# This file is the result of combining several RDB files, specifically # T0223.t04.dssp-ebghstl.rdb (weight 1.53986) # T0223.t04.stride-ebghtl.rdb (weight 1.24869) # T0223.t04.str2.rdb (weight 1.54758) # T0223.t04.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 T0223.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0223 # 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 T0223.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 97.3627 # # ============================================ # Comments from T0223.t04.stride-ebghtl.rdb # ============================================ # TARGET T0223 # 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 T0223.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 97.3627 # # ============================================ # Comments from T0223.t04.str2.rdb # ============================================ # TARGET T0223 # 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 T0223.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 97.3627 # # ============================================ # Comments from T0223.t04.alpha.rdb # ============================================ # TARGET T0223 # 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 T0223.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 97.3627 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0758 0.0676 0.8566 2 N 0.0938 0.2750 0.6312 3 I 0.0085 0.9299 0.0616 4 F 0.0051 0.9541 0.0409 5 E 0.0049 0.9595 0.0356 6 A 0.0050 0.9581 0.0369 7 I 0.0058 0.9510 0.0432 8 E 0.0063 0.9288 0.0649 9 N 0.0114 0.7568 0.2318 10 R 0.0529 0.5564 0.3907 11 H 0.0543 0.3069 0.6388 12 S 0.1140 0.2241 0.6619 13 V 0.0549 0.7594 0.1857 14 R 0.0518 0.8150 0.1332 15 D 0.0594 0.7897 0.1509 16 F 0.0638 0.7434 0.1927 17 L 0.0757 0.6004 0.3239 18 E 0.0736 0.3578 0.5685 19 R 0.1011 0.1557 0.7433 20 K 0.1004 0.0683 0.8313 21 M 0.0589 0.0156 0.9255 22 P 0.0525 0.0681 0.8794 23 E 0.0059 0.8757 0.1184 24 R 0.0064 0.8915 0.1021 25 V 0.0081 0.8866 0.1054 26 K 0.0111 0.8858 0.1031 27 D 0.0114 0.8023 0.1863 28 D 0.0123 0.7842 0.2035 29 I 0.0178 0.7113 0.2709 30 E 0.0108 0.6851 0.3041 31 N 0.0097 0.5317 0.4587 32 L 0.0281 0.6209 0.3510 33 L 0.0651 0.5677 0.3672 34 V 0.2354 0.6010 0.1637 35 K 0.3157 0.5936 0.0907 36 F 0.3371 0.5749 0.0880 37 I 0.2720 0.5779 0.1501 38 T 0.1308 0.6503 0.2189 39 K 0.0538 0.6594 0.2868 40 K 0.0349 0.6588 0.3063 41 L 0.0699 0.5073 0.4228 42 D 0.0728 0.4544 0.4728 43 W 0.0655 0.6159 0.3185 44 K 0.0864 0.5969 0.3167 45 I 0.1065 0.5934 0.3001 46 N 0.1106 0.5463 0.3431 47 L 0.0857 0.4952 0.4192 48 S 0.0464 0.3284 0.6252 49 S 0.0426 0.1466 0.8108 50 F 0.0923 0.0240 0.8836 51 P 0.1183 0.0358 0.8460 52 S 0.7108 0.0309 0.2582 53 Y 0.8934 0.0128 0.0938 54 I 0.9199 0.0123 0.0679 55 Y 0.9051 0.0175 0.0774 56 A 0.8421 0.0273 0.1306 57 K 0.5755 0.0387 0.3858 58 A 0.1794 0.0700 0.7506 59 E 0.0716 0.2236 0.7048 60 K 0.0404 0.3412 0.6184 61 H 0.0563 0.3605 0.5832 62 F 0.0476 0.6266 0.3258 63 D 0.0196 0.8106 0.1698 64 E 0.0246 0.8572 0.1181 65 L 0.0242 0.8934 0.0824 66 V 0.0220 0.9165 0.0615 67 E 0.0142 0.9352 0.0506 68 Y 0.0109 0.9474 0.0416 69 G 0.0069 0.9561 0.0370 70 F 0.0054 0.9590 0.0356 71 Q 0.0047 0.9608 0.0346 72 G 0.0047 0.9605 0.0348 73 E 0.0047 0.9609 0.0344 74 Q 0.0046 0.9611 0.0342 75 I 0.0047 0.9605 0.0348 76 V 0.0047 0.9610 0.0344 77 L 0.0047 0.9612 0.0342 78 F 0.0047 0.9603 0.0350 79 L 0.0048 0.9570 0.0383 80 T 0.0051 0.9432 0.0516 81 A 0.0068 0.9036 0.0896 82 Q 0.0439 0.4613 0.4949 83 G 0.0389 0.0645 0.8966 84 F 0.0696 0.0453 0.8850 85 G 0.2109 0.0598 0.7292 86 T 0.7093 0.0531 0.2377 87 C 0.8495 0.0355 0.1150 88 W 0.8375 0.0388 0.1237 89 M 0.7574 0.0538 0.1888 90 A 0.5265 0.0494 0.4240 91 R 0.3156 0.0449 0.6395 92 S 0.1787 0.0254 0.7959 93 P 0.1123 0.0590 0.8287 94 H 0.0739 0.0435 0.8827 95 P 0.0487 0.0902 0.8612 96 D 0.0678 0.0546 0.8776 97 V 0.1277 0.0138 0.8586 98 P 0.3508 0.0077 0.6415 99 Y 0.8896 0.0041 0.1063 100 I 0.9239 0.0033 0.0728 101 I 0.9211 0.0032 0.0756 102 V 0.8850 0.0045 0.1106 103 F 0.6766 0.0187 0.3047 104 G 0.3385 0.0217 0.6398 105 Y 0.2493 0.0245 0.7262 106 P 0.2052 0.0948 0.7000 107 R 0.1093 0.1531 0.7376 108 T 0.0923 0.1685 0.7392 109 R 0.0786 0.1540 0.7674 110 N 0.0579 0.1396 0.8025 111 F 0.0712 0.1296 0.7992 112 T 0.1063 0.0896 0.8040 113 R 0.0966 0.0577 0.8457 114 K 0.1123 0.0587 0.8290 115 R 0.1515 0.0488 0.7997 116 R 0.1349 0.0149 0.8502 117 P 0.1265 0.0268 0.8467 118 I 0.1146 0.3767 0.5087 119 T 0.1296 0.4915 0.3789 120 S 0.2798 0.4672 0.2530 121 F 0.5054 0.2984 0.1962 122 L 0.5690 0.2250 0.2061 123 E 0.4641 0.2358 0.3001 124 N 0.1993 0.2392 0.5615 125 D 0.1346 0.2231 0.6423 126 L 0.1273 0.3710 0.5017 127 E 0.1301 0.3076 0.5623 128 E 0.0856 0.2293 0.6851 129 L 0.0809 0.0425 0.8766 130 P 0.0556 0.0201 0.9243 131 P 0.0090 0.8038 0.1873 132 E 0.0090 0.8674 0.1236 133 I 0.0082 0.9138 0.0780 134 V 0.0094 0.9248 0.0659 135 K 0.0168 0.9106 0.0726 136 I 0.0084 0.9375 0.0541 137 V 0.0057 0.9511 0.0431 138 E 0.0055 0.9539 0.0406 139 M 0.0072 0.9446 0.0483 140 T 0.0088 0.9291 0.0622 141 I 0.0171 0.8449 0.1381 142 L 0.0231 0.6250 0.3519 143 A 0.0839 0.0946 0.8215 144 P 0.0232 0.3413 0.6355 145 S 0.0409 0.4128 0.5463 146 A 0.0312 0.5789 0.3899 147 L 0.0402 0.4522 0.5076 148 N 0.0735 0.1993 0.7272 149 R 0.0936 0.0681 0.8383 150 Q 0.1853 0.0157 0.7990 151 P 0.2805 0.0165 0.7030 152 W 0.6738 0.0154 0.3108 153 K 0.8754 0.0062 0.1184 154 I 0.9163 0.0049 0.0788 155 K 0.9030 0.0059 0.0910 156 Y 0.8313 0.0079 0.1608 157 T 0.4979 0.0230 0.4791 158 G 0.0923 0.0243 0.8833 159 G 0.1993 0.0421 0.7586 160 E 0.6315 0.0276 0.3409 161 L 0.7208 0.0155 0.2637 162 C 0.6145 0.0169 0.3686 163 I 0.4121 0.0578 0.5301 164 S 0.1807 0.0945 0.7248 165 S 0.0953 0.1054 0.7993 166 E 0.0974 0.0998 0.8029 167 R 0.1024 0.0792 0.8184 168 P 0.1091 0.2463 0.6445 169 V 0.1625 0.4520 0.3855 170 D 0.1192 0.6665 0.2144 171 L 0.0624 0.8609 0.0768 172 G 0.0492 0.8866 0.0642 173 I 0.0249 0.9202 0.0549 174 A 0.0239 0.9211 0.0551 175 L 0.0163 0.9232 0.0605 176 S 0.0189 0.9017 0.0794 177 H 0.0214 0.8936 0.0850 178 A 0.0413 0.8400 0.1187 179 Y 0.0736 0.7767 0.1497 180 L 0.1482 0.6349 0.2169 181 T 0.1191 0.4545 0.4264 182 A 0.0752 0.5449 0.3799 183 R 0.0678 0.5532 0.3790 184 E 0.0872 0.5507 0.3620 185 I 0.1326 0.4681 0.3993 186 F 0.2303 0.2921 0.4777 187 K 0.2705 0.1698 0.5597 188 R 0.2279 0.1362 0.6359 189 E 0.1368 0.1396 0.7236 190 P 0.1571 0.2453 0.5977 191 V 0.2193 0.3022 0.4785 192 I 0.3738 0.1880 0.4381 193 Q 0.4325 0.1414 0.4261 194 K 0.4588 0.0896 0.4516 195 R 0.2844 0.0901 0.6255 196 G 0.2007 0.0646 0.7347 197 E 0.2258 0.0742 0.7000 198 D 0.3965 0.0477 0.5559 199 T 0.7810 0.0098 0.2093 200 Y 0.9022 0.0046 0.0932 201 C 0.9256 0.0036 0.0708 202 L 0.9225 0.0037 0.0738 203 I 0.9025 0.0041 0.0934 204 L 0.7256 0.0191 0.2553 205 N 0.2961 0.0108 0.6932 206 P 0.0732 0.0813 0.8455