# This file is the result of combining several RDB files, specifically # T0183.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0183.t2k.stride-ebghtl.rdb (weight 1.24869) # T0183.t2k.str.rdb (weight 1.53983) # T0183.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 T0183.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0183 # 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 T0183.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 52 # # ============================================ # Comments from T0183.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0183 # 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 T0183.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 52 # # ============================================ # Comments from T0183.t2k.str.rdb # ============================================ # TARGET T0183 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0183.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 52 # # ============================================ # Comments from T0183.t2k.alpha.rdb # ============================================ # TARGET T0183 # 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 T0183.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 52 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0682 0.0408 0.8910 2 I 0.0914 0.0842 0.8244 3 E 0.0172 0.7113 0.2715 4 Y 0.0070 0.8588 0.1342 5 R 0.0052 0.9262 0.0685 6 I 0.0045 0.9379 0.0575 7 E 0.0053 0.9404 0.0543 8 E 0.0064 0.9361 0.0574 9 A 0.0055 0.9295 0.0650 10 V 0.0075 0.9125 0.0800 11 A 0.0121 0.8470 0.1408 12 K 0.0203 0.7161 0.2636 13 Y 0.0438 0.6426 0.3136 14 R 0.0459 0.5997 0.3544 15 E 0.0640 0.5451 0.3909 16 F 0.1351 0.3989 0.4660 17 Y 0.2275 0.2733 0.4992 18 E 0.3181 0.1945 0.4874 19 F 0.2229 0.1321 0.6450 20 K 0.1030 0.1230 0.7740 21 P 0.0486 0.4519 0.4995 22 V 0.0168 0.6794 0.3038 23 R 0.0167 0.6597 0.3236 24 E 0.0144 0.6688 0.3168 25 S 0.0114 0.7443 0.2444 26 A 0.0121 0.7302 0.2577 27 G 0.0104 0.8005 0.1891 28 I 0.0062 0.8972 0.0966 29 E 0.0069 0.9203 0.0729 30 D 0.0066 0.9288 0.0646 31 V 0.0055 0.9329 0.0616 32 K 0.0056 0.9315 0.0629 33 S 0.0052 0.9032 0.0915 34 A 0.0084 0.8779 0.1137 35 I 0.0319 0.8200 0.1481 36 E 0.0347 0.7699 0.1954 37 H 0.0244 0.7022 0.2734 38 T 0.0343 0.5162 0.4495 39 N 0.0620 0.2581 0.6799 40 L 0.1078 0.0950 0.7972 41 K 0.0679 0.0557 0.8764 42 P 0.0164 0.2035 0.7801 43 F 0.0185 0.1238 0.8577 44 A 0.0699 0.0507 0.8794 45 T 0.0617 0.0273 0.9111 46 P 0.0046 0.9234 0.0720 47 D 0.0044 0.9478 0.0477 48 D 0.0045 0.9532 0.0423 49 I 0.0044 0.9595 0.0361 50 K 0.0044 0.9596 0.0360 51 K 0.0044 0.9582 0.0374 52 L 0.0044 0.9553 0.0402 53 C 0.0044 0.9554 0.0402 54 L 0.0044 0.9544 0.0412 55 E 0.0046 0.9454 0.0500 56 A 0.0053 0.9344 0.0604 57 R 0.0067 0.8877 0.1056 58 E 0.0116 0.7320 0.2564 59 N 0.0476 0.3282 0.6241 60 R 0.0556 0.0433 0.9012 61 F 0.1747 0.0188 0.8065 62 H 0.5928 0.0187 0.3886 63 G 0.8700 0.0076 0.1224 64 V 0.9115 0.0046 0.0839 65 C 0.8876 0.0057 0.1068 66 V 0.6827 0.0121 0.3052 67 N 0.2217 0.0162 0.7620 68 P 0.0267 0.4123 0.5609 69 C 0.0248 0.5782 0.3970 70 Y 0.0224 0.6925 0.2852 71 V 0.0117 0.8613 0.1270 72 K 0.0046 0.9462 0.0492 73 L 0.0045 0.9520 0.0435 74 A 0.0045 0.9542 0.0413 75 R 0.0045 0.9519 0.0436 76 E 0.0048 0.9467 0.0485 77 E 0.0065 0.9172 0.0762 78 L 0.0233 0.8534 0.1232 79 E 0.0091 0.7537 0.2372 80 G 0.0175 0.4458 0.5368 81 T 0.0623 0.1404 0.7973 82 D 0.0641 0.0346 0.9013 83 V 0.3231 0.0079 0.6690 84 K 0.7720 0.0050 0.2230 85 V 0.9055 0.0045 0.0901 86 V 0.9056 0.0057 0.0886 87 T 0.8814 0.0074 0.1112 88 V 0.8078 0.0164 0.1758 89 V 0.4725 0.0433 0.4842 90 G 0.2466 0.0294 0.7240 91 F 0.1889 0.0270 0.7841 92 P 0.1582 0.0566 0.7852 93 L 0.0773 0.0929 0.8298 94 G 0.0526 0.0822 0.8652 95 A 0.0645 0.1195 0.8160 96 N 0.0944 0.1458 0.7598 97 E 0.0713 0.4700 0.4587 98 T 0.0385 0.7829 0.1786 99 R 0.0268 0.8957 0.0776 100 T 0.0233 0.9146 0.0621 101 K 0.0136 0.9391 0.0472 102 A 0.0083 0.9538 0.0379 103 H 0.0067 0.9576 0.0356 104 E 0.0056 0.9571 0.0373 105 A 0.0061 0.9552 0.0387 106 I 0.0054 0.9563 0.0383 107 F 0.0049 0.9541 0.0410 108 A 0.0048 0.9450 0.0502 109 V 0.0049 0.9167 0.0785 110 E 0.0059 0.8288 0.1653 111 S 0.0375 0.3402 0.6223 112 G 0.0480 0.0956 0.8564 113 A 0.0949 0.0587 0.8465 114 D 0.1933 0.1156 0.6911 115 E 0.5658 0.0696 0.3646 116 I 0.6876 0.0271 0.2853 117 D 0.7267 0.0404 0.2330 118 M 0.8252 0.0252 0.1496 119 V 0.7302 0.0387 0.2311 120 I 0.5801 0.0663 0.3537 121 N 0.3012 0.0836 0.6152 122 V 0.0324 0.7155 0.2521 123 G 0.0165 0.8006 0.1829 124 M 0.0196 0.8443 0.1361 125 L 0.0343 0.8295 0.1362 126 K 0.0372 0.6926 0.2702 127 A 0.0389 0.4297 0.5314 128 K 0.0375 0.1241 0.8384 129 E 0.0661 0.2384 0.6956 130 W 0.0137 0.8793 0.1071 131 E 0.0053 0.9300 0.0648 132 Y 0.0058 0.9357 0.0585 133 V 0.0049 0.9474 0.0477 134 Y 0.0044 0.9576 0.0380 135 E 0.0044 0.9584 0.0372 136 D 0.0044 0.9580 0.0376 137 I 0.0044 0.9600 0.0357 138 R 0.0044 0.9601 0.0355 139 S 0.0044 0.9589 0.0367 140 V 0.0045 0.9557 0.0399 141 V 0.0046 0.9484 0.0470 142 E 0.0050 0.9343 0.0607 143 S 0.0095 0.8630 0.1275 144 V 0.0510 0.5468 0.4023 145 K 0.0291 0.2160 0.7549 146 G 0.0243 0.0926 0.8831 147 K 0.2201 0.0525 0.7275 148 V 0.6342 0.0239 0.3419 149 V 0.8478 0.0238 0.1283 150 K 0.8601 0.0393 0.1006 151 V 0.8794 0.0280 0.0926 152 I 0.8405 0.0429 0.1166 153 I 0.7453 0.0813 0.1734 154 E 0.6205 0.1090 0.2705 155 T 0.4015 0.1507 0.4478 156 C 0.2969 0.1448 0.5583 157 Y 0.2830 0.1042 0.6128 158 L 0.1240 0.0963 0.7797 159 D 0.0656 0.0670 0.8674 160 T 0.0140 0.8514 0.1346 161 E 0.0068 0.9183 0.0749 162 E 0.0067 0.9406 0.0527 163 K 0.0049 0.9556 0.0395 164 I 0.0047 0.9577 0.0377 165 A 0.0044 0.9592 0.0364 166 A 0.0044 0.9584 0.0373 167 C 0.0044 0.9593 0.0363 168 V 0.0044 0.9600 0.0356 169 I 0.0044 0.9604 0.0353 170 S 0.0044 0.9592 0.0364 171 K 0.0048 0.9506 0.0447 172 L 0.0061 0.9142 0.0798 173 A 0.0412 0.5161 0.4427 174 G 0.0500 0.0493 0.9008 175 A 0.0869 0.0252 0.8879 176 H 0.1443 0.0882 0.7674 177 F 0.6179 0.1428 0.2393 178 V 0.6792 0.1313 0.1895 179 K 0.6482 0.0984 0.2534 180 T 0.3020 0.1394 0.5586 181 S 0.1191 0.1321 0.7488 182 T 0.0859 0.1022 0.8120 183 G 0.0755 0.0607 0.8638 184 F 0.1208 0.0721 0.8071 185 G 0.1387 0.0822 0.7791 186 T 0.0983 0.1079 0.7938 187 G 0.0639 0.1057 0.8303 188 G 0.0556 0.0635 0.8809 189 A 0.1013 0.0359 0.8628 190 T 0.0921 0.0893 0.8185 191 A 0.0061 0.9362 0.0577 192 E 0.0044 0.9551 0.0405 193 D 0.0044 0.9586 0.0369 194 V 0.0044 0.9604 0.0353 195 H 0.0044 0.9607 0.0349 196 L 0.0044 0.9603 0.0353 197 M 0.0044 0.9599 0.0357 198 K 0.0044 0.9564 0.0391 199 W 0.0049 0.9470 0.0481 200 I 0.0068 0.9039 0.0894 201 V 0.0240 0.7539 0.2221 202 G 0.0270 0.5488 0.4241 203 D 0.0225 0.4165 0.5610 204 E 0.0351 0.2873 0.6776 205 M 0.1352 0.1225 0.7423 206 G 0.2028 0.0328 0.7644 207 V 0.4969 0.0238 0.4792 208 K 0.5748 0.0254 0.3998 209 A 0.4407 0.0583 0.5010 210 S 0.2007 0.1016 0.6976 211 G 0.1099 0.0820 0.8081 212 G 0.1092 0.1173 0.7734 213 I 0.2093 0.1063 0.6844 214 R 0.1598 0.1068 0.7333 215 T 0.0973 0.0560 0.8467 216 F 0.0048 0.9265 0.0687 217 E 0.0045 0.9512 0.0443 218 D 0.0047 0.9542 0.0411 219 A 0.0044 0.9587 0.0369 220 V 0.0044 0.9589 0.0367 221 K 0.0044 0.9589 0.0367 222 M 0.0045 0.9572 0.0383 223 I 0.0048 0.9546 0.0406 224 M 0.0048 0.9411 0.0541 225 Y 0.0062 0.8934 0.1003 226 G 0.0084 0.8438 0.1477 227 A 0.0105 0.8158 0.1737 228 D 0.0173 0.8143 0.1684 229 R 0.0406 0.7489 0.2105 230 I 0.0605 0.5703 0.3691 231 G 0.0682 0.3441 0.5877 232 T 0.0584 0.4207 0.5209 233 S 0.0358 0.5398 0.4244 234 S 0.0183 0.7194 0.2623 235 G 0.0202 0.8423 0.1375 236 V 0.0140 0.9235 0.0625 237 K 0.0152 0.9345 0.0504 238 I 0.0130 0.9359 0.0510 239 V 0.0164 0.9069 0.0768 240 Q 0.0144 0.8395 0.1462 241 G 0.0161 0.6983 0.2856 242 G 0.0317 0.6754 0.2928 243 E 0.0613 0.6575 0.2812 244 E 0.0530 0.6636 0.2834 245 R 0.0601 0.5001 0.4398 246 Y 0.0823 0.2545 0.6632 247 G 0.0564 0.0728 0.8707 248 G 0.0421 0.0310 0.9269