# This file is the result of combining several RDB files, specifically # T0378.t04.dssp-ebghstl.rdb (weight 1.53986) # T0378.t04.stride-ebghtl.rdb (weight 1.24869) # T0378.t04.str2.rdb (weight 1.54758) # T0378.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 T0378.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0378 # 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 T0378.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 1385 # # ============================================ # Comments from T0378.t04.stride-ebghtl.rdb # ============================================ # TARGET T0378 # 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 T0378.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 1385 # # ============================================ # Comments from T0378.t04.str2.rdb # ============================================ # TARGET T0378 # 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 T0378.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 1385 # # ============================================ # Comments from T0378.t04.alpha.rdb # ============================================ # TARGET T0378 # 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 T0378.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 1385 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0784 0.1854 0.7362 2 L 0.0935 0.1950 0.7115 3 S 0.0550 0.2041 0.7409 4 A 0.0316 0.4661 0.5022 5 N 0.0134 0.6835 0.3031 6 Q 0.0231 0.7781 0.1989 7 I 0.0297 0.8414 0.1289 8 K 0.0224 0.8889 0.0887 9 F 0.0293 0.8862 0.0845 10 L 0.0199 0.8846 0.0956 11 R 0.0124 0.9022 0.0853 12 S 0.0112 0.8718 0.1169 13 L 0.0119 0.8267 0.1615 14 R 0.0142 0.7502 0.2356 15 E 0.0156 0.7436 0.2408 16 R 0.0201 0.7166 0.2633 17 K 0.0274 0.6277 0.3448 18 Y 0.0564 0.5559 0.3876 19 R 0.0919 0.4968 0.4113 20 L 0.0842 0.4314 0.4844 21 R 0.0570 0.4758 0.4672 22 E 0.0698 0.3380 0.5922 23 Q 0.1176 0.1946 0.6878 24 A 0.2948 0.0990 0.6063 25 F 0.6633 0.0574 0.2793 26 A 0.8201 0.0512 0.1287 27 V 0.7999 0.0541 0.1460 28 E 0.6274 0.0753 0.2973 29 G 0.1933 0.0758 0.7309 30 P 0.0445 0.4498 0.5058 31 K 0.0384 0.6274 0.3342 32 L 0.0282 0.8171 0.1547 33 V 0.0126 0.9014 0.0860 34 G 0.0087 0.9084 0.0828 35 E 0.0099 0.8807 0.1094 36 M 0.0117 0.8422 0.1461 37 L 0.0220 0.7232 0.2548 38 P 0.0156 0.5841 0.4003 39 F 0.0352 0.4048 0.5599 40 Y 0.0558 0.1464 0.7978 41 R 0.0815 0.1080 0.8106 42 C 0.2270 0.0651 0.7079 43 R 0.3181 0.1074 0.5745 44 M 0.8281 0.0493 0.1226 45 L 0.8938 0.0334 0.0728 46 V 0.8793 0.0390 0.0817 47 G 0.7838 0.0425 0.1737 48 T 0.3085 0.0812 0.6103 49 A 0.0344 0.7312 0.2344 50 A 0.0184 0.8118 0.1698 51 M 0.0161 0.8379 0.1460 52 L 0.0199 0.8509 0.1292 53 R 0.0169 0.8058 0.1773 54 A 0.0189 0.7039 0.2772 55 V 0.0418 0.4819 0.4763 56 S 0.0662 0.2971 0.6367 57 T 0.0583 0.1530 0.7887 58 P 0.0488 0.1969 0.7543 59 H 0.0817 0.1168 0.8015 60 D 0.0947 0.0481 0.8572 61 A 0.2518 0.0119 0.7362 62 E 0.6925 0.0071 0.3004 63 V 0.8810 0.0053 0.1137 64 V 0.8771 0.0061 0.1167 65 E 0.8395 0.0042 0.1563 66 L 0.4125 0.0093 0.5781 67 P 0.1320 0.0201 0.8479 68 E 0.0258 0.3204 0.6538 69 S 0.0352 0.4102 0.5546 70 F 0.0844 0.3048 0.6108 71 D 0.1358 0.3431 0.5211 72 F 0.0529 0.7361 0.2109 73 K 0.0257 0.8021 0.1722 74 R 0.0335 0.7992 0.1673 75 I 0.0507 0.6939 0.2554 76 S 0.0685 0.4193 0.5122 77 T 0.0483 0.2193 0.7325 78 Q 0.0681 0.1069 0.8249 79 T 0.1281 0.0778 0.7942 80 T 0.1257 0.0365 0.8378 81 P 0.1180 0.0570 0.8250 82 Q 0.1466 0.0805 0.7728 83 P 0.4025 0.0390 0.5586 84 L 0.8231 0.0138 0.1631 85 M 0.9149 0.0055 0.0796 86 A 0.9130 0.0055 0.0815 87 V 0.9080 0.0074 0.0846 88 F 0.8153 0.0105 0.1742 89 D 0.5485 0.0169 0.4346 90 L 0.2267 0.0145 0.7589 91 P 0.1139 0.0296 0.8565 92 A 0.0783 0.0307 0.8910 93 E 0.0697 0.0239 0.9064 94 P 0.0695 0.0589 0.8717 95 E 0.0804 0.0646 0.8550 96 P 0.1260 0.1222 0.7518 97 V 0.1656 0.2057 0.6286 98 V 0.1819 0.1437 0.6744 99 E 0.0869 0.1030 0.8101 100 G 0.1182 0.0343 0.8474 101 L 0.5904 0.0071 0.4024 102 T 0.9115 0.0036 0.0850 103 L 0.9310 0.0033 0.0657 104 L 0.9251 0.0036 0.0713 105 L 0.8733 0.0061 0.1206 106 D 0.5348 0.0437 0.4215 107 G 0.2165 0.0283 0.7552 108 V 0.2348 0.0477 0.7175 109 Q 0.2595 0.0470 0.6935 110 D 0.1119 0.0262 0.8618 111 P 0.0288 0.1618 0.8094 112 G 0.0444 0.2376 0.7181 113 N 0.0357 0.6640 0.3003 114 V 0.0072 0.9150 0.0778 115 G 0.0053 0.9465 0.0482 116 T 0.0048 0.9573 0.0378 117 I 0.0048 0.9587 0.0365 118 L 0.0048 0.9571 0.0381 119 R 0.0052 0.9525 0.0423 120 T 0.0048 0.9496 0.0456 121 A 0.0048 0.9468 0.0484 122 D 0.0051 0.9255 0.0694 123 W 0.0063 0.8900 0.1037 124 F 0.0468 0.4163 0.5370 125 G 0.0616 0.0168 0.9216 126 I 0.1061 0.0136 0.8803 127 R 0.1463 0.0493 0.8044 128 H 0.8356 0.0111 0.1533 129 V 0.9218 0.0040 0.0742 130 W 0.9257 0.0041 0.0702 131 L 0.8701 0.0079 0.1220 132 G 0.4532 0.0142 0.5326 133 T 0.1424 0.0404 0.8172 134 G 0.0710 0.0679 0.8611 135 S 0.0891 0.1242 0.7866 136 A 0.0934 0.1648 0.7418 137 D 0.0953 0.1552 0.7495 138 V 0.0808 0.2016 0.7176 139 F 0.0859 0.1273 0.7868 140 S 0.0756 0.0768 0.8477 141 P 0.0053 0.8888 0.1059 142 K 0.0061 0.9224 0.0714 143 V 0.0085 0.9374 0.0541 144 V 0.0092 0.9417 0.0491 145 Q 0.0140 0.9305 0.0556 146 A 0.0172 0.8848 0.0981 147 S 0.0251 0.8362 0.1387 148 M 0.0248 0.7816 0.1937 149 G 0.0466 0.6033 0.3501 150 A 0.0711 0.6188 0.3102 151 L 0.0844 0.6388 0.2768 152 A 0.1312 0.5002 0.3686 153 R 0.2002 0.2956 0.5042 154 V 0.2106 0.0476 0.7418 155 Q 0.1555 0.0169 0.8276 156 P 0.2077 0.0551 0.7372 157 T 0.3362 0.0468 0.6170 158 P 0.3854 0.0661 0.5485 159 L 0.1898 0.1288 0.6813 160 K 0.0902 0.1678 0.7420 161 N 0.1137 0.1492 0.7371 162 T 0.0052 0.9276 0.0673 163 V 0.0047 0.9568 0.0385 164 D 0.0047 0.9591 0.0363 165 T 0.0048 0.9573 0.0379 166 L 0.0047 0.9581 0.0372 167 A 0.0047 0.9553 0.0400 168 Y 0.0048 0.9557 0.0396 169 F 0.0048 0.9521 0.0431 170 R 0.0049 0.9435 0.0516 171 R 0.0061 0.8867 0.1073 172 Q 0.0417 0.3402 0.6181 173 G 0.0393 0.0142 0.9466 174 I 0.0813 0.0077 0.9111 175 P 0.5274 0.0046 0.4680 176 V 0.9260 0.0033 0.0707 177 Y 0.9261 0.0043 0.0696 178 G 0.9271 0.0035 0.0694 179 A 0.8935 0.0058 0.1008 180 F 0.6882 0.0060 0.3058 181 L 0.2818 0.0323 0.6859 182 D 0.1272 0.0424 0.8303 183 G 0.0696 0.1273 0.8030 184 Q 0.1011 0.1714 0.7275 185 S 0.2007 0.1805 0.6188 186 L 0.2478 0.1805 0.5718 187 Y 0.2263 0.1564 0.6173 188 E 0.1969 0.1355 0.6676 189 A 0.1097 0.0856 0.8047 190 P 0.1099 0.1246 0.7655 191 L 0.1122 0.1147 0.7731 192 P 0.0761 0.1353 0.7886 193 N 0.0747 0.1188 0.8065 194 F 0.0792 0.0796 0.8412 195 T 0.0698 0.0586 0.8716 196 E 0.0768 0.0387 0.8845 197 P 0.1478 0.0225 0.8297 198 A 0.7474 0.0078 0.2448 199 I 0.9263 0.0034 0.0704 200 L 0.9328 0.0032 0.0640 201 V 0.9279 0.0034 0.0687 202 L 0.8429 0.0164 0.1407 203 G 0.4144 0.0156 0.5701 204 S 0.1625 0.0548 0.7827 205 E 0.0937 0.1306 0.7757 206 G 0.0661 0.1572 0.7767 207 R 0.0535 0.1608 0.7857 208 G 0.0636 0.1010 0.8354 209 I 0.0953 0.0266 0.8781 210 S 0.0640 0.0476 0.8883 211 P 0.0050 0.9413 0.0537 212 E 0.0047 0.9547 0.0405 213 V 0.0050 0.9482 0.0467 214 A 0.0065 0.9388 0.0546 215 A 0.0073 0.8783 0.1144 216 E 0.0131 0.5860 0.4009 217 I 0.0519 0.3142 0.6339 218 T 0.0781 0.1770 0.7449 219 D 0.3668 0.1297 0.5036 220 R 0.7231 0.0514 0.2255 221 L 0.8393 0.0146 0.1462 222 T 0.8209 0.0093 0.1698 223 I 0.5993 0.0093 0.3914 224 P 0.2797 0.0166 0.7037 225 A 0.1109 0.0471 0.8420 226 S 0.0412 0.0993 0.8595 227 G 0.0416 0.1135 0.8449 228 L 0.1081 0.1094 0.7825 229 S 0.1656 0.0890 0.7454 230 V 0.1549 0.0810 0.7641 231 K 0.1104 0.1157 0.7739 232 G 0.0779 0.0972 0.8248 233 H 0.1327 0.1288 0.7384 234 T 0.1897 0.2432 0.5671 235 E 0.1577 0.3346 0.5078 236 S 0.1879 0.4459 0.3661 237 L 0.0735 0.7593 0.1672 238 N 0.0201 0.8928 0.0871 239 V 0.0050 0.9571 0.0379 240 A 0.0047 0.9604 0.0349 241 I 0.0047 0.9605 0.0348 242 A 0.0047 0.9610 0.0343 243 T 0.0046 0.9612 0.0342 244 A 0.0046 0.9614 0.0340 245 I 0.0046 0.9613 0.0340 246 L 0.0046 0.9609 0.0344 247 C 0.0047 0.9593 0.0360 248 S 0.0050 0.9551 0.0399 249 E 0.0057 0.9459 0.0484 250 W 0.0094 0.9116 0.0790 251 R 0.0248 0.7783 0.1968 252 R 0.0482 0.5289 0.4229 253 R 0.0540 0.1050 0.8410 254 S 0.0475 0.0335 0.9190