# This file is the result of combining several RDB files, specifically # T0487.t04.str2.rdb (weight 1.54425) # T0487.t04.str4.rdb (weight 0.924988) # T0487.t04.pb.rdb (weight 0.789901) # T0487.t04.bys.rdb (weight 0.748322) # T0487.t04.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 T0487.t04.str2.rdb # ============================================ # TARGET T0487 # Using neural net dunbrack-40pc-3157-t04-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 T0487.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 427 # # ============================================ # Comments from T0487.t04.str4.rdb # ============================================ # TARGET T0487 # Using neural net dunbrack-40pc-3157-t04-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 T0487.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 427 # # ============================================ # Comments from T0487.t04.pb.rdb # ============================================ # TARGET T0487 # Using neural net dunbrack-40pc-3157-t04-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 T0487.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 427 # # ============================================ # Comments from T0487.t04.bys.rdb # ============================================ # TARGET T0487 # Using neural net dunbrack-40pc-3157-t04-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 T0487.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 427 # # ============================================ # Comments from T0487.t04.alpha.rdb # ============================================ # TARGET T0487 # Using neural net dunbrack-40pc-3157-t04-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 T0487.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 427 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.1959 0.1044 0.6998 2 L 0.3114 0.0761 0.6125 3 Q 0.4336 0.0584 0.5081 4 V 0.5058 0.0642 0.4300 5 V 0.6015 0.0473 0.3512 6 A 0.6451 0.0365 0.3184 7 L 0.5227 0.0653 0.4121 8 S 0.3382 0.0906 0.5712 9 G 0.2419 0.0732 0.6849 10 A 0.2118 0.0865 0.7018 11 Y 0.2226 0.0398 0.7376 12 P 0.1808 0.1333 0.6859 13 A 0.2067 0.1495 0.6438 14 E 0.5121 0.0468 0.4411 15 L 0.7212 0.0134 0.2654 16 A 0.7936 0.0057 0.2007 17 V 0.7686 0.0144 0.2169 18 G 0.7237 0.0153 0.2610 19 F 0.7064 0.0295 0.2641 20 D 0.5770 0.0374 0.3856 21 A 0.4284 0.1328 0.4388 22 G 0.2365 0.1154 0.6480 23 G 0.1802 0.0815 0.7383 24 R 0.1371 0.1564 0.7065 25 E 0.1324 0.1776 0.6900 26 S 0.1767 0.1338 0.6895 27 F 0.2963 0.1108 0.5929 28 R 0.5417 0.0769 0.3815 29 F 0.6797 0.0613 0.2590 30 G 0.7148 0.0587 0.2264 31 G 0.7621 0.0359 0.2020 32 A 0.7846 0.0351 0.1802 33 A 0.7939 0.0259 0.1802 34 C 0.7856 0.0221 0.1923 35 A 0.7278 0.0424 0.2298 36 V 0.5879 0.0779 0.3343 37 G 0.2929 0.0641 0.6429 38 G 0.1282 0.1786 0.6932 39 D 0.1286 0.1479 0.7235 40 G 0.1651 0.1451 0.6898 41 G 0.3121 0.1333 0.5546 42 H 0.5539 0.0953 0.3508 43 L 0.6461 0.0646 0.2892 44 L 0.6409 0.0820 0.2771 45 W 0.6145 0.0692 0.3163 46 T 0.5405 0.0622 0.3974 47 L 0.4586 0.0455 0.4959 48 P 0.3802 0.1632 0.4566 49 E 0.3331 0.2936 0.3733 50 A 0.2931 0.2752 0.4317 51 Q 0.2276 0.2193 0.5530 52 A 0.1165 0.1846 0.6989 53 G 0.0631 0.1378 0.7990 54 E 0.2226 0.0998 0.6776 55 R 0.3232 0.0929 0.5839 56 I 0.3030 0.0448 0.6522 57 P 0.1616 0.1257 0.7127 58 Q 0.0205 0.7273 0.2522 59 E 0.0111 0.8497 0.1392 60 V 0.0099 0.9061 0.0840 61 V 0.0087 0.9109 0.0803 62 W 0.0085 0.9206 0.0709 63 D 0.0083 0.9213 0.0704 64 L 0.0084 0.9216 0.0699 65 L 0.0083 0.9186 0.0731 66 E 0.0083 0.9237 0.0680 67 E 0.0083 0.9244 0.0673 68 T 0.0083 0.9236 0.0681 69 L 0.0083 0.9227 0.0690 70 W 0.0083 0.9230 0.0687 71 A 0.0083 0.9224 0.0693 72 F 0.0085 0.9176 0.0740 73 R 0.0085 0.9159 0.0756 74 R 0.0093 0.8919 0.0989 75 K 0.0178 0.7617 0.2205 76 A 0.0636 0.2388 0.6976 77 G 0.0506 0.0909 0.8585 78 R 0.1617 0.0512 0.7871 79 L 0.2302 0.0227 0.7471 80 P 0.2690 0.0479 0.6831 81 S 0.4012 0.0682 0.5305 82 R 0.7276 0.0131 0.2593 83 V 0.7871 0.0055 0.2074 84 L 0.8122 0.0051 0.1827 85 L 0.8137 0.0044 0.1819 86 L 0.7419 0.0101 0.2479 87 R 0.5900 0.0299 0.3800 88 D 0.2891 0.0604 0.6505 89 G 0.2008 0.0715 0.7277 90 R 0.2886 0.0531 0.6583 91 V 0.2473 0.0296 0.7231 92 P 0.1519 0.0867 0.7614 93 Q 0.0290 0.6420 0.3289 94 D 0.0205 0.7607 0.2189 95 E 0.0213 0.8656 0.1131 96 F 0.0090 0.9124 0.0786 97 A 0.0086 0.9221 0.0693 98 L 0.0083 0.9234 0.0683 99 A 0.0084 0.9211 0.0705 100 L 0.0085 0.9200 0.0715 101 E 0.0084 0.9162 0.0754 102 A 0.0095 0.8941 0.0964 103 L 0.0213 0.7869 0.1918 104 A 0.0194 0.6083 0.3723 105 R 0.0415 0.4331 0.5253 106 E 0.0871 0.2212 0.6917 107 G 0.1197 0.0658 0.8146 108 I 0.2801 0.0393 0.6806 109 A 0.4321 0.0284 0.5395 110 Y 0.6912 0.0082 0.3006 111 D 0.7380 0.0092 0.2528 112 L 0.8159 0.0043 0.1798 113 V 0.8082 0.0057 0.1861 114 S 0.8124 0.0044 0.1832 115 V 0.7953 0.0054 0.1993 116 R 0.6708 0.0118 0.3174 117 K 0.4914 0.0426 0.4660 118 S 0.3141 0.0822 0.6037 119 G 0.2015 0.0889 0.7096 120 G 0.2032 0.0754 0.7214 121 G 0.3919 0.0472 0.5610 122 R 0.6276 0.0329 0.3395 123 V 0.6756 0.0274 0.2970 124 Y 0.6226 0.0180 0.3594 125 P 0.4395 0.0356 0.5249 126 V 0.2987 0.0474 0.6538 127 Q 0.2101 0.1423 0.6476 128 G 0.1957 0.0889 0.7154 129 R 0.4126 0.0397 0.5477 130 L 0.5785 0.0345 0.3870 131 A 0.5524 0.0572 0.3904 132 D 0.3583 0.0778 0.5639 133 G 0.2958 0.0660 0.6382 134 L 0.4981 0.0462 0.4557 135 Y 0.5861 0.0272 0.3866 136 V 0.5294 0.0206 0.4501 137 P 0.2602 0.0163 0.7236 138 L 0.1266 0.2970 0.5765 139 E 0.1031 0.2980 0.5989 140 D 0.1422 0.2167 0.6411 141 K 0.2528 0.1445 0.6027 142 T 0.5062 0.0978 0.3960 143 F 0.7439 0.0250 0.2311 144 L 0.7767 0.0157 0.2076 145 L 0.7989 0.0140 0.1871 146 L 0.7437 0.0399 0.2164 147 T 0.6328 0.0565 0.3107 148 V 0.4248 0.1472 0.4280 149 H 0.2909 0.1769 0.5322 150 R 0.2682 0.2404 0.4914 151 D 0.2490 0.2326 0.5184 152 F 0.2410 0.2375 0.5215 153 R 0.2069 0.1527 0.6404 154 G 0.1978 0.0873 0.7149 155 T 0.2612 0.0486 0.6902 156 P 0.2866 0.0827 0.6307 157 R 0.3733 0.0352 0.5915 158 P 0.3981 0.0681 0.5338 159 L 0.5719 0.0313 0.3968 160 K 0.7240 0.0207 0.2553 161 L 0.7511 0.0122 0.2367 162 V 0.7187 0.0581 0.2232 163 H 0.6433 0.0707 0.2861 164 E 0.3684 0.1587 0.4729 165 A 0.1618 0.1718 0.6664 166 G 0.0976 0.1276 0.7748 167 D 0.1230 0.1001 0.7769 168 T 0.2276 0.0339 0.7386 169 P 0.1731 0.0211 0.8058 170 L 0.0131 0.7223 0.2646 171 E 0.0095 0.8630 0.1275 172 A 0.0086 0.9132 0.0781 173 L 0.0084 0.9208 0.0708 174 A 0.0083 0.9217 0.0700 175 H 0.0083 0.9225 0.0692 176 Q 0.0087 0.9202 0.0711 177 I 0.0090 0.9168 0.0742 178 F 0.0093 0.9088 0.0819 179 H 0.0121 0.8752 0.1127 180 L 0.0211 0.7947 0.1842 181 T 0.0359 0.7469 0.2172 182 R 0.0741 0.6236 0.3023 183 L 0.1618 0.4220 0.4162 184 Y 0.2331 0.1906 0.5762 185 P 0.1108 0.4319 0.4573 186 A 0.1148 0.4072 0.4780 187 S 0.1513 0.2261 0.6226 188 G 0.1426 0.1729 0.6845 189 F 0.1883 0.1632 0.6486 190 A 0.2354 0.1057 0.6590 191 F 0.2829 0.0687 0.6484 192 P 0.2581 0.1199 0.6221 193 R 0.2859 0.0966 0.6175 194 L 0.2938 0.0459 0.6603 195 P 0.2484 0.0729 0.6787 196 A 0.3531 0.1136 0.5333 197 P 0.3340 0.2276 0.4384 198 L 0.1993 0.5597 0.2410 199 H 0.1154 0.7319 0.1527 200 L 0.0465 0.8208 0.1327 201 A 0.0116 0.8907 0.0977 202 D 0.0087 0.9150 0.0764 203 R 0.0084 0.9201 0.0715 204 L 0.0085 0.9177 0.0738 205 V 0.0084 0.9193 0.0724 206 K 0.0085 0.9195 0.0720 207 E 0.0102 0.8955 0.0942 208 V 0.0258 0.8411 0.1331 209 G 0.0144 0.8422 0.1433 210 R 0.0234 0.8045 0.1721 211 L 0.0642 0.6408 0.2949 212 G 0.0882 0.4878 0.4240 213 I 0.1184 0.5021 0.3795 214 R 0.1206 0.4687 0.4108 215 H 0.1511 0.3760 0.4729 216 L 0.1099 0.4397 0.4504 217 K 0.0955 0.4732 0.4313 218 E 0.1096 0.4859 0.4044 219 V 0.1536 0.4063 0.4401 220 D 0.1484 0.3309 0.5206 221 R 0.0790 0.4787 0.4423 222 E 0.0888 0.3747 0.5365 223 K 0.1999 0.2355 0.5645 224 L 0.3754 0.1403 0.4843 225 F 0.5560 0.0958 0.3482 226 F 0.6149 0.0658 0.3194 227 V 0.5062 0.0785 0.4153