# This file is the result of combining several RDB files, specifically # T0198.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0198.t2k.stride-ebghtl.rdb (weight 1.24869) # T0198.t2k.str2.rdb (weight 1.54758) # T0198.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 T0198.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0198 # 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 T0198.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 190 # # ============================================ # Comments from T0198.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0198 # 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 T0198.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 190 # # ============================================ # Comments from T0198.t2k.str2.rdb # ============================================ # TARGET T0198 # 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 T0198.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 190 # # ============================================ # Comments from T0198.t2k.alpha.rdb # ============================================ # TARGET T0198 # 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 T0198.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 190 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0229 0.2681 0.7090 2 N 0.0321 0.5715 0.3964 3 R 0.0273 0.6955 0.2772 4 L 0.0257 0.7166 0.2576 5 L 0.0305 0.6364 0.3331 6 N 0.0226 0.6613 0.3162 7 E 0.0128 0.7988 0.1884 8 K 0.0134 0.8253 0.1613 9 V 0.0067 0.8816 0.1116 10 E 0.0058 0.9150 0.0791 11 E 0.0054 0.9266 0.0680 12 F 0.0051 0.9424 0.0525 13 K 0.0049 0.9534 0.0417 14 K 0.0049 0.9530 0.0421 15 G 0.0048 0.9539 0.0413 16 V 0.0048 0.9558 0.0394 17 L 0.0049 0.9534 0.0417 18 K 0.0050 0.9431 0.0520 19 A 0.0052 0.9360 0.0589 20 G 0.0053 0.9486 0.0461 21 W 0.0052 0.9475 0.0473 22 F 0.0050 0.9505 0.0445 23 I 0.0047 0.9548 0.0405 24 E 0.0047 0.9565 0.0388 25 K 0.0048 0.9556 0.0396 26 M 0.0048 0.9539 0.0413 27 F 0.0047 0.9578 0.0375 28 R 0.0047 0.9589 0.0364 29 N 0.0047 0.9572 0.0380 30 S 0.0047 0.9565 0.0388 31 I 0.0047 0.9578 0.0375 32 S 0.0047 0.9548 0.0404 33 S 0.0049 0.9453 0.0498 34 L 0.0050 0.9253 0.0697 35 V 0.0062 0.8797 0.1141 36 E 0.0181 0.6838 0.2981 37 R 0.0277 0.3496 0.6227 38 N 0.0668 0.2090 0.7242 39 E 0.0054 0.8962 0.0983 40 S 0.0052 0.9264 0.0684 41 L 0.0050 0.9361 0.0589 42 A 0.0048 0.9488 0.0465 43 R 0.0048 0.9439 0.0513 44 E 0.0049 0.9403 0.0549 45 V 0.0055 0.9332 0.0613 46 I 0.0065 0.9212 0.0723 47 A 0.0068 0.8835 0.1096 48 D 0.0082 0.8615 0.1303 49 E 0.0081 0.8933 0.0987 50 E 0.0062 0.8963 0.0975 51 V 0.0063 0.9162 0.0774 52 V 0.0065 0.9329 0.0606 53 D 0.0066 0.9376 0.0557 54 Q 0.0049 0.9458 0.0493 55 M 0.0051 0.9500 0.0449 56 E 0.0047 0.9543 0.0410 57 V 0.0048 0.9545 0.0407 58 E 0.0047 0.9538 0.0414 59 I 0.0047 0.9552 0.0400 60 Q 0.0047 0.9571 0.0382 61 E 0.0049 0.9554 0.0397 62 K 0.0048 0.9550 0.0402 63 A 0.0047 0.9559 0.0393 64 M 0.0047 0.9576 0.0377 65 E 0.0048 0.9567 0.0385 66 V 0.0049 0.9533 0.0418 67 L 0.0052 0.9424 0.0524 68 G 0.0059 0.8935 0.1006 69 L 0.0093 0.7096 0.2811 70 F 0.0323 0.5061 0.4615 71 S 0.0480 0.1723 0.7797 72 P 0.0410 0.2464 0.7126 73 I 0.0263 0.3849 0.5888 74 G 0.0163 0.5801 0.4036 75 K 0.0143 0.5834 0.4023 76 P 0.0217 0.6896 0.2887 77 L 0.0049 0.9276 0.0675 78 L 0.0048 0.9498 0.0455 79 T 0.0047 0.9575 0.0378 80 V 0.0047 0.9600 0.0353 81 T 0.0047 0.9602 0.0351 82 A 0.0047 0.9596 0.0357 83 G 0.0047 0.9597 0.0357 84 I 0.0047 0.9596 0.0357 85 R 0.0047 0.9551 0.0401 86 V 0.0048 0.9461 0.0490 87 A 0.0050 0.9487 0.0463 88 E 0.0054 0.9263 0.0683 89 L 0.0054 0.9257 0.0689 90 I 0.0049 0.9474 0.0477 91 E 0.0051 0.9468 0.0481 92 N 0.0051 0.9320 0.0628 93 I 0.0051 0.9416 0.0533 94 A 0.0049 0.9517 0.0434 95 D 0.0049 0.9527 0.0424 96 K 0.0048 0.9541 0.0411 97 C 0.0047 0.9574 0.0379 98 H 0.0048 0.9582 0.0370 99 D 0.0048 0.9570 0.0382 100 I 0.0047 0.9565 0.0388 101 A 0.0047 0.9561 0.0392 102 K 0.0048 0.9532 0.0420 103 N 0.0048 0.9465 0.0487 104 V 0.0050 0.9385 0.0564 105 L 0.0055 0.9120 0.0826 106 E 0.0077 0.8541 0.1381 107 L 0.0185 0.7515 0.2300 108 M 0.0436 0.4772 0.4791 109 E 0.0286 0.3016 0.6698 110 E 0.0420 0.1853 0.7727 111 P 0.0585 0.1142 0.8273 112 P 0.0623 0.1449 0.7927 113 L 0.0255 0.5322 0.4423 114 K 0.0209 0.6141 0.3650 115 P 0.0177 0.7285 0.2538 116 L 0.0081 0.8628 0.1291 117 E 0.0063 0.8956 0.0981 118 D 0.0059 0.9128 0.0813 119 I 0.0049 0.9453 0.0498 120 P 0.0048 0.9563 0.0389 121 A 0.0049 0.9557 0.0394 122 M 0.0048 0.9550 0.0402 123 A 0.0047 0.9596 0.0357 124 N 0.0049 0.9574 0.0377 125 Q 0.0048 0.9563 0.0389 126 T 0.0047 0.9568 0.0385 127 S 0.0048 0.9578 0.0374 128 E 0.0048 0.9567 0.0385 129 M 0.0048 0.9541 0.0411 130 L 0.0047 0.9581 0.0372 131 K 0.0047 0.9592 0.0361 132 F 0.0047 0.9566 0.0387 133 A 0.0047 0.9555 0.0397 134 L 0.0048 0.9550 0.0402 135 R 0.0048 0.9455 0.0497 136 M 0.0054 0.9175 0.0771 137 F 0.0083 0.8352 0.1565 138 A 0.0127 0.6672 0.3201 139 D 0.0389 0.3598 0.6013 140 V 0.0318 0.1543 0.8139 141 N 0.0760 0.0761 0.8478 142 V 0.0053 0.9091 0.0857 143 E 0.0050 0.9385 0.0565 144 K 0.0049 0.9457 0.0494 145 S 0.0047 0.9547 0.0406 146 F 0.0048 0.9534 0.0418 147 E 0.0048 0.9510 0.0442 148 V 0.0048 0.9458 0.0494 149 C 0.0052 0.9371 0.0576 150 R 0.0060 0.9100 0.0840 151 M 0.0093 0.8894 0.1013 152 D 0.0093 0.8906 0.1001 153 S 0.0063 0.9068 0.0869 154 K 0.0067 0.9236 0.0697 155 V 0.0057 0.9401 0.0542 156 D 0.0054 0.9481 0.0465 157 D 0.0049 0.9528 0.0423 158 L 0.0050 0.9539 0.0411 159 Y 0.0048 0.9545 0.0407 160 E 0.0048 0.9555 0.0397 161 K 0.0048 0.9560 0.0391 162 V 0.0048 0.9567 0.0385 163 R 0.0048 0.9558 0.0394 164 E 0.0048 0.9573 0.0380 165 E 0.0048 0.9550 0.0401 166 L 0.0048 0.9536 0.0416 167 L 0.0049 0.9513 0.0438 168 L 0.0054 0.9427 0.0518 169 Y 0.0065 0.9189 0.0746 170 M 0.0114 0.8911 0.0975 171 M 0.0109 0.8065 0.1826 172 E 0.0200 0.5923 0.3878 173 S 0.0592 0.1579 0.7829 174 P 0.0195 0.4027 0.5779 175 K 0.0160 0.4409 0.5431 176 Y 0.0301 0.5386 0.4313 177 V 0.0073 0.9180 0.0746 178 K 0.0058 0.9408 0.0534 179 R 0.0052 0.9514 0.0434 180 A 0.0050 0.9563 0.0387 181 L 0.0050 0.9565 0.0385 182 L 0.0047 0.9578 0.0375 183 L 0.0047 0.9585 0.0367 184 L 0.0047 0.9585 0.0368 185 E 0.0048 0.9572 0.0380 186 I 0.0048 0.9548 0.0404 187 A 0.0048 0.9544 0.0407 188 G 0.0051 0.9447 0.0503 189 N 0.0052 0.9320 0.0628 190 I 0.0062 0.9400 0.0537 191 E 0.0064 0.9413 0.0523 192 I 0.0060 0.9257 0.0683 193 I 0.0069 0.9289 0.0641 194 A 0.0070 0.9276 0.0653 195 D 0.0064 0.9226 0.0711 196 Y 0.0062 0.9139 0.0798 197 A 0.0063 0.9129 0.0807 198 T 0.0069 0.9042 0.0889 199 N 0.0086 0.8804 0.1110 200 I 0.0073 0.9259 0.0668 201 V 0.0128 0.9256 0.0616 202 E 0.0119 0.9301 0.0580 203 V 0.0201 0.9232 0.0568 204 S 0.0264 0.9198 0.0537 205 V 0.0766 0.8611 0.0623 206 Y 0.1544 0.7660 0.0796 207 M 0.1804 0.7128 0.1067 208 V 0.2082 0.5784 0.2134 209 Q 0.1175 0.2876 0.5949 210 G 0.0779 0.0883 0.8338 211 E 0.2096 0.0734 0.7170 212 A 0.3985 0.0532 0.5482 213 Y 0.2690 0.0943 0.6366 214 K 0.2002 0.1233 0.6765 215 C 0.1500 0.1085 0.7416 216 Y 0.1240 0.0918 0.7842 217 H 0.1015 0.0592 0.8393 218 D 0.0966 0.1422 0.7611 219 E 0.0881 0.2705 0.6414 220 L 0.0772 0.2827 0.6401 221 L 0.0899 0.2760 0.6341 222 L 0.0795 0.3032 0.6173 223 F 0.1246 0.2788 0.5965 224 K 0.1571 0.2575 0.5854 225 K 0.1440 0.2594 0.5966 226 S 0.1229 0.2592 0.6179 227 G 0.0845 0.1493 0.7662 228 G 0.1088 0.1079 0.7833 229 V 0.3132 0.1279 0.5589 230 L 0.4081 0.1466 0.4452 231 F 0.3938 0.1810 0.4252 232 E 0.3254 0.2175 0.4572 233 S 0.2220 0.1908 0.5872 234 S 0.1518 0.1229 0.7254 235 D 0.0568 0.0437 0.8996