# This file is the result of combining several RDB files, specifically # T0296.t04.dssp-ebghstl.rdb (weight 1.53986) # T0296.t04.stride-ebghtl.rdb (weight 1.24869) # T0296.t04.str2.rdb (weight 1.54758) # T0296.t04.alpha.rdb (weight 0.659012) # 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 T0296.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0296 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0296.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 6.08683 # # ============================================ # Comments from T0296.t04.stride-ebghtl.rdb # ============================================ # TARGET T0296 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0296.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 6.08683 # # ============================================ # Comments from T0296.t04.str2.rdb # ============================================ # TARGET T0296 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0296.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 6.08683 # # ============================================ # Comments from T0296.t04.alpha.rdb # ============================================ # TARGET T0296 # Using neural net t04-2621-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 T0296.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 6.08683 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.1074 0.0535 0.8391 2 L 0.2252 0.0730 0.7018 3 S 0.3124 0.0524 0.6352 4 L 0.2865 0.0677 0.6458 5 A 0.1615 0.0379 0.8006 6 P 0.1331 0.0431 0.8237 7 T 0.1010 0.0280 0.8709 8 P 0.0655 0.1367 0.7978 9 A 0.0579 0.1497 0.7925 10 V 0.0582 0.2105 0.7312 11 G 0.0434 0.1477 0.8089 12 D 0.0478 0.3339 0.6182 13 S 0.1455 0.5072 0.3472 14 V 0.0137 0.9256 0.0607 15 A 0.0054 0.9549 0.0397 16 R 0.0049 0.9604 0.0347 17 V 0.0047 0.9605 0.0348 18 L 0.0047 0.9574 0.0379 19 E 0.0051 0.9481 0.0468 20 E 0.0072 0.8908 0.1020 21 M 0.0430 0.5688 0.3882 22 G 0.0552 0.2311 0.7137 23 L 0.0885 0.2544 0.6571 24 E 0.1423 0.4100 0.4477 25 T 0.2527 0.3758 0.3715 26 V 0.2228 0.2575 0.5197 27 G 0.1078 0.1032 0.7890 28 T 0.0796 0.1513 0.7690 29 H 0.0511 0.2929 0.6560 30 G 0.0425 0.4109 0.5466 31 T 0.0289 0.8097 0.1613 32 T 0.0056 0.9529 0.0414 33 A 0.0047 0.9599 0.0354 34 A 0.0047 0.9604 0.0349 35 L 0.0047 0.9603 0.0350 36 A 0.0047 0.9585 0.0368 37 L 0.0049 0.9466 0.0486 38 L 0.0052 0.9324 0.0624 39 N 0.0223 0.8916 0.0860 40 D 0.0067 0.9175 0.0758 41 Q 0.0075 0.9083 0.0842 42 V 0.0203 0.8491 0.1306 43 K 0.0230 0.8090 0.1680 44 K 0.0254 0.6648 0.3098 45 G 0.0471 0.3743 0.5786 46 G 0.1007 0.2584 0.6409 47 V 0.3180 0.2734 0.4086 48 M 0.4057 0.2969 0.2974 49 A 0.4854 0.2561 0.2585 50 C 0.4801 0.2462 0.2736 51 N 0.3543 0.2860 0.3596 52 Q 0.3426 0.2284 0.4290 53 V 0.3059 0.2005 0.4936 54 G 0.1944 0.1296 0.6760 55 G 0.1566 0.1114 0.7321 56 L 0.2329 0.1332 0.6340 57 S 0.2367 0.1561 0.6072 58 G 0.2846 0.1753 0.5401 59 A 0.5328 0.1187 0.3485 60 F 0.6976 0.0508 0.2515 61 I 0.5832 0.0296 0.3872 62 P 0.4327 0.0269 0.5404 63 V 0.2160 0.2757 0.5083 64 S 0.1174 0.4179 0.4647 65 E 0.0516 0.4775 0.4709 66 D 0.0573 0.5192 0.4235 67 E 0.0067 0.9134 0.0799 68 G 0.0070 0.9332 0.0599 69 M 0.0053 0.9515 0.0431 70 I 0.0052 0.9559 0.0389 71 A 0.0049 0.9578 0.0373 72 A 0.0051 0.9556 0.0393 73 V 0.0061 0.9476 0.0462 74 Q 0.0080 0.9093 0.0827 75 N 0.0402 0.5175 0.4423 76 G 0.0252 0.1060 0.8687 77 S 0.0849 0.0635 0.8516 78 L 0.2879 0.0292 0.6829 79 N 0.2256 0.0316 0.7428 80 L 0.0190 0.8548 0.1261 81 E 0.0076 0.8893 0.1031 82 K 0.0088 0.8970 0.0942 83 L 0.0274 0.8593 0.1133 84 E 0.0326 0.8237 0.1437 85 A 0.0473 0.8165 0.1362 86 M 0.0665 0.7727 0.1608 87 T 0.0852 0.7741 0.1407 88 A 0.1608 0.6971 0.1421 89 I 0.2187 0.6301 0.1512 90 C 0.2064 0.5568 0.2369 91 S 0.2280 0.3495 0.4225 92 V 0.1509 0.2897 0.5594 93 G 0.2131 0.1677 0.6192 94 L 0.3015 0.1555 0.5430 95 D 0.3699 0.1410 0.4891 96 M 0.6187 0.0986 0.2827 97 I 0.6731 0.0327 0.2942 98 A 0.6976 0.0233 0.2791 99 I 0.3801 0.0206 0.5993 100 P 0.1184 0.1098 0.7718 101 E 0.0253 0.1423 0.8324 102 D 0.0561 0.1308 0.8131 103 T 0.0656 0.0248 0.9096 104 P 0.0649 0.0721 0.8629 105 A 0.0060 0.9351 0.0588 106 E 0.0049 0.9545 0.0407 107 T 0.0048 0.9574 0.0378 108 I 0.0049 0.9596 0.0355 109 A 0.0047 0.9599 0.0354 110 A 0.0047 0.9551 0.0402 111 M 0.0047 0.9516 0.0437 112 I 0.0048 0.9482 0.0470 113 A 0.0052 0.9287 0.0662 114 D 0.0064 0.8838 0.1098 115 E 0.0068 0.9185 0.0747 116 A 0.0073 0.9331 0.0596 117 A 0.0109 0.9350 0.0541 118 I 0.0163 0.9253 0.0583 119 G 0.0384 0.8722 0.0895 120 V 0.0687 0.8071 0.1242 121 I 0.0771 0.6706 0.2523 122 N 0.0702 0.2730 0.6568 123 M 0.0583 0.0810 0.8607 124 K 0.2051 0.0215 0.7734 125 T 0.4264 0.0109 0.5627 126 T 0.7209 0.0189 0.2602 127 A 0.8986 0.0040 0.0973 128 V 0.9212 0.0035 0.0753 129 R 0.9249 0.0038 0.0712 130 I 0.8974 0.0043 0.0983 131 I 0.7427 0.0065 0.2509 132 P 0.4456 0.0145 0.5399 133 K 0.1076 0.0688 0.8236 134 G 0.0534 0.0422 0.9043 135 K 0.0833 0.0484 0.8683 136 E 0.0994 0.0474 0.8532 137 G 0.1089 0.0372 0.8539 138 D 0.2825 0.0366 0.6808 139 M 0.8063 0.0199 0.1738 140 I 0.8525 0.0177 0.1297 141 E 0.8581 0.0208 0.1211 142 F 0.7360 0.0455 0.2184 143 G 0.3174 0.0561 0.6265 144 G 0.1825 0.0575 0.7600 145 L 0.3211 0.0960 0.5829 146 L 0.3075 0.1167 0.5757 147 G 0.1866 0.0632 0.7502 148 T 0.2672 0.0362 0.6966 149 A 0.3141 0.0159 0.6700 150 P 0.3848 0.0216 0.5936 151 V 0.7044 0.0390 0.2567 152 M 0.7779 0.0303 0.1918 153 K 0.7910 0.0263 0.1827 154 V 0.6091 0.0382 0.3527 155 N 0.2662 0.0635 0.6702 156 G 0.1147 0.0555 0.8298 157 A 0.1654 0.0708 0.7638 158 S 0.1921 0.0728 0.7351 159 S 0.1540 0.3372 0.5089 160 V 0.1429 0.5021 0.3551 161 D 0.2028 0.5509 0.2463 162 F 0.2775 0.5295 0.1930 163 I 0.3086 0.4643 0.2271 164 S 0.2492 0.4111 0.3397 165 R 0.1296 0.2433 0.6271 166 G 0.0997 0.0797 0.8206 167 G 0.1409 0.0504 0.8088 168 Q 0.3682 0.0318 0.6000 169 I 0.3403 0.0194 0.6403 170 P 0.3213 0.0260 0.6527 171 A 0.3042 0.0536 0.6422 172 P 0.2822 0.0836 0.6342 173 I 0.1913 0.3670 0.4417 174 H 0.1380 0.4606 0.4014 175 S 0.1669 0.3863 0.4467 176 F 0.1853 0.2115 0.6033 177 K 0.1318 0.1355 0.7328 178 N 0.0685 0.0476 0.8838