# This file is the result of combining several RDB files, specifically # T0330.t04.dssp-ebghstl.rdb (weight 1.53986) # T0330.t04.stride-ebghtl.rdb (weight 1.24869) # T0330.t04.str2.rdb (weight 1.54758) # T0330.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 T0330.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0330 # Using neural net t06-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 T0330.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 2277 # # ============================================ # Comments from T0330.t04.stride-ebghtl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 2277 # # ============================================ # Comments from T0330.t04.str2.rdb # ============================================ # TARGET T0330 # Using neural net t04-2621-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 T0330.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 2277 # # ============================================ # Comments from T0330.t04.alpha.rdb # ============================================ # TARGET T0330 # 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 T0330.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 2277 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0671 0.0132 0.9198 2 S 0.1389 0.0173 0.8439 3 R 0.2232 0.0097 0.7670 4 T 0.4752 0.0364 0.4885 5 L 0.9183 0.0035 0.0781 6 V 0.9327 0.0032 0.0641 7 L 0.9326 0.0032 0.0642 8 F 0.9156 0.0039 0.0805 9 D 0.6312 0.0051 0.3637 10 I 0.2198 0.0487 0.7315 11 D 0.0752 0.0472 0.8776 12 G 0.0757 0.0629 0.8614 13 T 0.2584 0.0645 0.6770 14 L 0.5938 0.0817 0.3245 15 L 0.4728 0.1004 0.4268 16 K 0.3141 0.0955 0.5904 17 V 0.0837 0.3238 0.5925 18 E 0.0189 0.7483 0.2327 19 S 0.0080 0.9048 0.0872 20 M 0.0063 0.9276 0.0661 21 N 0.0053 0.9473 0.0474 22 R 0.0049 0.9571 0.0379 23 R 0.0049 0.9587 0.0364 24 V 0.0047 0.9585 0.0369 25 L 0.0047 0.9581 0.0372 26 A 0.0047 0.9567 0.0386 27 D 0.0048 0.9455 0.0497 28 A 0.0050 0.9307 0.0643 29 L 0.0050 0.9251 0.0700 30 I 0.0061 0.9335 0.0604 31 E 0.0074 0.9146 0.0780 32 V 0.0120 0.8689 0.1191 33 Y 0.0511 0.5065 0.4424 34 G 0.0336 0.0641 0.9023 35 T 0.0612 0.0292 0.9095 36 E 0.0997 0.0332 0.8671 37 G 0.0869 0.0313 0.8817 38 S 0.0773 0.0385 0.8842 39 T 0.0376 0.3414 0.6210 40 G 0.0534 0.2695 0.6771 41 S 0.0811 0.2817 0.6372 42 H 0.1115 0.1867 0.7018 43 D 0.1487 0.2196 0.6317 44 F 0.1960 0.2887 0.5153 45 S 0.1738 0.2214 0.6049 46 G 0.1153 0.1309 0.7538 47 K 0.0972 0.1380 0.7649 48 M 0.0818 0.1916 0.7267 49 D 0.0371 0.5241 0.4389 50 G 0.0125 0.8560 0.1314 51 A 0.0114 0.9220 0.0666 52 I 0.0088 0.9427 0.0485 53 I 0.0061 0.9529 0.0410 54 Y 0.0059 0.9557 0.0384 55 E 0.0053 0.9527 0.0421 56 V 0.0049 0.9521 0.0430 57 L 0.0054 0.9471 0.0474 58 S 0.0058 0.9297 0.0645 59 N 0.0077 0.8644 0.1279 60 V 0.0467 0.5565 0.3969 61 G 0.0400 0.1071 0.8529 62 L 0.0631 0.1297 0.8072 63 E 0.0791 0.2074 0.7135 64 R 0.0260 0.6815 0.2925 65 A 0.0090 0.8842 0.1068 66 E 0.0081 0.9169 0.0750 67 I 0.0082 0.9208 0.0710 68 A 0.0083 0.9210 0.0708 69 D 0.0059 0.9140 0.0801 70 K 0.0053 0.9004 0.0943 71 F 0.0058 0.9079 0.0863 72 D 0.0050 0.9259 0.0692 73 K 0.0054 0.9310 0.0636 74 A 0.0054 0.9271 0.0676 75 K 0.0049 0.9492 0.0458 76 E 0.0047 0.9567 0.0385 77 T 0.0047 0.9572 0.0381 78 Y 0.0047 0.9579 0.0374 79 I 0.0047 0.9600 0.0354 80 A 0.0047 0.9600 0.0353 81 L 0.0047 0.9584 0.0369 82 F 0.0047 0.9557 0.0395 83 R 0.0048 0.9491 0.0461 84 E 0.0052 0.9296 0.0652 85 R 0.0070 0.8763 0.1167 86 A 0.0172 0.7707 0.2120 87 R 0.0229 0.6266 0.3505 88 R 0.0304 0.4964 0.4732 89 E 0.0338 0.2990 0.6672 90 D 0.0584 0.1688 0.7728 91 I 0.1783 0.0769 0.7447 92 T 0.2499 0.0863 0.6639 93 L 0.2330 0.1282 0.6387 94 L 0.0812 0.1880 0.7309 95 E 0.0158 0.5241 0.4601 96 G 0.0124 0.5119 0.4757 97 V 0.0093 0.8747 0.1161 98 R 0.0065 0.9399 0.0536 99 E 0.0080 0.9422 0.0498 100 L 0.0050 0.9553 0.0397 101 L 0.0052 0.9561 0.0386 102 D 0.0047 0.9570 0.0383 103 A 0.0048 0.9505 0.0447 104 L 0.0050 0.9190 0.0760 105 S 0.0058 0.8266 0.1675 106 S 0.0088 0.6252 0.3660 107 R 0.0422 0.2750 0.6827 108 S 0.0434 0.0463 0.9103 109 D 0.0641 0.0367 0.8992 110 V 0.3545 0.0102 0.6352 111 L 0.6359 0.0067 0.3574 112 L 0.9191 0.0039 0.0770 113 G 0.9300 0.0036 0.0664 114 L 0.9289 0.0036 0.0674 115 L 0.8833 0.0086 0.1081 116 T 0.4768 0.0117 0.5116 117 G 0.0743 0.0506 0.8751 118 N 0.0791 0.0715 0.8494 119 F 0.0530 0.3650 0.5820 120 E 0.0319 0.6897 0.2784 121 A 0.0270 0.7828 0.1902 122 S 0.0286 0.7976 0.1738 123 G 0.0380 0.8047 0.1573 124 R 0.0446 0.8197 0.1357 125 H 0.0445 0.8434 0.1121 126 K 0.0390 0.8448 0.1162 127 L 0.0437 0.7697 0.1866 128 K 0.0343 0.5231 0.4426 129 L 0.0555 0.2779 0.6667 130 P 0.0375 0.2162 0.7463 131 G 0.0349 0.1579 0.8071 132 I 0.0736 0.2500 0.6763 133 D 0.0570 0.3723 0.5708 134 H 0.0668 0.3541 0.5791 135 Y 0.1221 0.2245 0.6534 136 F 0.2605 0.0405 0.6990 137 P 0.2218 0.1000 0.6782 138 F 0.7829 0.0445 0.1726 139 G 0.8945 0.0202 0.0853 140 A 0.8875 0.0180 0.0945 141 F 0.7236 0.0213 0.2550 142 A 0.2161 0.2018 0.5821 143 D 0.0547 0.3877 0.5576 144 D 0.0600 0.4766 0.4634 145 A 0.0589 0.5021 0.4389 146 L 0.0451 0.5226 0.4322 147 D 0.0386 0.4427 0.5188 148 R 0.0489 0.3230 0.6281 149 N 0.0627 0.1544 0.7829 150 E 0.0659 0.1515 0.7826 151 L 0.0846 0.0853 0.8300 152 P 0.0090 0.8647 0.1263 153 H 0.0060 0.9356 0.0584 154 I 0.0048 0.9524 0.0428 155 A 0.0050 0.9572 0.0378 156 L 0.0049 0.9592 0.0358 157 E 0.0047 0.9587 0.0367 158 R 0.0047 0.9560 0.0393 159 A 0.0048 0.9446 0.0506 160 R 0.0051 0.8843 0.1106 161 R 0.0072 0.7786 0.2143 162 M 0.0272 0.3615 0.6113 163 T 0.0276 0.2044 0.7680 164 G 0.0195 0.1312 0.8493 165 A 0.0604 0.1154 0.8242 166 N 0.0737 0.0404 0.8859 167 Y 0.1514 0.0104 0.8382 168 S 0.1274 0.0092 0.8635 169 P 0.0442 0.6219 0.3339 170 S 0.1093 0.5028 0.3879 171 Q 0.3447 0.3065 0.3488 172 I 0.8748 0.0110 0.1143 173 V 0.9083 0.0097 0.0820 174 I 0.9211 0.0050 0.0738 175 I 0.8507 0.0268 0.1224 176 G 0.5215 0.0185 0.4600 177 D 0.1890 0.0175 0.7935 178 T 0.0615 0.0643 0.8742 179 E 0.0082 0.7732 0.2186 180 H 0.0109 0.8451 0.1440 181 D 0.0087 0.8649 0.1264 182 I 0.0054 0.9477 0.0470 183 R 0.0047 0.9535 0.0418 184 C 0.0047 0.9571 0.0382 185 A 0.0047 0.9557 0.0395 186 R 0.0052 0.9495 0.0453 187 E 0.0056 0.9064 0.0880 188 L 0.0463 0.3800 0.5737 189 D 0.0488 0.0146 0.9367 190 A 0.0955 0.0075 0.8970 191 R 0.3842 0.0247 0.5911 192 S 0.9023 0.0037 0.0940 193 I 0.9249 0.0035 0.0716 194 A 0.9266 0.0034 0.0700 195 V 0.8839 0.0059 0.1102 196 A 0.6114 0.0121 0.3765 197 T 0.1786 0.0417 0.7797 198 G 0.0628 0.0571 0.8802 199 N 0.0776 0.0776 0.8449 200 F 0.1050 0.0525 0.8425 201 T 0.1134 0.0744 0.8123 202 M 0.0104 0.8931 0.0965 203 E 0.0064 0.9345 0.0591 204 E 0.0056 0.9403 0.0542 205 L 0.0065 0.9251 0.0683 206 A 0.0099 0.8785 0.1116 207 R 0.0127 0.7243 0.2631 208 H 0.0494 0.4507 0.4999 209 K 0.0692 0.0485 0.8823 210 P 0.0705 0.0729 0.8566 211 G 0.1505 0.0711 0.7784 212 T 0.7872 0.0252 0.1876 213 L 0.8793 0.0162 0.1044 214 F 0.8128 0.0168 0.1704 215 K 0.4871 0.0683 0.4446 216 N 0.1669 0.0417 0.7914 217 F 0.0145 0.7433 0.2422 218 A 0.0085 0.8336 0.1579 219 E 0.0115 0.8440 0.1446 220 T 0.0105 0.8474 0.1420 221 D 0.0051 0.9377 0.0572 222 E 0.0050 0.9478 0.0472 223 V 0.0048 0.9506 0.0447 224 L 0.0049 0.9439 0.0512 225 A 0.0051 0.9219 0.0730 226 S 0.0070 0.8393 0.1537 227 I 0.0155 0.6726 0.3118 228 L 0.0480 0.3458 0.6062 229 T 0.0539 0.1025 0.8436 230 P 0.0369 0.1455 0.8176 231 K 0.0513 0.1343 0.8144 232 H 0.0710 0.0620 0.8670 233 S 0.0489 0.0352 0.9160