# This file is the result of combining several RDB files, specifically # T0627.t06.str2.rdb (weight 1.54425) # T0627.t06.str4.rdb (weight 0.924988) # T0627.t06.pb.rdb (weight 0.789901) # T0627.t06.bys.rdb (weight 0.748322) # T0627.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 T0627.t06.str2.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1077 # # ============================================ # Comments from T0627.t06.str4.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1077 # # ============================================ # Comments from T0627.t06.pb.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1077 # # ============================================ # Comments from T0627.t06.bys.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1077 # # ============================================ # Comments from T0627.t06.alpha.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1077 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3394 0.1145 0.5460 2 I 0.3429 0.1113 0.5458 3 D 0.3247 0.1236 0.5517 4 T 0.2618 0.2159 0.5223 5 F 0.2294 0.2401 0.5305 6 E 0.2245 0.2148 0.5607 7 R 0.1858 0.2293 0.5849 8 T 0.1744 0.1535 0.6721 9 G 0.1688 0.1045 0.7267 10 P 0.1610 0.2009 0.6381 11 L 0.1834 0.2628 0.5538 12 M 0.2268 0.2106 0.5626 13 E 0.1962 0.1639 0.6399 14 A 0.1094 0.3391 0.5515 15 S 0.0959 0.3277 0.5764 16 S 0.1093 0.2687 0.6220 17 Y 0.1195 0.3504 0.5301 18 P 0.0338 0.6919 0.2743 19 A 0.0154 0.8457 0.1389 20 W 0.0114 0.8968 0.0918 21 A 0.0084 0.9186 0.0730 22 Q 0.0083 0.9224 0.0693 23 Q 0.0084 0.9216 0.0701 24 L 0.0086 0.9162 0.0752 25 I 0.0088 0.9000 0.0911 26 N 0.0102 0.8338 0.1559 27 D 0.0172 0.7191 0.2637 28 C 0.0414 0.5708 0.3879 29 S 0.0498 0.5344 0.4158 30 P 0.0191 0.7784 0.2025 31 A 0.0134 0.8626 0.1240 32 K 0.0105 0.9011 0.0885 33 A 0.0095 0.9009 0.0896 34 R 0.0113 0.8689 0.1198 35 V 0.0158 0.8267 0.1575 36 V 0.0270 0.7678 0.2052 37 E 0.0396 0.6162 0.3442 38 H 0.0959 0.4685 0.4356 39 E 0.0162 0.7807 0.2031 40 L 0.0130 0.8682 0.1188 41 Y 0.0125 0.9065 0.0810 42 Q 0.0089 0.9122 0.0789 43 Q 0.0109 0.8920 0.0972 44 M 0.0185 0.8536 0.1279 45 R 0.0254 0.7164 0.2582 46 D 0.0411 0.2818 0.6771 47 A 0.0678 0.1520 0.7802 48 K 0.1611 0.0951 0.7438 49 L 0.2303 0.0419 0.7277 50 S 0.1660 0.0214 0.8126 51 P 0.0118 0.7464 0.2418 52 Q 0.0092 0.8636 0.1272 53 I 0.0084 0.9218 0.0698 54 M 0.0083 0.9232 0.0685 55 R 0.0083 0.9219 0.0698 56 Q 0.0083 0.9188 0.0729 57 Y 0.0089 0.9110 0.0801 58 L 0.0147 0.8705 0.1148 59 I 0.0264 0.7592 0.2144 60 G 0.0342 0.5099 0.4558 61 G 0.0512 0.3587 0.5900 62 W 0.1324 0.3518 0.5158 63 P 0.1004 0.6059 0.2937 64 V 0.0830 0.7408 0.1763 65 V 0.0401 0.8498 0.1100 66 E 0.0225 0.8806 0.0970 67 Q 0.0185 0.8782 0.1033 68 F 0.0112 0.8956 0.0932 69 A 0.0084 0.9137 0.0779 70 V 0.0083 0.9223 0.0694 71 Y 0.0084 0.9221 0.0696 72 M 0.0084 0.9197 0.0719 73 A 0.0084 0.9177 0.0739 74 K 0.0085 0.9092 0.0822 75 N 0.0088 0.8765 0.1147 76 L 0.0113 0.8363 0.1523 77 T 0.0169 0.7891 0.1941 78 K 0.0263 0.7585 0.2152 79 T 0.0629 0.6695 0.2676 80 R 0.0925 0.5276 0.3800 81 F 0.1250 0.3880 0.4869 82 G 0.0927 0.3451 0.5622 83 R 0.1224 0.2026 0.6750 84 H 0.1836 0.0652 0.7512 85 P 0.0849 0.2736 0.6415 86 G 0.0624 0.2149 0.7228 87 E 0.0451 0.6028 0.3521 88 D 0.0125 0.8552 0.1324 89 M 0.0090 0.9025 0.0885 90 A 0.0083 0.9211 0.0705 91 R 0.0083 0.9220 0.0697 92 R 0.0083 0.9240 0.0677 93 W 0.0083 0.9233 0.0684 94 L 0.0083 0.9220 0.0697 95 M 0.0084 0.9174 0.0742 96 R 0.0088 0.9012 0.0901 97 N 0.0117 0.8644 0.1238 98 I 0.0197 0.8425 0.1378 99 R 0.0253 0.8113 0.1634 100 V 0.0405 0.7745 0.1851 101 E 0.0654 0.6423 0.2922 102 L 0.0940 0.4394 0.4666 103 N 0.0775 0.3393 0.5832 104 H 0.0777 0.5768 0.3455 105 A 0.0162 0.8269 0.1569 106 D 0.0113 0.8866 0.1021 107 Y 0.0100 0.9110 0.0790 108 W 0.0093 0.9163 0.0744 109 V 0.0084 0.9188 0.0729 110 N 0.0085 0.9190 0.0725 111 W 0.0085 0.9141 0.0774 112 C 0.0091 0.9127 0.0782 113 A 0.0093 0.8919 0.0989 114 A 0.0165 0.7651 0.2184 115 H 0.0631 0.2734 0.6635 116 D 0.0497 0.1005 0.8498 117 V 0.1774 0.0215 0.8011 118 T 0.1781 0.0174 0.8045 119 L 0.0209 0.7070 0.2720 120 E 0.0157 0.7922 0.1921 121 D 0.0266 0.8097 0.1637 122 L 0.0485 0.7581 0.1934 123 H 0.0350 0.6728 0.2923 124 D 0.0443 0.4322 0.5235 125 Q 0.1093 0.3447 0.5460 126 R 0.1551 0.1575 0.6874 127 V 0.1818 0.1313 0.6870 128 A 0.1576 0.1516 0.6908 129 P 0.0188 0.7390 0.2422 130 E 0.0130 0.8456 0.1414 131 L 0.0102 0.9104 0.0794 132 H 0.0087 0.9184 0.0729 133 A 0.0086 0.9205 0.0709 134 L 0.0084 0.9202 0.0713 135 S 0.0084 0.9191 0.0725 136 H 0.0084 0.9196 0.0720 137 W 0.0085 0.9188 0.0727 138 C 0.0088 0.9160 0.0752 139 W 0.0089 0.9050 0.0861 140 Q 0.0140 0.8615 0.1245 141 T 0.0284 0.7647 0.2069 142 S 0.0512 0.6263 0.3226 143 S 0.0680 0.4232 0.5088 144 S 0.0909 0.3072 0.6020 145 D 0.0725 0.3112 0.6163 146 S 0.0986 0.3623 0.5391 147 L 0.0202 0.7649 0.2149 148 A 0.0121 0.8676 0.1203 149 V 0.0136 0.9096 0.0767 150 A 0.0148 0.9102 0.0750 151 M 0.0139 0.9095 0.0766 152 A 0.0174 0.8972 0.0853 153 A 0.0259 0.8624 0.1117 154 T 0.0343 0.8095 0.1562 155 N 0.0331 0.7706 0.1963 156 Y 0.0235 0.7724 0.2041 157 A 0.0263 0.8069 0.1668 158 I 0.0239 0.8281 0.1480 159 E 0.0249 0.7919 0.1831 160 G 0.0441 0.7086 0.2473 161 A 0.0680 0.6588 0.2732 162 T 0.0585 0.7068 0.2347 163 G 0.0200 0.8196 0.1604 164 E 0.0202 0.8528 0.1270 165 W 0.0192 0.8592 0.1216 166 S 0.0124 0.8873 0.1003 167 A 0.0109 0.8991 0.0901 168 V 0.0128 0.8932 0.0940 169 V 0.0163 0.8686 0.1151 170 C 0.0211 0.8254 0.1534 171 S 0.0302 0.7049 0.2649 172 T 0.0524 0.5800 0.3676 173 G 0.0311 0.6189 0.3499 174 V 0.0398 0.7222 0.2380 175 Y 0.0409 0.7999 0.1593 176 A 0.0164 0.8651 0.1185 177 E 0.0185 0.8403 0.1412 178 A 0.0297 0.7347 0.2356 179 F 0.0728 0.5827 0.3445 180 A 0.0708 0.5021 0.4271 181 E 0.0752 0.4967 0.4281 182 E 0.0694 0.4626 0.4680 183 T 0.0820 0.4258 0.4922 184 R 0.0960 0.3597 0.5443 185 K 0.0601 0.5756 0.3643 186 K 0.0321 0.6916 0.2762 187 S 0.0342 0.7620 0.2037 188 M 0.0289 0.8438 0.1272 189 K 0.0277 0.8626 0.1097 190 W 0.0383 0.8476 0.1141 191 L 0.0502 0.8298 0.1201 192 K 0.0666 0.7705 0.1629 193 M 0.0833 0.6406 0.2761 194 H 0.1209 0.4320 0.4472 195 A 0.1395 0.3443 0.5162 196 Q 0.1476 0.2414 0.6110 197 Y 0.1086 0.3307 0.5607 198 D 0.0963 0.3276 0.5761 199 D 0.0690 0.3813 0.5496 200 A 0.0952 0.3179 0.5868 201 H 0.1581 0.2212 0.6207 202 P 0.0328 0.7244 0.2428 203 W 0.0107 0.8681 0.1212 204 E 0.0091 0.9105 0.0804 205 A 0.0084 0.9208 0.0708 206 L 0.0083 0.9217 0.0700 207 E 0.0083 0.9228 0.0689 208 I 0.0083 0.9229 0.0687 209 I 0.0084 0.9199 0.0717 210 C 0.0085 0.9150 0.0765 211 T 0.0089 0.9031 0.0880 212 L 0.0141 0.8324 0.1535 213 V 0.0288 0.6879 0.2832 214 G 0.0264 0.5205 0.4531 215 N 0.0581 0.3139 0.6279 216 K 0.1747 0.0771 0.7481 217 P 0.1148 0.1756 0.7096 218 S 0.1561 0.0706 0.7734 219 L 0.0120 0.7498 0.2382 220 Q 0.0092 0.8709 0.1199 221 L 0.0087 0.9194 0.0720 222 Q 0.0083 0.9221 0.0696 223 A 0.0083 0.9238 0.0679 224 E 0.0083 0.9245 0.0673 225 L 0.0083 0.9239 0.0679 226 R 0.0083 0.9208 0.0708 227 Q 0.0083 0.9235 0.0682 228 A 0.0083 0.9216 0.0701 229 V 0.0083 0.9217 0.0700 230 T 0.0083 0.9205 0.0711 231 K 0.0086 0.9142 0.0772 232 S 0.0091 0.9071 0.0839 233 Y 0.0090 0.9127 0.0783 234 D 0.0085 0.9175 0.0739 235 Y 0.0088 0.9205 0.0707 236 M 0.0083 0.9213 0.0703 237 Y 0.0084 0.9209 0.0708 238 L 0.0085 0.9169 0.0746 239 F 0.0088 0.9160 0.0752 240 L 0.0085 0.9155 0.0760 241 E 0.0084 0.9168 0.0748 242 R 0.0085 0.9126 0.0789 243 C 0.0098 0.9022 0.0880 244 I 0.0112 0.8782 0.1106 245 Q 0.0216 0.7900 0.1884 246 L 0.0528 0.6309 0.3163 247 D 0.0777 0.4668 0.4555 248 K 0.1263 0.3316 0.5420 249 V 0.2191 0.1564 0.6244 250 K 0.2138 0.1388 0.6474 251 S 0.2348 0.0514 0.7138 252 P 0.1697 0.1311 0.6992 253 R 0.0881 0.2337 0.6782 254 G 0.0717 0.1761 0.7523 255 R 0.2462 0.1354 0.6183 256 V 0.4006 0.1097 0.4897 257 A 0.3909 0.1622 0.4469 258 A 0.3808 0.2021 0.4171 259 L 0.2957 0.2534 0.4508 260 E 0.2363 0.2349 0.5287 261 M 0.2161 0.2015 0.5823