# This file is the result of combining several RDB files, specifically # T0386.t06.dssp-ebghstl.rdb (weight 1.53986) # T0386.t06.stride-ebghtl.rdb (weight 1.24869) # T0386.t06.str2.rdb (weight 1.54758) # T0386.t06.alpha.rdb (weight 0.659012) # T0386.t04.dssp-ebghstl.rdb (weight 1.53986) # T0386.t04.stride-ebghtl.rdb (weight 1.24869) # T0386.t04.str2.rdb (weight 1.54758) # T0386.t04.alpha.rdb (weight 0.659012) # T0386.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0386.t2k.stride-ebghtl.rdb (weight 1.24869) # T0386.t2k.str2.rdb (weight 1.54758) # T0386.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 T0386.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0386 # Using neural net t06-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 T0386.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 543 # # ============================================ # Comments from T0386.t06.stride-ebghtl.rdb # ============================================ # TARGET T0386 # Using neural net t06-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 T0386.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 543 # # ============================================ # Comments from T0386.t06.str2.rdb # ============================================ # TARGET T0386 # Using neural net 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 T0386.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 543 # # ============================================ # Comments from T0386.t06.alpha.rdb # ============================================ # TARGET T0386 # Using neural net 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 T0386.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 543 # # ============================================ # Comments from T0386.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0386 # Using neural net t06-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 T0386.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 538 # # ============================================ # Comments from T0386.t04.stride-ebghtl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 538 # # ============================================ # Comments from T0386.t04.str2.rdb # ============================================ # TARGET T0386 # Using neural net t04-2621-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 T0386.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 538 # # ============================================ # Comments from T0386.t04.alpha.rdb # ============================================ # TARGET T0386 # 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 T0386.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 538 # # ============================================ # Comments from T0386.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 191 # # ============================================ # Comments from T0386.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 191 # # ============================================ # Comments from T0386.t2k.str2.rdb # ============================================ # TARGET T0386 # 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 T0386.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 191 # # ============================================ # Comments from T0386.t2k.alpha.rdb # ============================================ # TARGET T0386 # 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 T0386.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 191 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0575 0.0629 0.8796 2 P 0.0832 0.1459 0.7709 3 K 0.0958 0.2564 0.6477 4 A 0.0907 0.4720 0.4373 5 K 0.1170 0.5554 0.3275 6 A 0.1431 0.5734 0.2835 7 K 0.1639 0.5419 0.2942 8 T 0.1610 0.5044 0.3346 9 K 0.1404 0.3967 0.4629 10 N 0.1209 0.2580 0.6212 11 T 0.1847 0.2207 0.5946 12 E 0.2800 0.2098 0.5101 13 I 0.2563 0.1825 0.5612 14 I 0.2394 0.1566 0.6040 15 S 0.2018 0.1198 0.6784 16 P 0.1651 0.1526 0.6823 17 H 0.1797 0.1117 0.7086 18 H 0.2336 0.0926 0.6738 19 Y 0.4478 0.0469 0.5052 20 V 0.5027 0.0355 0.4618 21 Y 0.2671 0.0469 0.6860 22 P 0.1095 0.1031 0.7874 23 N 0.0558 0.1907 0.7535 24 T 0.0621 0.4333 0.5046 25 T 0.0963 0.6171 0.2866 26 T 0.1105 0.7124 0.1771 27 L 0.0978 0.7401 0.1621 28 K 0.0722 0.7282 0.1996 29 N 0.0608 0.6586 0.2806 30 K 0.0582 0.5607 0.3811 31 Y 0.0804 0.2890 0.6306 32 G 0.0701 0.1192 0.8107 33 I 0.0763 0.1398 0.7839 34 K 0.0716 0.1390 0.7894 35 N 0.0659 0.1462 0.7880 36 L 0.0086 0.8407 0.1507 37 N 0.0083 0.8692 0.1225 38 A 0.0064 0.9012 0.0924 39 F 0.0054 0.9182 0.0763 40 L 0.0058 0.9173 0.0769 41 E 0.0050 0.9265 0.0685 42 K 0.0056 0.9253 0.0691 43 C 0.0058 0.9220 0.0722 44 S 0.0067 0.9059 0.0874 45 H 0.0065 0.9070 0.0865 46 D 0.0065 0.9172 0.0763 47 T 0.0056 0.9315 0.0628 48 A 0.0052 0.9415 0.0534 49 K 0.0052 0.9480 0.0468 50 A 0.0055 0.9439 0.0506 51 M 0.0055 0.9407 0.0538 52 I 0.0073 0.9325 0.0602 53 N 0.0075 0.9085 0.0840 54 L 0.0102 0.8707 0.1192 55 R 0.0142 0.8098 0.1760 56 E 0.0209 0.6633 0.3158 57 E 0.0501 0.4127 0.5373 58 S 0.0434 0.2317 0.7250 59 L 0.0515 0.1892 0.7593 60 P 0.0481 0.1667 0.7852 61 E 0.0674 0.1149 0.8177 62 Y 0.1462 0.0858 0.7680 63 F 0.2240 0.0343 0.7416 64 D 0.0937 0.0198 0.8864 65 T 0.0050 0.9323 0.0626 66 A 0.0047 0.9481 0.0471 67 Y 0.0048 0.9538 0.0415 68 L 0.0047 0.9577 0.0376 69 C 0.0047 0.9580 0.0373 70 H 0.0047 0.9566 0.0387 71 I 0.0048 0.9551 0.0402 72 H 0.0048 0.9532 0.0420 73 Q 0.0048 0.9459 0.0492 74 Q 0.0057 0.9190 0.0753 75 L 0.0074 0.8763 0.1163 76 F 0.0196 0.7385 0.2420 77 K 0.0219 0.5714 0.4067 78 N 0.0342 0.4112 0.5546 79 T 0.0611 0.3446 0.5944 80 F 0.0685 0.3968 0.5347 81 E 0.0400 0.4634 0.4966 82 W 0.0426 0.4343 0.5231 83 A 0.0529 0.2720 0.6751 84 G 0.0636 0.1116 0.8248 85 Y 0.2163 0.0816 0.7021 86 L 0.5140 0.0575 0.4285 87 R 0.4395 0.0761 0.4844 88 H 0.3980 0.0779 0.5240 89 I 0.3288 0.0800 0.5912 90 P 0.3446 0.0688 0.5866 91 F 0.5632 0.0576 0.3791 92 T 0.6355 0.0513 0.3132 93 F 0.5697 0.0821 0.3482 94 A 0.3838 0.0961 0.5201 95 D 0.2863 0.1147 0.5990 96 G 0.3236 0.1506 0.5258 97 T 0.4039 0.1703 0.4257 98 T 0.4128 0.2277 0.3595 99 A 0.3959 0.2478 0.3563 100 A 0.3375 0.2698 0.3927 101 M 0.2673 0.2455 0.4872 102 P 0.1685 0.2507 0.5808 103 E 0.1315 0.2578 0.6107 104 M 0.1245 0.2102 0.6653 105 K 0.1338 0.1359 0.7303 106 R 0.1775 0.1265 0.6961 107 T 0.2266 0.1150 0.6585 108 G 0.3586 0.0779 0.5635 109 W 0.5333 0.0430 0.4238 110 K 0.5770 0.0371 0.3859 111 N 0.5049 0.0329 0.4622 112 A 0.2719 0.0311 0.6970 113 F 0.1389 0.0225 0.8386 114 A 0.0965 0.0312 0.8723 115 I 0.0737 0.0440 0.8823 116 G 0.0173 0.6111 0.3716 117 D 0.0101 0.6367 0.3533 118 E 0.0192 0.6957 0.2852 119 I 0.0164 0.7938 0.1899 120 Q 0.0057 0.9206 0.0736 121 E 0.0051 0.9411 0.0538 122 G 0.0050 0.9446 0.0504 123 L 0.0048 0.9510 0.0442 124 Q 0.0049 0.9494 0.0457 125 R 0.0048 0.9447 0.0504 126 L 0.0048 0.9435 0.0517 127 D 0.0049 0.9340 0.0611 128 Q 0.0055 0.9038 0.0907 129 T 0.0056 0.8634 0.1310 130 L 0.0122 0.7883 0.1995 131 A 0.0126 0.6461 0.3413 132 E 0.0187 0.5431 0.4382 133 K 0.0162 0.6351 0.3486 134 N 0.0154 0.6763 0.3083 135 N 0.0158 0.6871 0.2971 136 L 0.0227 0.6337 0.3436 137 Q 0.0258 0.4807 0.4935 138 G 0.0309 0.3668 0.6023 139 L 0.0379 0.3520 0.6101 140 T 0.0403 0.2658 0.6939 141 R 0.0304 0.4235 0.5461 142 E 0.0231 0.5937 0.3832 143 E 0.0179 0.7011 0.2810 144 F 0.0092 0.8665 0.1243 145 N 0.0056 0.9357 0.0587 146 S 0.0053 0.9489 0.0458 147 E 0.0049 0.9549 0.0402 148 A 0.0047 0.9569 0.0384 149 I 0.0049 0.9575 0.0375 150 E 0.0054 0.9545 0.0400 151 L 0.0065 0.9450 0.0486 152 F 0.0083 0.9319 0.0597 153 N 0.0211 0.8872 0.0917 154 S 0.0362 0.8416 0.1223 155 L 0.0859 0.7609 0.1532 156 N 0.1364 0.6472 0.2164 157 Q 0.1931 0.4941 0.3128 158 L 0.2200 0.2668 0.5132 159 H 0.1758 0.0790 0.7452 160 P 0.0922 0.1439 0.7639 161 F 0.0968 0.1156 0.7876 162 R 0.0754 0.1375 0.7871 163 E 0.0402 0.1196 0.8403 164 G 0.0325 0.1423 0.8252 165 N 0.0383 0.4483 0.5134 166 G 0.0200 0.7375 0.2425 167 R 0.0152 0.9114 0.0734 168 T 0.0055 0.9490 0.0455 169 Q 0.0047 0.9566 0.0387 170 R 0.0047 0.9589 0.0364 171 L 0.0047 0.9602 0.0351 172 F 0.0047 0.9604 0.0349 173 F 0.0047 0.9601 0.0353 174 E 0.0047 0.9599 0.0354 175 N 0.0048 0.9571 0.0381 176 L 0.0047 0.9560 0.0393 177 A 0.0049 0.9493 0.0458 178 K 0.0055 0.9307 0.0639 179 A 0.0074 0.8889 0.1037 180 A 0.0433 0.4133 0.5433 181 G 0.0361 0.0375 0.9263 182 H 0.0737 0.0259 0.9003 183 Q 0.1977 0.0352 0.7671 184 L 0.2631 0.1120 0.6249 185 N 0.3252 0.1759 0.4989 186 F 0.3779 0.2234 0.3987 187 S 0.3417 0.2488 0.4095 188 L 0.2514 0.2658 0.4829 189 I 0.1568 0.2945 0.5487 190 T 0.0813 0.3223 0.5964 191 K 0.0426 0.4921 0.4653 192 E 0.0132 0.8061 0.1808 193 R 0.0092 0.9063 0.0845 194 M 0.0077 0.9271 0.0652 195 M 0.0072 0.9415 0.0513 196 V 0.0070 0.9499 0.0431 197 A 0.0066 0.9477 0.0457 198 S 0.0058 0.9468 0.0473 199 V 0.0056 0.9455 0.0488 200 A 0.0057 0.9378 0.0564 201 V 0.0062 0.9081 0.0857 202 A 0.0140 0.7781 0.2079 203 E 0.0214 0.5610 0.4176 204 N 0.0463 0.2925 0.6612 205 G 0.0275 0.1176 0.8548 206 D 0.0623 0.0988 0.8388 207 L 0.0453 0.3733 0.5815 208 E 0.0347 0.6631 0.3022 209 P 0.0188 0.8435 0.1377 210 M 0.0105 0.9097 0.0798 211 Q 0.0087 0.9323 0.0589 212 H 0.0093 0.9338 0.0569 213 L 0.0074 0.9286 0.0640 214 F 0.0086 0.9130 0.0784 215 E 0.0079 0.8971 0.0949 216 D 0.0095 0.8426 0.1480 217 I 0.0155 0.7566 0.2278 218 S 0.0223 0.7135 0.2642 219 N 0.0316 0.7117 0.2567 220 P 0.0081 0.8626 0.1292 221 E 0.0096 0.8883 0.1021 222 K 0.0073 0.9172 0.0755 223 I 0.0075 0.9304 0.0621 224 R 0.0064 0.9359 0.0577 225 L 0.0059 0.9337 0.0604 226 L 0.0056 0.9376 0.0568 227 K 0.0056 0.9370 0.0574 228 E 0.0061 0.9272 0.0667 229 F 0.0069 0.9152 0.0780 230 M 0.0083 0.8968 0.0949 231 H 0.0095 0.8555 0.1350 232 T 0.0128 0.7933 0.1939 233 M 0.0245 0.7303 0.2452 234 K 0.0269 0.6877 0.2854 235 N 0.0314 0.5471 0.4215 236 T 0.0416 0.4260 0.5324 237 G 0.0532 0.3209 0.6259 238 R 0.0530 0.3244 0.6226 239 N 0.0678 0.2822 0.6500 240 V 0.0650 0.4015 0.5335 241 N 0.0743 0.4529 0.4728 242 D 0.1426 0.4929 0.3645 243 R 0.2187 0.5336 0.2478 244 P 0.2813 0.5499 0.1688 245 V 0.3116 0.5643 0.1241 246 M 0.2878 0.6024 0.1097 247 V 0.2676 0.6203 0.1121 248 A 0.2091 0.6428 0.1481 249 K 0.1951 0.6231 0.1818 250 E 0.0853 0.5011 0.4136 251 G 0.0905 0.2061 0.7034 252 E 0.1684 0.2537 0.5778 253 T 0.2938 0.3154 0.3908 254 Y 0.2685 0.3830 0.3485 255 T 0.2672 0.3604 0.3724 256 G 0.3020 0.3342 0.3638 257 T 0.3268 0.3552 0.3180 258 Y 0.3125 0.3371 0.3503 259 R 0.2104 0.3032 0.4863 260 G 0.1728 0.2162 0.6111 261 A 0.1911 0.1700 0.6389 262 G 0.1602 0.2163 0.6235 263 L 0.1410 0.3040 0.5551 264 E 0.2546 0.3080 0.4374 265 G 0.3807 0.2519 0.3674 266 F 0.4733 0.1841 0.3427 267 A 0.4190 0.1964 0.3846 268 L 0.3957 0.2322 0.3721 269 N 0.3789 0.2078 0.4133 270 V 0.4274 0.1512 0.4214 271 K 0.3727 0.1681 0.4592 272 G 0.2435 0.2168 0.5398 273 A 0.3736 0.1899 0.4364 274 Y 0.6356 0.1494 0.2150 275 I 0.7232 0.1103 0.1666 276 I 0.5973 0.1309 0.2717 277 G 0.4037 0.0742 0.5220 278 N 0.2490 0.0819 0.6691 279 I 0.0340 0.5612 0.4047 280 D 0.0252 0.4740 0.5007 281 H 0.0383 0.4457 0.5161 282 L 0.0936 0.1072 0.7992 283 P 0.0574 0.0852 0.8574 284 P 0.0130 0.7061 0.2809 285 E 0.0129 0.7478 0.2392 286 Q 0.0218 0.7679 0.2103 287 L 0.0259 0.7544 0.2196 288 K 0.0408 0.6940 0.2653 289 I 0.0750 0.6393 0.2857 290 L 0.1561 0.2752 0.5687 291 K 0.0638 0.0816 0.8546 292 P 0.0358 0.1089 0.8554 293 G 0.0350 0.0752 0.8898 294 D 0.2150 0.0363 0.7487 295 K 0.6838 0.0225 0.2937 296 I 0.8271 0.0091 0.1638 297 T 0.7889 0.0132 0.1979 298 F 0.5628 0.0141 0.4231 299 T 0.0734 0.0221 0.9045