# This file is the result of combining several RDB files, specifically # T0441.t06.str2.rdb (weight 1.54425) # T0441.t06.str4.rdb (weight 0.924988) # T0441.t06.pb.rdb (weight 0.789901) # T0441.t06.bys.rdb (weight 0.748322) # T0441.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 T0441.t06.str2.rdb # ============================================ # TARGET T0441 # 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 T0441.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 5061 # # ============================================ # Comments from T0441.t06.str4.rdb # ============================================ # TARGET T0441 # 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 T0441.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 5061 # # ============================================ # Comments from T0441.t06.pb.rdb # ============================================ # TARGET T0441 # 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 T0441.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 5061 # # ============================================ # Comments from T0441.t06.bys.rdb # ============================================ # TARGET T0441 # 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 T0441.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 5061 # # ============================================ # Comments from T0441.t06.alpha.rdb # ============================================ # TARGET T0441 # 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 T0441.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 5061 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2823 0.0974 0.6203 2 S 0.2306 0.0887 0.6807 3 E 0.2219 0.1207 0.6574 4 P 0.1394 0.2966 0.5640 5 R 0.1687 0.3275 0.5038 6 K 0.2224 0.2644 0.5133 7 R 0.2008 0.2292 0.5700 8 R 0.1582 0.2543 0.5874 9 S 0.1064 0.2512 0.6423 10 T 0.1096 0.1802 0.7102 11 G 0.1086 0.1239 0.7675 12 N 0.2054 0.0807 0.7139 13 V 0.2843 0.0437 0.6721 14 T 0.2007 0.0333 0.7660 15 L 0.0269 0.6880 0.2851 16 A 0.0103 0.8625 0.1272 17 D 0.0091 0.9177 0.0732 18 V 0.0099 0.9125 0.0776 19 A 0.0084 0.9131 0.0785 20 K 0.0085 0.9126 0.0789 21 Q 0.0130 0.8227 0.1643 22 A 0.0611 0.3623 0.5765 23 G 0.0481 0.0940 0.8580 24 V 0.2139 0.0453 0.7407 25 G 0.2144 0.1056 0.6800 26 T 0.1507 0.3610 0.4883 27 M 0.2033 0.4235 0.3732 28 T 0.1808 0.5331 0.2861 29 V 0.1226 0.6853 0.1921 30 S 0.0768 0.7643 0.1589 31 R 0.0625 0.7814 0.1561 32 A 0.0873 0.7128 0.1999 33 L 0.1249 0.5201 0.3550 34 R 0.1296 0.2911 0.5793 35 T 0.1719 0.0856 0.7424 36 P 0.0701 0.3291 0.6008 37 E 0.0380 0.4721 0.4899 38 L 0.0705 0.4060 0.5235 39 V 0.1805 0.2524 0.5671 40 S 0.1671 0.1527 0.6802 41 D 0.0128 0.7292 0.2580 42 K 0.0096 0.8577 0.1328 43 L 0.0108 0.9106 0.0786 44 R 0.0083 0.9218 0.0699 45 E 0.0083 0.9234 0.0684 46 K 0.0083 0.9247 0.0671 47 I 0.0083 0.9224 0.0693 48 Q 0.0083 0.9213 0.0704 49 Q 0.0083 0.9238 0.0679 50 V 0.0083 0.9228 0.0689 51 V 0.0084 0.9150 0.0766 52 D 0.0087 0.9058 0.0855 53 E 0.0112 0.8174 0.1714 54 L 0.0609 0.3126 0.6265 55 G 0.0420 0.0849 0.8731 56 Y 0.1871 0.0557 0.7572 57 I 0.2684 0.0472 0.6844 58 P 0.1790 0.1456 0.6754 59 N 0.1427 0.2565 0.6008 60 K 0.0365 0.7015 0.2620 61 A 0.0302 0.7712 0.1986 62 A 0.0273 0.8353 0.1374 63 G 0.0215 0.8367 0.1418 64 A 0.0274 0.8092 0.1634 65 L 0.0483 0.7269 0.2248 66 A 0.0607 0.5954 0.3438 67 S 0.0930 0.3761 0.5309 68 A 0.0957 0.2588 0.6455 69 E 0.1455 0.1804 0.6741 70 S 0.2587 0.0931 0.6482 71 Y 0.4002 0.0433 0.5565 72 S 0.7301 0.0120 0.2579 73 I 0.7842 0.0074 0.2084 74 A 0.8126 0.0058 0.1816 75 L 0.8115 0.0054 0.1831 76 I 0.7718 0.0085 0.2197 77 I 0.5826 0.0102 0.4072 78 P 0.2772 0.0738 0.6489 79 S 0.1801 0.1629 0.6571 80 L 0.0976 0.2962 0.6063 81 F 0.1028 0.2770 0.6202 82 E 0.1158 0.3581 0.5261 83 K 0.0265 0.7096 0.2639 84 A 0.0281 0.7779 0.1941 85 C 0.0229 0.8467 0.1305 86 A 0.0129 0.8731 0.1140 87 H 0.0156 0.8526 0.1318 88 F 0.0241 0.7968 0.1790 89 L 0.0206 0.8351 0.1444 90 P 0.0093 0.8801 0.1106 91 S 0.0085 0.9117 0.0798 92 F 0.0086 0.9057 0.0856 93 Q 0.0084 0.9189 0.0727 94 Q 0.0083 0.9236 0.0681 95 A 0.0083 0.9235 0.0683 96 L 0.0084 0.9188 0.0728 97 N 0.0087 0.9047 0.0865 98 K 0.0128 0.7956 0.1916 99 A 0.0574 0.2296 0.7131 100 G 0.0526 0.0670 0.8805 101 Y 0.2578 0.0170 0.7253 102 Q 0.6140 0.0169 0.3691 103 L 0.7934 0.0061 0.2005 104 L 0.7958 0.0079 0.1963 105 L 0.7803 0.0092 0.2105 106 G 0.6814 0.0233 0.2952 107 Y 0.3970 0.0415 0.5614 108 S 0.2054 0.1130 0.6816 109 D 0.1202 0.1903 0.6896 110 Y 0.1287 0.1813 0.6900 111 S 0.1474 0.1473 0.7054 112 I 0.0165 0.7440 0.2396 113 E 0.0103 0.8558 0.1339 114 Q 0.0092 0.9127 0.0781 115 E 0.0088 0.9158 0.0754 116 E 0.0084 0.9197 0.0720 117 K 0.0083 0.9222 0.0695 118 L 0.0084 0.9205 0.0711 119 L 0.0084 0.9190 0.0726 120 S 0.0084 0.9173 0.0743 121 T 0.0085 0.9129 0.0786 122 F 0.0096 0.8969 0.0936 123 L 0.0121 0.8429 0.1450 124 E 0.0217 0.6504 0.3278 125 S 0.0583 0.3113 0.6304 126 R 0.1607 0.0751 0.7642 127 P 0.2274 0.0693 0.7032 128 A 0.3389 0.0766 0.5845 129 G 0.7696 0.0149 0.2155 130 V 0.7742 0.0061 0.2197 131 V 0.8075 0.0053 0.1872 132 L 0.7739 0.0088 0.2173 133 F 0.6682 0.0180 0.3138 134 G 0.3567 0.0412 0.6021 135 S 0.1897 0.1371 0.6732 136 E 0.1304 0.2171 0.6525 137 H 0.1209 0.2375 0.6416 138 S 0.1035 0.2857 0.6108 139 Q 0.0370 0.6652 0.2978 140 R 0.0209 0.8159 0.1632 141 T 0.0159 0.8790 0.1051 142 H 0.0097 0.9043 0.0860 143 Q 0.0086 0.9180 0.0734 144 L 0.0085 0.9200 0.0715 145 L 0.0101 0.9122 0.0777 146 E 0.0099 0.8938 0.0963 147 A 0.0134 0.7762 0.2104 148 S 0.0605 0.3168 0.6226 149 N 0.0429 0.0803 0.8768 150 T 0.2247 0.0129 0.7624 151 P 0.3979 0.0226 0.5795 152 V 0.7506 0.0077 0.2417 153 L 0.7877 0.0083 0.2041 154 E 0.7748 0.0061 0.2191 155 I 0.7276 0.0156 0.2568 156 A 0.4777 0.0591 0.4632 157 E 0.2819 0.1238 0.5943 158 L 0.2056 0.1740 0.6205 159 S 0.1818 0.1846 0.6336 160 S 0.1194 0.2564 0.6242 161 K 0.1245 0.2556 0.6199 162 A 0.1644 0.2415 0.5942 163 S 0.2188 0.1695 0.6117 164 Y 0.3396 0.0934 0.5670 165 L 0.3699 0.0970 0.5331 166 N 0.5621 0.0589 0.3790 167 I 0.6376 0.0434 0.3190 168 G 0.5297 0.0589 0.4114 169 V 0.3791 0.1614 0.4594 170 D 0.2000 0.2022 0.5978 171 H 0.0621 0.5749 0.3630 172 F 0.0183 0.8110 0.1707 173 E 0.0104 0.8975 0.0921 174 V 0.0092 0.9137 0.0771 175 G 0.0084 0.9193 0.0724 176 K 0.0083 0.9236 0.0682 177 A 0.0083 0.9244 0.0674 178 C 0.0083 0.9243 0.0675 179 T 0.0083 0.9225 0.0692 180 R 0.0083 0.9241 0.0677 181 H 0.0083 0.9248 0.0670 182 L 0.0083 0.9235 0.0681 183 I 0.0085 0.9142 0.0773 184 E 0.0114 0.8175 0.1711 185 Q 0.0525 0.3762 0.5712 186 G 0.0467 0.0896 0.8637 187 F 0.1465 0.0966 0.7569 188 K 0.2485 0.0980 0.6534 189 N 0.5519 0.0440 0.4041 190 V 0.7576 0.0124 0.2300 191 G 0.7874 0.0122 0.2003 192 F 0.7991 0.0062 0.1947 193 I 0.7634 0.0125 0.2241 194 G 0.6142 0.0206 0.3652 195 A 0.3619 0.0453 0.5927 196 R 0.1977 0.0949 0.7074 197 G 0.1004 0.2005 0.6992 198 N 0.1029 0.2053 0.6918 199 H 0.1310 0.2808 0.5882 200 S 0.0715 0.5659 0.3625 201 T 0.0490 0.7402 0.2107 202 L 0.0198 0.8594 0.1208 203 Q 0.0119 0.8997 0.0884 204 R 0.0102 0.9099 0.0799 205 Q 0.0109 0.9058 0.0833 206 L 0.0104 0.8991 0.0906 207 H 0.0091 0.8970 0.0939 208 G 0.0089 0.9121 0.0790 209 W 0.0084 0.9163 0.0752 210 Q 0.0083 0.9210 0.0707 211 S 0.0083 0.9217 0.0700 212 A 0.0083 0.9212 0.0704 213 M 0.0084 0.9190 0.0726 214 I 0.0086 0.9103 0.0811 215 E 0.0124 0.8075 0.1801 216 N 0.0365 0.3263 0.6372 217 Y 0.0494 0.1144 0.8362 218 L 0.1531 0.0522 0.7947 219 T 0.1986 0.0315 0.7698 220 P 0.1563 0.2479 0.5958 221 D 0.2110 0.2417 0.5473 222 H 0.3772 0.2056 0.4172 223 F 0.5085 0.1098 0.3816 224 L 0.5679 0.0776 0.3544 225 T 0.5523 0.0580 0.3897 226 T 0.4627 0.0607 0.4767 227 H 0.2981 0.0980 0.6038 228 E 0.2131 0.1127 0.6743 229 A 0.2011 0.0627 0.7362 230 P 0.1082 0.2480 0.6438 231 S 0.1277 0.3008 0.5715 232 S 0.0326 0.6771 0.2902 233 Q 0.0185 0.8057 0.1758 234 L 0.0174 0.8622 0.1204 235 G 0.0136 0.8913 0.0951 236 A 0.0087 0.9056 0.0857 237 E 0.0084 0.9193 0.0723 238 G 0.0083 0.9224 0.0693 239 L 0.0083 0.9223 0.0694 240 A 0.0083 0.9205 0.0711 241 K 0.0083 0.9207 0.0710 242 L 0.0087 0.9070 0.0843 243 L 0.0104 0.8657 0.1239 244 L 0.0133 0.7244 0.2624 245 R 0.0348 0.4525 0.5127 246 D 0.1153 0.1772 0.7075 247 S 0.0762 0.2547 0.6692 248 S 0.1835 0.0946 0.7219 249 L 0.3345 0.0521 0.6134 250 N 0.4845 0.0550 0.4605 251 A 0.8050 0.0072 0.1878 252 L 0.7667 0.0075 0.2258 253 V 0.8032 0.0063 0.1905 254 C 0.7279 0.0132 0.2588 255 S 0.4233 0.0851 0.4916 256 H 0.1680 0.2276 0.6045 257 E 0.0440 0.6376 0.3184 258 E 0.0169 0.8190 0.1641 259 I 0.0124 0.8889 0.0987 260 A 0.0088 0.9125 0.0787 261 I 0.0085 0.9188 0.0727 262 G 0.0083 0.9239 0.0678 263 A 0.0083 0.9236 0.0681 264 L 0.0083 0.9228 0.0689 265 F 0.0083 0.9240 0.0677 266 E 0.0083 0.9231 0.0686 267 C 0.0084 0.9204 0.0712 268 H 0.0086 0.9105 0.0809 269 R 0.0115 0.8233 0.1652 270 R 0.0404 0.4083 0.5513 271 V 0.0432 0.1699 0.7870 272 L 0.1612 0.0765 0.7624 273 K 0.2346 0.0623 0.7031 274 V 0.2475 0.0231 0.7294 275 P 0.1888 0.1118 0.6993 276 T 0.1585 0.2792 0.5623 277 D 0.3447 0.1090 0.5463 278 I 0.6535 0.0163 0.3302 279 A 0.7576 0.0104 0.2321 280 I 0.7987 0.0060 0.1953 281 I 0.7933 0.0084 0.1983 282 C 0.7319 0.0130 0.2551 283 L 0.5782 0.0540 0.3679 284 E 0.3138 0.0761 0.6100 285 G 0.1407 0.0995 0.7598 286 S 0.1962 0.1282 0.6757 287 S 0.1276 0.3428 0.5297 288 M 0.1148 0.4671 0.4181 289 G 0.1287 0.5082 0.3631 290 E 0.1259 0.4999 0.3743 291 H 0.1778 0.3757 0.4465 292 A 0.2361 0.2193 0.5446 293 Y 0.2428 0.0649 0.6923 294 P 0.1739 0.1706 0.6556 295 S 0.1933 0.1675 0.6392 296 L 0.2933 0.1485 0.5582 297 T 0.4017 0.1089 0.4893 298 S 0.5186 0.1014 0.3799 299 A 0.4532 0.1516 0.3952 300 E 0.3965 0.1258 0.4777 301 F 0.3201 0.1003 0.5796 302 D 0.1843 0.0669 0.7488 303 Y 0.0135 0.7452 0.2413 304 E 0.0095 0.8610 0.1295 305 R 0.0088 0.9120 0.0792 306 M 0.0088 0.9163 0.0748 307 G 0.0084 0.9181 0.0735 308 T 0.0083 0.9228 0.0689 309 K 0.0083 0.9241 0.0676 310 A 0.0083 0.9249 0.0669 311 A 0.0083 0.9241 0.0676 312 E 0.0083 0.9247 0.0670 313 K 0.0083 0.9245 0.0672 314 L 0.0083 0.9237 0.0681 315 L 0.0085 0.9142 0.0774 316 H 0.0085 0.9121 0.0793 317 A 0.0095 0.8723 0.1182 318 I 0.0230 0.7439 0.2331 319 K 0.0459 0.3107 0.6433 320 G 0.0326 0.0929 0.8745 321 E 0.1642 0.0263 0.8095 322 P 0.1949 0.0591 0.7459 323 E 0.2407 0.0678 0.6916 324 E 0.2425 0.0668 0.6906 325 R 0.3673 0.0357 0.5971 326 P 0.4406 0.0391 0.5203 327 T 0.6555 0.0326 0.3119 328 S 0.6657 0.0227 0.3116 329 M 0.6008 0.0299 0.3693 330 G 0.5044 0.0357 0.4598 331 F 0.5236 0.0316 0.4448 332 K 0.6842 0.0249 0.2909 333 L 0.7231 0.0167 0.2602 334 K 0.7159 0.0252 0.2589 335 R 0.6440 0.0300 0.3259 336 R 0.4641 0.0756 0.4603 337 A 0.3132 0.1400 0.5468 338 S 0.2767 0.1200 0.6033 339 T 0.2933 0.0939 0.6128 340 A 0.2605 0.1022 0.6373 341 I 0.2356 0.1280 0.6365 342 N 0.1943 0.1217 0.6840