390 0.0072 0.1537 61 I 0.8095 0.0082 0.1823 62 E 0.2084 0.0169 0.7747 63 P 0.0253 0.0957 0.8790 64 D 0.0440 0.0246 0.9314 65 G 0.0433 0.0289 0.9278 66 T 0.1590 0.0090 0.8320 67 P 0.7434 0.0048 0.2519 68 F 0.9035 0.0056 0.0910 69 F 0.9212 0.0048 0.0739 70 F 0.9051 0.0071 0.0878 71 A 0.7305 0.0194 0.2500 72 A 0.2768 0.0667 0.6565 73 G 0.0744 0.1853 0.7403 74 L 0.0592 0.3169 0.6239 75 T 0.0661 0.4705 0.4634 76 L 0.0544 0.6788 0.2668 77 H 0.0645 0.7369 0.1986 78 A 0.0590 0.7926 0.1484 79 R 0.0419 0.8193 0.1388 80 N 0.0615 0.7690 0.1695 81 M 0.0390 0.7932 0.1678 82 E 0.0413 0.6905 0.2682 83 T 0.0565 0.4782 0.4653 84 D 0.1144 0.0397 0.8459 85 A 0.0718 0.1225 0.8057 86 R 0.2291 0.0927 0.6782 87 I 0.7275 0.0233 0.2491 88 S 0.8754 0.0062 0.1184 89 V 0.9146 0.0037 0.0816 90 T 0.9118 0.0041 0.0841 91 L 0.8474 0.0072 0.1454 92 A 0.5212 0.0111 0.4677 93 P 0.2751 0.0348 0.6901 94 F 0.1130 0.0587 0.8284 95 G 0.0755 0.0547 0.8698 96 K 0.0561 0.0948 0.8490 97 G 0.0700 0.0874 0.8427 98 D 0.1241 0.1005 0.7754 99 A 0.0661 0.3721 0.5618 100 L 0.0811 0.3024 0.6165 101 T 0.1159 0.2020 0.6820 102 L 0.1365 0.0517 0.8118 103 P 0.1811 0.0510 0.7679 104 R 0.7490 0.0204 0.2306 105 L 0.8958 0.0039 0.1003 106 T 0.9221 0.0039 0.0739 107 L 0.9206 0.0037 0.0757 108 V 0.8761 0.0145 0.1094 109 G 0.8615 0.0061 0.1324 110 R 0.8657 0.0047 0.1296 111 A 0.8440 0.0062 0.1498 112 D 0.8207 0.0093 0.1700 113 R 0.7505 0.0082 0.2413 114 I 0.3533 0.0233 0.6234 115 G 0.0974 0.0128 0.8898 116 P 0.0157 0.4133 0.5710 117 D 0.0111 0.5772 0.4117 118 E 0.0151 0.6597 0.3252 119 V 0.0104 0.8037 0.1859 120 P 0.0052 0.9434 0.0515 121 L 0.0048 0.9554 0.0398 122 A 0.0050 0.9561 0.0389 123 I 0.0047 0.9558 0.0395 124 A 0.0049 0.9527 0.0425 125 R 0.0054 0.9402 0.0544 126 Y 0.0052 0.9302 0.0646 127 I 0.0065 0.9139 0.0796 128 A 0.0069 0.8639 0.1292 129 R 0.0166 0.7157 0.2677 130 Y 0.0793 0.1394 0.7813 131 P 0.0120 0.3663 0.6218 132 K 0.0222 0.3565 0.6213 133 A 0.0567 0.5233 0.4200 134 K 0.0686 0.5418 0.3896 135 L 0.1072 0.4987 0.3941 136 Y 0.1755 0.3443 0.4802 137 L 0.2096 0.1945 0.5959 138 S 0.2076 0.1090 0.6835 139 L 0.1055 0.0416 0.8529 140 P 0.0424 0.1075 0.8501 141 D 0.0796 0.0664 0.8540 142 T 0.4091 0.0236 0.5672 143 R 0.7734 0.0074 0.2192 144 L 0.9204 0.0032 0.0765 145 Y 0.9203 0.0037 0.0760 146 R 0.9290 0.0033 0.0677 147 L 0.9173 0.0038 0.0789 148 R 0.8763 0.0049 0.1188 149 T 0.7698 0.0082 0.2220 150 E 0.5999 0.0416 0.3585 151 G 0.7636 0.0200 0.2164 152 V 0.8776 0.0061 0.1163 153 Q 0.9168 0.0041 0.0791 154 I 0.8831 0.0073 0.1097 155 N 0.6237 0.0200 0.3563 156 G 0.2650 0.0300 0.7050 157 G 0.1670 0.0271 0.8059 158 P 0.1788 0.0769 0.7442 159 A 0.1668 0.1599 0.6733 160 R 0.1817 0.1894 0.6288 161 N 0.2709 0.1708 0.5583 162 A 0.2755 0.2695 0.4550 163 S 0.2738 0.2285 0.4977 164 N 0.3463 0.0775 0.5762 165 I 0.3298 0.0129 0.6573 166 T 0.1086 0.0100 0.8815 167 P 0.0053 0.9061 0.0886 168 A 0.0050 0.9223 0.0727 169 D 0.0054 0.9266 0.0679 170 L 0.0104 0.9037 0.0858 171 R 0.0133 0.8595 0.1272 172 T 0.0170 0.8081 0.1748 173 D 0.0253 0.7205 0.2542 174 L 0.0389 0.6143 0.3469 175 S 0.0394 0.5056 0.4549 176 G 0.0438 0.3375 0.6188 177 A 0.0433 0.4672 0.4895 178 E 0.0305 0.6640 0.3055 179 E 0.0114 0.8226 0.1661 180 L 0.0142 0.8174 0.1684 181 M 0.0194 0.8059 0.1747 182 A 0.0146 0.8128 0.1726 183 A 0.0132 0.7820 0.2048 184 A 0.0102 0.8260 0.1638 185 E 0.0068 0.8834 0.1098 186 S 0.0064 0.8759 0.1177 187 E 0.0077 0.8885 0.1039 188 A 0.0092 0.8986 0.0921 189 T 0.0070 0.8961 0.0968 190 R 0.0095 0.8536 0.1370 191 L 0.0114 0.8188 0.1697 192 N 0.0144 0.7130 0.2726 193 A 0.0077 0.7772 0.2151 194 I 0.0213 0.7333 0.2454 195 K 0.0369 0.7280 0.2352 196 G 0.0118 0.8790 0.1091 197 E 0.0117 0.9193 0.0690 198 A 0.0070 0.9461 0.0469 199 S 0.0066 0.9518 0.0416 200 R 0.0057 0.9542 0.0401 201 L 0.0072 0.9487 0.0440 202 A 0.0082 0.9330 0.0588 203 V 0.0155 0.9070 0.0775 204 L 0.0216 0.8467 0.1317 205 A 0.0412 0.5103 0.4485 206 G 0.0427 0.1007 0.8566 207 A 0.1006 0.0592 0.8403 208 K 0.1913 0.0710 0.7377 209 T 0.1749 0.1690 0.6561 210 G 0.1221 0.1270 0.7509 211 R 0.3188 0.0761 0.6051 212 W 0.6327 0.0140 0.3533 213 K 0.8053 0.0079 0.1867 214 I 0.8787 0.0069 0.1144 215 T 0.8376 0.0259 0.1364 216 S 0.8175 0.0113 0.1713 217 I 0.7596 0.0119 0.2286 218 D 0.3134 0.0122 0.6743 219 P 0.0291 0.1287 0.8423 220 D 0.0310 0.0766 0.8924 221 G 0.1830 0.1107 0.7062 222 I 0.5128 0.0263 0.4609 223 D 0.7991 0.0210 0.1799 224 L 0.8148 0.0303 0.1549 225 A 0.7772 0.0353 0.1875 226 S 0.6335 0.0411 0.3253 227 A 0.3895 0.0449 0.5656 228 S 0.2833 0.0505 0.6662 229 D 0.3910 0.0542 0.5548 230 L 0.7480 0.0257 0.2262 231 A 0.8479 0.0139 0.1382 232 R 0.8708 0.0171 0.1121 233 L 0.7334 0.0250 0.2416 234 W 0.5017 0.0314 0.4669 235 F 0.2799 0.0564 0.6637 236 A 0.1163 0.2283 0.6553 237 E 0.0970 0.2528 0.6502 238 R 0.0868 0.2771 0.6360 239 V 0.1084 0.2222 0.6693 240 E 0.1066 0.1769 0.7165 241 T 0.0867 0.0949 0.8184 242 L 0.0048 0.9453 0.0499 243 K 0.0047 0.9595 0.0358 244 Q 0.0047 0.9611 0.0342 245 F 0.0047 0.9607 0.0346 246 E 0.0046 0.9613 0.0341 247 K 0.0046 0.9617 0.0336 248 A 0.0046 0.9611 0.0343 249 L 0.0047 0.9604 0.0350 250 A 0.0047 0.9600 0.0354 251 Q 0.0047 0.9531 0.0422 252 L 0.0050 0.9023 0.0927 253 L 0.0069 0.7100 0.2831 254 K 0.0140 0.3566 0.6295