# This file is the result of combining several RDB files, specifically # T0341.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0341.t2k.stride-ebghtl.rdb (weight 1.24869) # T0341.t2k.str2.rdb (weight 1.54758) # T0341.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 T0341.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0341 # 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 T0341.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 857 # # ============================================ # Comments from T0341.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0341 # 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 T0341.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 857 # # ============================================ # Comments from T0341.t2k.str2.rdb # ============================================ # TARGET T0341 # 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 T0341.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 857 # # ============================================ # Comments from T0341.t2k.alpha.rdb # ============================================ # TARGET T0341 # 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 T0341.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 857 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0445 0.1808 0.7747 2 A 0.0545 0.4029 0.5426 3 A 0.0407 0.5123 0.4471 4 R 0.0337 0.5699 0.3964 5 R 0.0346 0.4228 0.5426 6 A 0.0702 0.2109 0.7189 7 L 0.1547 0.0152 0.8301 8 K 0.2517 0.0425 0.7057 9 A 0.9145 0.0044 0.0811 10 V 0.9316 0.0033 0.0651 11 L 0.9252 0.0038 0.0710 12 V 0.9042 0.0052 0.0907 13 D 0.5252 0.0065 0.4683 14 L 0.0797 0.0959 0.8244 15 N 0.0528 0.0441 0.9032 16 G 0.0825 0.0733 0.8443 17 T 0.3733 0.0461 0.5805 18 L 0.7214 0.0380 0.2407 19 H 0.5683 0.0667 0.3649 20 I 0.2928 0.0848 0.6224 21 E 0.0782 0.1364 0.7854 22 D 0.0562 0.2298 0.7140 23 A 0.0470 0.3706 0.5824 24 A 0.0528 0.4468 0.5004 25 V 0.0321 0.6109 0.3570 26 P 0.0081 0.8658 0.1262 27 G 0.0085 0.8861 0.1054 28 A 0.0063 0.9336 0.0601 29 Q 0.0058 0.9479 0.0463 30 E 0.0050 0.9537 0.0414 31 A 0.0047 0.9561 0.0391 32 L 0.0047 0.9531 0.0422 33 K 0.0048 0.9497 0.0455 34 R 0.0050 0.9373 0.0577 35 L 0.0063 0.9059 0.0879 36 R 0.0131 0.8341 0.1529 37 A 0.0162 0.6286 0.3551 38 T 0.0444 0.3578 0.5978 39 S 0.0430 0.1020 0.8549 40 V 0.0801 0.0427 0.8773 41 M 0.1888 0.0438 0.7674 42 V 0.4746 0.1170 0.4084 43 R 0.6161 0.1278 0.2561 44 F 0.6853 0.1126 0.2021 45 V 0.6078 0.1246 0.2676 46 T 0.4039 0.1538 0.4424 47 N 0.1809 0.2073 0.6118 48 T 0.1198 0.1959 0.6844 49 T 0.1106 0.2162 0.6732 50 K 0.1035 0.2237 0.6728 51 E 0.0887 0.2357 0.6755 52 T 0.0704 0.2265 0.7031 53 K 0.0113 0.8298 0.1589 54 K 0.0077 0.8913 0.1010 55 D 0.0069 0.9145 0.0786 56 L 0.0058 0.9263 0.0680 57 L 0.0055 0.9263 0.0682 58 E 0.0061 0.9212 0.0727 59 R 0.0057 0.9144 0.0798 60 L 0.0081 0.8886 0.1033 61 K 0.0071 0.8555 0.1374 62 K 0.0104 0.7659 0.2237 63 L 0.0413 0.4616 0.4971 64 E 0.0459 0.1502 0.8039 65 F 0.0794 0.1202 0.8004 66 E 0.1253 0.1386 0.7361 67 I 0.1120 0.2002 0.6877 68 S 0.1064 0.1921 0.7015 69 E 0.0489 0.5755 0.3756 70 D 0.0418 0.6401 0.3181 71 E 0.0661 0.6180 0.3159 72 I 0.1208 0.5327 0.3465 73 F 0.1287 0.4587 0.4125 74 T 0.1016 0.3952 0.5032 75 S 0.0326 0.6192 0.3482 76 L 0.0170 0.7640 0.2189 77 T 0.0108 0.8675 0.1216 78 A 0.0094 0.8929 0.0977 79 A 0.0069 0.9157 0.0774 80 R 0.0064 0.9308 0.0629 81 N 0.0065 0.9329 0.0606 82 L 0.0062 0.9277 0.0661 83 I 0.0074 0.9062 0.0865 84 E 0.0079 0.8706 0.1215 85 Q 0.0108 0.7810 0.2081 86 K 0.0309 0.6116 0.3575 87 Q 0.0491 0.4450 0.5058 88 V 0.0510 0.4134 0.5356 89 R 0.0648 0.4463 0.4889 90 P 0.0928 0.4913 0.4159 91 M 0.1767 0.4630 0.3603 92 L 0.2772 0.4110 0.3118 93 L 0.3053 0.3880 0.3067 94 L 0.2768 0.3659 0.3573 95 D 0.1790 0.3504 0.4706 96 D 0.1037 0.2944 0.6018 97 R 0.0672 0.4019 0.5309 98 A 0.0549 0.4978 0.4473 99 L 0.0519 0.5211 0.4270 100 P 0.0435 0.5855 0.3711 101 E 0.0334 0.6918 0.2748 102 F 0.0259 0.7425 0.2316 103 T 0.0246 0.7558 0.2195 104 G 0.0281 0.7345 0.2375 105 V 0.0271 0.7355 0.2374 106 Q 0.0315 0.7026 0.2659 107 T 0.0308 0.6700 0.2992 108 Q 0.0384 0.6620 0.2996 109 D 0.0453 0.6808 0.2739 110 P 0.0620 0.6807 0.2573 111 N 0.0964 0.6834 0.2202 112 A 0.1548 0.6554 0.1898 113 V 0.2111 0.5965 0.1924 114 V 0.2039 0.5578 0.2384 115 I 0.2189 0.4227 0.3584 116 G 0.1450 0.3540 0.5009 117 L 0.1085 0.2673 0.6241 118 A 0.0947 0.2824 0.6229 119 P 0.1090 0.2358 0.6552 120 E 0.0989 0.2296 0.6715 121 H 0.0942 0.2060 0.6998 122 F 0.0697 0.2516 0.6787 123 H 0.0174 0.5792 0.4034 124 Y 0.0233 0.5818 0.3949 125 Q 0.0140 0.8206 0.1655 126 L 0.0093 0.9182 0.0725 127 L 0.0066 0.9386 0.0547 128 N 0.0057 0.9454 0.0489 129 Q 0.0053 0.9465 0.0482 130 A 0.0054 0.9484 0.0463 131 F 0.0050 0.9490 0.0460 132 R 0.0052 0.9387 0.0561 133 L 0.0059 0.9148 0.0792 134 L 0.0082 0.8420 0.1497 135 L 0.0425 0.3262 0.6313 136 D 0.0361 0.0301 0.9338 137 G 0.0823 0.0118 0.9058 138 A 0.3080 0.0102 0.6818 139 P 0.8701 0.0045 0.1254 140 L 0.9208 0.0041 0.0751 141 I 0.9270 0.0035 0.0695 142 A 0.8916 0.0056 0.1028 143 I 0.5824 0.0217 0.3959 144 H 0.1596 0.0238 0.8167 145 K 0.0597 0.0878 0.8525 146 A 0.0907 0.1419 0.7674 147 R 0.0705 0.3090 0.6205 148 Y 0.0693 0.3516 0.5791 149 Y 0.0958 0.4012 0.5031 150 K 0.0840 0.4928 0.4232 151 R 0.0855 0.5477 0.3667 152 K 0.0655 0.6485 0.2861 153 D 0.0552 0.6476 0.2972 154 G 0.0649 0.5825 0.3527 155 L 0.0654 0.5462 0.3884 156 A 0.0747 0.4551 0.4703 157 L 0.0516 0.3610 0.5873 158 G 0.0564 0.2372 0.7063 159 P 0.0454 0.5290 0.4256 160 G 0.0197 0.7593 0.2210 161 P 0.0146 0.8518 0.1336 162 F 0.0131 0.9045 0.0824 163 V 0.0080 0.9342 0.0578 164 T 0.0081 0.9373 0.0546 165 A 0.0076 0.9374 0.0550 166 L 0.0102 0.9370 0.0528 167 E 0.0107 0.9257 0.0635 168 Y 0.0119 0.8884 0.0997 169 A 0.0211 0.8225 0.1564 170 T 0.0664 0.6103 0.3233 171 D 0.0805 0.3230 0.5965 172 T 0.0820 0.2636 0.6544 173 K 0.0981 0.2547 0.6471 174 A 0.1281 0.2997 0.5722 175 M 0.1740 0.2654 0.5605 176 V 0.1916 0.2119 0.5966 177 V 0.1632 0.1572 0.6796 178 G 0.1119 0.0820 0.8062 179 K 0.0980 0.0755 0.8265 180 P 0.0845 0.0828 0.8327 181 E 0.0660 0.0809 0.8531 182 K 0.0117 0.8064 0.1819 183 T 0.0075 0.8957 0.0968 184 F 0.0050 0.9420 0.0530 185 F 0.0048 0.9559 0.0393 186 L 0.0049 0.9577 0.0374 187 E 0.0047 0.9592 0.0360 188 A 0.0047 0.9591 0.0362 189 L 0.0048 0.9566 0.0385 190 R 0.0055 0.9407 0.0538 191 D 0.0077 0.8782 0.1142 192 A 0.0475 0.4836 0.4689 193 D 0.0404 0.0313 0.9283 194 C 0.0653 0.0088 0.9259 195 A 0.0687 0.0111 0.9203 196 P 0.0315 0.6529 0.3156 197 E 0.0279 0.6829 0.2892 198 E 0.1304 0.6020 0.2675 199 A 0.7383 0.0457 0.2161 200 V 0.8611 0.0169 0.1221 201 M 0.8790 0.0151 0.1060 202 I 0.7444 0.0567 0.1989 203 G 0.3744 0.0524 0.5732 204 D 0.1182 0.0672 0.8146 205 D 0.0729 0.0884 0.8387 206 C 0.0242 0.5084 0.4674 207 R 0.0156 0.6972 0.2872 208 D 0.0126 0.7920 0.1954 209 D 0.0135 0.8638 0.1227 210 V 0.0066 0.9345 0.0589 211 D 0.0054 0.9464 0.0482 212 G 0.0049 0.9503 0.0448 213 A 0.0053 0.9501 0.0446 214 Q 0.0058 0.9336 0.0607 215 N 0.0087 0.8502 0.1411 216 I 0.0458 0.3881 0.5660 217 G 0.0563 0.0292 0.9145 218 M 0.1287 0.0135 0.8578 219 L 0.3968 0.0366 0.5666 220 G 0.8877 0.0071 0.1052 221 I 0.9171 0.0062 0.0767 222 L 0.9212 0.0048 0.0739 223 V 0.8718 0.0104 0.1178 224 K 0.6051 0.0224 0.3725 225 T 0.1660 0.0562 0.7779 226 G 0.0870 0.0583 0.8547 227 K 0.1478 0.0849 0.7673 228 Y 0.1718 0.0848 0.7434 229 K 0.1097 0.1337 0.7566 230 A 0.0326 0.5529 0.4145 231 A 0.0243 0.6161 0.3595 232 D 0.0346 0.5959 0.3695 233 E 0.0534 0.4800 0.4666 234 E 0.0562 0.4088 0.5350 235 K 0.0566 0.3095 0.6339 236 I 0.0612 0.2218 0.7170 237 N 0.0797 0.1577 0.7626 238 P 0.1158 0.1124 0.7718 239 P 0.1206 0.0630 0.8165 240 P 0.1620 0.0604 0.7776 241 Y 0.2877 0.0774 0.6349 242 L 0.7312 0.0290 0.2398 243 T 0.8267 0.0126 0.1607 244 C 0.6746 0.0163 0.3091 245 E 0.2420 0.0730 0.6849 246 S 0.1070 0.0237 0.8693 247 F 0.0106 0.7764 0.2130 248 P 0.0061 0.8959 0.0980 249 H 0.0088 0.8959 0.0953 250 A 0.0058 0.9362 0.0579 251 V 0.0057 0.9507 0.0436 252 D 0.0049 0.9498 0.0453 253 H 0.0049 0.9517 0.0434 254 I 0.0054 0.9425 0.0522 255 L 0.0054 0.8925 0.1021 256 Q 0.0082 0.7588 0.2331 257 H 0.0214 0.5258 0.4528 258 L 0.0520 0.2734 0.6746 259 L 0.0339 0.0727 0.8933