# This file is the result of combining several RDB files, specifically # T0241.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0241.t2k.stride-ebghtl.rdb (weight 1.24869) # T0241.t2k.str2.rdb (weight 1.54758) # T0241.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 T0241.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0241 # 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 T0241.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 48 # # ============================================ # Comments from T0241.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0241 # 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 T0241.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 48 # # ============================================ # Comments from T0241.t2k.str2.rdb # ============================================ # TARGET T0241 # 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 T0241.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 48 # # ============================================ # Comments from T0241.t2k.alpha.rdb # ============================================ # TARGET T0241 # 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 T0241.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 48 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.0533 0.0409 0.9059 2 K 0.0948 0.0897 0.8155 3 N 0.1306 0.1481 0.7213 4 V 0.3830 0.3207 0.2963 5 L 0.4871 0.3429 0.1700 6 F 0.4679 0.3459 0.1862 7 Q 0.3780 0.4388 0.1832 8 Y 0.1517 0.6477 0.2006 9 S 0.0675 0.7676 0.1649 10 T 0.0228 0.8687 0.1085 11 I 0.0079 0.9418 0.0503 12 N 0.0091 0.9464 0.0445 13 A 0.0064 0.9457 0.0478 14 L 0.0071 0.9332 0.0597 15 M 0.0091 0.8990 0.0919 16 L 0.0226 0.7075 0.2699 17 G 0.0296 0.4858 0.4846 18 Q 0.0846 0.4331 0.4823 19 F 0.1399 0.3386 0.5215 20 E 0.0915 0.1909 0.7176 21 G 0.1157 0.1263 0.7580 22 D 0.3008 0.0843 0.6149 23 L 0.5389 0.0271 0.4340 24 T 0.3971 0.0448 0.5580 25 L 0.0062 0.9288 0.0650 26 K 0.0051 0.9473 0.0477 27 D 0.0049 0.9454 0.0497 28 L 0.0066 0.9397 0.0537 29 K 0.0112 0.9097 0.0791 30 L 0.0159 0.8210 0.1631 31 R 0.0482 0.5328 0.4190 32 G 0.0600 0.1316 0.8084 33 D 0.0675 0.0745 0.8579 34 M 0.2136 0.0730 0.7134 35 G 0.3535 0.0708 0.5757 36 L 0.5123 0.1023 0.3853 37 G 0.5761 0.0798 0.3440 38 T 0.5029 0.0821 0.4150 39 I 0.2987 0.1694 0.5319 40 N 0.1772 0.1928 0.6300 41 D 0.1556 0.1564 0.6880 42 L 0.1809 0.0764 0.7426 43 D 0.2041 0.0630 0.7330 44 G 0.3854 0.0671 0.5475 45 E 0.6702 0.0573 0.2725 46 M 0.8067 0.0601 0.1332 47 I 0.8529 0.0476 0.0996 48 Q 0.8157 0.0505 0.1338 49 M 0.6556 0.0480 0.2965 50 G 0.2350 0.0281 0.7369 51 T 0.2066 0.0454 0.7480 52 K 0.6356 0.0290 0.3354 53 F 0.8416 0.0157 0.1427 54 Y 0.8585 0.0174 0.1241 55 Q 0.8786 0.0085 0.1129 56 I 0.8490 0.0071 0.1439 57 D 0.5154 0.0238 0.4608 58 S 0.1337 0.0920 0.7743 59 T 0.0643 0.0192 0.9164 60 G 0.1725 0.0284 0.7991 61 K 0.6580 0.0091 0.3329 62 L 0.9042 0.0038 0.0920 63 S 0.8693 0.0062 0.1245 64 E 0.8496 0.0051 0.1453 65 L 0.5127 0.0086 0.4787 66 P 0.1928 0.0204 0.7868 67 E 0.0254 0.1869 0.7878 68 S 0.0409 0.1518 0.8073 69 V 0.2310 0.1390 0.6300 70 K 0.4610 0.0537 0.4853 71 T 0.4472 0.0192 0.5336 72 P 0.4423 0.0293 0.5284 73 F 0.6678 0.0323 0.2999 74 A 0.7883 0.0193 0.1924 75 V 0.8696 0.0105 0.1199 76 T 0.8529 0.0090 0.1381 77 T 0.7185 0.0174 0.2641 78 H 0.5639 0.0278 0.4083 79 F 0.3874 0.0389 0.5737 80 E 0.2441 0.0254 0.7305 81 P 0.1814 0.1377 0.6809 82 K 0.2635 0.1704 0.5660 83 E 0.4889 0.1273 0.3838 84 K 0.6286 0.0781 0.2934 85 T 0.6890 0.0479 0.2632 86 T 0.6339 0.0597 0.3064 87 L 0.3499 0.1544 0.4957 88 T 0.1872 0.1522 0.6606 89 N 0.1422 0.1624 0.6954 90 V 0.1386 0.1092 0.7521 91 Q 0.1632 0.0645 0.7723 92 D 0.1102 0.0424 0.8474 93 Y 0.0074 0.8991 0.0935 94 N 0.0051 0.9360 0.0589 95 Q 0.0052 0.9454 0.0494 96 L 0.0047 0.9527 0.0426 97 T 0.0047 0.9538 0.0415 98 K 0.0048 0.9498 0.0454 99 M 0.0051 0.9427 0.0522 100 L 0.0061 0.9298 0.0640 101 E 0.0062 0.8904 0.1033 102 E 0.0091 0.7888 0.2020 103 K 0.0199 0.6362 0.3439 104 F 0.0700 0.1842 0.7458 105 E 0.0399 0.1239 0.8361 106 N 0.0821 0.0965 0.8213 107 K 0.1305 0.1219 0.7476 108 N 0.3045 0.0795 0.6160 109 V 0.5414 0.0864 0.3722 110 F 0.6635 0.0850 0.2515 111 Y 0.7423 0.0828 0.1749 112 A 0.8547 0.0316 0.1138 113 V 0.8978 0.0114 0.0908 114 K 0.9053 0.0069 0.0878 115 L 0.8918 0.0115 0.0967 116 T 0.7863 0.0362 0.1775 117 G 0.7004 0.0228 0.2768 118 T 0.7328 0.0267 0.2405 119 F 0.6791 0.0400 0.2810 120 K 0.5118 0.0871 0.4011 121 M 0.5908 0.0342 0.3750 122 V 0.7239 0.0099 0.2662 123 K 0.8412 0.0068 0.1520 124 A 0.8762 0.0058 0.1180 125 R 0.8280 0.0122 0.1598 126 T 0.7187 0.0120 0.2693 127 V 0.3844 0.0196 0.5961 128 P 0.1801 0.1187 0.7012 129 K 0.1094 0.1803 0.7102 130 Q 0.1642 0.1485 0.6874 131 T 0.1217 0.0789 0.7994 132 R 0.0737 0.0803 0.8460 133 P 0.0757 0.0987 0.8256 134 Y 0.0564 0.1862 0.7574 135 P 0.0303 0.5482 0.4215 136 Q 0.0264 0.6668 0.3069 137 L 0.0098 0.8756 0.1145 138 T 0.0088 0.9168 0.0744 139 E 0.0085 0.9248 0.0667 140 V 0.0082 0.9101 0.0818 141 T 0.0148 0.8742 0.1110 142 K 0.0149 0.6844 0.3007 143 K 0.0314 0.3905 0.5781 144 Q 0.0919 0.0919 0.8163 145 S 0.1287 0.1235 0.7478 146 E 0.3316 0.1631 0.5054 147 F 0.4626 0.1266 0.4108 148 E 0.5706 0.0855 0.3438 149 F 0.4375 0.1588 0.4037 150 K 0.2346 0.1793 0.5861 151 N 0.2034 0.0962 0.7004 152 V 0.3784 0.0380 0.5837 153 K 0.5200 0.0397 0.4403 154 G 0.7580 0.0133 0.2287 155 T 0.8532 0.0090 0.1378 156 L 0.8939 0.0080 0.0981 157 I 0.8378 0.0228 0.1394 158 G 0.7797 0.0261 0.1942 159 F 0.7218 0.0394 0.2388 160 Y 0.5394 0.0460 0.4145 161 T 0.2441 0.0483 0.7076 162 P 0.1036 0.4395 0.4569 163 N 0.0471 0.5720 0.3809 164 Y 0.0494 0.6111 0.3394 165 A 0.1163 0.4154 0.4683 166 A 0.0831 0.3310 0.5858 167 A 0.1088 0.1784 0.7128 168 L 0.2072 0.1188 0.6740 169 N 0.2610 0.0812 0.6577 170 V 0.1972 0.0926 0.7102 171 P 0.1255 0.1226 0.7519 172 G 0.2138 0.1001 0.6861 173 F 0.5158 0.0694 0.4148 174 H 0.6746 0.0459 0.2795 175 L 0.7587 0.0434 0.1979 176 H 0.8034 0.0275 0.1692 177 F 0.7772 0.0241 0.1987 178 I 0.6799 0.0251 0.2950 179 T 0.3264 0.0348 0.6388 180 E 0.0711 0.1487 0.7802 181 D 0.0722 0.1065 0.8213 182 K 0.1143 0.0941 0.7916 183 T 0.1862 0.0685 0.7452 184 S 0.2498 0.0549 0.6953 185 G 0.2190 0.0416 0.7394 186 G 0.3848 0.0390 0.5762 187 H 0.5938 0.0320 0.3742 188 V 0.7303 0.0313 0.2385 189 L 0.7732 0.0226 0.2041 190 N 0.8046 0.0140 0.1813 191 L 0.8695 0.0072 0.1233 192 Q 0.8805 0.0049 0.1145 193 F 0.8386 0.0088 0.1526 194 D 0.6548 0.0401 0.3051 195 N 0.6032 0.0258 0.3711 196 A 0.7670 0.0061 0.2269 197 N 0.9048 0.0033 0.0919 198 L 0.9244 0.0035 0.0721 199 E 0.9208 0.0040 0.0752 200 I 0.8938 0.0057 0.1005 201 S 0.7048 0.0094 0.2858 202 P 0.4920 0.0354 0.4725 203 I 0.3827 0.0775 0.5398 204 H 0.3377 0.1112 0.5511 205 E 0.4191 0.0925 0.4885 206 F 0.7001 0.0320 0.2679 207 D 0.7854 0.0213 0.1932 208 V 0.7675 0.0254 0.2070 209 Q 0.6491 0.0315 0.3194 210 L 0.4202 0.0224 0.5574 211 P 0.2654 0.0335 0.7010 212 H 0.1289 0.0778 0.7934 213 T 0.0738 0.0766 0.8496 214 D 0.0370 0.4664 0.4967 215 D 0.0178 0.6233 0.3589 216 F 0.0284 0.6798 0.2919 217 A 0.0351 0.6137 0.3512 218 H 0.0502 0.4475 0.5024 219 S 0.0561 0.3900 0.5539 220 D 0.0740 0.2289 0.6971 221 L 0.1026 0.1133 0.7841 222 T 0.0834 0.0474 0.8691 223 Q 0.0269 0.6067 0.3664 224 V 0.0129 0.6888 0.2983 225 T 0.0282 0.6950 0.2768 226 T 0.0101 0.8885 0.1013 227 S 0.0092 0.9127 0.0781 228 Q 0.0098 0.9133 0.0769 229 V 0.0150 0.9037 0.0813 230 H 0.0315 0.8622 0.1062 231 Q 0.0389 0.8047 0.1564 232 A 0.0402 0.7053 0.2545 233 E 0.0379 0.6676 0.2945 234 S 0.0391 0.5150 0.4459 235 E 0.0435 0.3155 0.6409 236 R 0.0585 0.1451 0.7964 237 K 0.0378 0.0471 0.9151