# This file is the result of combining several RDB files, specifically # T0640.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0640.t2k.stride-ebghtl.rdb (weight 1.24869) # T0640.t2k.str.rdb (weight 1.53983) # 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 T0640.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0640 # 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 T0640.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 1286 # # ============================================ # Comments from T0640.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0640 # 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 T0640.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 1286 # # ============================================ # Comments from T0640.t2k.str.rdb # ============================================ # TARGET T0640 # 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 T0640.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 1286 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0247 0.0104 0.9649 2 S 0.1597 0.0389 0.8014 3 L 0.2477 0.1101 0.6423 4 E 0.2222 0.1065 0.6714 5 K 0.1292 0.1490 0.7218 6 Q 0.0312 0.1214 0.8475 7 K 0.0257 0.0451 0.9293 8 G 0.3288 0.0119 0.6593 9 L 0.9214 0.0025 0.0761 10 A 0.9764 0.0024 0.0211 11 I 0.9749 0.0024 0.0227 12 I 0.9389 0.0031 0.0580 13 T 0.5744 0.0081 0.4176 14 G 0.1224 0.0422 0.8355 15 A 0.0304 0.1489 0.8207 16 S 0.0306 0.2193 0.7501 17 Q 0.0156 0.3787 0.6058 18 G 0.0098 0.6761 0.3141 19 I 0.0047 0.9386 0.0566 20 G 0.0040 0.9669 0.0291 21 A 0.0037 0.9746 0.0217 22 V 0.0037 0.9759 0.0204 23 I 0.0037 0.9759 0.0204 24 A 0.0037 0.9752 0.0211 25 A 0.0037 0.9734 0.0229 26 G 0.0037 0.9721 0.0242 27 L 0.0037 0.9715 0.0248 28 A 0.0038 0.9609 0.0353 29 T 0.0038 0.8706 0.1256 30 D 0.0045 0.3400 0.6555 31 G 0.0091 0.0101 0.9808 32 Y 0.0326 0.0054 0.9620 33 R 0.5253 0.0038 0.4710 34 V 0.9736 0.0024 0.0240 35 V 0.9819 0.0024 0.0157 36 L 0.9811 0.0024 0.0165 37 I 0.9550 0.0029 0.0421 38 A 0.6330 0.0070 0.3600 39 R 0.1148 0.0129 0.8723 40 S 0.0654 0.0160 0.9186 41 K 0.0053 0.8079 0.1869 42 Q 0.0043 0.8829 0.1128 43 N 0.0039 0.9364 0.0597 44 L 0.0038 0.9602 0.0359 45 E 0.0041 0.9621 0.0338 46 K 0.0038 0.9596 0.0366 47 V 0.0041 0.9606 0.0353 48 H 0.0038 0.9665 0.0298 49 D 0.0038 0.9588 0.0375 50 E 0.0038 0.9457 0.0505 51 I 0.0051 0.9223 0.0726 52 M 0.0046 0.8936 0.1018 53 R 0.0054 0.8181 0.1764 54 S 0.0074 0.7201 0.2725 55 N 0.0144 0.4887 0.4968 56 K 0.0172 0.3364 0.6464 57 H 0.0184 0.2513 0.7303 58 V 0.0231 0.0633 0.9136 59 Q 0.0945 0.0508 0.8547 60 E 0.3923 0.0205 0.5871 61 P 0.6463 0.0067 0.3470 62 I 0.8929 0.0032 0.1038 63 V 0.9275 0.0028 0.0697 64 L 0.8993 0.0030 0.0977 65 P 0.8324 0.0052 0.1624 66 L 0.5891 0.0100 0.4009 67 D 0.4108 0.0210 0.5682 68 I 0.2025 0.0616 0.7360 69 T 0.0911 0.0414 0.8675 70 D 0.0338 0.0396 0.9267 71 C 0.0048 0.8295 0.1657 72 T 0.0053 0.9017 0.0930 73 K 0.0040 0.9378 0.0583 74 A 0.0039 0.9618 0.0343 75 D 0.0038 0.9699 0.0263 76 T 0.0038 0.9696 0.0266 77 E 0.0038 0.9708 0.0254 78 I 0.0037 0.9723 0.0240 79 K 0.0037 0.9717 0.0245 80 D 0.0038 0.9677 0.0286 81 I 0.0038 0.9667 0.0295 82 H 0.0039 0.9491 0.0470 83 Q 0.0040 0.9290 0.0670 84 K 0.0044 0.8320 0.1636 85 Y 0.0077 0.4373 0.5549 86 G 0.0263 0.0575 0.9162 87 A 0.0900 0.0243 0.8857 88 V 0.2484 0.0121 0.7394 89 D 0.3941 0.0103 0.5957 90 I 0.9579 0.0088 0.0333 91 L 0.9677 0.0125 0.0197 92 V 0.9509 0.0204 0.0287 93 N 0.8325 0.0499 0.1176 94 A 0.3079 0.0825 0.6096 95 A 0.1430 0.1568 0.7002 96 A 0.1263 0.2395 0.6342 97 M 0.1747 0.2453 0.5799 98 F 0.1702 0.1947 0.6351 99 M 0.1156 0.2010 0.6834 100 D 0.0956 0.2280 0.6764 101 G 0.1176 0.2422 0.6402 102 S 0.1308 0.3983 0.4709 103 L 0.1699 0.3007 0.5294 104 S 0.1876 0.2331 0.5792 105 E 0.1273 0.0292 0.8435 106 P 0.0609 0.0224 0.9166 107 V 0.0039 0.9324 0.0638 108 D 0.0038 0.9491 0.0472 109 N 0.0038 0.9556 0.0406 110 F 0.0044 0.9618 0.0338 111 R 0.0055 0.9454 0.0491 112 K 0.0048 0.9390 0.0562 113 I 0.0069 0.9439 0.0491 114 M 0.0091 0.9478 0.0431 115 E 0.0073 0.9540 0.0387 116 I 0.0077 0.9538 0.0385 117 N 0.0088 0.9487 0.0426 118 V 0.0048 0.9605 0.0347 119 I 0.0037 0.9612 0.0350 120 A 0.0037 0.9650 0.0312 121 Q 0.0037 0.9752 0.0211 122 Y 0.0037 0.9767 0.0196 123 G 0.0037 0.9766 0.0197 124 I 0.0037 0.9748 0.0215 125 L 0.0037 0.9737 0.0225 126 K 0.0037 0.9669 0.0294 127 T 0.0038 0.9458 0.0504 128 V 0.0042 0.9394 0.0565 129 T 0.0043 0.9417 0.0541 130 E 0.0037 0.9663 0.0300 131 I 0.0037 0.9645 0.0318 132 M 0.0037 0.9658 0.0305 133 K 0.0045 0.9438 0.0517 134 V 0.0061 0.8601 0.1338 135 Q 0.0076 0.5681 0.4243 136 K 0.0183 0.1008 0.8808 137 N 0.0561 0.0409 0.9031 138 G 0.2224 0.0244 0.7531 139 Y 0.6829 0.0226 0.2945 140 I 0.9627 0.0058 0.0315 141 F 0.9602 0.0064 0.0334 142 N 0.9139 0.0140 0.0721 143 V 0.6461 0.0675 0.2864 144 A 0.3099 0.1602 0.5298 145 S 0.1676 0.3290 0.5035 146 R 0.1345 0.5070 0.3585 147 A 0.1173 0.4935 0.3892 148 A 0.1613 0.4079 0.4308 149 K 0.2231 0.3171 0.4598 150 Y 0.1946 0.2333 0.5722 151 G 0.1541 0.2025 0.6434 152 F 0.0730 0.0887 0.8383 153 A 0.0235 0.1543 0.8222 154 D 0.0160 0.1629 0.8210 155 G 0.0528 0.3986 0.5486 156 G 0.0820 0.4900 0.4280 157 I 0.0399 0.8050 0.1551 158 Y 0.0198 0.8768 0.1035 159 G 0.0117 0.9038 0.0845 160 S 0.0063 0.9335 0.0602 161 T 0.0045 0.9580 0.0375 162 K 0.0037 0.9738 0.0225 163 F 0.0037 0.9748 0.0215 164 A 0.0037 0.9752 0.0211 165 L 0.0037 0.9741 0.0222 166 L 0.0037 0.9706 0.0257 167 G 0.0037 0.9643 0.0320 168 L 0.0038 0.9643 0.0319 169 A 0.0038 0.9676 0.0286 170 E 0.0037 0.9721 0.0242 171 S 0.0037 0.9693 0.0270 172 L 0.0037 0.9696 0.0267 173 Y 0.0038 0.9605 0.0357 174 R 0.0038 0.9484 0.0478 175 E 0.0038 0.9231 0.0731 176 L 0.0061 0.8933 0.1006 177 A 0.0087 0.7801 0.2112 178 P 0.0098 0.6133 0.3770 179 L 0.0129 0.2356 0.7514 180 G 0.0392 0.0163 0.9445 181 I 0.3244 0.0042 0.6714 182 R 0.8722 0.0025 0.1252 183 V 0.9564 0.0024 0.0412 184 T 0.9559 0.0032 0.0409 185 T 0.9613 0.0025 0.0361 186 L 0.9301 0.0028 0.0671 187 C 0.7314 0.0049 0.2638 188 P 0.3169 0.0205 0.6627 189 G 0.1827 0.0342 0.7831 190 W 0.2597 0.0963 0.6441 191 V 0.3463 0.0976 0.5561 192 N 0.2606 0.1121 0.6273 193 T 0.0949 0.1851 0.7201 194 D 0.0391 0.5214 0.4395 195 M 0.0323 0.6519 0.3158 196 A 0.0283 0.7004 0.2713 197 K 0.0279 0.6167 0.3553 198 K 0.0265 0.5652 0.4083 199 A 0.0327 0.4209 0.5465 200 G 0.0283 0.2933 0.6785 201 T 0.0163 0.4419 0.5418 202 P 0.0118 0.5597 0.4285 203 F 0.0100 0.6631 0.3270 204 K 0.0100 0.6976 0.2924 205 D 0.0103 0.7173 0.2724 206 E 0.0100 0.6935 0.2964 207 E 0.0112 0.6392 0.3495 208 M 0.0173 0.5770 0.4057 209 I 0.0209 0.4956 0.4835 210 Q 0.0162 0.3550 0.6288 211 P 0.0056 0.8313 0.1631 212 D 0.0049 0.8904 0.1046 213 D 0.0044 0.9148 0.0808 214 L 0.0048 0.9307 0.0645 215 L 0.0043 0.9299 0.0658 216 N 0.0050 0.9196 0.0754 217 T 0.0058 0.9115 0.0827 218 I 0.0094 0.9139 0.0768 219 R 0.0082 0.9206 0.0711 220 C 0.0075 0.8955 0.0970 221 L 0.0091 0.8568 0.1341 222 L 0.0213 0.7352 0.2435 223 N 0.0258 0.5752 0.3991 224 L 0.0227 0.3996 0.5777 225 S 0.0278 0.2174 0.7549 226 E 0.0275 0.1801 0.7924 227 N 0.0433 0.1511 0.8057 228 V 0.1179 0.0897 0.7924 229 C 0.0858 0.0576 0.8565 230 I 0.0248 0.1824 0.7928 231 K 0.0135 0.1627 0.8237 232 D 0.0322 0.1861 0.7817 233 I 0.0074 0.8896 0.1030 234 V 0.0045 0.9516 0.0439 235 F 0.0049 0.9595 0.0356 236 E 0.0041 0.9697 0.0263 237 M 0.0041 0.9724 0.0235 238 K 0.0041 0.9741 0.0218 239 K 0.0051 0.9723 0.0225 240 S 0.0048 0.9709 0.0243 241 I 0.0048 0.9677 0.0275 242 I 0.0044 0.9574 0.0382 243 E 0.0048 0.8801 0.1151 244 G 0.0070 0.6854 0.3076 245 H 0.0154 0.4943 0.4903 246 H 0.0365 0.4153 0.5482 247 H 0.0524 0.2691 0.6785 248 H 0.0580 0.1642 0.7778 249 H 0.0775 0.0892 0.8332 250 H 0.0103 0.0090 0.9807