# This file is the result of combining several RDB files, specifically # T0582.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0582.t2k.stride-ebghtl.rdb (weight 1.24869) # T0582.t2k.str2.rdb (weight 1.54758) # T0582.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 T0582.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0582 # 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 T0582.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 396 # # ============================================ # Comments from T0582.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0582 # 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 T0582.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 396 # # ============================================ # Comments from T0582.t2k.str2.rdb # ============================================ # TARGET T0582 # 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 T0582.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 396 # # ============================================ # Comments from T0582.t2k.alpha.rdb # ============================================ # TARGET T0582 # 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 T0582.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 396 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1191 0.0222 0.8586 2 E 0.2554 0.0272 0.7174 3 I 0.2728 0.0567 0.6706 4 N 0.1869 0.0449 0.7681 5 A 0.1111 0.1584 0.7305 6 D 0.1029 0.1301 0.7670 7 F 0.0621 0.2392 0.6987 8 T 0.0585 0.2270 0.7144 9 K 0.1476 0.1938 0.6586 10 P 0.3728 0.0759 0.5513 11 V 0.6882 0.0327 0.2791 12 V 0.8071 0.0181 0.1748 13 I 0.7429 0.0180 0.2391 14 D 0.4738 0.0224 0.5038 15 T 0.0518 0.4434 0.5048 16 D 0.0207 0.3944 0.5849 17 Q 0.0520 0.4789 0.4691 18 L 0.1537 0.1662 0.6801 19 E 0.2222 0.0988 0.6789 20 W 0.4518 0.0690 0.4792 21 R 0.5147 0.0414 0.4438 22 P 0.5132 0.0459 0.4409 23 S 0.2921 0.0363 0.6715 24 P 0.1337 0.0598 0.8065 25 M 0.0818 0.0659 0.8523 26 K 0.0728 0.1088 0.8184 27 G 0.1525 0.1120 0.7355 28 V 0.4335 0.1039 0.4626 29 E 0.6842 0.0822 0.2335 30 R 0.6368 0.1178 0.2454 31 R 0.5998 0.1250 0.2752 32 M 0.5496 0.1769 0.2735 33 L 0.4143 0.2393 0.3465 34 D 0.3795 0.2045 0.4160 35 R 0.2469 0.1762 0.5769 36 I 0.1337 0.1424 0.7239 37 G 0.0863 0.0956 0.8180 38 G 0.0652 0.1427 0.7921 39 E 0.1027 0.1883 0.7090 40 V 0.1881 0.1437 0.6682 41 A 0.3047 0.0782 0.6171 42 R 0.5711 0.0403 0.3886 43 A 0.8129 0.0157 0.1714 44 T 0.8793 0.0078 0.1129 45 S 0.9102 0.0049 0.0849 46 I 0.9242 0.0036 0.0721 47 V 0.9133 0.0043 0.0824 48 R 0.8950 0.0044 0.1005 49 Y 0.7497 0.0083 0.2420 50 A 0.2706 0.0176 0.7118 51 P 0.0316 0.0690 0.8994 52 G 0.0380 0.0426 0.9195 53 S 0.1548 0.0307 0.8145 54 R 0.3001 0.0330 0.6669 55 F 0.3187 0.0232 0.6582 56 S 0.2320 0.0400 0.7280 57 A 0.2567 0.0918 0.6515 58 H 0.3105 0.0674 0.6222 59 T 0.3111 0.0552 0.6336 60 H 0.1627 0.0353 0.8020 61 D 0.0639 0.0754 0.8607 62 G 0.0772 0.0549 0.8678 63 G 0.2140 0.0395 0.7466 64 E 0.5761 0.0128 0.4112 65 E 0.8607 0.0048 0.1346 66 F 0.9096 0.0042 0.0862 67 I 0.9266 0.0033 0.0702 68 V 0.9232 0.0035 0.0733 69 L 0.8992 0.0085 0.0923 70 D 0.8134 0.0202 0.1663 71 G 0.7135 0.0127 0.2738 72 V 0.7675 0.0147 0.2177 73 F 0.7342 0.0211 0.2447 74 Q 0.6179 0.0234 0.3587 75 D 0.3708 0.0466 0.5826 76 E 0.0987 0.1188 0.7825 77 H 0.0827 0.0785 0.8388 78 G 0.1017 0.0604 0.8379 79 D 0.2329 0.0367 0.7304 80 Y 0.3881 0.0225 0.5894 81 P 0.1753 0.0219 0.8028 82 A 0.1455 0.0904 0.7642 83 G 0.1663 0.0865 0.7473 84 T 0.4608 0.0415 0.4977 85 Y 0.7711 0.0143 0.2146 86 V 0.8084 0.0153 0.1763 87 R 0.7691 0.0167 0.2142 88 N 0.4586 0.0180 0.5234 89 P 0.1216 0.0227 0.8558 90 P 0.0331 0.0777 0.8892 91 T 0.0495 0.0556 0.8950 92 T 0.1543 0.0343 0.8115 93 S 0.2221 0.0554 0.7225 94 H 0.3248 0.0472 0.6280 95 V 0.3161 0.0355 0.6484 96 P 0.3709 0.0634 0.5656 97 G 0.3912 0.0657 0.5431 98 S 0.2820 0.0421 0.6758 99 A 0.0908 0.0787 0.8304 100 E 0.0342 0.0951 0.8706 101 G 0.0552 0.0625 0.8823 102 C 0.3612 0.0453 0.5935 103 T 0.7729 0.0266 0.2005 104 I 0.8740 0.0225 0.1035 105 F 0.9067 0.0168 0.0765 106 V 0.8984 0.0236 0.0780 107 K 0.8830 0.0302 0.0868 108 L 0.8325 0.0534 0.1140 109 W 0.7630 0.0740 0.1630 110 Q 0.5781 0.0963 0.3256 111 F 0.2590 0.0703 0.6707 112 D 0.1022 0.0414 0.8564 113 P 0.0323 0.3130 0.6546 114 A 0.0347 0.3458 0.6195 115 D 0.0695 0.3596 0.5709 116 R 0.1457 0.2223 0.6320 117 T 0.2132 0.1823 0.6045 118 Q 0.3355 0.1339 0.5306 119 F 0.4835 0.1083 0.4082 120 S 0.5591 0.0867 0.3542 121 K 0.4927 0.1339 0.3733 122 N 0.3508 0.1371 0.5121 123 M 0.1987 0.2302 0.5711 124 E 0.1292 0.1989 0.6719 125 A 0.1300 0.1290 0.7410 126 E 0.0882 0.3271 0.5847 127 L 0.1085 0.3326 0.5589 128 G 0.1346 0.2994 0.5660 129 A 0.1653 0.1568 0.6779 130 P 0.1563 0.1126 0.7311 131 V 0.1303 0.1129 0.7568 132 E 0.0910 0.1139 0.7951 133 G 0.1626 0.1062 0.7311 134 I 0.5084 0.0717 0.4199 135 S 0.7376 0.0468 0.2156 136 T 0.7703 0.0436 0.1861 137 S 0.7165 0.0356 0.2479 138 L 0.6606 0.0566 0.2828 139 L 0.4642 0.1078 0.4279 140 H 0.3484 0.1068 0.5448 141 E 0.1481 0.1297 0.7222 142 D 0.0885 0.0731 0.8385 143 E 0.0835 0.0899 0.8266 144 R 0.1492 0.0687 0.7821 145 E 0.4771 0.0320 0.4910 146 T 0.7865 0.0113 0.2023 147 V 0.8784 0.0094 0.1123 148 T 0.9043 0.0073 0.0883 149 H 0.9059 0.0080 0.0861 150 R 0.8846 0.0077 0.1077 151 K 0.8541 0.0073 0.1386 152 L 0.6107 0.0145 0.3748 153 E 0.2072 0.0265 0.7663 154 P 0.0405 0.0824 0.8771 155 G 0.0506 0.0511 0.8983 156 A 0.3130 0.0250 0.6621 157 N 0.6273 0.0190 0.3537 158 L 0.6326 0.0206 0.3468 159 T 0.5287 0.0321 0.4392 160 S 0.4640 0.0499 0.4861 161 E 0.3788 0.0517 0.5695 162 A 0.2079 0.0561 0.7360 163 A 0.1102 0.1041 0.7857 164 G 0.1203 0.0544 0.8254 165 G 0.3007 0.0398 0.6596 166 I 0.6759 0.0121 0.3120 167 E 0.8931 0.0036 0.1033 168 V 0.9101 0.0038 0.0861 169 L 0.9262 0.0032 0.0706 170 V 0.9254 0.0035 0.0711 171 L 0.9052 0.0084 0.0864 172 D 0.8368 0.0199 0.1433 173 G 0.7938 0.0079 0.1983 174 D 0.8581 0.0068 0.1351 175 V 0.8508 0.0093 0.1399 176 T 0.7583 0.0189 0.2228 177 V 0.5132 0.0452 0.4416 178 N 0.0875 0.0806 0.8318 179 D 0.0742 0.0606 0.8652 180 E 0.3317 0.0653 0.6031 181 V 0.6023 0.0314 0.3663 182 L 0.5533 0.0156 0.4311 183 G 0.1939 0.0191 0.7870 184 R 0.0726 0.0850 0.8424 185 N 0.0723 0.0791 0.8486 186 A 0.3607 0.0416 0.5977 187 W 0.7243 0.0231 0.2526 188 L 0.7566 0.0258 0.2176 189 R 0.7169 0.0205 0.2627 190 L 0.4276 0.0152 0.5572 191 P 0.1581 0.0249 0.8170 192 E 0.0563 0.0724 0.8713 193 G 0.0523 0.0681 0.8796 194 E 0.1005 0.0568 0.8427 195 A 0.2187 0.1013 0.6800 196 L 0.2894 0.1166 0.5940 197 S 0.3947 0.0892 0.5161 198 A 0.5893 0.1037 0.3070 199 T 0.6054 0.0929 0.3018 200 A 0.6287 0.0547 0.3166 201 G 0.3356 0.0347 0.6297 202 A 0.0531 0.1277 0.8192 203 R 0.0599 0.0876 0.8525 204 G 0.1216 0.0709 0.8075 205 A 0.4848 0.0205 0.4947 206 K 0.8659 0.0136 0.1205 207 I 0.9116 0.0134 0.0750 208 W 0.9115 0.0136 0.0750 209 M 0.8811 0.0199 0.0990 210 K 0.7280 0.0528 0.2191 211 T 0.4421 0.0661 0.4918 212 G 0.2297 0.0476 0.7227 213 H 0.2161 0.0745 0.7094 214 L 0.2034 0.1441 0.6525 215 R 0.1128 0.2298 0.6573 216 F 0.1223 0.2160 0.6617 217 V 0.1319 0.0814 0.7867 218 R 0.1080 0.0522 0.8398 219 T 0.0908 0.0614 0.8479 220 P 0.0838 0.1605 0.7557 221 E 0.1010 0.1403 0.7588 222 V 0.0623 0.0366 0.9011