# This file is the result of combining several RDB files, specifically # T0393.t06.str2.rdb (weight 1.54425) # T0393.t06.str4.rdb (weight 0.924988) # T0393.t06.pb.rdb (weight 0.789901) # T0393.t06.bys.rdb (weight 0.748322) # T0393.t06.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 T0393.t06.str2.rdb # ============================================ # TARGET T0393 # 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 T0393.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 3171 # # ============================================ # Comments from T0393.t06.str4.rdb # ============================================ # TARGET T0393 # 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 T0393.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 3171 # # ============================================ # Comments from T0393.t06.pb.rdb # ============================================ # TARGET T0393 # 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 T0393.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 3171 # # ============================================ # Comments from T0393.t06.bys.rdb # ============================================ # TARGET T0393 # 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 T0393.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 3171 # # ============================================ # Comments from T0393.t06.alpha.rdb # ============================================ # TARGET T0393 # 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 T0393.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 3171 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2794 0.0998 0.6208 2 K 0.2752 0.0921 0.6328 3 R 0.2838 0.1076 0.6086 4 S 0.2190 0.0942 0.6868 5 I 0.1035 0.3678 0.5287 6 E 0.1028 0.2985 0.5987 7 D 0.1469 0.1391 0.7140 8 T 0.2821 0.0313 0.6867 9 P 0.4122 0.0361 0.5516 10 I 0.7747 0.0141 0.2112 11 V 0.8013 0.0097 0.1890 12 L 0.7845 0.0082 0.2074 13 I 0.7236 0.0202 0.2562 14 G 0.5218 0.0540 0.4242 15 A 0.2355 0.2036 0.5609 16 G 0.1294 0.3309 0.5397 17 N 0.0472 0.6271 0.3257 18 L 0.0231 0.7994 0.1775 19 A 0.0111 0.8859 0.1030 20 T 0.0084 0.9153 0.0763 21 N 0.0083 0.9224 0.0693 22 L 0.0083 0.9237 0.0680 23 A 0.0083 0.9233 0.0684 24 K 0.0083 0.9235 0.0682 25 A 0.0083 0.9232 0.0685 26 L 0.0084 0.9206 0.0710 27 Y 0.0087 0.9087 0.0825 28 R 0.0129 0.8057 0.1814 29 K 0.0532 0.2891 0.6578 30 G 0.0530 0.0762 0.8708 31 F 0.2097 0.0300 0.7603 32 R 0.4875 0.0307 0.4818 33 I 0.7039 0.0252 0.2710 34 V 0.6796 0.0512 0.2693 35 Q 0.7352 0.0233 0.2414 36 V 0.7062 0.0325 0.2613 37 Y 0.6226 0.0495 0.3279 38 S 0.3429 0.0573 0.5998 39 R 0.1538 0.1606 0.6856 40 T 0.1790 0.0465 0.7745 41 E 0.0137 0.7264 0.2599 42 E 0.0099 0.8428 0.1473 43 S 0.0117 0.8915 0.0967 44 A 0.0087 0.9084 0.0829 45 R 0.0084 0.9174 0.0742 46 E 0.0083 0.9198 0.0719 47 L 0.0087 0.9140 0.0773 48 A 0.0088 0.9021 0.0891 49 Q 0.0103 0.8675 0.1223 50 K 0.0211 0.7180 0.2610 51 V 0.0777 0.2962 0.6262 52 E 0.0846 0.1513 0.7641 53 A 0.3022 0.0516 0.6462 54 E 0.4168 0.0560 0.5272 55 Y 0.5640 0.0627 0.3733 56 T 0.4073 0.0865 0.5062 57 T 0.3299 0.0862 0.5839 58 D 0.2144 0.0316 0.7540 59 L 0.0213 0.6802 0.2985 60 A 0.0134 0.7692 0.2174 61 E 0.0166 0.7856 0.1978 62 V 0.0536 0.6410 0.3054 63 N 0.0896 0.4392 0.4712 64 P 0.0418 0.5120 0.4462 65 Y 0.0684 0.2689 0.6627 66 A 0.2265 0.1320 0.6415 67 K 0.4088 0.0459 0.5452 68 L 0.8060 0.0052 0.1888 69 Y 0.7772 0.0061 0.2167 70 I 0.8204 0.0043 0.1752 71 V 0.7975 0.0088 0.1937 72 S 0.7138 0.0145 0.2717 73 L 0.4857 0.0215 0.4928 74 K 0.2356 0.0245 0.7399 75 D 0.0917 0.2977 0.6105 76 S 0.0195 0.6607 0.3198 77 A 0.0211 0.7694 0.2094 78 F 0.0122 0.8810 0.1068 79 A 0.0085 0.9151 0.0764 80 E 0.0084 0.9190 0.0726 81 L 0.0086 0.9161 0.0753 82 L 0.0094 0.9047 0.0860 83 Q 0.0094 0.8692 0.1214 84 G 0.0132 0.8283 0.1585 85 I 0.0271 0.7692 0.2037 86 V 0.0372 0.6746 0.2882 87 E 0.0377 0.4975 0.4649 88 G 0.0552 0.3313 0.6135 89 K 0.1560 0.1560 0.6880 90 R 0.1684 0.0893 0.7423 91 E 0.0588 0.3508 0.5904 92 E 0.0845 0.1861 0.7294 93 A 0.4248 0.0394 0.5358 94 L 0.7359 0.0116 0.2525 95 M 0.7956 0.0069 0.1975 96 V 0.8088 0.0064 0.1849 97 H 0.7123 0.0170 0.2707 98 T 0.5300 0.0869 0.3831 99 A 0.2824 0.1308 0.5869 100 G 0.1900 0.1418 0.6682 101 S 0.2095 0.1208 0.6697 102 I 0.2571 0.0684 0.6745 103 P 0.1756 0.1845 0.6399 104 M 0.0687 0.5744 0.3569 105 N 0.0434 0.7444 0.2122 106 V 0.0472 0.7831 0.1697 107 W 0.0400 0.7888 0.1712 108 E 0.0284 0.7755 0.1961 109 G 0.0280 0.6840 0.2880 110 H 0.0630 0.5588 0.3782 111 V 0.1641 0.1940 0.6419 112 P 0.0859 0.3454 0.5686 113 H 0.0787 0.3045 0.6169 114 Y 0.1206 0.1772 0.7022 115 G 0.1911 0.0818 0.7271 116 V 0.5604 0.0262 0.4133 117 F 0.6906 0.0205 0.2889 118 Y 0.6940 0.0163 0.2896 119 P 0.5721 0.0520 0.3759 120 M 0.4349 0.0758 0.4893 121 Q 0.3462 0.0662 0.5876 122 T 0.2276 0.1650 0.6074 123 F 0.1945 0.1826 0.6229 124 S 0.1950 0.1189 0.6861 125 K 0.0983 0.3220 0.5797 126 Q 0.1397 0.3454 0.5149 127 R 0.2069 0.3639 0.4291 128 E 0.2102 0.4093 0.3806 129 V 0.2082 0.4079 0.3838 130 D 0.1672 0.3680 0.4649 131 F 0.1635 0.2909 0.5456 132 K 0.2427 0.1552 0.6021 133 E 0.2476 0.1025 0.6499 134 I 0.3441 0.0484 0.6075 135 P 0.4044 0.0806 0.5150 136 F 0.6770 0.0462 0.2768 137 F 0.7142 0.0318 0.2540 138 I 0.6345 0.0415 0.3239 139 E 0.4401 0.0750 0.4849 140 A 0.2365 0.0930 0.6705 141 S 0.1864 0.0860 0.7276 142 S 0.1731 0.0581 0.7687 143 T 0.0155 0.7188 0.2657 144 E 0.0107 0.8408 0.1485 145 D 0.0121 0.8826 0.1053 146 A 0.0087 0.9081 0.0832 147 A 0.0084 0.9158 0.0759 148 F 0.0083 0.9207 0.0709 149 L 0.0084 0.9200 0.0716 150 K 0.0084 0.9156 0.0760 151 A 0.0083 0.9160 0.0757 152 I 0.0088 0.9067 0.0845 153 A 0.0100 0.8850 0.1050 154 S 0.0128 0.8059 0.1813 155 T 0.0294 0.6285 0.3421 156 L 0.0791 0.3732 0.5477 157 S 0.1034 0.2376 0.6589 158 N 0.1754 0.1595 0.6651 159 R 0.3575 0.0864 0.5562 160 V 0.5426 0.0542 0.4031 161 Y 0.6027 0.0479 0.3494 162 D 0.5392 0.0447 0.4161 163 A 0.3394 0.1012 0.5594 164 D 0.2148 0.0680 0.7172 165 S 0.0412 0.5119 0.4468 166 E 0.0337 0.6083 0.3580 167 Q 0.0494 0.6041 0.3465 168 R 0.0531 0.6792 0.2677 169 K 0.0383 0.6996 0.2621 170 S 0.0719 0.6578 0.2703 171 L 0.1421 0.6118 0.2461 172 H 0.1618 0.6466 0.1916 173 L 0.2422 0.6070 0.1507 174 A 0.2156 0.6314 0.1531 175 A 0.1348 0.6963 0.1689 176 V 0.0890 0.7033 0.2077 177 F 0.0553 0.7405 0.2042 178 T 0.0249 0.8365 0.1386 179 C 0.0104 0.8906 0.0990 180 N 0.0091 0.9078 0.0831 181 F 0.0084 0.9199 0.0717 182 T 0.0083 0.9214 0.0703 183 N 0.0083 0.9231 0.0686 184 H 0.0083 0.9239 0.0679 185 M 0.0083 0.9243 0.0674 186 Y 0.0083 0.9240 0.0677 187 A 0.0083 0.9247 0.0670 188 L 0.0083 0.9240 0.0677 189 A 0.0083 0.9234 0.0683 190 A 0.0083 0.9200 0.0717 191 E 0.0083 0.9247 0.0670 192 L 0.0083 0.9243 0.0674 193 L 0.0084 0.9214 0.0703 194 K 0.0085 0.9114 0.0801 195 K 0.0120 0.8181 0.1699 196 Y 0.0576 0.3129 0.6295 197 N 0.0374 0.0878 0.8748 198 L 0.1609 0.0169 0.8221 199 P 0.1562 0.0228 0.8210 200 F 0.0172 0.7024 0.2804 201 D 0.0116 0.8123 0.1761 202 V 0.0143 0.8721 0.1136 203 M 0.0172 0.8806 0.1022 204 L 0.0108 0.8950 0.0942 205 P 0.0096 0.8968 0.0937 206 L 0.0114 0.8849 0.1037 207 I 0.0168 0.8649 0.1183 208 D 0.0142 0.8510 0.1348 209 E 0.0135 0.8083 0.1781 210 T 0.0201 0.7955 0.1844 211 A 0.0183 0.8138 0.1680 212 R 0.0178 0.7882 0.1939 213 K 0.0267 0.6924 0.2809 214 V 0.0623 0.6607 0.2771 215 H 0.0672 0.6540 0.2788 216 E 0.0985 0.5183 0.3833 217 L 0.1607 0.3483 0.4911 218 E 0.1887 0.2167 0.5946 219 P 0.1170 0.3658 0.5172 220 K 0.1019 0.3464 0.5518 221 T 0.1308 0.2662 0.6030 222 A 0.0999 0.3120 0.5881 223 Q 0.1410 0.2365 0.6224 224 T 0.1528 0.1308 0.7164 225 G 0.1402 0.2704 0.5894 226 P 0.0951 0.5151 0.3898 227 A 0.1350 0.5202 0.3447 228 I 0.2004 0.4492 0.3505 229 R 0.1783 0.4093 0.4123 230 Y 0.1554 0.4224 0.4222 231 D 0.1547 0.3116 0.5337 232 E 0.0321 0.6141 0.3538 233 N 0.0307 0.6792 0.2901 234 V 0.0347 0.8023 0.1630 235 I 0.0156 0.8843 0.1001 236 G 0.0093 0.9089 0.0818 237 N 0.0087 0.9151 0.0762 238 H 0.0087 0.9170 0.0744 239 L 0.0088 0.9144 0.0768 240 R 0.0087 0.9090 0.0822 241 M 0.0110 0.8584 0.1306 242 L 0.0302 0.7284 0.2414 243 A 0.0298 0.5815 0.3887 244 D 0.0564 0.4337 0.5099 245 D 0.1306 0.2965 0.5729 246 P 0.0183 0.6905 0.2911 247 A 0.0152 0.7844 0.2004 248 M 0.0127 0.8749 0.1124 249 Q 0.0087 0.9104 0.0809 250 R 0.0084 0.9201 0.0715 251 L 0.0083 0.9218 0.0699 252 Y 0.0083 0.9220 0.0697 253 E 0.0083 0.9240 0.0678 254 L 0.0083 0.9238 0.0680 255 L 0.0083 0.9222 0.0695 256 S 0.0084 0.9175 0.0741 257 R 0.0084 0.9179 0.0737 258 S 0.0089 0.9046 0.0865 259 I 0.0107 0.8810 0.1083 260 H 0.0142 0.7975 0.1884 261 E 0.0333 0.5882 0.3785 262 R 0.0942 0.3076 0.5982 263 Q 0.1230 0.1893 0.6878