# This file is the result of combining several RDB files, specifically # T0268.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0268.t2k.stride-ebghtl.rdb (weight 1.24869) # T0268.t2k.str2.rdb (weight 1.54758) # T0268.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 T0268.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0268 # 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 T0268.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 180 # # ============================================ # Comments from T0268.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0268 # 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 T0268.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 180 # # ============================================ # Comments from T0268.t2k.str2.rdb # ============================================ # TARGET T0268 # 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 T0268.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 180 # # ============================================ # Comments from T0268.t2k.alpha.rdb # ============================================ # TARGET T0268 # 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 T0268.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 180 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0590 0.0577 0.8832 2 R 0.1094 0.0805 0.8101 3 P 0.1076 0.0949 0.7975 4 M 0.0974 0.1534 0.7492 5 T 0.0925 0.1724 0.7350 6 H 0.1762 0.1984 0.6254 7 V 0.2088 0.3074 0.4838 8 P 0.1959 0.5493 0.2548 9 V 0.1543 0.6240 0.2218 10 L 0.1203 0.6594 0.2203 11 Y 0.0116 0.9005 0.0880 12 Q 0.0057 0.9453 0.0490 13 E 0.0059 0.9469 0.0472 14 A 0.0072 0.9428 0.0500 15 L 0.0108 0.9085 0.0807 16 D 0.0138 0.8282 0.1580 17 L 0.0229 0.7103 0.2668 18 L 0.1256 0.3461 0.5283 19 A 0.2226 0.1004 0.6770 20 V 0.2880 0.0520 0.6600 21 R 0.0989 0.0260 0.8750 22 P 0.0297 0.0730 0.8973 23 G 0.0391 0.0387 0.9223 24 G 0.2582 0.0363 0.7055 25 V 0.8181 0.0072 0.1747 26 Y 0.9092 0.0047 0.0860 27 V 0.9016 0.0055 0.0929 28 D 0.8148 0.0195 0.1656 29 A 0.6849 0.0386 0.2766 30 T 0.5484 0.0562 0.3954 31 L 0.2974 0.0866 0.6160 32 G 0.1208 0.0906 0.7885 33 G 0.0860 0.1758 0.7382 34 A 0.0556 0.2751 0.6693 35 G 0.0467 0.5623 0.3910 36 H 0.0408 0.7174 0.2419 37 A 0.0256 0.7979 0.1765 38 R 0.0399 0.7960 0.1641 39 G 0.0524 0.7152 0.2324 40 I 0.1030 0.6274 0.2696 41 L 0.1378 0.3764 0.4858 42 E 0.0804 0.1763 0.7433 43 R 0.0309 0.1364 0.8326 44 G 0.0412 0.0546 0.9042 45 G 0.2928 0.0117 0.6955 46 R 0.8012 0.0045 0.1943 47 V 0.9294 0.0031 0.0675 48 I 0.9227 0.0043 0.0730 49 G 0.9161 0.0048 0.0791 50 L 0.8223 0.0112 0.1665 51 D 0.4813 0.0161 0.5026 52 Q 0.0895 0.0527 0.8579 53 D 0.0945 0.0419 0.8636 54 P 0.0053 0.8883 0.1063 55 E 0.0051 0.9280 0.0669 56 A 0.0051 0.9399 0.0551 57 V 0.0051 0.9455 0.0494 58 A 0.0066 0.9331 0.0604 59 R 0.0069 0.9127 0.0804 60 A 0.0106 0.8712 0.1182 61 K 0.0167 0.8428 0.1405 62 G 0.0283 0.7511 0.2206 63 L 0.0551 0.5353 0.4097 64 H 0.0823 0.2124 0.7052 65 L 0.0518 0.0972 0.8510 66 P 0.0295 0.1113 0.8592 67 G 0.4063 0.0623 0.5314 68 L 0.8530 0.0071 0.1399 69 T 0.8833 0.0083 0.1084 70 V 0.8706 0.0114 0.1180 71 V 0.7088 0.0362 0.2550 72 Q 0.3679 0.0824 0.5496 73 G 0.1338 0.1338 0.7324 74 N 0.1102 0.1277 0.7620 75 F 0.0228 0.6706 0.3066 76 R 0.0116 0.7186 0.2698 77 H 0.0132 0.7132 0.2736 78 L 0.0071 0.9041 0.0889 79 K 0.0054 0.9454 0.0492 80 R 0.0049 0.9491 0.0460 81 H 0.0051 0.9491 0.0458 82 L 0.0056 0.9451 0.0493 83 A 0.0051 0.9254 0.0695 84 A 0.0064 0.8765 0.1172 85 L 0.0451 0.5753 0.3796 86 G 0.0447 0.0857 0.8696 87 V 0.0770 0.0593 0.8637 88 E 0.1576 0.1008 0.7416 89 R 0.3277 0.0768 0.5955 90 V 0.4823 0.0082 0.5095 91 D 0.5586 0.0339 0.4076 92 G 0.8849 0.0058 0.1092 93 I 0.9267 0.0037 0.0696 94 L 0.9142 0.0100 0.0758 95 A 0.8839 0.0109 0.1052 96 D 0.5898 0.0198 0.3904 97 L 0.2640 0.0581 0.6779 98 G 0.1544 0.0695 0.7761 99 V 0.1818 0.0845 0.7337 100 S 0.1363 0.0887 0.7750 101 S 0.1217 0.2285 0.6498 102 F 0.1162 0.2559 0.6279 103 H 0.1772 0.2288 0.5940 104 L 0.2006 0.1810 0.6185 105 D 0.0949 0.1270 0.7780 106 D 0.0641 0.2314 0.7046 107 P 0.0374 0.3353 0.6273 108 S 0.0620 0.3195 0.6185 109 R 0.1051 0.2319 0.6630 110 G 0.1225 0.1104 0.7672 111 F 0.2518 0.0712 0.6770 112 S 0.3363 0.0758 0.5879 113 Y 0.2696 0.1597 0.5707 114 Q 0.1825 0.1654 0.6521 115 K 0.1104 0.1457 0.7439 116 E 0.0916 0.0874 0.8209 117 G 0.0997 0.0392 0.8610 118 P 0.1570 0.0900 0.7530 119 L 0.2018 0.1615 0.6366 120 D 0.2502 0.1990 0.5508 121 M 0.2589 0.2020 0.5391 122 R 0.2627 0.1175 0.6198 123 M 0.1956 0.0576 0.7468 124 G 0.0896 0.0321 0.8784 125 L 0.0364 0.1042 0.8594 126 E 0.0318 0.0854 0.8828 127 G 0.0689 0.0466 0.8845 128 P 0.1552 0.0218 0.8231 129 T 0.1734 0.0337 0.7928 130 A 0.0054 0.9293 0.0653 131 K 0.0048 0.9472 0.0480 132 E 0.0051 0.9458 0.0491 133 V 0.0057 0.9418 0.0525 134 V 0.0089 0.8671 0.1240 135 N 0.0110 0.5935 0.3956 136 R 0.0302 0.3028 0.6670 137 L 0.0891 0.0454 0.8654 138 P 0.0632 0.0341 0.9026 139 L 0.0051 0.9325 0.0624 140 E 0.0048 0.9435 0.0518 141 A 0.0048 0.9515 0.0437 142 L 0.0047 0.9579 0.0374 143 A 0.0047 0.9582 0.0371 144 R 0.0047 0.9554 0.0400 145 L 0.0047 0.9550 0.0403 146 L 0.0047 0.9496 0.0457 147 R 0.0050 0.9198 0.0753 148 E 0.0068 0.8337 0.1595 149 L 0.0348 0.5555 0.4097 150 G 0.0357 0.1911 0.7732 151 E 0.0339 0.3206 0.6454 152 E 0.0461 0.5213 0.4326 153 P 0.0246 0.6490 0.3263 154 Q 0.0240 0.6979 0.2780 155 A 0.0092 0.8658 0.1251 156 Y 0.0082 0.9223 0.0695 157 R 0.0058 0.9480 0.0461 158 I 0.0049 0.9554 0.0397 159 A 0.0048 0.9585 0.0367 160 R 0.0047 0.9593 0.0360 161 A 0.0047 0.9590 0.0364 162 I 0.0047 0.9582 0.0371 163 V 0.0049 0.9512 0.0439 164 A 0.0052 0.8994 0.0954 165 A 0.0074 0.7917 0.2010 166 R 0.0182 0.6727 0.3091 167 E 0.0158 0.5855 0.3987 168 K 0.0245 0.4477 0.5278 169 A 0.0541 0.1240 0.8219 170 P 0.0743 0.1211 0.8046 171 I 0.1922 0.2216 0.5862 172 E 0.1667 0.3288 0.5045 173 T 0.1729 0.4143 0.4128 174 T 0.0255 0.8674 0.1072 175 T 0.0060 0.9455 0.0485 176 Q 0.0053 0.9524 0.0423 177 L 0.0049 0.9551 0.0400 178 A 0.0047 0.9580 0.0373 179 E 0.0047 0.9558 0.0395 180 I 0.0047 0.9526 0.0427 181 V 0.0048 0.9427 0.0524 182 R 0.0053 0.8979 0.0968 183 K 0.0074 0.8068 0.1859 184 A 0.0202 0.6095 0.3703 185 V 0.0792 0.1264 0.7944 186 G 0.0619 0.1318 0.8063 187 F 0.0860 0.1712 0.7428 188 R 0.0881 0.1473 0.7646 189 R 0.0560 0.1236 0.8203 190 A 0.0623 0.0751 0.8625 191 G 0.0863 0.0428 0.8709 192 H 0.1067 0.0495 0.8438 193 P 0.0362 0.6203 0.3434 194 A 0.0494 0.7049 0.2456 195 R 0.0674 0.7977 0.1350 196 K 0.0690 0.8448 0.0862 197 T 0.0582 0.8751 0.0666 198 F 0.0704 0.8781 0.0515 199 Q 0.0988 0.8493 0.0519 200 A 0.0818 0.8633 0.0549 201 L 0.0804 0.8693 0.0503 202 R 0.1114 0.8277 0.0609 203 I 0.1022 0.7979 0.0999 204 Y 0.1499 0.6425 0.2076 205 V 0.1144 0.5493 0.3362 206 N 0.0514 0.5313 0.4174 207 D 0.0347 0.4901 0.4752 208 E 0.0161 0.6553 0.3286 209 L 0.0098 0.8390 0.1512 210 N 0.0081 0.8458 0.1461 211 A 0.0061 0.8879 0.1060 212 L 0.0051 0.9265 0.0684 213 K 0.0048 0.9446 0.0506 214 E 0.0048 0.9407 0.0544 215 F 0.0048 0.9388 0.0563 216 L 0.0048 0.9448 0.0504 217 E 0.0049 0.9334 0.0617 218 Q 0.0051 0.9199 0.0749 219 A 0.0050 0.9141 0.0810 220 A 0.0054 0.9145 0.0800 221 E 0.0083 0.8376 0.1541 222 V 0.0167 0.6253 0.3580 223 L 0.1157 0.1992 0.6852 224 A 0.0960 0.0330 0.8711 225 P 0.0775 0.0946 0.8279 226 G 0.0485 0.0501 0.9015 227 G 0.3722 0.0177 0.6101 228 R 0.8028 0.0054 0.1919 229 L 0.9227 0.0032 0.0741 230 V 0.9312 0.0033 0.0656 231 V 0.9285 0.0037 0.0678 232 I 0.9053 0.0094 0.0853 233 A 0.8420 0.0084 0.1495 234 F 0.5348 0.0357 0.4295 235 H 0.2806 0.0417 0.6777 236 S 0.1199 0.0460 0.8341 237 L 0.0148 0.7547 0.2305 238 E 0.0139 0.8453 0.1408 239 D 0.0131 0.8833 0.1036 240 R 0.0097 0.9218 0.0684 241 V 0.0093 0.9275 0.0631 242 V 0.0064 0.9351 0.0584 243 K 0.0063 0.9376 0.0561 244 R 0.0064 0.9260 0.0676 245 F 0.0072 0.8839 0.1089 246 L 0.0189 0.7568 0.2243 247 R 0.0233 0.6342 0.3425 248 E 0.0436 0.2779 0.6785 249 S 0.0566 0.1537 0.7898 250 G 0.0688 0.1613 0.7699 251 L 0.1787 0.1651 0.6562 252 K 0.3586 0.1305 0.5110 253 V 0.5469 0.1041 0.3491 254 L 0.5372 0.0859 0.3769 255 T 0.4232 0.0612 0.5156 256 K 0.2359 0.0415 0.7226 257 K 0.2026 0.0173 0.7801 258 P 0.2062 0.0113 0.7826 259 L 0.2582 0.0190 0.7228 260 V 0.1864 0.0104 0.8032 261 P 0.0906 0.0262 0.8832 262 S 0.0663 0.0186 0.9151 263 E 0.0058 0.8875 0.1068 264 K 0.0054 0.9142 0.0804 265 E 0.0095 0.9150 0.0755 266 A 0.0131 0.9095 0.0774 267 A 0.0188 0.8622 0.1190 268 Q 0.0290 0.7528 0.2182 269 N 0.0817 0.2341 0.6842 270 P 0.0149 0.3304 0.6548 271 R 0.0188 0.3309 0.6502 272 A 0.0583 0.3536 0.5881 273 R 0.0598 0.4939 0.4463 274 S 0.1200 0.5146 0.3654 275 A 0.1385 0.5771 0.2844 276 K 0.1753 0.6695 0.1552 277 L 0.2377 0.6072 0.1551 278 R 0.2349 0.6293 0.1358 279 A 0.2796 0.5912 0.1292 280 A 0.2850 0.5472 0.1678 281 E 0.3059 0.4842 0.2099 282 K 0.2387 0.4450 0.3163 283 E 0.1905 0.2462 0.5634 284 A 0.0806 0.0398 0.8796 285 P 0.0458 0.0296 0.9246