# This file is the result of combining several RDB files, specifically # T0440.t06.str2.rdb (weight 1.54425) # T0440.t06.str4.rdb (weight 0.924988) # T0440.t06.pb.rdb (weight 0.789901) # T0440.t06.bys.rdb (weight 0.748322) # T0440.t06.alpha.rdb (weight 0.678173) # T0440.t04.str2.rdb (weight 1.54425) # T0440.t04.str4.rdb (weight 0.924988) # T0440.t04.pb.rdb (weight 0.789901) # T0440.t04.bys.rdb (weight 0.748322) # T0440.t04.alpha.rdb (weight 0.678173) # T0440.t2k.str2.rdb (weight 1.54425) # T0440.t2k.str4.rdb (weight 0.924988) # T0440.t2k.pb.rdb (weight 0.789901) # T0440.t2k.bys.rdb (weight 0.748322) # T0440.t2k.alpha.rdb (weight 0.678173) # 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 T0440.t06.str2.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t06-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 T0440.t06-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 1611 # # ============================================ # Comments from T0440.t06.str4.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0440.t06-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 1611 # # ============================================ # Comments from T0440.t06.pb.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0440.t06-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 1611 # # ============================================ # Comments from T0440.t06.bys.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0440.t06-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 1611 # # ============================================ # Comments from T0440.t06.alpha.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t06-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 T0440.t06-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 1611 # # ============================================ # Comments from T0440.t04.str2.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t04-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 T0440.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 1436 # # ============================================ # Comments from T0440.t04.str4.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0440.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 1436 # # ============================================ # Comments from T0440.t04.pb.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0440.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 1436 # # ============================================ # Comments from T0440.t04.bys.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0440.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 1436 # # ============================================ # Comments from T0440.t04.alpha.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t04-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 T0440.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 1436 # # ============================================ # Comments from T0440.t2k.str2.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t2k-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 T0440.t2k-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 193 # # ============================================ # Comments from T0440.t2k.str4.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0440.t2k-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 193 # # ============================================ # Comments from T0440.t2k.pb.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0440.t2k-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 193 # # ============================================ # Comments from T0440.t2k.bys.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0440.t2k-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 193 # # ============================================ # Comments from T0440.t2k.alpha.rdb # ============================================ # TARGET T0440 # Using neural net dunbrack-40pc-3157-t2k-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 T0440.t2k-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 193 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3215 0.0934 0.5851 2 K 0.3113 0.1012 0.5875 3 R 0.2892 0.1511 0.5597 4 D 0.2428 0.1488 0.6083 5 G 0.2325 0.1822 0.5853 6 H 0.3322 0.1383 0.5295 7 T 0.3593 0.1317 0.5090 8 H 0.2972 0.1110 0.5918 9 T 0.2219 0.1412 0.6368 10 E 0.1275 0.3042 0.5683 11 F 0.1727 0.2081 0.6192 12 C 0.1757 0.1200 0.7043 13 P 0.1001 0.3530 0.5469 14 H 0.0900 0.2325 0.6775 15 G 0.0887 0.1539 0.7574 16 T 0.1316 0.1628 0.7055 17 H 0.1104 0.2413 0.6483 18 D 0.0884 0.3016 0.6100 19 D 0.1060 0.3643 0.5297 20 V 0.0112 0.7812 0.2076 21 E 0.0089 0.8842 0.1069 22 E 0.0083 0.9250 0.0668 23 M 0.0083 0.9239 0.0678 24 V 0.0083 0.9240 0.0677 25 L 0.0083 0.9243 0.0674 26 K 0.0083 0.9242 0.0675 27 A 0.0086 0.9187 0.0727 28 I 0.0085 0.9059 0.0856 29 E 0.0113 0.8308 0.1578 30 L 0.0495 0.3496 0.6009 31 D 0.0514 0.0801 0.8685 32 F 0.1733 0.0844 0.7423 33 D 0.2931 0.1039 0.6029 34 E 0.6534 0.0581 0.2885 35 Y 0.7299 0.0207 0.2494 36 S 0.7617 0.0157 0.2225 37 I 0.7128 0.0298 0.2574 38 V 0.5925 0.0636 0.3439 39 E 0.3508 0.1735 0.4756 40 H 0.2224 0.1611 0.6165 41 A 0.2305 0.1004 0.6691 42 P 0.2102 0.1347 0.6552 43 L 0.2272 0.1037 0.6690 44 S 0.1551 0.1932 0.6517 45 S 0.0633 0.4649 0.4718 46 E 0.0577 0.5151 0.4272 47 F 0.0926 0.4508 0.4566 48 M 0.1468 0.3381 0.5151 49 K 0.1735 0.2281 0.5984 50 N 0.1748 0.1544 0.6708 51 T 0.1536 0.2275 0.6189 52 A 0.0643 0.4757 0.4601 53 G 0.0745 0.3941 0.5313 54 D 0.0986 0.4693 0.4320 55 K 0.0634 0.6351 0.3015 56 E 0.0712 0.6394 0.2894 57 A 0.0912 0.5815 0.3273 58 V 0.1182 0.5410 0.3408 59 T 0.1107 0.5027 0.3866 60 T 0.0925 0.5065 0.4010 61 A 0.0468 0.6484 0.3048 62 S 0.0615 0.5990 0.3395 63 M 0.1082 0.5369 0.3549 64 A 0.1090 0.4478 0.4432 65 M 0.0414 0.6392 0.3193 66 S 0.0249 0.6168 0.3582 67 D 0.0380 0.4309 0.5311 68 L 0.0678 0.4623 0.4699 69 P 0.0129 0.8265 0.1606 70 Y 0.0093 0.8905 0.1002 71 Y 0.0092 0.9105 0.0803 72 F 0.0085 0.9146 0.0770 73 K 0.0083 0.9213 0.0704 74 K 0.0084 0.9187 0.0729 75 M 0.0084 0.9176 0.0740 76 N 0.0083 0.9209 0.0708 77 H 0.0083 0.9221 0.0696 78 I 0.0084 0.9176 0.0739 79 K 0.0084 0.9176 0.0740 80 K 0.0085 0.9139 0.0776 81 K 0.0124 0.8706 0.1170 82 Y 0.0341 0.7487 0.2172 83 A 0.0481 0.6508 0.3011 84 S 0.0460 0.3789 0.5751 85 D 0.0971 0.1690 0.7339 86 L 0.3486 0.0411 0.6104 87 L 0.5522 0.0282 0.4196 88 I 0.7307 0.0164 0.2529 89 H 0.7145 0.0154 0.2701 90 I 0.7160 0.0267 0.2573 91 G 0.6738 0.0278 0.2985 92 F 0.7196 0.0241 0.2563 93 E 0.7114 0.0264 0.2623 94 V 0.6390 0.0615 0.2995 95 D 0.5195 0.1086 0.3719 96 Y 0.4216 0.1319 0.4464 97 L 0.2546 0.1200 0.6254 98 I 0.1466 0.2094 0.6440 99 G 0.0870 0.1938 0.7192 100 Y 0.1182 0.3221 0.5598 101 E 0.0641 0.6431 0.2928 102 D 0.0372 0.7726 0.1902 103 F 0.0279 0.8320 0.1401 104 T 0.0264 0.8575 0.1161 105 R 0.0111 0.8923 0.0966 106 D 0.0097 0.9067 0.0836 107 F 0.0113 0.8850 0.1037 108 L 0.0125 0.8633 0.1242 109 N 0.0166 0.7768 0.2067 110 E 0.0258 0.6167 0.3575 111 Y 0.0571 0.2814 0.6615 112 G 0.0941 0.1035 0.8024 113 P 0.1481 0.0911 0.7608 114 Q 0.1763 0.1503 0.6734 115 T 0.2406 0.1685 0.5909 116 D 0.3022 0.1596 0.5381 117 D 0.5246 0.1280 0.3474 118 G 0.6663 0.0736 0.2601 119 V 0.6843 0.0632 0.2525 120 L 0.6633 0.0522 0.2845 121 S 0.6783 0.0427 0.2790 122 L 0.6031 0.0786 0.3183 123 H 0.6273 0.0662 0.3065 124 F 0.5706 0.0772 0.3522 125 L 0.4238 0.1012 0.4750 126 E 0.2424 0.1339 0.6237 127 G 0.1656 0.1193 0.7152 128 Q 0.1687 0.1297 0.7016 129 G 0.1392 0.1501 0.7106 130 G 0.1617 0.1846 0.6536 131 F 0.2566 0.1712 0.5721 132 R 0.3120 0.1521 0.5360 133 S 0.2512 0.1831 0.5657 134 I 0.1562 0.4540 0.3898 135 D 0.1386 0.4403 0.4211 136 F 0.1703 0.3671 0.4626 137 S 0.1590 0.2978 0.5432 138 A 0.0496 0.6166 0.3339 139 E 0.0275 0.7372 0.2352 140 D 0.0320 0.7399 0.2281 141 Y 0.0310 0.7279 0.2411 142 N 0.0346 0.7035 0.2619 143 E 0.0482 0.5936 0.3582 144 G 0.0543 0.5799 0.3658 145 I 0.1027 0.6761 0.2212 146 V 0.1166 0.7002 0.1833 147 Q 0.1223 0.6758 0.2019 148 F 0.1132 0.6189 0.2679 149 Y 0.1290 0.4289 0.4421 150 G 0.0911 0.2773 0.6316 151 G 0.1123 0.2408 0.6469 152 F 0.1278 0.3051 0.5671 153 E 0.0873 0.4887 0.4240 154 Q 0.0695 0.6309 0.2996 155 A 0.0491 0.7585 0.1923 156 Q 0.0188 0.8729 0.1084 157 L 0.0097 0.9133 0.0771 158 A 0.0087 0.9192 0.0721 159 Y 0.0089 0.9188 0.0723 160 L 0.0088 0.9185 0.0727 161 E 0.0084 0.9160 0.0756 162 G 0.0085 0.9095 0.0820 163 V 0.0084 0.9158 0.0757 164 K 0.0084 0.9189 0.0727 165 Q 0.0083 0.9230 0.0687 166 S 0.0083 0.9230 0.0687 167 I 0.0083 0.9221 0.0696 168 E 0.0084 0.9191 0.0725 169 A 0.0084 0.9144 0.0772 170 D 0.0119 0.8443 0.1438 171 L 0.0295 0.6941 0.2764 172 G 0.0357 0.5176 0.4467 173 L 0.0755 0.3742 0.5504 174 F 0.1112 0.1594 0.7294 175 K 0.2248 0.0644 0.7108 176 P 0.2767 0.0900 0.6333 177 R 0.4787 0.0871 0.4343 178 R 0.6667 0.0615 0.2718 179 M 0.6415 0.0663 0.2922 180 G 0.5890 0.0591 0.3519 181 H 0.3867 0.1176 0.4957 182 I 0.1609 0.3951 0.4440 183 S 0.0807 0.6057 0.3135 184 L 0.0484 0.7591 0.1925 185 C 0.0392 0.8232 0.1376 186 Q 0.0429 0.8212 0.1359 187 K 0.0490 0.7513 0.1997 188 F 0.0781 0.5968 0.3251 189 Q 0.1032 0.5195 0.3772 190 Q 0.0956 0.4698 0.4346 191 F 0.1364 0.3494 0.5142 192 F 0.1373 0.2401 0.6226 193 G 0.1119 0.1879 0.7002 194 E 0.1053 0.3312 0.5635 195 D 0.1310 0.2613 0.6077 196 T 0.1352 0.3476 0.5172 197 S 0.0949 0.4646 0.4406 198 D 0.0653 0.5462 0.3885 199 F 0.0813 0.4942 0.4246 200 S 0.0880 0.5925 0.3195 201 E 0.0125 0.8129 0.1746 202 E 0.0109 0.8712 0.1179 203 V 0.0095 0.9097 0.0808 204 M 0.0084 0.9194 0.0722 205 E 0.0083 0.9237 0.0680 206 K 0.0083 0.9243 0.0674 207 F 0.0083 0.9228 0.0689 208 R 0.0083 0.9238 0.0680 209 V 0.0082 0.9251 0.0666 210 I 0.0083 0.9231 0.0686 211 L 0.0083 0.9219 0.0697 212 A 0.0083 0.9247 0.0670 213 L 0.0083 0.9244 0.0673 214 V 0.0084 0.9191 0.0725 215 K 0.0089 0.8857 0.1054 216 K 0.0126 0.8162 0.1712 217 R 0.0533 0.2712 0.6755 218 D 0.0517 0.0716 0.8767 219 Y 0.2342 0.0329 0.7330 220 E 0.5637 0.0279 0.4084 221 L 0.7727 0.0137 0.2136 222 D 0.7722 0.0112 0.2166 223 F 0.7486 0.0218 0.2296 224 N 0.5212 0.0416 0.4372 225 T 0.3196 0.1751 0.5053 226 A 0.1527 0.3244 0.5229 227 G 0.1461 0.3327 0.5212 228 L 0.2010 0.3302 0.4688 229 F 0.2424 0.2311 0.5265 230 K 0.2260 0.2326 0.5414 231 P 0.0983 0.4160 0.4857 232 L 0.1063 0.3696 0.5241 233 C 0.1447 0.2239 0.6314 234 G 0.1258 0.1216 0.7526 235 E 0.2325 0.1060 0.6616 236 T 0.3076 0.1169 0.5755 237 Y 0.2881 0.0553 0.6566 238 P 0.1790 0.0809 0.7402 239 P 0.0799 0.4018 0.5184 240 K 0.0139 0.7765 0.2096 241 K 0.0109 0.8710 0.1181 242 I 0.0084 0.9155 0.0761 243 V 0.0083 0.9210 0.0707 244 T 0.0083 0.9244 0.0673 245 L 0.0083 0.9234 0.0683 246 A 0.0084 0.9177 0.0739 247 S 0.0087 0.9007 0.0906 248 E 0.0133 0.8204 0.1663 249 L 0.0578 0.3546 0.5875 250 Q 0.0509 0.0669 0.8821 251 I 0.2140 0.0180 0.7680 252 P 0.4704 0.0230 0.5066 253 F 0.7260 0.0139 0.2602 254 V 0.7495 0.0146 0.2359 255 Y 0.7234 0.0245 0.2521 256 G 0.5745 0.0299 0.3956 257 S 0.2861 0.1340 0.5799 258 D 0.1460 0.2300 0.6240 259 S 0.0911 0.3545 0.5544 260 H 0.1055 0.2691 0.6253 261 G 0.1174 0.2542 0.6283 262 V 0.0543 0.5886 0.3571 263 Q 0.0442 0.6709 0.2849 264 D 0.0568 0.7032 0.2400 265 I 0.0724 0.6475 0.2801 266 G 0.0786 0.5476 0.3738 267 R 0.0600 0.5082 0.4317 268 G 0.0657 0.3882 0.5462 269 Y 0.0650 0.6299 0.3051 270 S 0.0245 0.8324 0.1431 271 T 0.0209 0.8585 0.1206 272 Y 0.0288 0.8377 0.1335 273 C 0.0522 0.7683 0.1795 274 Q 0.0800 0.6360 0.2840 275 K 0.1049 0.4173 0.4778