# This file is the result of combining several RDB files, specifically # T0238.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0238.t2k.stride-ebghtl.rdb (weight 1.24869) # T0238.t2k.str2.rdb (weight 1.54758) # T0238.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 T0238.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0238 # 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 T0238.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 13 # # ============================================ # Comments from T0238.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0238 # 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 T0238.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 13 # # ============================================ # Comments from T0238.t2k.str2.rdb # ============================================ # TARGET T0238 # 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 T0238.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 13 # # ============================================ # Comments from T0238.t2k.alpha.rdb # ============================================ # TARGET T0238 # 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 T0238.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 13 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0457 0.0848 0.8694 2 K 0.0551 0.1915 0.7534 3 K 0.0652 0.3633 0.5715 4 A 0.0638 0.4508 0.4854 5 K 0.1143 0.5128 0.3729 6 L 0.1428 0.5836 0.2735 7 N 0.1300 0.6184 0.2516 8 I 0.1795 0.6581 0.1625 9 I 0.1222 0.7408 0.1370 10 K 0.1038 0.7590 0.1372 11 I 0.0352 0.8603 0.1045 12 N 0.0231 0.8523 0.1247 13 I 0.0130 0.9275 0.0595 14 I 0.0095 0.9439 0.0467 15 A 0.0108 0.9389 0.0503 16 M 0.0125 0.9356 0.0519 17 I 0.0276 0.9201 0.0523 18 L 0.0437 0.8946 0.0616 19 T 0.0870 0.8471 0.0658 20 L 0.0985 0.8329 0.0686 21 I 0.0811 0.8373 0.0816 22 C 0.1164 0.7574 0.1262 23 T 0.1372 0.6227 0.2401 24 S 0.1688 0.4241 0.4071 25 C 0.1562 0.2854 0.5584 26 A 0.1099 0.1684 0.7217 27 P 0.0401 0.2272 0.7326 28 F 0.0456 0.2017 0.7528 29 S 0.0608 0.1623 0.7769 30 K 0.1075 0.1169 0.7756 31 I 0.2186 0.0683 0.7131 32 D 0.1232 0.0420 0.8347 33 P 0.0279 0.3122 0.6599 34 K 0.0392 0.2899 0.6708 35 A 0.0593 0.4148 0.5259 36 N 0.1118 0.3419 0.5463 37 A 0.1363 0.3212 0.5424 38 N 0.1147 0.1946 0.6907 39 T 0.0788 0.2771 0.6441 40 K 0.1231 0.2676 0.6093 41 P 0.1294 0.2831 0.5876 42 K 0.1374 0.2124 0.6503 43 K 0.1833 0.1751 0.6416 44 I 0.1959 0.1115 0.6926 45 T 0.1852 0.0593 0.7555 46 N 0.1249 0.0336 0.8415 47 P 0.0353 0.2694 0.6953 48 G 0.0388 0.2314 0.7298 49 E 0.0792 0.1954 0.7254 50 N 0.1231 0.1093 0.7676 51 T 0.2561 0.0995 0.6443 52 Q 0.3781 0.0957 0.5261 53 N 0.3462 0.0866 0.5673 54 F 0.2009 0.2310 0.5681 55 E 0.1568 0.2664 0.5768 56 D 0.1696 0.2229 0.6075 57 K 0.1490 0.2505 0.6006 58 S 0.1919 0.1864 0.6217 59 G 0.1362 0.2021 0.6616 60 D 0.1327 0.1442 0.7230 61 L 0.1541 0.1872 0.6587 62 S 0.1425 0.1636 0.6939 63 T 0.1200 0.1979 0.6821 64 S 0.0447 0.3416 0.6138 65 D 0.0454 0.3463 0.6084 66 E 0.0614 0.4761 0.4625 67 K 0.0897 0.5505 0.3599 68 I 0.1427 0.5707 0.2865 69 M 0.1344 0.6659 0.1997 70 E 0.1229 0.7435 0.1336 71 T 0.1032 0.7723 0.1245 72 I 0.0438 0.8544 0.1018 73 A 0.0082 0.9309 0.0609 74 S 0.0066 0.9311 0.0623 75 E 0.0063 0.9167 0.0770 76 L 0.0121 0.9005 0.0874 77 K 0.0086 0.8789 0.1125 78 A 0.0124 0.7934 0.1942 79 I 0.0318 0.5476 0.4207 80 G 0.0396 0.3004 0.6601 81 K 0.0199 0.5621 0.4180 82 E 0.0262 0.6686 0.3053 83 L 0.0119 0.8167 0.1713 84 E 0.0139 0.8244 0.1617 85 D 0.0155 0.8240 0.1606 86 Q 0.0194 0.8191 0.1615 87 K 0.0239 0.7874 0.1886 88 K 0.0281 0.7194 0.2524 89 E 0.0388 0.6551 0.3061 90 E 0.0541 0.5526 0.3933 91 N 0.0626 0.4114 0.5261 92 I 0.0964 0.4283 0.4753 93 Q 0.1209 0.4208 0.4584 94 I 0.1047 0.5875 0.3078 95 A 0.1069 0.5902 0.3030 96 K 0.1129 0.5193 0.3678 97 I 0.1069 0.4422 0.4509 98 A 0.0596 0.4810 0.4594 99 K 0.0342 0.5294 0.4364 100 E 0.0390 0.5405 0.4205 101 K 0.0665 0.4991 0.4344 102 F 0.1088 0.4334 0.4577 103 D 0.1117 0.3754 0.5129 104 F 0.0821 0.5238 0.3941 105 L 0.0816 0.6097 0.3087 106 S 0.1036 0.5543 0.3421 107 T 0.1880 0.4198 0.3922 108 F 0.3434 0.1410 0.5156 109 K 0.3322 0.0651 0.6027 110 V 0.2431 0.1039 0.6530 111 G 0.1264 0.0938 0.7798 112 P 0.0867 0.2160 0.6973 113 Y 0.0608 0.4513 0.4878 114 D 0.0743 0.5422 0.3834 115 L 0.0674 0.6050 0.3277 116 I 0.0662 0.5995 0.3344 117 D 0.0518 0.6781 0.2701 118 E 0.0253 0.7366 0.2380 119 D 0.0290 0.7120 0.2590 120 I 0.0180 0.8088 0.1732 121 Q 0.0151 0.8520 0.1329 122 M 0.0161 0.8651 0.1187 123 K 0.0194 0.8691 0.1115 124 I 0.0177 0.9002 0.0820 125 K 0.0167 0.9088 0.0744 126 R 0.0218 0.8911 0.0871 127 T 0.0376 0.8540 0.1084 128 L 0.0771 0.8132 0.1098 129 Y 0.0842 0.7879 0.1279 130 S 0.1203 0.7105 0.1691 131 S 0.1644 0.5734 0.2623 132 L 0.1898 0.3598 0.4504 133 D 0.1911 0.1038 0.7050 134 Y 0.0473 0.1801 0.7725 135 K 0.0616 0.1176 0.8208 136 K 0.0147 0.7160 0.2694 137 E 0.0131 0.8019 0.1850 138 N 0.0156 0.8478 0.1366 139 I 0.0216 0.8696 0.1088 140 E 0.0267 0.8723 0.1011 141 K 0.0272 0.8601 0.1127 142 L 0.0064 0.9423 0.0513 143 K 0.0052 0.9535 0.0413 144 E 0.0047 0.9564 0.0388 145 I 0.0047 0.9571 0.0382 146 L 0.0047 0.9536 0.0417 147 E 0.0048 0.9393 0.0558 148 I 0.0053 0.9148 0.0798 149 L 0.0108 0.8626 0.1266 150 K 0.0177 0.7365 0.2458 151 K 0.0215 0.4268 0.5517 152 N 0.0461 0.2942 0.6597 153 S 0.0305 0.3361 0.6333 154 E 0.0268 0.4015 0.5717 155 H 0.0317 0.5497 0.4186 156 Y 0.0253 0.7932 0.1815 157 N 0.0105 0.8938 0.0957 158 I 0.0071 0.9306 0.0623 159 I 0.0055 0.9489 0.0456 160 G 0.0050 0.9550 0.0400 161 R 0.0049 0.9546 0.0405 162 L 0.0048 0.9508 0.0443 163 I 0.0054 0.9354 0.0591 164 Y 0.0068 0.9062 0.0870 165 H 0.0122 0.8379 0.1499 166 I 0.0225 0.7608 0.2167 167 S 0.0215 0.6884 0.2902 168 W 0.0288 0.7802 0.1909 169 G 0.0279 0.8032 0.1689 170 I 0.0190 0.8799 0.1011 171 Q 0.0183 0.9043 0.0774 172 F 0.0152 0.9186 0.0662 173 Q 0.0123 0.9124 0.0753 174 I 0.0066 0.9303 0.0631 175 E 0.0057 0.9395 0.0548 176 Q 0.0052 0.9400 0.0548 177 N 0.0048 0.9405 0.0547 178 L 0.0049 0.9349 0.0603 179 E 0.0050 0.9136 0.0814 180 L 0.0058 0.8773 0.1169 181 I 0.0081 0.8467 0.1452 182 Q 0.0089 0.8401 0.1509 183 N 0.0101 0.7594 0.2304 184 G 0.0141 0.6528 0.3331 185 V 0.0305 0.6369 0.3326 186 E 0.0388 0.5645 0.3967 187 N 0.0914 0.5202 0.3884 188 L 0.1379 0.2620 0.6001 189 S 0.0899 0.1327 0.7774 190 Q 0.0077 0.8824 0.1098 191 E 0.0060 0.9049 0.0891 192 E 0.0055 0.9111 0.0834 193 S 0.0051 0.9410 0.0539 194 K 0.0052 0.9482 0.0466 195 S 0.0050 0.9452 0.0498 196 L 0.0053 0.9401 0.0546 197 L 0.0052 0.9410 0.0538 198 M 0.0060 0.9152 0.0788 199 Q 0.0082 0.8639 0.1279 200 I 0.0097 0.8984 0.0919 201 K 0.0088 0.8989 0.0923 202 S 0.0084 0.8728 0.1188 203 N 0.0081 0.8943 0.0976 204 L 0.0101 0.8992 0.0907 205 E 0.0092 0.9073 0.0835 206 I 0.0088 0.9074 0.0839 207 K 0.0071 0.9348 0.0581 208 Q 0.0052 0.9515 0.0433 209 R 0.0050 0.9497 0.0454 210 L 0.0048 0.9475 0.0477 211 K 0.0047 0.9534 0.0419 212 K 0.0048 0.9506 0.0446 213 T 0.0048 0.9462 0.0490 214 L 0.0048 0.9452 0.0500 215 N 0.0048 0.9483 0.0469 216 E 0.0051 0.9404 0.0546 217 T 0.0050 0.9361 0.0589 218 L 0.0050 0.9412 0.0539 219 K 0.0049 0.9368 0.0583 220 V 0.0053 0.9280 0.0667 221 Y 0.0062 0.9182 0.0756 222 N 0.0065 0.8996 0.0939 223 Q 0.0060 0.8392 0.1548 224 N 0.0091 0.7809 0.2100 225 T 0.0141 0.7784 0.2074 226 Q 0.0119 0.8134 0.1747 227 D 0.0133 0.8351 0.1516 228 N 0.0113 0.8699 0.1188 229 E 0.0103 0.9050 0.0846 230 K 0.0083 0.9115 0.0802 231 I 0.0103 0.8984 0.0913 232 L 0.0076 0.9182 0.0742 233 A 0.0067 0.9309 0.0623 234 E 0.0060 0.9344 0.0596 235 H 0.0061 0.9309 0.0629 236 F 0.0062 0.9182 0.0756 237 N 0.0081 0.8808 0.1111 238 K 0.0117 0.8101 0.1782 239 Y 0.0325 0.6919 0.2756 240 Y 0.0551 0.4616 0.4832 241 K 0.0468 0.3650 0.5883 242 D 0.0618 0.2280 0.7102 243 F 0.0430 0.3134 0.6436 244 D 0.0358 0.3995 0.5648 245 T 0.0402 0.4725 0.4873 246 L 0.0527 0.4455 0.5017 247 K 0.0570 0.4425 0.5005 248 P 0.0640 0.5270 0.4090 249 A 0.0708 0.4139 0.5153 250 F 0.1048 0.2484 0.6468 251 Y 0.0437 0.0522 0.9041