# This file is the result of combining several RDB files, specifically # T0202.t04.dssp-ebghstl.rdb (weight 1.53986) # T0202.t04.stride-ebghtl.rdb (weight 1.24869) # T0202.t04.str2.rdb (weight 1.54758) # T0202.t04.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 T0202.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0202 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0202.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 244 # # ============================================ # Comments from T0202.t04.stride-ebghtl.rdb # ============================================ # TARGET T0202 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0202.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 244 # # ============================================ # Comments from T0202.t04.str2.rdb # ============================================ # TARGET T0202 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0202.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 244 # # ============================================ # Comments from T0202.t04.alpha.rdb # ============================================ # TARGET T0202 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0202.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 244 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0824 0.1131 0.8045 2 R 0.2461 0.1981 0.5558 3 A 0.4394 0.2297 0.3310 4 A 0.5760 0.2329 0.1910 5 V 0.6891 0.1881 0.1228 6 V 0.7505 0.1444 0.1051 7 Y 0.6573 0.1770 0.1656 8 K 0.4229 0.1970 0.3800 9 T 0.2105 0.2104 0.5791 10 D 0.0914 0.1810 0.7276 11 G 0.0722 0.2405 0.6873 12 H 0.1869 0.3859 0.4272 13 V 0.2572 0.5647 0.1781 14 K 0.2269 0.6621 0.1110 15 R 0.2406 0.6613 0.0981 16 I 0.1663 0.7283 0.1054 17 E 0.0742 0.8390 0.0868 18 E 0.0372 0.8819 0.0809 19 A 0.0319 0.8736 0.0945 20 L 0.0319 0.8705 0.0977 21 K 0.0340 0.8541 0.1119 22 R 0.0415 0.8265 0.1320 23 L 0.0768 0.7332 0.1900 24 E 0.1334 0.6261 0.2404 25 V 0.1996 0.5012 0.2992 26 E 0.2338 0.3898 0.3764 27 V 0.2805 0.3348 0.3847 28 E 0.2802 0.3155 0.4043 29 L 0.2399 0.2985 0.4616 30 F 0.1812 0.1889 0.6299 31 N 0.1250 0.0936 0.7814 32 Q 0.0905 0.0466 0.8629 33 P 0.0774 0.1008 0.8218 34 S 0.0379 0.5117 0.4503 35 E 0.0354 0.6255 0.3391 36 E 0.0424 0.6381 0.3195 37 L 0.0631 0.5505 0.3865 38 E 0.0496 0.4008 0.5495 39 N 0.1020 0.1126 0.7854 40 F 0.1635 0.0131 0.8233 41 D 0.1894 0.0373 0.7732 42 F 0.9180 0.0034 0.0786 43 I 0.9337 0.0032 0.0631 44 V 0.9336 0.0032 0.0632 45 S 0.9122 0.0035 0.0842 46 V 0.5490 0.0216 0.4294 47 G 0.1303 0.0338 0.8359 48 G 0.0428 0.0708 0.8864 49 D 0.0221 0.3260 0.6519 50 G 0.0059 0.8433 0.1508 51 T 0.0049 0.9465 0.0486 52 I 0.0047 0.9599 0.0355 53 L 0.0046 0.9610 0.0344 54 R 0.0047 0.9597 0.0356 55 I 0.0047 0.9570 0.0383 56 L 0.0048 0.9540 0.0412 57 Q 0.0054 0.9465 0.0482 58 K 0.0073 0.9054 0.0873 59 L 0.0193 0.8140 0.1666 60 K 0.0193 0.5683 0.4124 61 R 0.0228 0.2014 0.7757 62 C 0.0591 0.0186 0.9223 63 P 0.0668 0.0200 0.9132 64 P 0.2266 0.0175 0.7559 65 I 0.8132 0.0097 0.1771 66 F 0.8912 0.0119 0.0969 67 G 0.9065 0.0052 0.0883 68 I 0.8580 0.0096 0.1323 69 N 0.6733 0.0115 0.3152 70 T 0.3365 0.0425 0.6210 71 G 0.1556 0.0433 0.8011 72 R 0.2074 0.0929 0.6997 73 V 0.2416 0.1446 0.6137 74 G 0.2821 0.1581 0.5598 75 L 0.4194 0.1704 0.4102 76 L 0.3704 0.1368 0.4928 77 T 0.2423 0.0965 0.6612 78 H 0.1722 0.0630 0.7648 79 A 0.1493 0.0374 0.8133 80 S 0.0889 0.0186 0.8926 81 P 0.0108 0.7406 0.2486 82 E 0.0086 0.7780 0.2134 83 N 0.0134 0.7947 0.1918 84 F 0.0080 0.9099 0.0820 85 E 0.0070 0.9434 0.0495 86 V 0.0052 0.9555 0.0393 87 E 0.0057 0.9547 0.0396 88 L 0.0048 0.9539 0.0413 89 K 0.0048 0.9511 0.0441 90 K 0.0051 0.9209 0.0741 91 A 0.0078 0.8809 0.1113 92 V 0.0157 0.7461 0.2382 93 E 0.0204 0.4853 0.4943 94 K 0.0406 0.2956 0.6639 95 F 0.1511 0.1131 0.7358 96 E 0.3470 0.0577 0.5952 97 V 0.6335 0.0604 0.3061 98 E 0.6187 0.0579 0.3234 99 R 0.6290 0.0392 0.3319 100 F 0.4337 0.0174 0.5490 101 P 0.4430 0.0246 0.5324 102 R 0.6976 0.0218 0.2806 103 V 0.8351 0.0081 0.1568 104 S 0.8778 0.0073 0.1149 105 C 0.8869 0.0052 0.1080 106 S 0.8520 0.0064 0.1416 107 A 0.6991 0.0113 0.2896 108 M 0.2376 0.0205 0.7419 109 P 0.0600 0.0923 0.8477 110 D 0.0729 0.0860 0.8411 111 V 0.3119 0.0741 0.6139 112 L 0.5940 0.0474 0.3586 113 A 0.8407 0.0213 0.1381 114 L 0.8586 0.0201 0.1214 115 N 0.7918 0.0300 0.1782 116 E 0.8206 0.0219 0.1575 117 I 0.8293 0.0296 0.1411 118 A 0.8585 0.0326 0.1088 119 V 0.7846 0.0468 0.1686 120 L 0.5449 0.0469 0.4082 121 S 0.2238 0.0749 0.7013 122 R 0.1006 0.0653 0.8341 123 K 0.1064 0.0299 0.8637 124 P 0.1387 0.0945 0.7668 125 A 0.1789 0.1383 0.6828 126 K 0.3921 0.0921 0.5158 127 M 0.7925 0.0181 0.1894 128 I 0.8792 0.0061 0.1147 129 D 0.9126 0.0036 0.0839 130 V 0.9174 0.0034 0.0792 131 A 0.9279 0.0032 0.0688 132 L 0.9268 0.0036 0.0696 133 R 0.9192 0.0036 0.0773 134 V 0.8265 0.0134 0.1602 135 D 0.1333 0.0264 0.8403 136 G 0.0705 0.0330 0.8965 137 V 0.7580 0.0106 0.2314 138 E 0.8766 0.0065 0.1169 139 V 0.8222 0.0120 0.1658 140 D 0.7277 0.0500 0.2223 141 R 0.7775 0.0308 0.1917 142 I 0.7832 0.0198 0.1970 143 R 0.7292 0.0220 0.2488 144 C 0.5327 0.0200 0.4473 145 D 0.2878 0.0352 0.6770 146 G 0.7648 0.0104 0.2249 147 F 0.9175 0.0034 0.0790 148 I 0.9317 0.0033 0.0650 149 V 0.9174 0.0040 0.0786 150 A 0.7544 0.0122 0.2335 151 T 0.3328 0.0224 0.6448 152 Q 0.1470 0.0495 0.8035 153 I 0.1062 0.0946 0.7991 154 G 0.0737 0.1681 0.7582 155 S 0.0662 0.4215 0.5123 156 T 0.0621 0.5949 0.3429 157 G 0.0529 0.7269 0.2202 158 Y 0.0519 0.7165 0.2315 159 A 0.0617 0.6822 0.2561 160 F 0.0665 0.5850 0.3485 161 S 0.0894 0.3293 0.5813 162 A 0.0752 0.2310 0.6938 163 G 0.0617 0.1204 0.8179 164 G 0.0851 0.0846 0.8303 165 P 0.1595 0.1690 0.6715 166 V 0.3593 0.1553 0.4854 167 V 0.3568 0.1029 0.5403 168 E 0.1349 0.0490 0.8160 169 P 0.0335 0.1693 0.7971 170 Y 0.0440 0.1052 0.8508 171 L 0.1512 0.1307 0.7181 172 E 0.1624 0.0999 0.7377 173 C 0.7473 0.0397 0.2130 174 F 0.8899 0.0076 0.1025 175 I 0.9192 0.0041 0.0767 176 L 0.8928 0.0050 0.1022 177 I 0.7730 0.0108 0.2161 178 P 0.6179 0.0128 0.3693 179 I 0.3134 0.0384 0.6482 180 A 0.2037 0.0202 0.7760 181 P 0.1102 0.0846 0.8052 182 F 0.1714 0.0791 0.7494 183 R 0.2435 0.0849 0.6715 184 F 0.2121 0.1110 0.6770 185 G 0.2383 0.0595 0.7022 186 W 0.2625 0.0404 0.6971 187 K 0.2357 0.0175 0.7468 188 P 0.4002 0.0225 0.5773 189 Y 0.7234 0.0181 0.2586 190 V 0.8716 0.0061 0.1223 191 V 0.7302 0.0072 0.2627 192 S 0.3477 0.0126 0.6397 193 M 0.0353 0.1334 0.8314 194 E 0.0508 0.0798 0.8693 195 R 0.3831 0.0281 0.5888 196 K 0.7942 0.0056 0.2003 197 I 0.9097 0.0038 0.0865 198 E 0.9267 0.0035 0.0698 199 V 0.9215 0.0034 0.0751 200 I 0.8799 0.0040 0.1161 201 A 0.6840 0.0099 0.3061 202 E 0.3140 0.0430 0.6430 203 K 0.2694 0.0215 0.7091 204 A 0.7309 0.0077 0.2614 205 I 0.9165 0.0036 0.0799 206 V 0.9277 0.0034 0.0689 207 V 0.9197 0.0038 0.0765 208 A 0.8730 0.0126 0.1145 209 D 0.4242 0.0142 0.5616 210 G 0.1417 0.0357 0.8226 211 Q 0.6687 0.0243 0.3070 212 K 0.8381 0.0141 0.1478 213 S 0.8536 0.0126 0.1338 214 V 0.8637 0.0060 0.1303 215 D 0.7184 0.0088 0.2728 216 F 0.4203 0.0511 0.5286 217 D 0.0760 0.0345 0.8895 218 G 0.1362 0.0424 0.8214 219 E 0.7193 0.0096 0.2711 220 I 0.9175 0.0033 0.0792 221 T 0.9204 0.0042 0.0754 222 I 0.9227 0.0033 0.0740 223 E 0.8779 0.0090 0.1131 224 K 0.7278 0.0090 0.2632 225 S 0.3336 0.0176 0.6488 226 E 0.1373 0.0550 0.8077 227 F 0.2092 0.0177 0.7731 228 P 0.2486 0.0250 0.7264 229 A 0.4621 0.0332 0.5047 230 V 0.6522 0.0408 0.3070 231 F 0.8263 0.0288 0.1449 232 F 0.7725 0.0251 0.2023 233 K 0.5558 0.0278 0.4165 234 N 0.2218 0.0827 0.6955 235 E 0.0409 0.4385 0.5206 236 K 0.0183 0.6326 0.3491 237 R 0.0235 0.7966 0.1799 238 F 0.0141 0.9006 0.0853 239 R 0.0090 0.9338 0.0573 240 N 0.0117 0.9310 0.0572 241 L 0.0103 0.9368 0.0529 242 F 0.0115 0.9316 0.0569 243 G 0.0128 0.9129 0.0744 244 K 0.0169 0.8801 0.1030 245 V 0.0448 0.7978 0.1574 246 R 0.0770 0.6290 0.2940 247 S 0.1034 0.4901 0.4066 248 I 0.1022 0.2109 0.6869 249 G 0.0567 0.0475 0.8958