# This file is the result of combining several RDB files, specifically # T0321.t06.dssp-ebghstl.rdb (weight 1.53986) # T0321.t06.stride-ebghtl.rdb (weight 1.24869) # T0321.t06.str2.rdb (weight 1.54758) # T0321.t06.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 T0321.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0321 # 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 T0321.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 65 # # ============================================ # Comments from T0321.t06.stride-ebghtl.rdb # ============================================ # TARGET T0321 # 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 T0321.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 65 # # ============================================ # Comments from T0321.t06.str2.rdb # ============================================ # TARGET T0321 # 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 T0321.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 65 # # ============================================ # Comments from T0321.t06.alpha.rdb # ============================================ # TARGET T0321 # 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 T0321.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 65 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0177 0.2791 0.7033 2 W 0.0216 0.7577 0.2207 3 E 0.0190 0.8507 0.1303 4 I 0.0073 0.9317 0.0610 5 Y 0.0061 0.9410 0.0529 6 D 0.0056 0.9412 0.0531 7 A 0.0060 0.9365 0.0575 8 M 0.0073 0.9149 0.0778 9 I 0.0169 0.8158 0.1673 10 N 0.0191 0.5748 0.4061 11 G 0.0249 0.2727 0.7025 12 I 0.0618 0.0398 0.8985 13 P 0.0497 0.0720 0.8782 14 E 0.0270 0.3009 0.6720 15 D 0.0466 0.2398 0.7136 16 F 0.2016 0.0768 0.7216 17 L 0.3967 0.0349 0.5684 18 V 0.5291 0.0989 0.3719 19 D 0.5235 0.1326 0.3439 20 E 0.6412 0.1315 0.2273 21 L 0.7734 0.0662 0.1604 22 V 0.8288 0.0393 0.1320 23 C 0.7370 0.0388 0.2242 24 G 0.4345 0.0280 0.5375 25 T 0.3178 0.0296 0.6527 26 T 0.3583 0.0419 0.5998 27 H 0.5309 0.0385 0.4305 28 S 0.7601 0.0252 0.2147 29 V 0.8652 0.0185 0.1163 30 I 0.8722 0.0149 0.1129 31 R 0.7509 0.0314 0.2177 32 S 0.4086 0.0373 0.5541 33 G 0.0774 0.0439 0.8786 34 N 0.1232 0.0538 0.8230 35 G 0.5574 0.0336 0.4089 36 V 0.7664 0.0288 0.2048 37 G 0.8159 0.0192 0.1649 38 L 0.8223 0.0187 0.1590 39 G 0.6458 0.0144 0.3398 40 P 0.4382 0.0226 0.5392 41 N 0.2205 0.0252 0.7543 42 R 0.1133 0.0377 0.8490 43 P 0.0876 0.0958 0.8166 44 F 0.0855 0.1703 0.7442 45 E 0.0683 0.2191 0.7126 46 T 0.0954 0.1837 0.7209 47 R 0.1496 0.1551 0.6953 48 M 0.1423 0.1073 0.7504 49 P 0.1401 0.1651 0.6948 50 M 0.1092 0.2644 0.6264 51 L 0.1128 0.2932 0.5940 52 T 0.0629 0.4488 0.4883 53 Q 0.0471 0.5022 0.4507 54 N 0.0637 0.5044 0.4319 55 L 0.0945 0.4370 0.4685 56 L 0.0490 0.2205 0.7305 57 G 0.0375 0.0758 0.8868 58 L 0.1332 0.0282 0.8387 59 P 0.1685 0.0335 0.7980 60 L 0.0069 0.9315 0.0616 61 R 0.0081 0.9468 0.0450 62 V 0.0085 0.9442 0.0473 63 A 0.0151 0.9275 0.0575 64 A 0.0131 0.8937 0.0932 65 G 0.0168 0.7434 0.2398 66 C 0.0208 0.6899 0.2893 67 V 0.0387 0.6580 0.3033 68 K 0.0346 0.5264 0.4391 69 S 0.0498 0.3669 0.5834 70 W 0.0255 0.4256 0.5489 71 N 0.0441 0.4237 0.5322 72 Y 0.0064 0.9191 0.0746 73 V 0.0048 0.9542 0.0411 74 E 0.0048 0.9573 0.0379 75 A 0.0048 0.9572 0.0380 76 S 0.0047 0.9589 0.0363 77 I 0.0047 0.9593 0.0360 78 G 0.0047 0.9600 0.0353 79 L 0.0047 0.9600 0.0353 80 A 0.0047 0.9604 0.0350 81 A 0.0047 0.9590 0.0364 82 I 0.0048 0.9557 0.0396 83 N 0.0052 0.9450 0.0498 84 A 0.0059 0.9120 0.0821 85 Y 0.0096 0.8389 0.1515 86 Y 0.0292 0.6186 0.3522 87 N 0.0369 0.3544 0.6087 88 N 0.0767 0.0868 0.8365 89 P 0.0212 0.5436 0.4351 90 Q 0.0370 0.5942 0.3688 91 V 0.0918 0.6529 0.2553 92 A 0.1553 0.5649 0.2798 93 R 0.1088 0.4754 0.4159 94 E 0.0869 0.3307 0.5824 95 H 0.1404 0.1950 0.6646 96 G 0.2654 0.0776 0.6570 97 V 0.4837 0.0579 0.4584 98 I 0.5050 0.0543 0.4407 99 F 0.2696 0.0952 0.6351 100 S 0.1098 0.1546 0.7356 101 D 0.0548 0.2424 0.7028 102 A 0.0650 0.3954 0.5397 103 K 0.0740 0.4215 0.5045 104 R 0.0958 0.4633 0.4409 105 V 0.0928 0.5298 0.3773 106 E 0.0608 0.6229 0.3162 107 D 0.0470 0.6216 0.3314 108 R 0.0441 0.5237 0.4323 109 M 0.0730 0.3413 0.5857 110 N 0.0498 0.2261 0.7240 111 D 0.1017 0.0901 0.8082 112 P 0.0264 0.7113 0.2623 113 F 0.0477 0.7577 0.1945 114 I 0.1104 0.7084 0.1811 115 M 0.1933 0.5828 0.2239 116 S 0.2623 0.4268 0.3109 117 Q 0.2278 0.3793 0.3929 118 N 0.2236 0.3501 0.4264 119 E 0.2001 0.3105 0.4894 120 V 0.1980 0.2268 0.5752 121 K 0.0644 0.1046 0.8310 122 G 0.0499 0.0437 0.9064 123 K 0.2559 0.0139 0.7302 124 K 0.8056 0.0046 0.1898 125 V 0.9174 0.0038 0.0788 126 G 0.9310 0.0034 0.0656 127 V 0.9302 0.0032 0.0666 128 V 0.8691 0.0195 0.1114 129 G 0.5694 0.0175 0.4131 130 H 0.1909 0.0388 0.7704 131 F 0.0957 0.1042 0.8001 132 P 0.0616 0.3009 0.6375 133 H 0.0791 0.5078 0.4131 134 L 0.0168 0.8461 0.1371 135 E 0.0106 0.8867 0.1027 136 S 0.0142 0.8458 0.1400 137 L 0.0243 0.7758 0.1999 138 L 0.0653 0.5944 0.3403 139 E 0.0657 0.4524 0.4819 140 P 0.0603 0.3490 0.5907 141 I 0.1344 0.1894 0.6762 142 C 0.2326 0.0435 0.7240 143 D 0.5061 0.0232 0.4706 144 L 0.8023 0.0052 0.1925 145 S 0.8972 0.0053 0.0975 146 I 0.9164 0.0039 0.0797 147 L 0.8956 0.0062 0.0982 148 E 0.8261 0.0063 0.1675 149 W 0.4809 0.0201 0.4990 150 S 0.1749 0.0106 0.8145 151 P 0.0501 0.0871 0.8628 152 E 0.0563 0.0836 0.8601 153 E 0.0622 0.1768 0.7610 154 G 0.0917 0.0888 0.8195 155 D 0.1829 0.0669 0.7502 156 Y 0.1439 0.0370 0.8191 157 P 0.0935 0.0477 0.8588 158 L 0.0512 0.2524 0.6964 159 P 0.0249 0.4792 0.4959 160 A 0.0153 0.6801 0.3046 161 S 0.0320 0.6445 0.3235 162 E 0.0222 0.6523 0.3254 163 F 0.0338 0.5489 0.4173 164 I 0.0716 0.4603 0.4681 165 L 0.0595 0.3386 0.6019 166 P 0.0146 0.5327 0.4528 167 E 0.0245 0.4675 0.5080 168 C 0.1800 0.1371 0.6829 169 D 0.0862 0.1312 0.7826 170 Y 0.7783 0.0955 0.1262 171 V 0.8210 0.1004 0.0786 172 Y 0.8045 0.1205 0.0750 173 I 0.6927 0.1672 0.1401 174 T 0.3112 0.2399 0.4489 175 C 0.0946 0.5284 0.3770 176 A 0.0657 0.7158 0.2185 177 S 0.0629 0.8180 0.1191 178 V 0.0469 0.8252 0.1280 179 V 0.0365 0.7325 0.2310 180 D 0.0400 0.5047 0.4553 181 K 0.0144 0.3846 0.6010 182 T 0.0312 0.5100 0.4588 183 L 0.0056 0.8997 0.0946 184 P 0.0048 0.9491 0.0461 185 R 0.0048 0.9519 0.0433 186 L 0.0049 0.9488 0.0464 187 L 0.0049 0.9296 0.0655 188 E 0.0054 0.8129 0.1818 189 L 0.0088 0.6982 0.2929 190 S 0.0368 0.4025 0.5607 191 R 0.0178 0.3790 0.6033 192 N 0.0271 0.2346 0.7383 193 A 0.0810 0.1192 0.7997 194 R 0.1867 0.0252 0.7881 195 R 0.6901 0.0081 0.3019 196 I 0.9142 0.0039 0.0819 197 T 0.9305 0.0035 0.0660 198 L 0.9273 0.0038 0.0689 199 V 0.8408 0.0196 0.1396 200 G 0.4470 0.0145 0.5385 201 P 0.1274 0.0526 0.8200 202 G 0.0782 0.0994 0.8224 203 T 0.0554 0.2296 0.7150 204 P 0.0451 0.3869 0.5680 205 L 0.0499 0.5338 0.4163 206 A 0.0375 0.6320 0.3305 207 P 0.0169 0.8146 0.1685 208 V 0.0252 0.8305 0.1442 209 L 0.0233 0.8525 0.1242 210 F 0.0188 0.7982 0.1830 211 E 0.0122 0.7248 0.2631 212 H 0.0443 0.5233 0.4324 213 G 0.0585 0.1537 0.7878 214 L 0.1867 0.1824 0.6310 215 Q 0.3588 0.2006 0.4406 216 E 0.7322 0.1425 0.1253 217 L 0.6852 0.1383 0.1765 218 S 0.5992 0.0901 0.3107 219 G 0.5521 0.0544 0.3935 220 F 0.6473 0.0267 0.3260 221 M 0.7640 0.0272 0.2088 222 V 0.6894 0.0245 0.2861 223 K 0.4733 0.0407 0.4860 224 D 0.2196 0.0418 0.7386 225 N 0.0078 0.8535 0.1387 226 A 0.0071 0.9140 0.0789 227 R 0.0072 0.9315 0.0613 228 A 0.0082 0.9420 0.0498 229 F 0.0109 0.9424 0.0468 230 R 0.0127 0.9439 0.0434 231 I 0.0170 0.9408 0.0422 232 V 0.0167 0.9294 0.0539 233 A 0.0246 0.8458 0.1297 234 G 0.0391 0.5937 0.3672 235 A 0.0672 0.2580 0.6748 236 E 0.0699 0.1933 0.7368 237 K 0.1970 0.1938 0.6092 238 V 0.4695 0.1293 0.4012 239 K 0.6411 0.1053 0.2535 240 I 0.6675 0.1081 0.2244 241 Y 0.5343 0.1117 0.3540 242 S 0.3674 0.1069 0.5257 243 A 0.2496 0.1105 0.6399 244 G 0.3929 0.0463 0.5608 245 Q 0.7094 0.0226 0.2680 246 K 0.8697 0.0111 0.1192 247 V 0.8854 0.0091 0.1056 248 T 0.8990 0.0089 0.0921 249 I 0.8425 0.0111 0.1463 250 K 0.5244 0.0196 0.4560 251 K 0.1309 0.0194 0.8497