# This file is the result of combining several RDB files, specifically # T0202.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0202.t2k.stride-ebghtl.rdb (weight 1.24869) # T0202.t2k.str2.rdb (weight 1.54758) # T0202.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 T0202.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0202 # 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 T0202.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 219 # # ============================================ # Comments from T0202.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0202 # 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 T0202.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 219 # # ============================================ # Comments from T0202.t2k.str2.rdb # ============================================ # TARGET T0202 # 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 T0202.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 219 # # ============================================ # Comments from T0202.t2k.alpha.rdb # ============================================ # TARGET T0202 # 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 T0202.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 219 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1617 0.1027 0.7356 2 R 0.3983 0.1247 0.4770 3 A 0.6205 0.1164 0.2630 4 A 0.7057 0.1214 0.1729 5 V 0.8150 0.0759 0.1091 6 V 0.8221 0.0652 0.1127 7 Y 0.7528 0.0714 0.1758 8 K 0.5649 0.0901 0.3450 9 T 0.2078 0.1015 0.6907 10 D 0.1630 0.0639 0.7731 11 G 0.3803 0.1039 0.5158 12 H 0.7085 0.0637 0.2278 13 V 0.8201 0.0482 0.1317 14 K 0.8147 0.0516 0.1337 15 R 0.7029 0.0881 0.2090 16 I 0.5306 0.1331 0.3364 17 E 0.2486 0.2882 0.4632 18 E 0.1452 0.3027 0.5521 19 A 0.0791 0.4832 0.4378 20 L 0.0595 0.5831 0.3573 21 K 0.0520 0.6669 0.2812 22 R 0.0464 0.7314 0.2223 23 L 0.0527 0.7384 0.2089 24 E 0.0607 0.7153 0.2240 25 V 0.0707 0.6848 0.2445 26 E 0.0833 0.6572 0.2594 27 V 0.1034 0.6270 0.2695 28 E 0.1112 0.5680 0.3207 29 L 0.1071 0.5092 0.3837 30 F 0.0938 0.4543 0.4518 31 N 0.0886 0.3765 0.5349 32 Q 0.1060 0.3147 0.5792 33 P 0.0873 0.4245 0.4883 34 S 0.0724 0.4784 0.4492 35 E 0.0584 0.4807 0.4609 36 E 0.0632 0.4361 0.5007 37 L 0.0387 0.4190 0.5423 38 E 0.0501 0.3201 0.6299 39 N 0.1202 0.1240 0.7558 40 F 0.1791 0.0103 0.8106 41 D 0.2471 0.0414 0.7115 42 F 0.9285 0.0033 0.0682 43 I 0.9336 0.0032 0.0632 44 V 0.9309 0.0034 0.0657 45 S 0.9165 0.0041 0.0794 46 V 0.5506 0.0229 0.4266 47 G 0.1060 0.0340 0.8600 48 G 0.0582 0.1248 0.8169 49 D 0.0335 0.5861 0.3804 50 G 0.0078 0.8818 0.1105 51 T 0.0063 0.9378 0.0559 52 I 0.0047 0.9552 0.0401 53 L 0.0048 0.9552 0.0400 54 R 0.0049 0.9497 0.0455 55 I 0.0050 0.9448 0.0503 56 L 0.0060 0.9212 0.0728 57 Q 0.0074 0.8250 0.1676 58 K 0.0147 0.6740 0.3112 59 L 0.0673 0.2590 0.6737 60 K 0.0336 0.1023 0.8641 61 R 0.0463 0.0966 0.8571 62 C 0.0720 0.0423 0.8858 63 P 0.2308 0.0125 0.7567 64 P 0.6104 0.0059 0.3837 65 I 0.8963 0.0049 0.0987 66 F 0.9032 0.0081 0.0887 67 G 0.8973 0.0059 0.0968 68 I 0.8431 0.0130 0.1439 69 N 0.6469 0.0157 0.3374 70 T 0.2123 0.0732 0.7145 71 G 0.1149 0.0702 0.8149 72 R 0.1644 0.1141 0.7215 73 V 0.2577 0.1174 0.6250 74 G 0.3553 0.1359 0.5089 75 L 0.4492 0.1686 0.3822 76 L 0.4528 0.1620 0.3852 77 T 0.3773 0.1069 0.5158 78 H 0.2943 0.0637 0.6420 79 A 0.2125 0.0362 0.7512 80 S 0.1216 0.0214 0.8570 81 P 0.0158 0.7067 0.2774 82 E 0.0084 0.7500 0.2416 83 N 0.0120 0.7966 0.1913 84 F 0.0070 0.8996 0.0934 85 E 0.0057 0.9302 0.0641 86 V 0.0058 0.9370 0.0572 87 E 0.0055 0.9398 0.0547 88 L 0.0071 0.9307 0.0622 89 K 0.0066 0.9097 0.0837 90 K 0.0083 0.8472 0.1445 91 A 0.0171 0.7143 0.2686 92 V 0.0459 0.4121 0.5421 93 E 0.0355 0.1954 0.7691 94 K 0.0558 0.1310 0.8132 95 F 0.3438 0.0662 0.5899 96 E 0.6743 0.0240 0.3017 97 V 0.7900 0.0211 0.1888 98 E 0.7437 0.0325 0.2238 99 R 0.7163 0.0328 0.2509 100 F 0.6157 0.0460 0.3383 101 P 0.6393 0.0373 0.3234 102 R 0.7761 0.0243 0.1997 103 V 0.8599 0.0125 0.1276 104 S 0.9013 0.0064 0.0923 105 C 0.9042 0.0061 0.0897 106 S 0.9006 0.0072 0.0922 107 A 0.8456 0.0124 0.1421 108 M 0.5346 0.0301 0.4354 109 P 0.1512 0.0413 0.8075 110 D 0.1013 0.0581 0.8406 111 V 0.3466 0.0515 0.6018 112 L 0.4777 0.0449 0.4774 113 A 0.6461 0.0356 0.3183 114 L 0.7098 0.0280 0.2622 115 N 0.7165 0.0353 0.2482 116 E 0.7854 0.0409 0.1737 117 I 0.8497 0.0276 0.1227 118 A 0.8559 0.0261 0.1180 119 V 0.7871 0.0325 0.1803 120 L 0.5598 0.0334 0.4069 121 S 0.2271 0.0791 0.6938 122 R 0.1006 0.0616 0.8377 123 K 0.0956 0.0704 0.8340 124 P 0.0988 0.1075 0.7938 125 A 0.1017 0.1805 0.7179 126 K 0.2990 0.1233 0.5777 127 M 0.6850 0.0185 0.2965 128 I 0.8581 0.0059 0.1360 129 D 0.9176 0.0031 0.0793 130 V 0.9198 0.0038 0.0764 131 A 0.9291 0.0032 0.0678 132 L 0.9256 0.0035 0.0709 133 R 0.9175 0.0036 0.0789 134 V 0.8429 0.0118 0.1454 135 D 0.1735 0.0201 0.8064 136 G 0.0648 0.0524 0.8828 137 V 0.6002 0.0256 0.3742 138 E 0.8313 0.0112 0.1575 139 V 0.8298 0.0145 0.1557 140 D 0.8070 0.0373 0.1557 141 R 0.8376 0.0244 0.1380 142 I 0.8036 0.0184 0.1780 143 R 0.7495 0.0222 0.2283 144 C 0.5151 0.0142 0.4706 145 D 0.3605 0.0415 0.5980 146 G 0.7412 0.0091 0.2497 147 F 0.9133 0.0041 0.0825 148 I 0.9209 0.0046 0.0744 149 V 0.8762 0.0054 0.1185 150 A 0.5772 0.0137 0.4091 151 T 0.1925 0.0122 0.7953 152 Q 0.0758 0.0628 0.8614 153 I 0.0513 0.0666 0.8821 154 G 0.0687 0.1095 0.8217 155 S 0.0989 0.2243 0.6768 156 T 0.1400 0.4386 0.4214 157 G 0.1558 0.5989 0.2453 158 Y 0.1456 0.6510 0.2034 159 A 0.1129 0.6764 0.2107 160 F 0.0721 0.6697 0.2581 161 S 0.0933 0.4262 0.4805 162 A 0.0680 0.1767 0.7554 163 G 0.0659 0.0484 0.8857 164 G 0.0982 0.0354 0.8664 165 P 0.2108 0.0369 0.7523 166 V 0.4097 0.0434 0.5469 167 V 0.4085 0.0292 0.5623 168 E 0.1625 0.0292 0.8083 169 P 0.0219 0.1239 0.8542 170 Y 0.0361 0.0750 0.8889 171 L 0.1253 0.0437 0.8309 172 E 0.1481 0.0674 0.7846 173 C 0.8101 0.0119 0.1780 174 F 0.8900 0.0074 0.1026 175 I 0.9066 0.0049 0.0885 176 L 0.8554 0.0066 0.1380 177 I 0.6447 0.0139 0.3414 178 P 0.5975 0.0256 0.3769 179 I 0.3974 0.0586 0.5440 180 A 0.2470 0.0385 0.7145 181 P 0.0966 0.1345 0.7689 182 F 0.1165 0.1216 0.7619 183 R 0.1696 0.1003 0.7301 184 F 0.1303 0.1671 0.7026 185 G 0.1030 0.1328 0.7641 186 W 0.1638 0.0650 0.7712 187 K 0.2342 0.0196 0.7461 188 P 0.4624 0.0127 0.5249 189 Y 0.8103 0.0083 0.1814 190 V 0.8570 0.0059 0.1371 191 V 0.6917 0.0070 0.3013 192 S 0.1896 0.0179 0.7925 193 M 0.0182 0.0910 0.8907 194 E 0.0231 0.0556 0.9213 195 R 0.2557 0.0130 0.7313 196 K 0.7791 0.0038 0.2171 197 I 0.9085 0.0037 0.0878 198 E 0.9249 0.0032 0.0719 199 V 0.9129 0.0035 0.0837 200 I 0.8662 0.0047 0.1291 201 A 0.7313 0.0081 0.2606 202 E 0.3486 0.0568 0.5946 203 K 0.1438 0.2256 0.6307 204 A 0.0902 0.3713 0.5384 205 I 0.0947 0.3142 0.5911 206 V 0.1053 0.2451 0.6496 207 V 0.1001 0.1924 0.7074 208 A 0.0943 0.2301 0.6756 209 D 0.1071 0.1565 0.7364 210 G 0.2091 0.0599 0.7310 211 Q 0.3373 0.0274 0.6353 212 K 0.6875 0.0101 0.3024 213 S 0.8712 0.0052 0.1236 214 V 0.9127 0.0039 0.0834 215 D 0.8994 0.0046 0.0960 216 F 0.8332 0.0099 0.1569 217 D 0.3276 0.0329 0.6395 218 G 0.1213 0.0532 0.8255 219 E 0.4787 0.0566 0.4647 220 I 0.7610 0.0208 0.2182 221 T 0.7738 0.0175 0.2087 222 I 0.8224 0.0098 0.1678 223 E 0.8294 0.0063 0.1643 224 K 0.6294 0.0106 0.3600 225 S 0.2381 0.0183 0.7436 226 E 0.0449 0.0758 0.8794 227 F 0.0391 0.0501 0.9108 228 P 0.2511 0.0293 0.7196 229 A 0.8337 0.0038 0.1625 230 V 0.9162 0.0034 0.0804 231 F 0.9243 0.0033 0.0724 232 F 0.9083 0.0038 0.0879 233 K 0.8510 0.0073 0.1418 234 N 0.6836 0.0151 0.3013 235 E 0.3249 0.0213 0.6538 236 K 0.1314 0.0849 0.7838 237 R 0.1744 0.0464 0.7792 238 F 0.3574 0.0434 0.5992 239 R 0.4777 0.0297 0.4926 240 N 0.5753 0.0433 0.3813 241 L 0.7695 0.0328 0.1977 242 F 0.7670 0.0215 0.2114 243 G 0.6972 0.0129 0.2899 244 K 0.4289 0.0375 0.5336 245 V 0.1689 0.0824 0.7487 246 R 0.0854 0.1281 0.7865 247 S 0.1092 0.1075 0.7833 248 I 0.1231 0.0855 0.7915 249 G 0.0462 0.0338 0.9200