# This file is the result of combining several RDB files, specifically # T0337.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0337.t2k.stride-ebghtl.rdb (weight 1.24869) # T0337.t2k.str2.rdb (weight 1.54758) # T0337.t2k.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 T0337.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0337 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0337.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1092 # # ============================================ # Comments from T0337.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0337 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0337.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1092 # # ============================================ # Comments from T0337.t2k.str2.rdb # ============================================ # TARGET T0337 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0337.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1092 # # ============================================ # Comments from T0337.t2k.alpha.rdb # ============================================ # TARGET T0337 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0337.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1092 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0731 0.0510 0.8759 2 D 0.1191 0.0732 0.8077 3 C 0.0892 0.1888 0.7220 4 M 0.0708 0.3257 0.6035 5 R 0.0568 0.3615 0.5818 6 K 0.0834 0.2821 0.6346 7 L 0.0816 0.1665 0.7519 8 D 0.0560 0.1375 0.8064 9 R 0.0065 0.9241 0.0694 10 V 0.0055 0.9439 0.0507 11 D 0.0051 0.9519 0.0429 12 M 0.0047 0.9595 0.0359 13 Q 0.0047 0.9602 0.0351 14 L 0.0047 0.9597 0.0356 15 V 0.0047 0.9599 0.0354 16 K 0.0047 0.9591 0.0363 17 I 0.0048 0.9558 0.0394 18 L 0.0053 0.9445 0.0502 19 S 0.0071 0.9089 0.0840 20 E 0.0154 0.7465 0.2380 21 N 0.0457 0.3628 0.5915 22 S 0.0410 0.1361 0.8229 23 R 0.0547 0.0838 0.8615 24 L 0.0833 0.0373 0.8795 25 T 0.0751 0.0231 0.9018 26 Y 0.0057 0.9209 0.0734 27 R 0.0048 0.9469 0.0483 28 E 0.0050 0.9535 0.0415 29 L 0.0047 0.9562 0.0391 30 A 0.0048 0.9521 0.0431 31 D 0.0052 0.9273 0.0675 32 I 0.0063 0.8718 0.1220 33 L 0.0506 0.4178 0.5316 34 N 0.0457 0.0468 0.9075 35 T 0.0645 0.0207 0.9148 36 T 0.0571 0.0144 0.9285 37 R 0.0169 0.7724 0.2107 38 Q 0.0061 0.9112 0.0827 39 R 0.0054 0.9460 0.0486 40 I 0.0048 0.9570 0.0382 41 A 0.0047 0.9594 0.0358 42 R 0.0047 0.9600 0.0353 43 R 0.0047 0.9593 0.0360 44 I 0.0047 0.9598 0.0355 45 D 0.0047 0.9603 0.0350 46 K 0.0047 0.9600 0.0353 47 L 0.0047 0.9588 0.0365 48 K 0.0049 0.9495 0.0456 49 K 0.0053 0.9119 0.0828 50 L 0.0429 0.3014 0.6557 51 G 0.0356 0.0446 0.9199 52 I 0.1875 0.0732 0.7393 53 I 0.6229 0.0330 0.3441 54 R 0.5950 0.0537 0.3513 55 K 0.6110 0.0409 0.3481 56 F 0.7013 0.0289 0.2698 57 T 0.7727 0.0256 0.2017 58 I 0.8383 0.0195 0.1422 59 I 0.8347 0.0193 0.1460 60 P 0.7095 0.0254 0.2651 61 D 0.4049 0.0300 0.5651 62 I 0.0152 0.6946 0.2902 63 D 0.0099 0.6848 0.3052 64 K 0.0167 0.7567 0.2266 65 L 0.0662 0.4253 0.5085 66 G 0.0955 0.0794 0.8250 67 Y 0.2677 0.0325 0.6997 68 M 0.5205 0.0174 0.4621 69 Y 0.8363 0.0051 0.1586 70 A 0.9050 0.0038 0.0911 71 I 0.9267 0.0033 0.0700 72 V 0.9317 0.0031 0.0652 73 L 0.9258 0.0033 0.0709 74 I 0.9154 0.0033 0.0813 75 K 0.8792 0.0047 0.1161 76 S 0.7764 0.0065 0.2172 77 K 0.3750 0.0128 0.6121 78 V 0.1060 0.0179 0.8761 79 P 0.0260 0.3516 0.6224 80 S 0.0192 0.4742 0.5065 81 D 0.0280 0.5902 0.3817 82 A 0.0083 0.8884 0.1033 83 D 0.0059 0.9339 0.0602 84 K 0.0060 0.9425 0.0516 85 V 0.0058 0.9506 0.0436 86 I 0.0050 0.9542 0.0408 87 S 0.0048 0.9517 0.0435 88 E 0.0049 0.9443 0.0508 89 I 0.0054 0.9270 0.0676 90 S 0.0053 0.8089 0.1857 91 D 0.0114 0.5842 0.4043 92 I 0.0605 0.1687 0.7708 93 E 0.0243 0.2825 0.6932 94 Y 0.1481 0.2873 0.5646 95 V 0.5163 0.2190 0.2647 96 K 0.6510 0.1688 0.1802 97 S 0.7595 0.1217 0.1188 98 V 0.7465 0.1350 0.1186 99 E 0.7205 0.1360 0.1436 100 K 0.6604 0.1405 0.1991 101 G 0.5009 0.1278 0.3713 102 V 0.3086 0.0674 0.6240 103 G 0.1046 0.0412 0.8542 104 R 0.1221 0.0773 0.8006 105 Y 0.3107 0.0379 0.6514 106 N 0.4689 0.0278 0.5033 107 I 0.8804 0.0041 0.1156 108 I 0.9233 0.0035 0.0732 109 V 0.9280 0.0035 0.0685 110 R 0.9263 0.0037 0.0700 111 L 0.8998 0.0043 0.0959 112 L 0.8209 0.0079 0.1712 113 L 0.5105 0.0095 0.4800 114 P 0.1415 0.0239 0.8346 115 K 0.0311 0.1708 0.7982 116 D 0.0441 0.1194 0.8365 117 I 0.0136 0.7672 0.2192 118 K 0.0060 0.9059 0.0881 119 D 0.0061 0.9215 0.0724 120 A 0.0053 0.9390 0.0556 121 E 0.0052 0.9461 0.0487 122 N 0.0050 0.9468 0.0483 123 L 0.0049 0.9509 0.0442 124 I 0.0049 0.9495 0.0456 125 S 0.0049 0.9474 0.0478 126 E 0.0051 0.9392 0.0557 127 F 0.0054 0.9229 0.0716 128 L 0.0096 0.8662 0.1242 129 Q 0.0088 0.6919 0.2993 130 R 0.0210 0.4467 0.5323 131 I 0.0650 0.1090 0.8260 132 K 0.0216 0.1538 0.8246 133 N 0.0452 0.0957 0.8590 134 A 0.3201 0.0665 0.6135 135 E 0.5197 0.0760 0.4044 136 N 0.6641 0.0393 0.2967 137 V 0.7185 0.0307 0.2508 138 E 0.7922 0.0236 0.1842 139 V 0.8455 0.0240 0.1304 140 I 0.8746 0.0228 0.1026 141 L 0.8871 0.0237 0.0892 142 I 0.8734 0.0290 0.0976 143 S 0.7795 0.0835 0.1370 144 E 0.6936 0.1198 0.1866 145 V 0.6330 0.1493 0.2177 146 R 0.4764 0.1932 0.3303 147 K 0.3383 0.2124 0.4493 148 F 0.1681 0.2015 0.6304 149 E 0.1027 0.1282 0.7691 150 I 0.0649 0.0433 0.8917 151 I 0.0469 0.0344 0.9186