# This file is the result of combining several RDB files, specifically # T0489.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0489.t2k.stride-ebghtl.rdb (weight 1.24869) # T0489.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 T0489.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0489 # 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 T0489.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 154 # # ============================================ # Comments from T0489.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0489 # 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 T0489.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 154 # # ============================================ # Comments from T0489.t2k.str.rdb # ============================================ # TARGET T0489 # 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 T0489.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 154 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0104 0.0161 0.9734 2 M 0.0659 0.2793 0.6548 3 F 0.0506 0.3853 0.5641 4 K 0.0424 0.4743 0.4833 5 W 0.0394 0.5233 0.4373 6 P 0.0358 0.5568 0.4074 7 W 0.0530 0.5696 0.3774 8 K 0.0426 0.5789 0.3786 9 A 0.0359 0.5414 0.4227 10 D 0.0271 0.4321 0.5408 11 D 0.0198 0.2854 0.6948 12 E 0.0162 0.1581 0.8258 13 S 0.0200 0.0717 0.9084 14 G 0.0231 0.0204 0.9565 15 N 0.0129 0.0231 0.9640 16 A 0.0044 0.8393 0.1564 17 E 0.0041 0.8833 0.1127 18 M 0.0040 0.9307 0.0654 19 P 0.0038 0.9563 0.0399 20 W 0.0042 0.9530 0.0429 21 E 0.0038 0.9586 0.0377 22 Q 0.0038 0.9523 0.0439 23 A 0.0038 0.9376 0.0586 24 L 0.0039 0.7671 0.2290 25 A 0.0050 0.5890 0.4060 26 I 0.0232 0.2342 0.7426 27 P 0.0243 0.2983 0.6774 28 V 0.0198 0.6463 0.3339 29 L 0.0079 0.8207 0.1713 30 A 0.0073 0.6713 0.3214 31 H 0.0151 0.4128 0.5721 32 L 0.0200 0.0291 0.9509 33 S 0.0122 0.0209 0.9669 34 S 0.0038 0.9291 0.0671 35 T 0.0037 0.9573 0.0390 36 E 0.0037 0.9663 0.0300 37 Q 0.0037 0.9738 0.0225 38 H 0.0037 0.9703 0.0260 39 K 0.0037 0.9675 0.0288 40 L 0.0037 0.9711 0.0252 41 T 0.0037 0.9752 0.0211 42 Q 0.0037 0.9755 0.0207 43 M 0.0037 0.9746 0.0217 44 A 0.0037 0.9759 0.0204 45 A 0.0037 0.9749 0.0214 46 R 0.0037 0.9698 0.0265 47 F 0.0038 0.9544 0.0419 48 L 0.0044 0.9122 0.0835 49 Q 0.0095 0.8134 0.1772 50 Q 0.0182 0.6421 0.3398 51 K 0.0817 0.3743 0.5440 52 R 0.2221 0.1906 0.5874 53 L 0.4797 0.0961 0.4243 54 V 0.5746 0.0606 0.3648 55 A 0.4108 0.0588 0.5303 56 L 0.1436 0.1040 0.7524 57 Q 0.0396 0.0686 0.8917 58 G 0.0553 0.0514 0.8933 59 L 0.3043 0.0160 0.6797 60 E 0.5275 0.0088 0.4637 61 L 0.3965 0.0127 0.5907 62 T 0.0461 0.0220 0.9318 63 P 0.0038 0.9361 0.0601 64 L 0.0037 0.9640 0.0322 65 H 0.0037 0.9727 0.0236 66 Q 0.0037 0.9760 0.0203 67 A 0.0037 0.9762 0.0200 68 R 0.0037 0.9770 0.0193 69 I 0.0037 0.9770 0.0193 70 A 0.0037 0.9767 0.0196 71 M 0.0037 0.9736 0.0227 72 L 0.0037 0.9706 0.0256 73 F 0.0037 0.9613 0.0350 74 C 0.0037 0.9654 0.0309 75 L 0.0037 0.9682 0.0281 76 P 0.0038 0.9599 0.0363 77 V 0.0041 0.9430 0.0528 78 L 0.0066 0.8588 0.1346 79 E 0.0103 0.5657 0.4240 80 L 0.0168 0.2747 0.7084 81 G 0.0214 0.2844 0.6942 82 I 0.0150 0.6351 0.3500 83 E 0.0231 0.6203 0.3567 84 W 0.0424 0.5671 0.3904 85 L 0.0724 0.3333 0.5943 86 D 0.0235 0.2515 0.7251 87 G 0.0449 0.1217 0.8334 88 F 0.2334 0.0272 0.7394 89 H 0.5199 0.0095 0.4706 90 E 0.9454 0.0035 0.0512 91 V 0.9740 0.0024 0.0236 92 L 0.9751 0.0024 0.0225 93 I 0.9392 0.0025 0.0583 94 Y 0.6146 0.0035 0.3819 95 P 0.1816 0.0401 0.7784 96 A 0.0581 0.1060 0.8359 97 P 0.0949 0.1955 0.7096 98 F 0.2637 0.1268 0.6095 99 I 0.4846 0.0591 0.4563 100 V 0.4821 0.0428 0.4751 101 D 0.3406 0.0582 0.6012 102 D 0.3257 0.1403 0.5340 103 E 0.4527 0.1409 0.4065 104 W 0.4748 0.1480 0.3773 105 E 0.4513 0.1220 0.4267 106 D 0.2322 0.1204 0.6474 107 D 0.1057 0.1254 0.7689 108 I 0.0923 0.0734 0.8343 109 G 0.2329 0.0322 0.7349 110 L 0.6016 0.0175 0.3810 111 V 0.7829 0.0121 0.2049 112 H 0.5263 0.0238 0.4499 113 N 0.2787 0.1043 0.6171 114 Q 0.1924 0.1523 0.6554 115 R 0.3380 0.1388 0.5232 116 V 0.4885 0.1191 0.3924 117 V 0.5670 0.1202 0.3127 118 Q 0.6297 0.1043 0.2660 119 S 0.5299 0.0981 0.3720 120 G 0.4283 0.1072 0.4645 121 Q 0.4152 0.1459 0.4389 122 S 0.3226 0.1830 0.4945 123 W 0.2086 0.2709 0.5205 124 Q 0.1100 0.2366 0.6535 125 Q 0.0897 0.1499 0.7604 126 G 0.1355 0.0289 0.8356 127 P 0.3658 0.0126 0.6216 128 V 0.8703 0.0073 0.1224 129 V 0.9070 0.0048 0.0882 130 L 0.7955 0.0067 0.1978 131 N 0.3778 0.0156 0.6066 132 W 0.0148 0.7639 0.2213 133 L 0.0052 0.9129 0.0819 134 D 0.0050 0.9112 0.0837 135 I 0.0072 0.9172 0.0756 136 Q 0.0123 0.8574 0.1303 137 D 0.0121 0.5554 0.4325 138 S 0.0299 0.2222 0.7479 139 F 0.0564 0.0533 0.8903 140 D 0.0493 0.0783 0.8724 141 A 0.0142 0.1298 0.8560 142 S 0.0183 0.1268 0.8549 143 G 0.0563 0.1114 0.8323 144 F 0.1607 0.1426 0.6967 145 N 0.2804 0.3189 0.4007 146 L 0.3084 0.5343 0.1574 147 V 0.1573 0.7862 0.0566 148 V 0.0632 0.9003 0.0365 149 H 0.0446 0.9207 0.0347 150 E 0.0396 0.9243 0.0361 151 V 0.0272 0.9393 0.0335 152 A 0.0172 0.9503 0.0325 153 H 0.0112 0.9506 0.0382 154 K 0.0095 0.9426 0.0480 155 L 0.0111 0.8931 0.0958 156 D 0.0150 0.7597 0.2253 157 T 0.0092 0.6649 0.3259 158 R 0.0104 0.4203 0.5692 159 N 0.0102 0.2176 0.7722 160 G 0.0320 0.1358 0.8323 161 D 0.0727 0.1323 0.7950 162 R 0.0734 0.1361 0.7904 163 A 0.0328 0.0936 0.8735 164 S 0.0383 0.0588 0.9029 165 G 0.0923 0.0404 0.8672 166 V 0.1072 0.0664 0.8263 167 P 0.0819 0.1281 0.7900 168 L 0.0623 0.1449 0.7928 169 I 0.0295 0.1792 0.7913 170 P 0.0198 0.2550 0.7252 171 L 0.0162 0.3121 0.6717 172 R 0.0234 0.3177 0.6590 173 E 0.0296 0.3454 0.6250 174 V 0.0079 0.8269 0.1652 175 A 0.0055 0.9056 0.0889 176 G 0.0045 0.9365 0.0590 177 W 0.0038 0.9557 0.0405 178 E 0.0038 0.9600 0.0362 179 H 0.0038 0.9548 0.0414 180 D 0.0039 0.9368 0.0593 181 L 0.0040 0.9393 0.0567 182 H 0.0039 0.9477 0.0484 183 A 0.0038 0.9585 0.0377 184 A 0.0037 0.9619 0.0344 185 M 0.0037 0.9643 0.0320 186 N 0.0038 0.9557 0.0406 187 N 0.0038 0.9445 0.0517 188 I 0.0037 0.9485 0.0477 189 Q 0.0037 0.9528 0.0435 190 D 0.0037 0.9493 0.0469 191 E 0.0037 0.9469 0.0494 192 I 0.0044 0.9389 0.0567 193 D 0.0041 0.9202 0.0757 194 L 0.0043 0.8443 0.1513 195 V 0.0057 0.6486 0.3457 196 G 0.0092 0.3086 0.6822 197 E 0.0106 0.2299 0.7595 198 S 0.0168 0.2565 0.7266 199 A 0.0339 0.2682 0.6979 200 A 0.0674 0.2372 0.6954 201 S 0.1153 0.2478 0.6369 202 I 0.1887 0.2068 0.6044 203 D 0.1087 0.2056 0.6857 204 A 0.0349 0.6257 0.3394 205 Y 0.0280 0.5909 0.3811 206 A 0.0510 0.5192 0.4298 207 A 0.0632 0.4015 0.5353 208 T 0.0578 0.2384 0.7038 209 D 0.0246 0.1197 0.8556 210 P 0.0057 0.8485 0.1459 211 A 0.0070 0.9280 0.0651 212 E 0.0107 0.9366 0.0527 213 C 0.0113 0.9490 0.0397 214 F 0.0130 0.9518 0.0352 215 A 0.0184 0.9491 0.0324 216 V 0.0201 0.9362 0.0437 217 L 0.0365 0.9156 0.0479 218 S 0.0187 0.9180 0.0633 219 E 0.0194 0.9133 0.0673 220 Y 0.0272 0.8641 0.1087 221 F 0.0395 0.7856 0.1750 222 F 0.0532 0.6554 0.2914 223 S 0.0753 0.4620 0.4627 224 A 0.0403 0.1994 0.7602 225 P 0.0082 0.7052 0.2866 226 E 0.0042 0.8894 0.1064 227 L 0.0039 0.9169 0.0792 228 F 0.0038 0.9128 0.0834 229 A 0.0042 0.9002 0.0955 230 P 0.0044 0.7958 0.1998 231 R 0.0042 0.7653 0.2305 232 F 0.0074 0.5733 0.4193 233 P 0.0041 0.9222 0.0737 234 A 0.0038 0.9496 0.0466 235 L 0.0037 0.9679 0.0284 236 W 0.0037 0.9746 0.0216 237 Q 0.0037 0.9751 0.0212 238 R 0.0037 0.9734 0.0229 239 F 0.0037 0.9738 0.0225 240 C 0.0037 0.9711 0.0252 241 H 0.0038 0.9606 0.0356 242 F 0.0039 0.9339 0.0622 243 Y 0.0056 0.8144 0.1800 244 R 0.0093 0.5530 0.4376 245 Q 0.0141 0.3876 0.5983 246 D 0.0127 0.0719 0.9154 247 P 0.0046 0.8615 0.1339 248 L 0.0039 0.9162 0.0799 249 A 0.0046 0.9178 0.0777 250 R 0.0056 0.9091 0.0854 251 R 0.0113 0.8375 0.1512 252 R 0.0148 0.7580 0.2272 253 E 0.0122 0.7020 0.2858 254 N 0.0264 0.5941 0.3795 255 G 0.0266 0.5765 0.3969 256 L 0.0285 0.5004 0.4711 257 Q 0.0343 0.3354 0.6303 258 D 0.0255 0.1609 0.8136 259 E 0.0109 0.2921 0.6970 260 G 0.0158 0.3281 0.6560 261 D 0.1429 0.3451 0.5120 262 R 0.3089 0.2866 0.4045 263 R 0.4251 0.2866 0.2883 264 I 0.4419 0.2340 0.3241 265 V 0.3265 0.1420 0.5315 266 H 0.0127 0.0236 0.9637