# This file is the result of combining several RDB files, specifically # T0398.t06.str2.rdb (weight 1.54425) # T0398.t06.str4.rdb (weight 0.924988) # T0398.t06.pb.rdb (weight 0.789901) # T0398.t06.bys.rdb (weight 0.748322) # T0398.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 T0398.t06.str2.rdb # ============================================ # TARGET T0398 # 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 T0398.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 10322 # # ============================================ # Comments from T0398.t06.str4.rdb # ============================================ # TARGET T0398 # 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 T0398.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 10322 # # ============================================ # Comments from T0398.t06.pb.rdb # ============================================ # TARGET T0398 # 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 T0398.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 10322 # # ============================================ # Comments from T0398.t06.bys.rdb # ============================================ # TARGET T0398 # 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 T0398.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 10322 # # ============================================ # Comments from T0398.t06.alpha.rdb # ============================================ # TARGET T0398 # 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 T0398.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 10322 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3033 0.1025 0.5942 2 L 0.1912 0.1803 0.6285 3 T 0.1552 0.1420 0.7028 4 G 0.2162 0.1237 0.6600 5 K 0.4024 0.0726 0.5249 6 H 0.6445 0.0384 0.3171 7 V 0.7108 0.0336 0.2556 8 V 0.7195 0.0316 0.2489 9 I 0.6602 0.0371 0.3028 10 I 0.3670 0.0330 0.6000 11 G 0.1599 0.3034 0.5367 12 G 0.0571 0.5206 0.4224 13 D 0.0570 0.6474 0.2956 14 A 0.0291 0.8157 0.1551 15 R 0.0206 0.8457 0.1338 16 Q 0.0196 0.8927 0.0877 17 L 0.0171 0.8992 0.0837 18 E 0.0203 0.8958 0.0840 19 I 0.0282 0.8778 0.0940 20 I 0.0360 0.8403 0.1237 21 R 0.0560 0.6928 0.2511 22 K 0.0611 0.4067 0.5321 23 L 0.1004 0.1950 0.7046 24 S 0.2701 0.1009 0.6289 25 T 0.4437 0.0609 0.4954 26 F 0.5256 0.0830 0.3914 27 D 0.5800 0.0675 0.3525 28 A 0.6755 0.0699 0.2545 29 K 0.6947 0.0552 0.2501 30 I 0.7554 0.0327 0.2119 31 S 0.7135 0.0440 0.2425 32 L 0.6894 0.0502 0.2604 33 V 0.5383 0.0761 0.3855 34 G 0.3368 0.0977 0.5656 35 F 0.2337 0.1398 0.6265 36 D 0.1970 0.1230 0.6801 37 Q 0.1267 0.2411 0.6322 38 L 0.1362 0.2726 0.5912 39 D 0.1276 0.2826 0.5899 40 D 0.0798 0.4421 0.4780 41 G 0.1009 0.5329 0.3662 42 F 0.1893 0.5116 0.2992 43 I 0.2165 0.5206 0.2629 44 G 0.1502 0.6103 0.2395 45 V 0.1490 0.6167 0.2343 46 T 0.1216 0.6352 0.2431 47 K 0.0911 0.6832 0.2257 48 M 0.1403 0.6286 0.2311 49 R 0.1284 0.5818 0.2898 50 I 0.1506 0.5310 0.3185 51 D 0.1084 0.5200 0.3715 52 E 0.1202 0.4866 0.3932 53 V 0.1880 0.2909 0.5211 54 D 0.1700 0.2268 0.6031 55 W 0.1684 0.4335 0.3981 56 N 0.1672 0.4014 0.4314 57 T 0.2045 0.3551 0.4403 58 V 0.1781 0.3638 0.4581 59 D 0.2147 0.3133 0.4720 60 A 0.3132 0.2681 0.4188 61 I 0.4157 0.1777 0.4066 62 L 0.4486 0.1028 0.4486 63 L 0.3544 0.0673 0.5783 64 P 0.3080 0.1232 0.5687 65 I 0.2742 0.1593 0.5666 66 S 0.2157 0.1044 0.6799 67 G 0.1782 0.0765 0.7453 68 T 0.1411 0.2514 0.6074 69 N 0.1473 0.2751 0.5776 70 E 0.1036 0.5111 0.3853 71 A 0.0865 0.5548 0.3587 72 G 0.0939 0.5230 0.3831 73 K 0.1586 0.5005 0.3408 74 V 0.2040 0.4919 0.3041 75 D 0.2025 0.4585 0.3390 76 T 0.2464 0.4055 0.3480 77 I 0.2355 0.3446 0.4199 78 F 0.1890 0.3235 0.4875 79 S 0.1500 0.2513 0.5987 80 N 0.1751 0.2123 0.6126 81 E 0.2036 0.2340 0.5624 82 S 0.2587 0.2584 0.4829 83 I 0.3680 0.2058 0.4261 84 V 0.4184 0.1510 0.4307 85 L 0.3539 0.1471 0.4990 86 T 0.2783 0.2019 0.5199 87 E 0.2104 0.3332 0.4565 88 E 0.1676 0.4318 0.4006 89 M 0.1473 0.4419 0.4109 90 I 0.1747 0.3223 0.5030 91 E 0.1601 0.2316 0.6083 92 K 0.1532 0.1752 0.6716 93 T 0.2008 0.0602 0.7390 94 P 0.1365 0.2080 0.6555 95 N 0.1462 0.2658 0.5881 96 H 0.2808 0.2777 0.4414 97 C 0.4017 0.2606 0.3377 98 V 0.4173 0.2877 0.2949 99 V 0.3327 0.3423 0.3251 100 Y 0.2663 0.3329 0.4008 101 S 0.2105 0.2482 0.5413 102 G 0.1976 0.1718 0.6306 103 I 0.2755 0.1430 0.5814 104 S 0.2588 0.1847 0.5565 105 N 0.1821 0.3862 0.4317 106 T 0.1934 0.4555 0.3511 107 Y 0.2337 0.4694 0.2969 108 L 0.1514 0.5905 0.2581 109 N 0.1385 0.5888 0.2726 110 Q 0.1648 0.5345 0.3006 111 C 0.1559 0.4817 0.3625 112 M 0.1418 0.4414 0.4168 113 K 0.1320 0.4131 0.4549 114 K 0.1226 0.3105 0.5669 115 T 0.1990 0.2240 0.5769 116 N 0.1679 0.2069 0.6252 117 R 0.1558 0.3670 0.4772 118 T 0.1978 0.3930 0.4092 119 L 0.2142 0.3468 0.4390 120 V 0.1697 0.4972 0.3331 121 K 0.0956 0.6243 0.2801 122 L 0.1156 0.5753 0.3090 123 M 0.1697 0.3876 0.4427 124 E 0.1256 0.3137 0.5607 125 R 0.0982 0.2869 0.6149 126 D 0.1464 0.1998 0.6538 127 D 0.2203 0.1464 0.6333 128 I 0.4830 0.0710 0.4459 129 A 0.5924 0.0680 0.3396 130 I 0.6675 0.0506 0.2819 131 Y 0.5864 0.0687 0.3448 132 N 0.4345 0.0688 0.4967 133 S 0.3180 0.0901 0.5919 134 I 0.2846 0.0685 0.6468 135 P 0.2033 0.1678 0.6289 136 T 0.1817 0.2499 0.5684 137 A 0.1210 0.4140 0.4649 138 E 0.0628 0.6123 0.3249 139 G 0.0622 0.7016 0.2362 140 T 0.0793 0.7469 0.1738 141 I 0.0764 0.7900 0.1335 142 M 0.0574 0.8200 0.1226 143 M 0.0533 0.8200 0.1267 144 A 0.0606 0.7797 0.1597 145 I 0.0792 0.7069 0.2139 146 Q 0.0930 0.5931 0.3139 147 H 0.1206 0.4015 0.4779 148 T 0.1524 0.2367 0.6109 149 D 0.1841 0.1409 0.6750 150 F 0.3305 0.1103 0.5591 151 T 0.3555 0.1163 0.5282 152 I 0.3142 0.1391 0.5466 153 H 0.1589 0.1206 0.7206 154 G 0.0873 0.0847 0.8280 155 A 0.3167 0.0282 0.6551 156 N 0.6525 0.0190 0.3285 157 V 0.8119 0.0055 0.1826 158 A 0.8112 0.0056 0.1832 159 V 0.7711 0.0056 0.2233 160 L 0.6837 0.0213 0.2950 161 G 0.4783 0.0370 0.4847 162 L 0.2389 0.1537 0.6074 163 G 0.1593 0.2449 0.5959 164 R 0.0618 0.5355 0.4027 165 V 0.0281 0.7308 0.2411 166 G 0.0118 0.8708 0.1174 167 M 0.0086 0.9070 0.0845 168 S 0.0083 0.9231 0.0686 169 V 0.0083 0.9241 0.0676 170 A 0.0083 0.9232 0.0685 171 R 0.0083 0.9242 0.0676 172 K 0.0083 0.9236 0.0681 173 F 0.0084 0.9216 0.0700 174 A 0.0086 0.9081 0.0833 175 A 0.0134 0.8039 0.1828 176 L 0.0564 0.2330 0.7106 177 G 0.0529 0.0661 0.8810 178 A 0.2421 0.0175 0.7403 179 K 0.5501 0.0210 0.4288 180 V 0.7704 0.0068 0.2227 181 K 0.7828 0.0088 0.2084 182 V 0.7781 0.0111 0.2108 183 G 0.6967 0.0323 0.2709 184 A 0.4642 0.0442 0.4916 185 R 0.1901 0.1298 0.6801 186 E 0.1620 0.1042 0.7338 187 S 0.0194 0.6604 0.3202 188 D 0.0129 0.8095 0.1776 189 L 0.0140 0.8735 0.1125 190 L 0.0092 0.9022 0.0886 191 A 0.0085 0.9189 0.0726 192 R 0.0084 0.9204 0.0712 193 I 0.0087 0.9203 0.0711 194 A 0.0089 0.9106 0.0805 195 E 0.0129 0.8182 0.1688 196 M 0.0569 0.2969 0.6463 197 G 0.0494 0.0717 0.8788 198 M 0.1770 0.0244 0.7986 199 E 0.2483 0.0420 0.7097 200 P 0.3625 0.0692 0.5683 201 F 0.3895 0.0643 0.5462 202 H 0.2744 0.0276 0.6980 203 I 0.0518 0.5854 0.3627 204 S 0.0162 0.7848 0.1990 205 K 0.0226 0.8114 0.1660 206 A 0.0189 0.8384 0.1427 207 A 0.0104 0.8866 0.1030 208 Q 0.0096 0.8755 0.1149 209 E 0.0146 0.8371 0.1484 210 L 0.0462 0.7002 0.2536 211 R 0.0364 0.5406 0.4230 212 D 0.0620 0.2621 0.6759 213 V 0.2521 0.1146 0.6333 214 D 0.3459 0.0840 0.5701 215 V 0.8051 0.0123 0.1827 216 C 0.7665 0.0146 0.2189 217 I 0.7746 0.0234 0.2020 218 N 0.6873 0.0528 0.2600 219 T 0.5182 0.0679 0.4139 220 I 0.3585 0.0418 0.5998 221 P 0.1916 0.0927 0.7157 222 A 0.1141 0.2650 0.6210 223 L 0.1210 0.3160 0.5630 224 V 0.2429 0.2400 0.5172 225 V 0.3065 0.1531 0.5404 226 T 0.1950 0.1002 0.7048 227 A 0.0165 0.7280 0.2555 228 N 0.0146 0.8246 0.1609 229 V 0.0179 0.8487 0.1334 230 L 0.0210 0.8322 0.1468 231 A 0.0186 0.6294 0.3519 232 E 0.0305 0.4588 0.5106 233 M 0.1921 0.0854 0.7225 234 P 0.1385 0.0964 0.7651 235 S 0.0951 0.2106 0.6943 236 H 0.1146 0.0964 0.7890 237 T 0.5139 0.0211 0.4651 238 F 0.7522 0.0101 0.2377 239 V 0.7950 0.0073 0.1976 240 I 0.7889 0.0114 0.1997 241 D 0.6934 0.0236 0.2830 242 L 0.5608 0.0980 0.3412 243 A 0.4184 0.0940 0.4876 244 S 0.3010 0.0829 0.6161 245 K 0.2099 0.0476 0.7425 246 P 0.0985 0.2154 0.6861 247 G 0.0687 0.1574 0.7739 248 G 0.1124 0.1087 0.7790 249 T 0.2490 0.0525 0.6985 250 D 0.1963 0.0422 0.7616 251 F 0.0289 0.7111 0.2600 252 R 0.0166 0.8403 0.1431 253 Y 0.0221 0.8813 0.0966 254 A 0.0203 0.8841 0.0956 255 E 0.0166 0.8784 0.1050 256 K 0.0205 0.7698 0.2096 257 R 0.0621 0.3429 0.5949 258 G 0.0624 0.0940 0.8435 259 I 0.2859 0.0586 0.6555 260 K 0.5250 0.0707 0.4043 261 A 0.6906 0.0588 0.2506 262 L 0.7183 0.0384 0.2434 263 L 0.6603 0.0450 0.2947 264 V 0.4473 0.0393 0.5134 265 P 0.2152 0.1398 0.6449 266 G 0.1144 0.1358 0.7498 267 L 0.2112 0.0467 0.7421 268 P 0.1790 0.1182 0.7028 269 G 0.1689 0.1252 0.7059 270 I 0.3047 0.1027 0.5926 271 V 0.4096 0.0836 0.5068 272 A 0.3503 0.0523 0.5974 273 P 0.2341 0.1485 0.6174 274 K 0.1714 0.2232 0.6054 275 T 0.1583 0.2359 0.6058 276 A 0.0532 0.5761 0.3707 277 G 0.0379 0.6831 0.2790 278 R 0.0354 0.7943 0.1703 279 I 0.0316 0.8194 0.1490 280 L 0.0198 0.8413 0.1389 281 A 0.0126 0.8683 0.1192 282 D 0.0133 0.8429 0.1438 283 V 0.0169 0.8298 0.1533 284 L 0.0166 0.8584 0.1250 285 V 0.0126 0.8550 0.1324 286 K 0.0217 0.7844 0.1940 287 L 0.0600 0.6497 0.2903 288 L 0.1048 0.4083 0.4868 289 A 0.1431 0.1844 0.6725 290 E 0.1831 0.1025 0.7143 291 P 0.1297 0.2008 0.6695 292 S 0.1365 0.2130 0.6505