# This file is the result of combining several RDB files, specifically # T0185.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0185.t2k.stride-ebghtl.rdb (weight 1.24869) # T0185.t2k.str.rdb (weight 1.53983) # T0185.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 T0185.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0185 # 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 T0185.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 248 # # ============================================ # Comments from T0185.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0185 # 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 T0185.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 248 # # ============================================ # Comments from T0185.t2k.str.rdb # ============================================ # TARGET T0185 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0185.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 248 # # ============================================ # Comments from T0185.t2k.alpha.rdb # ============================================ # TARGET T0185 # 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 T0185.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 248 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0645 0.2728 0.6627 2 E 0.0664 0.2431 0.6905 3 R 0.0624 0.1024 0.8352 4 V 0.1204 0.0684 0.8112 5 P 0.3365 0.1100 0.5535 6 I 0.4314 0.2420 0.3266 7 E 0.4304 0.2644 0.3051 8 N 0.2788 0.3217 0.3994 9 R 0.0875 0.6602 0.2522 10 L 0.0273 0.8469 0.1259 11 H 0.0142 0.8881 0.0977 12 Y 0.0123 0.8921 0.0956 13 F 0.0104 0.8648 0.1249 14 R 0.0125 0.8149 0.1726 15 D 0.0156 0.7480 0.2364 16 T 0.0233 0.6755 0.3012 17 L 0.0378 0.5161 0.4461 18 K 0.0213 0.4265 0.5522 19 R 0.0324 0.3007 0.6669 20 E 0.0635 0.1772 0.7593 21 K 0.0648 0.0658 0.8694 22 K 0.1619 0.0183 0.8198 23 E 0.4802 0.0240 0.4957 24 E 0.8956 0.0058 0.0986 25 F 0.9234 0.0042 0.0724 26 A 0.9216 0.0040 0.0744 27 V 0.8910 0.0088 0.1002 28 T 0.7212 0.0190 0.2599 29 G 0.2478 0.0225 0.7297 30 T 0.0520 0.0811 0.8669 31 D 0.0485 0.0592 0.8923 32 G 0.0364 0.0718 0.8918 33 K 0.0405 0.4479 0.5116 34 T 0.0326 0.7642 0.2032 35 T 0.0173 0.8845 0.0982 36 T 0.0055 0.9417 0.0529 37 T 0.0044 0.9587 0.0369 38 A 0.0044 0.9602 0.0354 39 M 0.0043 0.9608 0.0349 40 V 0.0044 0.9601 0.0356 41 A 0.0044 0.9594 0.0362 42 H 0.0044 0.9591 0.0365 43 V 0.0044 0.9577 0.0379 44 L 0.0045 0.9513 0.0441 45 K 0.0051 0.9215 0.0735 46 H 0.0074 0.8360 0.1567 47 L 0.0437 0.4152 0.5411 48 R 0.0413 0.0405 0.9182 49 K 0.0807 0.0280 0.8913 50 S 0.1283 0.0381 0.8336 51 P 0.1867 0.1857 0.6277 52 T 0.2644 0.2443 0.4914 53 V 0.3701 0.2296 0.4003 54 F 0.4012 0.1781 0.4207 55 L 0.2458 0.1740 0.5802 56 G 0.1471 0.1436 0.7093 57 G 0.1558 0.1881 0.6561 58 I 0.2185 0.2453 0.5362 59 M 0.2142 0.2579 0.5279 60 D 0.1975 0.3047 0.4978 61 S 0.2165 0.3857 0.3978 62 L 0.1782 0.4758 0.3459 63 E 0.1981 0.4828 0.3191 64 H 0.1738 0.5257 0.3005 65 G 0.1491 0.5481 0.3028 66 N 0.1744 0.4399 0.3857 67 Y 0.1690 0.3294 0.5017 68 E 0.1094 0.2462 0.6445 69 K 0.0532 0.1611 0.7857 70 G 0.0620 0.0802 0.8577 71 N 0.1942 0.0231 0.7827 72 G 0.3522 0.0337 0.6142 73 P 0.8815 0.0047 0.1138 74 V 0.9217 0.0037 0.0747 75 V 0.9262 0.0036 0.0702 76 Y 0.9006 0.0071 0.0922 77 E 0.8761 0.0052 0.1187 78 L 0.7031 0.0139 0.2830 79 D 0.3005 0.0383 0.6612 80 E 0.0959 0.1610 0.7431 81 S 0.0742 0.1191 0.8067 82 E 0.0971 0.1143 0.7886 83 E 0.1517 0.1223 0.7260 84 F 0.2915 0.1508 0.5577 85 F 0.3497 0.1392 0.5111 86 S 0.3632 0.1665 0.4703 87 E 0.4477 0.0972 0.4551 88 F 0.4145 0.0417 0.5438 89 S 0.3008 0.0192 0.6800 90 P 0.3020 0.0220 0.6760 91 N 0.3695 0.0454 0.5851 92 Y 0.9105 0.0042 0.0853 93 L 0.9265 0.0038 0.0697 94 I 0.9272 0.0037 0.0691 95 I 0.9041 0.0050 0.0908 96 T 0.7179 0.0253 0.2568 97 N 0.4019 0.0205 0.5777 98 A 0.2001 0.0394 0.7605 99 R 0.1060 0.0408 0.8532 100 G 0.0220 0.6532 0.3248 101 D 0.0139 0.7087 0.2774 102 H 0.0247 0.7387 0.2366 103 L 0.0236 0.7266 0.2498 104 E 0.0265 0.6347 0.3388 105 N 0.0327 0.5156 0.4518 106 Y 0.0517 0.2481 0.7002 107 G 0.0396 0.1262 0.8342 108 N 0.0451 0.0961 0.8588 109 S 0.0638 0.1846 0.7516 110 L 0.0059 0.9362 0.0578 111 T 0.0048 0.9522 0.0430 112 R 0.0046 0.9540 0.0414 113 Y 0.0044 0.9576 0.0380 114 R 0.0045 0.9558 0.0397 115 S 0.0045 0.9500 0.0455 116 A 0.0046 0.9443 0.0512 117 F 0.0045 0.9477 0.0477 118 E 0.0050 0.9434 0.0515 119 K 0.0051 0.9332 0.0618 120 I 0.0059 0.9141 0.0800 121 S 0.0109 0.8703 0.1188 122 R 0.0144 0.7549 0.2307 123 N 0.0278 0.4517 0.5205 124 T 0.1054 0.1044 0.7901 125 D 0.1043 0.0521 0.8436 126 L 0.6486 0.0167 0.3347 127 V 0.8673 0.0067 0.1260 128 V 0.8936 0.0060 0.1004 129 T 0.8136 0.0127 0.1737 130 F 0.4024 0.0179 0.5797 131 A 0.0420 0.1163 0.8417 132 E 0.0380 0.0679 0.8941 133 D 0.0749 0.1039 0.8213 134 E 0.0121 0.6161 0.3717 135 L 0.0228 0.6094 0.3678 136 T 0.0561 0.6364 0.3076 137 S 0.0815 0.5007 0.4178 138 H 0.1308 0.3133 0.5558 139 L 0.2119 0.0789 0.7092 140 G 0.2506 0.0509 0.6985 141 D 0.6509 0.0278 0.3213 142 V 0.7844 0.0179 0.1977 143 T 0.8079 0.0161 0.1759 144 F 0.7151 0.0266 0.2583 145 G 0.5183 0.0292 0.4525 146 V 0.3202 0.0474 0.6324 147 K 0.1634 0.0426 0.7940 148 K 0.0879 0.1361 0.7760 149 G 0.0694 0.1815 0.7491 150 T 0.2068 0.1997 0.5935 151 Y 0.4043 0.1554 0.4403 152 T 0.5735 0.1212 0.3053 153 L 0.6343 0.1585 0.2071 154 E 0.6007 0.1712 0.2281 155 M 0.6291 0.1424 0.2285 156 R 0.6650 0.1112 0.2238 157 S 0.6901 0.1000 0.2098 158 A 0.6551 0.1060 0.2390 159 S 0.4913 0.1137 0.3950 160 R 0.2793 0.1491 0.5716 161 A 0.1743 0.1181 0.7076 162 E 0.2403 0.0634 0.6963 163 Q 0.4541 0.0306 0.5153 164 K 0.7080 0.0171 0.2749 165 A 0.8362 0.0102 0.1536 166 M 0.8850 0.0068 0.1082 167 V 0.8972 0.0061 0.0967 168 E 0.8710 0.0087 0.1202 169 K 0.7075 0.0154 0.2772 170 N 0.1926 0.0741 0.7333 171 G 0.1153 0.0825 0.8022 172 K 0.4360 0.0600 0.5040 173 R 0.6612 0.0391 0.2998 174 Y 0.6965 0.0331 0.2704 175 L 0.6593 0.0418 0.2989 176 E 0.7433 0.0281 0.2286 177 L 0.7764 0.0194 0.2042 178 K 0.7303 0.0195 0.2502 179 L 0.5837 0.0231 0.3932 180 K 0.3703 0.0406 0.5891 181 V 0.2491 0.0696 0.6813 182 P 0.1389 0.1310 0.7301 183 G 0.0836 0.2449 0.6714 184 F 0.0309 0.7272 0.2419 185 H 0.0301 0.7710 0.1989 186 N 0.0139 0.8718 0.1143 187 V 0.0045 0.9458 0.0498 188 L 0.0044 0.9530 0.0426 189 N 0.0044 0.9578 0.0378 190 A 0.0044 0.9599 0.0357 191 L 0.0043 0.9610 0.0346 192 A 0.0043 0.9613 0.0344 193 V 0.0043 0.9612 0.0344 194 I 0.0043 0.9611 0.0345 195 A 0.0043 0.9615 0.0342 196 L 0.0043 0.9612 0.0344 197 F 0.0045 0.9590 0.0365 198 D 0.0050 0.9485 0.0465 199 S 0.0067 0.8868 0.1066 200 L 0.0438 0.4144 0.5418 201 G 0.0427 0.0268 0.9305 202 Y 0.0568 0.0089 0.9343 203 D 0.0742 0.0106 0.9152 204 L 0.0050 0.9188 0.0762 205 A 0.0045 0.9488 0.0468 206 P 0.0045 0.9526 0.0429 207 V 0.0044 0.9568 0.0388 208 L 0.0044 0.9525 0.0430 209 E 0.0045 0.9396 0.0559 210 A 0.0047 0.9238 0.0715 211 L 0.0072 0.9003 0.0924 212 E 0.0054 0.8343 0.1603 213 E 0.0098 0.6292 0.3611 214 F 0.0655 0.2895 0.6449 215 R 0.0510 0.2053 0.7437 216 G 0.0663 0.1589 0.7748 217 V 0.0811 0.1225 0.7963 218 H 0.0700 0.1214 0.8086 219 R 0.0629 0.0592 0.8779 220 R 0.0470 0.0279 0.9251