# This file is the result of combining several RDB files, specifically # T0336.t04.dssp-ebghstl.rdb (weight 1.53986) # T0336.t04.stride-ebghtl.rdb (weight 1.24869) # T0336.t04.str2.rdb (weight 1.54758) # T0336.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 T0336.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0336 # 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 T0336.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 41.2849 # # ============================================ # Comments from T0336.t04.stride-ebghtl.rdb # ============================================ # TARGET T0336 # 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 T0336.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 41.2849 # # ============================================ # Comments from T0336.t04.str2.rdb # ============================================ # TARGET T0336 # 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 T0336.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 41.2849 # # ============================================ # Comments from T0336.t04.alpha.rdb # ============================================ # TARGET T0336 # 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 T0336.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 41.2849 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1124 0.0134 0.8742 2 S 0.1587 0.0173 0.8240 3 M 0.1074 0.4347 0.4579 4 E 0.0623 0.6123 0.3254 5 E 0.0171 0.8676 0.1154 6 E 0.0169 0.8807 0.1024 7 E 0.0157 0.9173 0.0670 8 F 0.0160 0.9141 0.0699 9 D 0.0228 0.8917 0.0855 10 I 0.0076 0.9347 0.0578 11 R 0.0057 0.9493 0.0449 12 E 0.0049 0.9514 0.0437 13 A 0.0055 0.9462 0.0484 14 L 0.0087 0.9092 0.0822 15 A 0.0097 0.7497 0.2406 16 N 0.0367 0.3987 0.5646 17 G 0.0300 0.2117 0.7582 18 E 0.0269 0.3473 0.6258 19 H 0.0534 0.4003 0.5462 20 L 0.0502 0.5704 0.3794 21 E 0.0383 0.6911 0.2706 22 K 0.0408 0.7654 0.1939 23 I 0.0488 0.7816 0.1696 24 L 0.0694 0.7579 0.1727 25 I 0.0632 0.7263 0.2105 26 M 0.0372 0.7143 0.2485 27 A 0.0275 0.7158 0.2568 28 K 0.0262 0.7141 0.2597 29 Y 0.0399 0.6078 0.3522 30 D 0.0658 0.5016 0.4326 31 E 0.0063 0.8608 0.1329 32 S 0.0067 0.8671 0.1262 33 V 0.0059 0.9035 0.0907 34 L 0.0052 0.9357 0.0591 35 K 0.0047 0.9352 0.0600 36 K 0.0053 0.9263 0.0684 37 L 0.0054 0.9159 0.0787 38 I 0.0069 0.9098 0.0832 39 E 0.0079 0.8526 0.1396 40 L 0.0164 0.7012 0.2824 41 L 0.0701 0.3101 0.6198 42 D 0.0533 0.1083 0.8384 43 D 0.0136 0.2920 0.6944 44 D 0.0269 0.2904 0.6827 45 L 0.0483 0.4067 0.5450 46 W 0.0452 0.4959 0.4589 47 T 0.0420 0.6315 0.3265 48 V 0.0060 0.9174 0.0766 49 V 0.0047 0.9510 0.0443 50 K 0.0047 0.9600 0.0353 51 N 0.0047 0.9593 0.0360 52 A 0.0047 0.9593 0.0360 53 I 0.0047 0.9609 0.0344 54 S 0.0046 0.9612 0.0341 55 I 0.0046 0.9612 0.0341 56 I 0.0047 0.9608 0.0345 57 M 0.0046 0.9612 0.0342 58 V 0.0047 0.9598 0.0355 59 I 0.0048 0.9558 0.0395 60 A 0.0050 0.9374 0.0576 61 K 0.0061 0.8725 0.1214 62 T 0.0171 0.7466 0.2363 63 R 0.0470 0.6056 0.3475 64 E 0.0216 0.6056 0.3728 65 D 0.0255 0.6440 0.3306 66 L 0.0344 0.6536 0.3120 67 Y 0.0574 0.6236 0.3189 68 E 0.0348 0.7563 0.2090 69 P 0.0249 0.8121 0.1630 70 M 0.0254 0.8173 0.1573 71 L 0.0225 0.8429 0.1346 72 K 0.0110 0.8791 0.1099 73 K 0.0088 0.8798 0.1115 74 L 0.0099 0.8694 0.1207 75 F 0.0110 0.9058 0.0833 76 S 0.0124 0.9004 0.0871 77 L 0.0163 0.8919 0.0918 78 L 0.0235 0.8569 0.1196 79 K 0.0251 0.8281 0.1469 80 K 0.0248 0.6840 0.2912 81 S 0.0510 0.3256 0.6233 82 E 0.0386 0.2275 0.7339 83 A 0.0403 0.1770 0.7827 84 I 0.0759 0.0425 0.8816 85 P 0.0401 0.4641 0.4958 86 L 0.0670 0.6508 0.2822 87 T 0.0336 0.7843 0.1821 88 Q 0.0078 0.9365 0.0557 89 E 0.0080 0.9458 0.0463 90 I 0.0068 0.9503 0.0429 91 A 0.0071 0.9505 0.0424 92 K 0.0065 0.9444 0.0491 93 A 0.0078 0.9273 0.0649 94 F 0.0077 0.9233 0.0690 95 G 0.0099 0.8991 0.0910 96 Q 0.0105 0.9101 0.0794 97 M 0.0134 0.8930 0.0936 98 A 0.0166 0.8498 0.1336 99 K 0.0178 0.7409 0.2414 100 E 0.0305 0.5431 0.4264 101 K 0.0620 0.1843 0.7537 102 P 0.0401 0.3323 0.6276 103 E 0.0592 0.4148 0.5260 104 L 0.0847 0.5459 0.3694 105 V 0.0996 0.5849 0.3155 106 K 0.0911 0.6330 0.2760 107 S 0.1001 0.5965 0.3035 108 M 0.0923 0.5994 0.3084 109 I 0.1179 0.5452 0.3370 110 P 0.1128 0.6346 0.2526 111 V 0.1459 0.6621 0.1920 112 L 0.1726 0.6536 0.1738 113 F 0.1966 0.6037 0.1997 114 A 0.1237 0.5800 0.2962 115 N 0.1619 0.4414 0.3966 116 Y 0.2275 0.1300 0.6426 117 R 0.1989 0.0804 0.7207 118 I 0.1428 0.1410 0.7162 119 G 0.1241 0.0808 0.7951 120 D 0.0871 0.0300 0.8829 121 E 0.0206 0.2118 0.7676 122 K 0.0511 0.1779 0.7710 123 T 0.1992 0.2056 0.5952 124 K 0.4228 0.1939 0.3832 125 I 0.6159 0.1745 0.2096 126 N 0.4203 0.2593 0.3204 127 V 0.2218 0.6040 0.1742 128 S 0.1509 0.7122 0.1369 129 Y 0.1254 0.7719 0.1027 130 A 0.0848 0.8280 0.0872 131 L 0.0399 0.8842 0.0759 132 E 0.0173 0.9145 0.0682 133 E 0.0096 0.9271 0.0633 134 I 0.0103 0.9081 0.0816 135 A 0.0115 0.8727 0.1158 136 K 0.0131 0.7633 0.2236 137 A 0.0333 0.5509 0.4158 138 N 0.0809 0.0943 0.8248 139 P 0.0076 0.7079 0.2845 140 M 0.0094 0.7601 0.2305 141 L 0.0116 0.8245 0.1639 142 M 0.0118 0.8467 0.1415 143 A 0.0058 0.9202 0.0740 144 S 0.0048 0.9293 0.0659 145 I 0.0047 0.9415 0.0537 146 V 0.0047 0.9560 0.0393 147 R 0.0047 0.9580 0.0373 148 D 0.0047 0.9563 0.0390 149 F 0.0047 0.9551 0.0402 150 M 0.0047 0.9520 0.0433 151 S 0.0048 0.9398 0.0553 152 M 0.0055 0.9067 0.0878 153 L 0.0103 0.8155 0.1742 154 S 0.0199 0.5304 0.4497 155 S 0.0310 0.2936 0.6754 156 K 0.0365 0.1262 0.8373 157 N 0.0359 0.1335 0.8306 158 R 0.0522 0.3388 0.6090 159 E 0.0573 0.5772 0.3654 160 D 0.0489 0.6014 0.3497 161 K 0.0911 0.6838 0.2251 162 L 0.1672 0.7018 0.1309 163 T 0.1679 0.7084 0.1238 164 A 0.1331 0.7695 0.0974 165 L 0.0803 0.8262 0.0935 166 N 0.0382 0.8500 0.1118 167 F 0.0288 0.8524 0.1188 168 I 0.0187 0.8812 0.1001 169 E 0.0177 0.8705 0.1118 170 A 0.0208 0.7943 0.1849 171 M 0.0533 0.5218 0.4248 172 G 0.0365 0.1925 0.7710 173 E 0.0533 0.2078 0.7389 174 N 0.0452 0.2035 0.7514 175 S 0.0518 0.2221 0.7261 176 F 0.0919 0.2326 0.6755 177 K 0.1327 0.2649 0.6024 178 Y 0.1762 0.2830 0.5408 179 V 0.1503 0.2464 0.6033 180 N 0.0677 0.2494 0.6828 181 P 0.0115 0.5675 0.4210 182 F 0.0140 0.6272 0.3588 183 L 0.0088 0.8639 0.1273 184 P 0.0052 0.9312 0.0636 185 R 0.0062 0.9354 0.0584 186 I 0.0063 0.9350 0.0587 187 I 0.0061 0.9319 0.0620 188 N 0.0060 0.8889 0.1051 189 L 0.0079 0.8368 0.1553 190 L 0.0258 0.6787 0.2955 191 H 0.0398 0.4119 0.5482 192 D 0.0695 0.2188 0.7116 193 G 0.0296 0.2836 0.6868 194 D 0.0295 0.4512 0.5193 195 E 0.0351 0.6937 0.2712 196 I 0.0490 0.7745 0.1765 197 V 0.0643 0.7754 0.1603 198 R 0.0344 0.8378 0.1279 199 A 0.0090 0.9253 0.0656 200 S 0.0072 0.9288 0.0641 201 A 0.0050 0.9513 0.0437 202 V 0.0047 0.9588 0.0365 203 E 0.0047 0.9573 0.0380 204 A 0.0048 0.9519 0.0433 205 L 0.0048 0.9444 0.0508 206 V 0.0051 0.9287 0.0662 207 H 0.0052 0.9138 0.0810 208 L 0.0099 0.9018 0.0884 209 A 0.0250 0.8086 0.1664 210 T 0.0337 0.6872 0.2792 211 L 0.0073 0.8688 0.1239 212 N 0.0110 0.8671 0.1218 213 D 0.0080 0.9187 0.0733 214 K 0.0075 0.9326 0.0599 215 L 0.0053 0.9451 0.0495 216 R 0.0047 0.9554 0.0399 217 K 0.0047 0.9587 0.0366 218 V 0.0053 0.9553 0.0394 219 V 0.0060 0.9474 0.0466 220 I 0.0071 0.9199 0.0731 221 K 0.0081 0.8637 0.1282 222 R 0.0113 0.7871 0.2016 223 L 0.0121 0.8547 0.1332 224 E 0.0070 0.8233 0.1698 225 E 0.0101 0.7559 0.2340 226 L 0.0443 0.4702 0.4855 227 N 0.0195 0.4526 0.5279 228 D 0.0360 0.4183 0.5457 229 T 0.0437 0.5272 0.4291 230 S 0.0512 0.6417 0.3071 231 S 0.0444 0.7874 0.1682 232 L 0.0512 0.8463 0.1025 233 V 0.0381 0.8763 0.0856 234 N 0.0310 0.8644 0.1045 235 K 0.0146 0.9140 0.0714 236 T 0.0147 0.9102 0.0751 237 V 0.0076 0.9453 0.0471 238 K 0.0066 0.9452 0.0482 239 E 0.0057 0.9353 0.0590 240 G 0.0053 0.9295 0.0652 241 I 0.0057 0.9361 0.0583 242 S 0.0063 0.9267 0.0670 243 R 0.0072 0.9236 0.0692 244 L 0.0126 0.8989 0.0885 245 L 0.0187 0.8333 0.1480 246 L 0.0244 0.7006 0.2749 247 L 0.0526 0.5500 0.3973 248 E 0.0438 0.4572 0.4990 249 G 0.0483 0.2906 0.6611 250 H 0.0796 0.2201 0.7003 251 S 0.1237 0.1293 0.7470 252 S 0.0873 0.0724 0.8403 253 S 0.0719 0.0412 0.8869