# This file is the result of combining several RDB files, specifically # T0329.t04.dssp-ebghstl.rdb (weight 1.53986) # T0329.t04.stride-ebghtl.rdb (weight 1.24869) # T0329.t04.str2.rdb (weight 1.54758) # T0329.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 T0329.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0329 # 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 T0329.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 2251 # # ============================================ # Comments from T0329.t04.stride-ebghtl.rdb # ============================================ # TARGET T0329 # 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 T0329.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 2251 # # ============================================ # Comments from T0329.t04.str2.rdb # ============================================ # TARGET T0329 # 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 T0329.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 2251 # # ============================================ # Comments from T0329.t04.alpha.rdb # ============================================ # TARGET T0329 # 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 T0329.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 2251 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0742 0.0142 0.9115 2 K 0.1616 0.0153 0.8231 3 Y 0.3926 0.0061 0.6014 4 K 0.6078 0.0320 0.3602 5 A 0.9134 0.0036 0.0830 6 A 0.9301 0.0032 0.0667 7 I 0.9321 0.0032 0.0647 8 F 0.9051 0.0039 0.0910 9 D 0.5533 0.0065 0.4402 10 M 0.1505 0.0493 0.8002 11 D 0.0580 0.0444 0.8976 12 G 0.0938 0.0634 0.8428 13 T 0.3717 0.0666 0.5617 14 I 0.6683 0.0639 0.2678 15 L 0.5579 0.0767 0.3654 16 D 0.2758 0.0682 0.6560 17 T 0.0653 0.1646 0.7701 18 S 0.0265 0.5572 0.4163 19 A 0.0071 0.8673 0.1256 20 D 0.0094 0.8813 0.1094 21 L 0.0048 0.9543 0.0410 22 T 0.0047 0.9598 0.0355 23 S 0.0047 0.9603 0.0351 24 A 0.0047 0.9612 0.0341 25 L 0.0047 0.9601 0.0352 26 N 0.0047 0.9600 0.0354 27 Y 0.0048 0.9583 0.0369 28 A 0.0047 0.9582 0.0370 29 F 0.0049 0.9574 0.0377 30 E 0.0052 0.9493 0.0455 31 Q 0.0087 0.9024 0.0888 32 T 0.0454 0.5729 0.3817 33 G 0.0335 0.0471 0.9194 34 H 0.0566 0.0277 0.9157 35 R 0.0720 0.0410 0.8870 36 H 0.0913 0.0568 0.8519 37 D 0.1217 0.0376 0.8407 38 F 0.1159 0.0211 0.8631 39 T 0.0738 0.0206 0.9056 40 V 0.0048 0.9457 0.0495 41 E 0.0047 0.9578 0.0375 42 D 0.0047 0.9581 0.0371 43 I 0.0048 0.9557 0.0395 44 K 0.0053 0.9423 0.0524 45 N 0.0067 0.9000 0.0932 46 F 0.0116 0.8362 0.1523 47 F 0.0330 0.6905 0.2766 48 G 0.0323 0.3691 0.5986 49 S 0.0386 0.4134 0.5480 50 G 0.0351 0.4839 0.4809 51 V 0.0214 0.8465 0.1322 52 V 0.0189 0.9001 0.0810 53 V 0.0169 0.9308 0.0523 54 A 0.0153 0.9365 0.0482 55 V 0.0177 0.9310 0.0513 56 T 0.0160 0.9287 0.0553 57 R 0.0140 0.9058 0.0802 58 A 0.0167 0.8487 0.1346 59 L 0.0368 0.6651 0.2981 60 A 0.0525 0.5838 0.3638 61 Y 0.0411 0.5857 0.3732 62 E 0.0450 0.5592 0.3957 63 A 0.0455 0.4290 0.5255 64 G 0.0378 0.2675 0.6947 65 S 0.0632 0.2032 0.7336 66 S 0.0852 0.1969 0.7179 67 R 0.0697 0.4250 0.5052 68 E 0.0536 0.6539 0.2926 69 S 0.0710 0.7225 0.2065 70 L 0.0951 0.7445 0.1604 71 V 0.1093 0.7188 0.1720 72 A 0.0939 0.7287 0.1774 73 F 0.0826 0.6060 0.3114 74 G 0.0768 0.3388 0.5844 75 T 0.0972 0.2592 0.6437 76 K 0.0758 0.4118 0.5123 77 D 0.0438 0.6183 0.3380 78 E 0.0273 0.6460 0.3267 79 Q 0.0405 0.5921 0.3674 80 I 0.0665 0.4383 0.4952 81 P 0.0288 0.6035 0.3677 82 E 0.0235 0.6547 0.3219 83 A 0.0306 0.5803 0.3891 84 V 0.0620 0.4441 0.4939 85 T 0.0521 0.3490 0.5989 86 Q 0.0079 0.8255 0.1666 87 T 0.0081 0.8112 0.1807 88 E 0.0105 0.8279 0.1616 89 V 0.0053 0.9386 0.0560 90 N 0.0053 0.9499 0.0448 91 R 0.0053 0.9460 0.0486 92 V 0.0052 0.9462 0.0487 93 L 0.0053 0.9470 0.0477 94 E 0.0058 0.9361 0.0580 95 V 0.0066 0.9009 0.0924 96 F 0.0099 0.8420 0.1481 97 K 0.0093 0.8324 0.1583 98 P 0.0054 0.9125 0.0821 99 Y 0.0069 0.9054 0.0877 100 Y 0.0073 0.9172 0.0755 101 A 0.0071 0.9122 0.0807 102 D 0.0075 0.8618 0.1307 103 H 0.0133 0.7823 0.2044 104 C 0.0388 0.6079 0.3533 105 Q 0.0452 0.5238 0.4309 106 I 0.0528 0.4763 0.4709 107 K 0.0664 0.3489 0.5847 108 T 0.0865 0.0924 0.8211 109 G 0.0727 0.0531 0.8742 110 P 0.0804 0.0767 0.8429 111 F 0.0605 0.0529 0.8865 112 P 0.0153 0.3800 0.6047 113 G 0.0181 0.4015 0.5805 114 I 0.0071 0.8906 0.1023 115 L 0.0058 0.9501 0.0441 116 D 0.0061 0.9517 0.0422 117 L 0.0057 0.9561 0.0382 118 M 0.0047 0.9603 0.0350 119 K 0.0046 0.9598 0.0355 120 N 0.0047 0.9596 0.0358 121 L 0.0047 0.9589 0.0364 122 R 0.0048 0.9500 0.0452 123 Q 0.0055 0.9154 0.0791 124 K 0.0417 0.3079 0.6503 125 G 0.0389 0.0143 0.9469 126 V 0.0929 0.0077 0.8994 127 K 0.6250 0.0066 0.3684 128 L 0.9272 0.0038 0.0690 129 A 0.9321 0.0034 0.0645 130 V 0.9320 0.0032 0.0647 131 V 0.8765 0.0064 0.1171 132 S 0.4743 0.0135 0.5122 133 N 0.0699 0.0395 0.8906 134 K 0.0622 0.0315 0.9063 135 P 0.0468 0.1989 0.7543 136 N 0.0146 0.7129 0.2725 137 E 0.0070 0.9154 0.0776 138 A 0.0053 0.9444 0.0503 139 V 0.0052 0.9564 0.0383 140 Q 0.0059 0.9578 0.0363 141 V 0.0054 0.9567 0.0379 142 L 0.0049 0.9551 0.0400 143 V 0.0048 0.9510 0.0441 144 E 0.0054 0.9358 0.0588 145 E 0.0069 0.8403 0.1528 146 L 0.0167 0.6255 0.3578 147 F 0.0464 0.1230 0.8306 148 P 0.0290 0.2355 0.7356 149 G 0.0282 0.2440 0.7278 150 S 0.1260 0.2829 0.5910 151 F 0.3595 0.0857 0.5548 152 D 0.2850 0.0741 0.6409 153 F 0.8283 0.0224 0.1492 154 A 0.8918 0.0129 0.0953 155 L 0.8883 0.0131 0.0986 156 G 0.7176 0.0168 0.2656 157 E 0.2639 0.1298 0.6063 158 K 0.1032 0.1831 0.7137 159 S 0.0782 0.2399 0.6819 160 G 0.0960 0.1779 0.7261 161 I 0.1381 0.2080 0.6539 162 R 0.1289 0.1948 0.6763 163 R 0.1463 0.0877 0.7660 164 K 0.1205 0.0250 0.8546 165 P 0.0953 0.0241 0.8806 166 A 0.0767 0.0312 0.8921 167 P 0.0126 0.8114 0.1760 168 D 0.0082 0.9103 0.0815 169 M 0.0053 0.9427 0.0519 170 T 0.0048 0.9566 0.0386 171 S 0.0047 0.9609 0.0345 172 E 0.0047 0.9606 0.0347 173 C 0.0047 0.9609 0.0344 174 V 0.0047 0.9597 0.0356 175 K 0.0049 0.9549 0.0402 176 V 0.0065 0.9289 0.0646 177 L 0.0456 0.5110 0.4433 178 G 0.0397 0.0193 0.9410 179 V 0.0649 0.0088 0.9263 180 P 0.0759 0.0115 0.9126 181 R 0.0202 0.6958 0.2840 182 D 0.0229 0.6939 0.2832 183 K 0.1722 0.5294 0.2984 184 C 0.8187 0.0251 0.1561 185 V 0.8781 0.0146 0.1073 186 Y 0.9101 0.0064 0.0835 187 I 0.8063 0.0256 0.1681 188 G 0.3757 0.0218 0.6025 189 D 0.1389 0.0218 0.8393 190 S 0.0640 0.1044 0.8316 191 E 0.0135 0.7151 0.2714 192 I 0.0159 0.8097 0.1744 193 D 0.0218 0.8075 0.1707 194 I 0.0071 0.9457 0.0473 195 Q 0.0051 0.9532 0.0418 196 T 0.0050 0.9558 0.0392 197 A 0.0058 0.9518 0.0425 198 R 0.0065 0.9346 0.0589 199 N 0.0082 0.8199 0.1719 200 S 0.0473 0.3378 0.6150 201 E 0.0487 0.0237 0.9276 202 M 0.1076 0.0084 0.8839 203 D 0.3200 0.0445 0.6354 204 E 0.9027 0.0049 0.0924 205 I 0.9261 0.0037 0.0702 206 A 0.9271 0.0036 0.0693 207 V 0.8832 0.0075 0.1093 208 N 0.5879 0.0108 0.4014 209 W 0.1730 0.0522 0.7748 210 G 0.0752 0.0654 0.8594 211 F 0.0782 0.1205 0.8012 212 R 0.0810 0.1068 0.8122 213 S 0.0915 0.1307 0.7778 214 V 0.0576 0.3981 0.5443 215 P 0.0258 0.7707 0.2035 216 F 0.0190 0.8412 0.1398 217 L 0.0207 0.8542 0.1251 218 Q 0.0182 0.8379 0.1439 219 K 0.0212 0.7069 0.2719 220 H 0.0535 0.3504 0.5961 221 G 0.0695 0.0360 0.8945 222 A 0.1422 0.0182 0.8396 223 T 0.4471 0.0408 0.5121 224 V 0.8355 0.0111 0.1534 225 I 0.8812 0.0140 0.1048 226 V 0.8162 0.0199 0.1640 227 D 0.3936 0.0695 0.5369 228 T 0.1236 0.0772 0.7993 229 A 0.0114 0.7922 0.1965 230 E 0.0054 0.9139 0.0807 231 K 0.0057 0.9152 0.0791 232 L 0.0061 0.9224 0.0716 233 E 0.0063 0.9330 0.0607 234 E 0.0061 0.9260 0.0680 235 A 0.0088 0.8902 0.1010 236 I 0.0200 0.7248 0.2552 237 L 0.0256 0.4435 0.5310 238 G 0.0288 0.1399 0.8313 239 E 0.0388 0.0829 0.8783