# This file is the result of combining several RDB files, specifically # T0378.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0378.t2k.stride-ebghtl.rdb (weight 1.24869) # T0378.t2k.str2.rdb (weight 1.54758) # T0378.t2k.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.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0378 # 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 T0378.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 913 # # ============================================ # Comments from T0378.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0378 # 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 T0378.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 913 # # ============================================ # Comments from T0378.t2k.str2.rdb # ============================================ # TARGET T0378 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0378.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 913 # # ============================================ # Comments from T0378.t2k.alpha.rdb # ============================================ # TARGET T0378 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0378.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 913 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0390 0.0809 0.8801 2 L 0.0497 0.1889 0.7614 3 S 0.0502 0.2674 0.6824 4 A 0.0424 0.4821 0.4755 5 N 0.0233 0.6980 0.2787 6 Q 0.0157 0.7481 0.2362 7 I 0.0084 0.9139 0.0777 8 K 0.0076 0.9301 0.0622 9 F 0.0054 0.9449 0.0496 10 L 0.0059 0.9416 0.0525 11 R 0.0065 0.9333 0.0602 12 S 0.0060 0.9200 0.0740 13 L 0.0096 0.8628 0.1276 14 R 0.0120 0.7627 0.2253 15 E 0.0185 0.6583 0.3232 16 R 0.0214 0.6949 0.2837 17 K 0.0239 0.7122 0.2639 18 Y 0.0451 0.6710 0.2840 19 R 0.0794 0.6782 0.2425 20 L 0.0600 0.7053 0.2347 21 R 0.0434 0.6476 0.3090 22 E 0.0520 0.2814 0.6665 23 Q 0.0467 0.0882 0.8651 24 A 0.3409 0.0810 0.5782 25 F 0.7356 0.0601 0.2042 26 A 0.7731 0.0908 0.1361 27 V 0.7134 0.1364 0.1503 28 E 0.5080 0.2020 0.2900 29 G 0.2747 0.2808 0.4445 30 P 0.1372 0.5154 0.3473 31 K 0.1075 0.6388 0.2537 32 L 0.0377 0.8156 0.1467 33 V 0.0128 0.9088 0.0784 34 G 0.0075 0.9385 0.0540 35 E 0.0058 0.9443 0.0499 36 M 0.0053 0.9387 0.0560 37 L 0.0059 0.9148 0.0793 38 P 0.0078 0.8126 0.1796 39 F 0.0426 0.4515 0.5058 40 Y 0.0405 0.1177 0.8418 41 R 0.0671 0.0702 0.8627 42 C 0.1583 0.1099 0.7318 43 R 0.2595 0.3068 0.4337 44 M 0.3250 0.3907 0.2843 45 L 0.4593 0.3440 0.1968 46 V 0.4252 0.3754 0.1994 47 G 0.3930 0.3682 0.2388 48 T 0.2768 0.4005 0.3228 49 A 0.1705 0.3701 0.4594 50 A 0.0423 0.7225 0.2352 51 M 0.0190 0.8265 0.1545 52 L 0.0140 0.8526 0.1334 53 R 0.0107 0.8768 0.1124 54 A 0.0092 0.8921 0.0986 55 V 0.0086 0.8985 0.0929 56 S 0.0076 0.9021 0.0904 57 T 0.0097 0.8883 0.1021 58 P 0.0093 0.8535 0.1372 59 H 0.0137 0.7520 0.2344 60 D 0.0442 0.3153 0.6405 61 A 0.0401 0.0350 0.9249 62 E 0.1155 0.0125 0.8720 63 V 0.4316 0.0076 0.5608 64 V 0.8128 0.0059 0.1813 65 E 0.8803 0.0057 0.1140 66 L 0.8712 0.0048 0.1240 67 P 0.6531 0.0082 0.3387 68 E 0.2082 0.0115 0.7803 69 S 0.0062 0.8490 0.1448 70 F 0.0052 0.8969 0.0979 71 D 0.0060 0.9230 0.0710 72 F 0.0058 0.9301 0.0641 73 K 0.0083 0.9028 0.0889 74 R 0.0096 0.8616 0.1288 75 I 0.0215 0.7800 0.1984 76 S 0.0494 0.5477 0.4028 77 T 0.0403 0.2332 0.7265 78 Q 0.0713 0.0976 0.8312 79 T 0.1315 0.0838 0.7847 80 T 0.1793 0.0627 0.7580 81 P 0.1806 0.1171 0.7023 82 Q 0.2361 0.1041 0.6598 83 P 0.4423 0.0593 0.4984 84 L 0.7779 0.0199 0.2022 85 M 0.8854 0.0115 0.1031 86 A 0.8982 0.0083 0.0935 87 V 0.8966 0.0101 0.0933 88 F 0.7837 0.0135 0.2028 89 D 0.5061 0.0214 0.4725 90 L 0.1999 0.0539 0.7462 91 P 0.1070 0.1058 0.7872 92 A 0.0911 0.1378 0.7710 93 E 0.0779 0.1922 0.7299 94 P 0.0696 0.2024 0.7280 95 E 0.0851 0.2188 0.6960 96 P 0.0517 0.3521 0.5962 97 V 0.0520 0.3034 0.6446 98 V 0.0694 0.1867 0.7439 99 E 0.0988 0.0458 0.8554 100 G 0.1233 0.0447 0.8320 101 L 0.7009 0.0114 0.2878 102 T 0.9049 0.0045 0.0906 103 L 0.9255 0.0036 0.0710 104 L 0.9186 0.0037 0.0776 105 L 0.8679 0.0080 0.1241 106 D 0.5140 0.0510 0.4350 107 G 0.1951 0.0401 0.7648 108 V 0.1471 0.0570 0.7958 109 Q 0.0913 0.0645 0.8442 110 D 0.0895 0.0383 0.8722 111 P 0.0221 0.2606 0.7172 112 G 0.0335 0.3022 0.6643 113 N 0.0630 0.4942 0.4428 114 V 0.0182 0.8438 0.1379 115 G 0.0136 0.9196 0.0668 116 T 0.0131 0.9376 0.0493 117 I 0.0090 0.9509 0.0400 118 L 0.0075 0.9537 0.0388 119 R 0.0091 0.9455 0.0454 120 T 0.0088 0.9368 0.0544 121 A 0.0051 0.9398 0.0550 122 D 0.0065 0.9188 0.0747 123 W 0.0086 0.8182 0.1732 124 F 0.0447 0.4302 0.5251 125 G 0.0646 0.0447 0.8907 126 I 0.1109 0.0112 0.8779 127 R 0.1787 0.0404 0.7809 128 H 0.8806 0.0064 0.1131 129 V 0.9259 0.0034 0.0707 130 W 0.9203 0.0044 0.0753 131 L 0.8711 0.0056 0.1233 132 G 0.4659 0.0230 0.5111 133 T 0.0833 0.0668 0.8499 134 G 0.0416 0.1332 0.8251 135 S 0.0794 0.1561 0.7645 136 A 0.1230 0.1142 0.7628 137 D 0.0953 0.1040 0.8006 138 V 0.0630 0.1720 0.7650 139 F 0.0759 0.1496 0.7746 140 S 0.0829 0.1050 0.8122 141 P 0.0062 0.8955 0.0983 142 K 0.0065 0.9247 0.0689 143 V 0.0114 0.9370 0.0516 144 V 0.0150 0.9340 0.0509 145 Q 0.0258 0.9123 0.0619 146 A 0.0252 0.8842 0.0905 147 S 0.0465 0.7833 0.1702 148 M 0.0315 0.6426 0.3259 149 G 0.0465 0.3557 0.5978 150 A 0.1153 0.3391 0.5456 151 L 0.2578 0.2737 0.4685 152 A 0.3432 0.2478 0.4089 153 R 0.4492 0.1412 0.4096 154 V 0.5020 0.0337 0.4643 155 Q 0.5240 0.0196 0.4564 156 P 0.7346 0.0224 0.2430 157 T 0.7777 0.0246 0.1977 158 P 0.7866 0.0156 0.1978 159 L 0.5105 0.0197 0.4698 160 K 0.1499 0.0608 0.7894 161 N 0.1156 0.0165 0.8679 162 T 0.0083 0.8696 0.1221 163 V 0.0051 0.9457 0.0492 164 D 0.0048 0.9536 0.0416 165 T 0.0048 0.9559 0.0392 166 L 0.0049 0.9552 0.0399 167 A 0.0049 0.9507 0.0444 168 Y 0.0050 0.9498 0.0451 169 F 0.0056 0.9468 0.0476 170 R 0.0050 0.9303 0.0647 171 R 0.0061 0.8488 0.1451 172 Q 0.0446 0.2689 0.6865 173 G 0.0404 0.0166 0.9430 174 I 0.1370 0.0078 0.8553 175 P 0.7557 0.0042 0.2401 176 V 0.9228 0.0031 0.0741 177 Y 0.9224 0.0045 0.0731 178 G 0.9119 0.0042 0.0839 179 A 0.8392 0.0086 0.1522 180 F 0.4698 0.0145 0.5158 181 L 0.1281 0.0736 0.7983 182 D 0.0834 0.0947 0.8219 183 G 0.0617 0.2204 0.7180 184 Q 0.0689 0.2459 0.6853 185 S 0.1256 0.2447 0.6298 186 L 0.1891 0.2118 0.5991 187 Y 0.2136 0.1934 0.5929 188 E 0.2141 0.1888 0.5971 189 A 0.1214 0.4675 0.4111 190 P 0.1197 0.4915 0.3888 191 L 0.1277 0.4470 0.4253 192 P 0.1538 0.2668 0.5794 193 N 0.1267 0.1373 0.7360 194 F 0.1035 0.1026 0.7939 195 T 0.0664 0.0882 0.8454 196 E 0.0747 0.0382 0.8871 197 P 0.1695 0.0279 0.8026 198 A 0.8456 0.0042 0.1502 199 I 0.9274 0.0033 0.0693 200 L 0.9288 0.0033 0.0678 201 V 0.9182 0.0033 0.0784 202 L 0.7247 0.0210 0.2543 203 G 0.2995 0.0191 0.6814 204 S 0.1542 0.0660 0.7798 205 E 0.0763 0.1810 0.7426 206 G 0.0591 0.2130 0.7280 207 R 0.0445 0.1508 0.8047 208 G 0.0590 0.0790 0.8620 209 I 0.1151 0.0403 0.8447 210 S 0.0536 0.0344 0.9120 211 P 0.0057 0.9274 0.0669 212 E 0.0049 0.9422 0.0529 213 V 0.0054 0.9438 0.0509 214 A 0.0053 0.9437 0.0510 215 A 0.0078 0.8759 0.1163 216 E 0.0168 0.6483 0.3349 217 I 0.0714 0.2990 0.6296 218 T 0.0704 0.1508 0.7788 219 D 0.3986 0.1146 0.4867 220 R 0.7701 0.0379 0.1920 221 L 0.8743 0.0106 0.1151 222 T 0.8736 0.0091 0.1173 223 I 0.6711 0.0101 0.3188 224 P 0.3283 0.0253 0.6464 225 A 0.1338 0.0725 0.7937 226 S 0.0847 0.1582 0.7571 227 G 0.0598 0.2192 0.7210 228 L 0.0587 0.2332 0.7080 229 S 0.0618 0.1863 0.7519 230 V 0.0605 0.2188 0.7208 231 K 0.0755 0.2207 0.7038 232 G 0.0835 0.1904 0.7261 233 H 0.1362 0.2283 0.6355 234 T 0.2189 0.2997 0.4814 235 E 0.2126 0.3384 0.4490 236 S 0.2093 0.4573 0.3334 237 L 0.0596 0.7992 0.1412 238 N 0.0179 0.8985 0.0836 239 V 0.0054 0.9465 0.0481 240 A 0.0047 0.9556 0.0397 241 I 0.0047 0.9588 0.0365 242 A 0.0047 0.9602 0.0351 243 T 0.0047 0.9602 0.0351 244 A 0.0047 0.9605 0.0349 245 I 0.0047 0.9606 0.0348 246 L 0.0047 0.9606 0.0347 247 C 0.0047 0.9595 0.0358 248 S 0.0048 0.9570 0.0383 249 E 0.0052 0.9499 0.0449 250 W 0.0066 0.9350 0.0585 251 R 0.0115 0.8795 0.1090 252 R 0.0189 0.6014 0.3797 253 R 0.0366 0.3577 0.6057 254 S 0.0306 0.0717 0.8976