# This file is the result of combining several RDB files, specifically # T0296.t06.dssp-ebghstl.rdb (weight 1.53986) # T0296.t06.stride-ebghtl.rdb (weight 1.24869) # T0296.t06.str2.rdb (weight 1.54758) # T0296.t06.alpha.rdb (weight 0.659012) # T0296.t04.dssp-ebghstl.rdb (weight 1.53986) # T0296.t04.stride-ebghtl.rdb (weight 1.24869) # T0296.t04.str2.rdb (weight 1.54758) # T0296.t04.alpha.rdb (weight 0.659012) # T0296.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0296.t2k.stride-ebghtl.rdb (weight 1.24869) # T0296.t2k.str2.rdb (weight 1.54758) # T0296.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 T0296.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0296 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0296.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 4.62916 # # ============================================ # Comments from T0296.t06.stride-ebghtl.rdb # ============================================ # TARGET T0296 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0296.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 4.62916 # # ============================================ # Comments from T0296.t06.str2.rdb # ============================================ # TARGET T0296 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0296.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 4.62916 # # ============================================ # Comments from T0296.t06.alpha.rdb # ============================================ # TARGET T0296 # Using neural net t04-2621-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 T0296.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 4.62916 # # ============================================ # Comments from T0296.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0296 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0296.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 4.62834 # # ============================================ # Comments from T0296.t04.stride-ebghtl.rdb # ============================================ # TARGET T0296 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0296.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 4.62834 # # ============================================ # Comments from T0296.t04.str2.rdb # ============================================ # TARGET T0296 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0296.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 4.62834 # # ============================================ # Comments from T0296.t04.alpha.rdb # ============================================ # TARGET T0296 # Using neural net t04-2621-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 T0296.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 4.62834 # # ============================================ # Comments from T0296.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0296 # 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 T0296.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 50 # # ============================================ # Comments from T0296.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0296 # 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 T0296.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 50 # # ============================================ # Comments from T0296.t2k.str2.rdb # ============================================ # TARGET T0296 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0296.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 5.65553 # # ============================================ # Comments from T0296.t2k.alpha.rdb # ============================================ # TARGET T0296 # 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 T0296.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 50 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0726 0.0521 0.8753 2 D 0.0788 0.0530 0.8682 3 I 0.0075 0.8929 0.0997 4 R 0.0054 0.9274 0.0672 5 Q 0.0055 0.9407 0.0539 6 V 0.0050 0.9552 0.0398 7 T 0.0047 0.9525 0.0428 8 E 0.0047 0.9404 0.0549 9 T 0.0050 0.9403 0.0547 10 I 0.0050 0.9403 0.0547 11 A 0.0047 0.9550 0.0403 12 M 0.0047 0.9551 0.0403 13 I 0.0054 0.9481 0.0465 14 E 0.0059 0.9275 0.0666 15 E 0.0064 0.8450 0.1485 16 Q 0.0219 0.6012 0.3769 17 N 0.0364 0.3596 0.6040 18 F 0.0868 0.1856 0.7276 19 D 0.1933 0.1346 0.6721 20 I 0.3692 0.2888 0.3420 21 R 0.3931 0.3194 0.2875 22 T 0.4612 0.2909 0.2479 23 I 0.4696 0.2740 0.2564 24 T 0.4458 0.2617 0.2925 25 M 0.3647 0.2425 0.3928 26 G 0.3840 0.1295 0.4865 27 I 0.4402 0.0912 0.4686 28 S 0.4393 0.0532 0.5075 29 L 0.0996 0.6012 0.2992 30 L 0.0534 0.6784 0.2682 31 D 0.0724 0.6327 0.2949 32 C 0.1161 0.4281 0.4558 33 I 0.1431 0.2413 0.6156 34 D 0.0761 0.1615 0.7624 35 P 0.0256 0.3287 0.6457 36 D 0.0861 0.2519 0.6620 37 I 0.0055 0.8877 0.1068 38 N 0.0053 0.9370 0.0577 39 R 0.0049 0.9394 0.0557 40 A 0.0048 0.9438 0.0514 41 A 0.0048 0.9454 0.0498 42 E 0.0049 0.9476 0.0474 43 K 0.0049 0.9454 0.0497 44 I 0.0047 0.9530 0.0423 45 Y 0.0047 0.9561 0.0391 46 Q 0.0048 0.9538 0.0414 47 K 0.0048 0.9505 0.0447 48 I 0.0048 0.9483 0.0470 49 T 0.0066 0.9256 0.0678 50 T 0.0056 0.9176 0.0768 51 K 0.0055 0.9196 0.0749 52 A 0.0050 0.9200 0.0750 53 A 0.0051 0.9015 0.0934 54 N 0.0054 0.8423 0.1523 55 L 0.0086 0.8864 0.1050 56 V 0.0059 0.9104 0.0837 57 A 0.0064 0.8982 0.0953 58 V 0.0069 0.9236 0.0694 59 G 0.0050 0.9497 0.0453 60 D 0.0047 0.9575 0.0378 61 E 0.0047 0.9601 0.0352 62 I 0.0047 0.9595 0.0358 63 A 0.0048 0.9549 0.0403 64 A 0.0059 0.9370 0.0571 65 E 0.0121 0.8622 0.1257 66 L 0.0493 0.4978 0.4529 67 G 0.0437 0.0208 0.9355 68 I 0.0812 0.0112 0.9076 69 P 0.4075 0.0160 0.5765 70 I 0.8076 0.0112 0.1812 71 V 0.8183 0.0211 0.1607 72 N 0.7387 0.0162 0.2451 73 K 0.5632 0.0267 0.4101 74 R 0.5098 0.0221 0.4681 75 V 0.6249 0.0257 0.3494 76 S 0.6122 0.0253 0.3625 77 V 0.5475 0.0370 0.4155 78 T 0.2846 0.0403 0.6751 79 P 0.0683 0.6437 0.2881 80 I 0.0243 0.8687 0.1070 81 S 0.0324 0.8894 0.0781 82 L 0.0372 0.8767 0.0861 83 I 0.0486 0.7895 0.1619 84 G 0.0447 0.6929 0.2624 85 A 0.0407 0.5541 0.4052 86 A 0.0517 0.4354 0.5129 87 T 0.0755 0.2240 0.7005 88 D 0.0514 0.1216 0.8270 89 A 0.0304 0.5101 0.4596 90 T 0.0149 0.6566 0.3284 91 D 0.0264 0.7512 0.2224 92 Y 0.0136 0.9121 0.0744 93 V 0.0083 0.9437 0.0481 94 V 0.0079 0.9492 0.0429 95 L 0.0050 0.9548 0.0402 96 A 0.0048 0.9544 0.0408 97 K 0.0049 0.9331 0.0620 98 A 0.0048 0.9256 0.0696 99 L 0.0052 0.9359 0.0589 100 D 0.0051 0.9536 0.0412 101 K 0.0049 0.9565 0.0387 102 A 0.0047 0.9574 0.0379 103 A 0.0048 0.9529 0.0423 104 K 0.0054 0.9388 0.0557 105 E 0.0070 0.8934 0.0996 106 I 0.0482 0.4644 0.4874 107 G 0.0559 0.0301 0.9140 108 V 0.1453 0.0131 0.8416 109 D 0.5306 0.0268 0.4426 110 F 0.8349 0.0237 0.1414 111 I 0.8137 0.0304 0.1558 112 G 0.6873 0.0266 0.2861 113 G 0.3021 0.1564 0.5416 114 F 0.2395 0.2349 0.5256 115 S 0.2888 0.3956 0.3157 116 A 0.3122 0.4752 0.2126 117 L 0.3692 0.4469 0.1840 118 V 0.3831 0.4157 0.2012 119 Q 0.2629 0.3455 0.3916 120 K 0.0919 0.1833 0.7247 121 G 0.0619 0.0653 0.8728 122 Y 0.1050 0.0386 0.8564 123 Q 0.1082 0.0351 0.8567 124 K 0.0235 0.3061 0.6704 125 G 0.0191 0.3003 0.6806 126 D 0.0192 0.6774 0.3035 127 E 0.0080 0.9207 0.0712 128 I 0.0117 0.9261 0.0622 129 L 0.0063 0.9354 0.0584 130 I 0.0056 0.9290 0.0653 131 N 0.0061 0.8863 0.1076 132 S 0.0106 0.8396 0.1498 133 I 0.0100 0.8150 0.1750 134 P 0.0061 0.9080 0.0859 135 R 0.0059 0.9003 0.0938 136 A 0.0087 0.8911 0.1001 137 L 0.0128 0.8358 0.1514 138 A 0.0113 0.7267 0.2621 139 E 0.0198 0.4696 0.5106 140 T 0.0764 0.1601 0.7635 141 D 0.1004 0.1458 0.7537 142 K 0.4462 0.1114 0.4425 143 V 0.6409 0.0757 0.2834 144 C 0.6585 0.0654 0.2761 145 S 0.6550 0.0526 0.2924 146 S 0.5774 0.0595 0.3631 147 V 0.5673 0.0435 0.3892 148 N 0.4851 0.0461 0.4688 149 I 0.3599 0.1047 0.5354 150 G 0.3433 0.0911 0.5656 151 S 0.2735 0.0972 0.6293 152 T 0.1407 0.1282 0.7311 153 K 0.0759 0.2858 0.6383 154 S 0.0652 0.2736 0.6612 155 G 0.1158 0.2232 0.6610 156 I 0.2259 0.2592 0.5149 157 N 0.1736 0.3330 0.4933 158 M 0.0077 0.9141 0.0782 159 T 0.0048 0.9372 0.0580 160 A 0.0051 0.9418 0.0532 161 V 0.0059 0.9478 0.0462 162 A 0.0049 0.9512 0.0439 163 D 0.0050 0.9424 0.0526 164 M 0.0054 0.9237 0.0709 165 G 0.0055 0.8993 0.0952 166 R 0.0087 0.9135 0.0778 167 I 0.0110 0.9193 0.0697 168 I 0.0170 0.9172 0.0659 169 K 0.0150 0.9120 0.0730 170 E 0.0189 0.8769 0.1042 171 T 0.0254 0.7696 0.2050 172 A 0.0562 0.3971 0.5467 173 N 0.0503 0.2165 0.7331 174 L 0.0405 0.1875 0.7720 175 S 0.0499 0.0925 0.8575 176 D 0.0551 0.1808 0.7641 177 M 0.1437 0.2057 0.6506 178 G 0.2369 0.2289 0.5342 179 V 0.3934 0.2526 0.3540 180 A 0.5576 0.2184 0.2240 181 K 0.6588 0.2155 0.1257 182 L 0.7497 0.1660 0.0844 183 V 0.8025 0.1114 0.0861 184 V 0.7656 0.1357 0.0987 185 F 0.7287 0.1344 0.1369 186 A 0.5568 0.1448 0.2983 187 N 0.3351 0.0978 0.5671 188 A 0.1794 0.0815 0.7392 189 V 0.1148 0.1331 0.7521 190 E 0.0558 0.1572 0.7870 191 D 0.0641 0.1025 0.8334 192 N 0.0656 0.0551 0.8792 193 P 0.0511 0.2140 0.7349 194 F 0.0938 0.2317 0.6745 195 M 0.1810 0.2581 0.5609 196 A 0.2197 0.2811 0.4992 197 G 0.2559 0.2793 0.4648 198 A 0.2909 0.3197 0.3894 199 F 0.3206 0.2568 0.4225 200 H 0.2282 0.1916 0.5801 201 G 0.1344 0.0882 0.7774 202 V 0.1476 0.0921 0.7603 203 G 0.1263 0.0624 0.8113 204 E 0.1313 0.2074 0.6613 205 A 0.1548 0.1845 0.6607 206 D 0.2746 0.1915 0.5340 207 V 0.7510 0.0532 0.1958 208 I 0.8457 0.0329 0.1214 209 I 0.8553 0.0350 0.1097 210 N 0.7703 0.0535 0.1761 211 V 0.5238 0.0943 0.3819 212 G 0.3061 0.0900 0.6039 213 V 0.2062 0.1261 0.6677 214 S 0.1078 0.1492 0.7430 215 G 0.0444 0.2632 0.6924 216 P 0.0184 0.8161 0.1655 217 G 0.0107 0.9000 0.0893 218 V 0.0068 0.9511 0.0421 219 V 0.0051 0.9568 0.0381 220 K 0.0048 0.9573 0.0379 221 R 0.0049 0.9571 0.0380 222 A 0.0049 0.9529 0.0422 223 L 0.0055 0.9344 0.0601 224 E 0.0056 0.8862 0.1083 225 K 0.0097 0.7745 0.2158 226 V 0.0439 0.2756 0.6805 227 R 0.0163 0.1786 0.8051 228 G 0.0253 0.0991 0.8756 229 Q 0.0850 0.0619 0.8532 230 S 0.1132 0.0709 0.8159 231 F 0.0098 0.8925 0.0977 232 D 0.0051 0.9416 0.0533 233 V 0.0061 0.9437 0.0502 234 V 0.0047 0.9523 0.0430 235 A 0.0048 0.9554 0.0398 236 E 0.0048 0.9516 0.0436 237 T 0.0049 0.9484 0.0467 238 V 0.0051 0.9449 0.0500 239 K 0.0052 0.9342 0.0606 240 K 0.0060 0.8912 0.1028 241 T 0.0077 0.7847 0.2076 242 A 0.0249 0.5850 0.3901 243 F 0.0857 0.4226 0.4917 244 K 0.1915 0.3751 0.4334 245 I 0.3036 0.3566 0.3398 246 T 0.2483 0.3070 0.4447 247 R 0.2004 0.3044 0.4953 248 I 0.0507 0.5213 0.4280 249 G 0.0375 0.5045 0.4580 250 Q 0.0575 0.6678 0.2747 251 L 0.0666 0.8039 0.1295 252 V 0.0390 0.8636 0.0974 253 G 0.0147 0.9203 0.0649 254 Q 0.0056 0.9494 0.0450 255 M 0.0051 0.9562 0.0387 256 A 0.0050 0.9565 0.0386 257 S 0.0049 0.9529 0.0422 258 E 0.0066 0.9325 0.0609 259 R 0.0083 0.8860 0.1057 260 L 0.0472 0.5069 0.4459 261 G 0.0395 0.0387 0.9218 262 V 0.0670 0.0127 0.9202 263 E 0.1126 0.0351 0.8523 264 F 0.4003 0.0590 0.5406 265 G 0.7027 0.0437 0.2536 266 I 0.8314 0.0352 0.1334 267 V 0.7717 0.0619 0.1665 268 D 0.6816 0.0704 0.2479 269 L 0.4099 0.1753 0.4148 270 S 0.2924 0.1617 0.5459 271 L 0.1572 0.1944 0.6484 272 A 0.0674 0.1122 0.8205