# This file is the result of combining several RDB files, specifically # T0225.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0225.t2k.stride-ebghtl.rdb (weight 1.24869) # T0225.t2k.str2.rdb (weight 1.54758) # T0225.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 T0225.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0225 # 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 T0225.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 1309 # # ============================================ # Comments from T0225.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0225 # 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 T0225.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 1309 # # ============================================ # Comments from T0225.t2k.str2.rdb # ============================================ # TARGET T0225 # 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 T0225.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 1309 # # ============================================ # Comments from T0225.t2k.alpha.rdb # ============================================ # TARGET T0225 # 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 T0225.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 1309 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0919 0.0249 0.8832 2 K 0.5783 0.0073 0.4144 3 I 0.8902 0.0050 0.1048 4 L 0.9190 0.0047 0.0763 5 I 0.8969 0.0086 0.0945 6 T 0.6966 0.0388 0.2645 7 G 0.2125 0.0378 0.7497 8 A 0.0526 0.1197 0.8277 9 N 0.0374 0.2094 0.7532 10 G 0.0418 0.3169 0.6413 11 Q 0.0234 0.7961 0.1805 12 L 0.0131 0.8830 0.1039 13 G 0.0057 0.9336 0.0607 14 R 0.0048 0.9556 0.0396 15 E 0.0047 0.9586 0.0367 16 I 0.0047 0.9598 0.0355 17 Q 0.0047 0.9588 0.0365 18 K 0.0047 0.9583 0.0370 19 Q 0.0047 0.9565 0.0388 20 L 0.0048 0.9521 0.0430 21 K 0.0051 0.9328 0.0621 22 G 0.0066 0.8430 0.1504 23 K 0.0408 0.3318 0.6274 24 N 0.0415 0.0199 0.9386 25 V 0.1137 0.0115 0.8748 26 E 0.6533 0.0052 0.3415 27 V 0.8800 0.0032 0.1169 28 I 0.9100 0.0039 0.0861 29 P 0.9039 0.0035 0.0926 30 T 0.8237 0.0084 0.1679 31 D 0.4718 0.0201 0.5081 32 V 0.1354 0.0567 0.8079 33 Q 0.0822 0.0735 0.8444 34 D 0.0836 0.1202 0.7962 35 L 0.1542 0.0784 0.7673 36 D 0.1535 0.0573 0.7891 37 I 0.1333 0.2603 0.6064 38 T 0.1508 0.2113 0.6379 39 N 0.1485 0.1593 0.6922 40 V 0.0060 0.9088 0.0852 41 L 0.0063 0.9272 0.0666 42 A 0.0052 0.9407 0.0541 43 V 0.0049 0.9495 0.0456 44 N 0.0049 0.9506 0.0445 45 K 0.0050 0.9429 0.0521 46 F 0.0054 0.9321 0.0625 47 F 0.0074 0.9165 0.0761 48 N 0.0076 0.8264 0.1660 49 E 0.0133 0.5266 0.4601 50 K 0.0681 0.2524 0.6795 51 K 0.0889 0.0272 0.8839 52 P 0.0925 0.0628 0.8447 53 N 0.1215 0.0812 0.7973 54 V 0.8762 0.0195 0.1042 55 V 0.9262 0.0078 0.0660 56 I 0.9176 0.0108 0.0716 57 N 0.8562 0.0264 0.1174 58 C 0.4120 0.1401 0.4479 59 A 0.2047 0.3062 0.4892 60 A 0.1630 0.3698 0.4672 61 H 0.1529 0.3529 0.4941 62 T 0.1238 0.2962 0.5800 63 A 0.1376 0.1857 0.6767 64 V 0.0959 0.1919 0.7121 65 D 0.0876 0.3090 0.6034 66 K 0.0559 0.4738 0.4702 67 C 0.0625 0.4603 0.4772 68 E 0.0624 0.4354 0.5022 69 E 0.0521 0.3851 0.5628 70 Q 0.0700 0.1824 0.7476 71 Y 0.0161 0.7873 0.1966 72 D 0.0116 0.8604 0.1280 73 L 0.0123 0.8942 0.0935 74 A 0.0192 0.8974 0.0834 75 Y 0.0204 0.9036 0.0760 76 K 0.0173 0.9046 0.0782 77 I 0.0135 0.8996 0.0869 78 N 0.0170 0.8430 0.1400 79 A 0.0092 0.9066 0.0842 80 I 0.0090 0.9202 0.0708 81 G 0.0065 0.9355 0.0580 82 P 0.0048 0.9546 0.0406 83 K 0.0048 0.9585 0.0367 84 N 0.0047 0.9593 0.0360 85 L 0.0047 0.9586 0.0366 86 A 0.0047 0.9595 0.0358 87 A 0.0048 0.9593 0.0360 88 A 0.0047 0.9580 0.0373 89 A 0.0048 0.9565 0.0387 90 Y 0.0051 0.9396 0.0553 91 S 0.0056 0.8695 0.1249 92 V 0.0441 0.3792 0.5767 93 G 0.0416 0.0196 0.9388 94 A 0.1042 0.0079 0.8879 95 E 0.5890 0.0076 0.4033 96 I 0.9179 0.0033 0.0788 97 V 0.9274 0.0038 0.0688 98 Q 0.9230 0.0036 0.0734 99 I 0.8493 0.0072 0.1436 100 S 0.5122 0.0110 0.4769 101 T 0.2070 0.0748 0.7182 102 D 0.1377 0.2667 0.5956 103 Y 0.2059 0.3245 0.4697 104 V 0.2498 0.2688 0.4814 105 F 0.2206 0.1285 0.6509 106 D 0.1082 0.0745 0.8172 107 G 0.0783 0.0776 0.8440 108 E 0.0875 0.1005 0.8120 109 A 0.0838 0.1169 0.7993 110 K 0.1011 0.0914 0.8075 111 E 0.1855 0.0426 0.7719 112 P 0.2696 0.0343 0.6961 113 I 0.3107 0.0369 0.6524 114 T 0.1940 0.0507 0.7553 115 E 0.0720 0.2090 0.7189 116 F 0.0572 0.1784 0.7644 117 D 0.0877 0.0885 0.8239 118 E 0.0954 0.0595 0.8450 119 V 0.1674 0.0733 0.7593 120 N 0.0995 0.0611 0.8394 121 P 0.0812 0.0891 0.8297 122 Q 0.0762 0.1072 0.8166 123 S 0.0774 0.1111 0.8115 124 A 0.0141 0.7762 0.2097 125 Y 0.0133 0.8465 0.1402 126 G 0.0116 0.8974 0.0910 127 K 0.0073 0.9299 0.0629 128 T 0.0065 0.9305 0.0630 129 K 0.0052 0.9519 0.0429 130 L 0.0051 0.9552 0.0397 131 E 0.0047 0.9553 0.0400 132 G 0.0047 0.9568 0.0385 133 E 0.0047 0.9582 0.0371 134 N 0.0047 0.9571 0.0382 135 F 0.0047 0.9558 0.0395 136 V 0.0049 0.9475 0.0476 137 K 0.0056 0.9259 0.0685 138 A 0.0076 0.8496 0.1428 139 L 0.0466 0.3956 0.5578 140 N 0.0417 0.0339 0.9243 141 P 0.0707 0.0154 0.9139 142 K 0.1938 0.0446 0.7616 143 Y 0.8821 0.0048 0.1131 144 Y 0.9264 0.0037 0.0699 145 I 0.9301 0.0035 0.0664 146 V 0.9178 0.0046 0.0776 147 R 0.8046 0.0059 0.1895 148 T 0.4546 0.0230 0.5224 149 A 0.2103 0.0806 0.7090 150 W 0.2012 0.1426 0.6563 151 L 0.1877 0.1914 0.6209 152 Y 0.1501 0.1296 0.7203 153 G 0.0787 0.0830 0.8384 154 D 0.0497 0.1272 0.8231 155 G 0.0416 0.2035 0.7549 156 N 0.0351 0.2641 0.7009 157 N 0.0491 0.3201 0.6308 158 F 0.0535 0.6796 0.2668 159 V 0.0211 0.8601 0.1188 160 K 0.0062 0.9387 0.0551 161 T 0.0055 0.9500 0.0446 162 M 0.0050 0.9528 0.0422 163 I 0.0047 0.9541 0.0412 164 N 0.0053 0.9521 0.0426 165 L 0.0050 0.9449 0.0502 166 G 0.0066 0.9231 0.0703 167 K 0.0076 0.8712 0.1212 168 T 0.0410 0.4548 0.5042 169 H 0.0365 0.0720 0.8915 170 D 0.0705 0.0249 0.9046 171 E 0.2809 0.0246 0.6945 172 L 0.3783 0.0300 0.5917 173 K 0.4480 0.0342 0.5179 174 V 0.3476 0.0375 0.6149 175 V 0.1831 0.0509 0.7661 176 H 0.1068 0.0953 0.7980 177 D 0.1271 0.0982 0.7747 178 Q 0.2520 0.0739 0.6741 179 V 0.3951 0.0827 0.5222 180 G 0.3713 0.0644 0.5643 181 T 0.3025 0.0555 0.6420 182 P 0.3645 0.0850 0.5504 183 T 0.4215 0.0478 0.5307 184 S 0.2912 0.0540 0.6548 185 T 0.0075 0.9020 0.0905 186 V 0.0052 0.9293 0.0654 187 D 0.0049 0.9434 0.0517 188 L 0.0047 0.9574 0.0379 189 A 0.0047 0.9600 0.0354 190 R 0.0046 0.9603 0.0350 191 V 0.0047 0.9609 0.0345 192 V 0.0047 0.9603 0.0350 193 L 0.0047 0.9595 0.0358 194 K 0.0047 0.9547 0.0405 195 V 0.0050 0.9386 0.0564 196 I 0.0064 0.8884 0.1052 197 D 0.0132 0.7160 0.2709 198 E 0.0554 0.3169 0.6277 199 K 0.0526 0.1038 0.8436 200 N 0.0466 0.1004 0.8530 201 Y 0.0729 0.0671 0.8600 202 G 0.2441 0.0439 0.7119 203 T 0.7875 0.0124 0.2002 204 F 0.8695 0.0087 0.1218 205 H 0.8605 0.0059 0.1336 206 C 0.6597 0.0242 0.3161 207 T 0.2760 0.0389 0.6851 208 C 0.0746 0.0580 0.8674 209 K 0.0483 0.0612 0.8905 210 G 0.1463 0.0547 0.7991 211 I 0.3108 0.0335 0.6557 212 C 0.4360 0.0185 0.5454 213 S 0.3026 0.0274 0.6700 214 W 0.0051 0.9331 0.0619 215 Y 0.0047 0.9531 0.0422 216 D 0.0047 0.9582 0.0372 217 F 0.0047 0.9602 0.0351 218 A 0.0047 0.9606 0.0348 219 V 0.0047 0.9593 0.0360 220 E 0.0047 0.9597 0.0356 221 I 0.0047 0.9584 0.0369 222 F 0.0048 0.9545 0.0407 223 R 0.0054 0.9351 0.0595 224 L 0.0081 0.8875 0.1044 225 T 0.0466 0.5600 0.3934 226 G 0.0367 0.0609 0.9024 227 I 0.0747 0.0434 0.8818 228 D 0.1282 0.0480 0.8238 229 V 0.1662 0.0561 0.7777 230 K 0.2811 0.0467 0.6722 231 V 0.4808 0.0509 0.4682 232 T 0.4971 0.0421 0.4608 233 P 0.4188 0.0478 0.5334 234 C 0.2798 0.0543 0.6659 235 T 0.2034 0.0842 0.7124 236 T 0.1487 0.2065 0.6448 237 E 0.1743 0.2101 0.6156 238 E 0.1906 0.2143 0.5951 239 F 0.1482 0.1529 0.6989 240 P 0.1207 0.1288 0.7506 241 R 0.1163 0.1246 0.7592 242 P 0.0892 0.1051 0.8057 243 A 0.0523 0.1816 0.7661 244 K 0.0523 0.1444 0.8033 245 R 0.0762 0.0878 0.8360 246 P 0.0834 0.1894 0.7273 247 K 0.0899 0.2957 0.6143 248 Y 0.1295 0.3216 0.5489 249 S 0.2445 0.2083 0.5471 250 V 0.3787 0.1228 0.4986 251 L 0.4360 0.0673 0.4966 252 R 0.2416 0.0555 0.7029 253 N 0.0054 0.9266 0.0679 254 Y 0.0049 0.9515 0.0436 255 M 0.0048 0.9562 0.0389 256 L 0.0047 0.9580 0.0373 257 E 0.0048 0.9552 0.0400 258 L 0.0056 0.9392 0.0552 259 T 0.0087 0.8948 0.0966 260 T 0.0457 0.5723 0.3820 261 G 0.0412 0.0547 0.9040 262 D 0.0696 0.0188 0.9116 263 I 0.0842 0.0188 0.8970 264 T 0.0995 0.0264 0.8741 265 R 0.0925 0.0288 0.8786 266 E 0.0984 0.0348 0.8667 267 W 0.0066 0.8824 0.1110 268 K 0.0048 0.9300 0.0651 269 E 0.0049 0.9411 0.0540 270 S 0.0051 0.9419 0.0530 271 L 0.0047 0.9512 0.0441 272 K 0.0047 0.9524 0.0428 273 E 0.0048 0.9472 0.0480 274 Y 0.0048 0.9398 0.0554 275 I 0.0051 0.9229 0.0720 276 D 0.0059 0.8896 0.1045 277 L 0.0072 0.8206 0.1722 278 L 0.0300 0.6003 0.3697 279 Q 0.0364 0.4175 0.5461 280 M 0.0310 0.1115 0.8574