# This file is the result of combining several RDB files, specifically # T0627.t04.dssp-ebghstl.rdb (weight 1.53986) # T0627.t04.stride-ebghtl.rdb (weight 1.24869) # T0627.t04.str2.rdb (weight 1.54758) # T0627.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 T0627.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0627 # Using neural net t04-2621-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 T0627.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 1054 # # ============================================ # Comments from T0627.t04.stride-ebghtl.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1054 # # ============================================ # Comments from T0627.t04.str2.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1054 # # ============================================ # Comments from T0627.t04.alpha.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1054 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1764 0.0850 0.7386 2 I 0.2618 0.1191 0.6192 3 D 0.2215 0.1604 0.6181 4 T 0.1587 0.2267 0.6146 5 F 0.1695 0.2703 0.5602 6 E 0.1674 0.2704 0.5622 7 R 0.1576 0.2313 0.6111 8 T 0.1317 0.1432 0.7250 9 G 0.0978 0.0638 0.8384 10 P 0.1176 0.1101 0.7723 11 L 0.1132 0.2664 0.6204 12 M 0.1223 0.2847 0.5930 13 E 0.1126 0.2636 0.6237 14 A 0.0739 0.3043 0.6218 15 S 0.0566 0.2386 0.7047 16 S 0.0487 0.1998 0.7515 17 Y 0.0456 0.1718 0.7826 18 P 0.0228 0.5754 0.4019 19 A 0.0112 0.8144 0.1744 20 W 0.0058 0.9192 0.0750 21 A 0.0047 0.9521 0.0431 22 Q 0.0047 0.9571 0.0382 23 Q 0.0050 0.9560 0.0390 24 L 0.0048 0.9539 0.0413 25 I 0.0050 0.9431 0.0519 26 N 0.0062 0.8935 0.1003 27 D 0.0099 0.7445 0.2456 28 C 0.0217 0.5658 0.4125 29 S 0.0196 0.4692 0.5112 30 P 0.0057 0.8298 0.1645 31 A 0.0065 0.8857 0.1078 32 K 0.0066 0.9158 0.0776 33 A 0.0069 0.9185 0.0745 34 R 0.0080 0.9069 0.0850 35 V 0.0118 0.8830 0.1053 36 V 0.0177 0.7813 0.2010 37 E 0.0226 0.5975 0.3800 38 H 0.0489 0.4230 0.5282 39 E 0.0064 0.8617 0.1319 40 L 0.0064 0.9099 0.0836 41 Y 0.0056 0.9430 0.0514 42 Q 0.0049 0.9462 0.0489 43 Q 0.0052 0.9221 0.0727 44 M 0.0104 0.8698 0.1198 45 R 0.0109 0.7425 0.2466 46 D 0.0407 0.3706 0.5887 47 A 0.0492 0.1247 0.8260 48 K 0.0900 0.0272 0.8829 49 L 0.1186 0.0111 0.8702 50 S 0.0595 0.0110 0.9295 51 P 0.0049 0.9483 0.0468 52 Q 0.0047 0.9605 0.0348 53 I 0.0047 0.9604 0.0349 54 M 0.0047 0.9609 0.0344 55 R 0.0047 0.9594 0.0359 56 Q 0.0047 0.9589 0.0364 57 Y 0.0047 0.9561 0.0392 58 L 0.0059 0.9447 0.0493 59 I 0.0090 0.9068 0.0842 60 G 0.0268 0.6828 0.2904 61 G 0.0181 0.5548 0.4271 62 W 0.0342 0.7144 0.2514 63 P 0.0299 0.8487 0.1214 64 V 0.0210 0.9096 0.0693 65 V 0.0101 0.9410 0.0489 66 E 0.0069 0.9431 0.0500 67 Q 0.0057 0.9451 0.0492 68 F 0.0050 0.9470 0.0480 69 A 0.0047 0.9578 0.0375 70 V 0.0047 0.9609 0.0344 71 Y 0.0047 0.9614 0.0339 72 M 0.0047 0.9579 0.0374 73 A 0.0047 0.9566 0.0387 74 K 0.0048 0.9507 0.0445 75 N 0.0051 0.9142 0.0808 76 L 0.0057 0.8586 0.1356 77 T 0.0108 0.7209 0.2682 78 K 0.0211 0.5604 0.4185 79 T 0.0651 0.1898 0.7451 80 R 0.0834 0.1590 0.7576 81 F 0.0777 0.1077 0.8146 82 G 0.0463 0.1014 0.8522 83 R 0.0674 0.0856 0.8470 84 H 0.0547 0.0526 0.8928 85 P 0.0293 0.1831 0.7876 86 G 0.0371 0.2375 0.7254 87 E 0.0336 0.5551 0.4113 88 D 0.0065 0.9298 0.0638 89 M 0.0047 0.9521 0.0432 90 A 0.0047 0.9584 0.0369 91 R 0.0047 0.9604 0.0350 92 R 0.0046 0.9608 0.0345 93 W 0.0047 0.9589 0.0364 94 L 0.0047 0.9562 0.0391 95 M 0.0047 0.9557 0.0396 96 R 0.0050 0.9402 0.0548 97 N 0.0060 0.9114 0.0826 98 I 0.0095 0.8922 0.0983 99 R 0.0204 0.8300 0.1495 100 V 0.0234 0.8211 0.1554 101 E 0.0296 0.8074 0.1630 102 L 0.0321 0.7247 0.2432 103 N 0.0300 0.6174 0.3526 104 H 0.0254 0.7399 0.2347 105 A 0.0078 0.9210 0.0712 106 D 0.0059 0.9503 0.0437 107 Y 0.0050 0.9560 0.0390 108 W 0.0050 0.9567 0.0383 109 V 0.0047 0.9599 0.0354 110 N 0.0047 0.9598 0.0355 111 W 0.0047 0.9605 0.0348 112 C 0.0047 0.9582 0.0371 113 A 0.0049 0.9485 0.0466 114 A 0.0057 0.9132 0.0811 115 H 0.0456 0.4410 0.5134 116 D 0.0473 0.0155 0.9372 117 V 0.0701 0.0078 0.9221 118 T 0.0781 0.0081 0.9138 119 L 0.0052 0.9165 0.0783 120 E 0.0051 0.9333 0.0616 121 D 0.0057 0.9363 0.0580 122 L 0.0139 0.9105 0.0756 123 H 0.0180 0.7900 0.1920 124 D 0.0235 0.5028 0.4737 125 Q 0.0540 0.2105 0.7355 126 R 0.0774 0.0796 0.8431 127 V 0.0727 0.0511 0.8763 128 A 0.0613 0.0503 0.8883 129 P 0.0080 0.8754 0.1166 130 E 0.0073 0.9174 0.0752 131 L 0.0052 0.9429 0.0519 132 H 0.0050 0.9516 0.0434 133 A 0.0048 0.9520 0.0432 134 L 0.0048 0.9530 0.0422 135 S 0.0048 0.9568 0.0384 136 H 0.0047 0.9582 0.0371 137 W 0.0047 0.9574 0.0379 138 C 0.0047 0.9558 0.0395 139 W 0.0047 0.9538 0.0415 140 Q 0.0048 0.9414 0.0538 141 T 0.0057 0.8995 0.0948 142 S 0.0117 0.7491 0.2392 143 S 0.0237 0.4683 0.5079 144 S 0.0525 0.2617 0.6858 145 D 0.0312 0.2011 0.7676 146 S 0.0517 0.2769 0.6714 147 L 0.0068 0.9159 0.0773 148 A 0.0069 0.9461 0.0469 149 V 0.0123 0.9404 0.0473 150 A 0.0217 0.9355 0.0428 151 M 0.0253 0.9257 0.0489 152 A 0.0388 0.9010 0.0602 153 A 0.0583 0.8578 0.0840 154 T 0.0404 0.8427 0.1169 155 N 0.0276 0.8284 0.1440 156 Y 0.0236 0.8080 0.1684 157 A 0.0425 0.7456 0.2119 158 I 0.0532 0.7163 0.2304 159 E 0.0574 0.5982 0.3444 160 G 0.0505 0.4602 0.4893 161 A 0.0656 0.4403 0.4941 162 T 0.0631 0.4474 0.4895 163 G 0.0386 0.6026 0.3588 164 E 0.0444 0.6955 0.2601 165 W 0.0464 0.8228 0.1308 166 S 0.0473 0.8368 0.1159 167 A 0.0339 0.8894 0.0767 168 V 0.0372 0.8914 0.0714 169 V 0.0387 0.8837 0.0777 170 C 0.0374 0.8463 0.1163 171 S 0.0188 0.8154 0.1658 172 T 0.0131 0.8205 0.1664 173 G 0.0104 0.7789 0.2107 174 V 0.0186 0.7979 0.1834 175 Y 0.0207 0.7948 0.1845 176 A 0.0168 0.8340 0.1492 177 E 0.0159 0.8065 0.1776 178 A 0.0238 0.7162 0.2600 179 F 0.0550 0.4705 0.4746 180 A 0.0376 0.3506 0.6117 181 E 0.0202 0.6273 0.3526 182 E 0.0269 0.6579 0.3152 183 T 0.0405 0.5639 0.3956 184 R 0.0405 0.4817 0.4778 185 K 0.0169 0.7783 0.2048 186 K 0.0157 0.8239 0.1603 187 S 0.0194 0.8545 0.1262 188 M 0.0184 0.9004 0.0811 189 K 0.0264 0.8991 0.0745 190 W 0.0515 0.8851 0.0634 191 L 0.0558 0.8850 0.0592 192 K 0.0536 0.8688 0.0776 193 M 0.0510 0.8214 0.1276 194 H 0.0734 0.6529 0.2737 195 A 0.0850 0.4222 0.4928 196 Q 0.0846 0.3241 0.5913 197 Y 0.0716 0.3474 0.5810 198 D 0.0587 0.3191 0.6222 199 D 0.0271 0.3540 0.6189 200 A 0.0350 0.3627 0.6023 201 H 0.0575 0.2602 0.6823 202 P 0.0128 0.8392 0.1480 203 W 0.0067 0.9430 0.0503 204 E 0.0054 0.9526 0.0420 205 A 0.0048 0.9581 0.0372 206 L 0.0047 0.9593 0.0359 207 E 0.0047 0.9606 0.0347 208 I 0.0047 0.9596 0.0357 209 I 0.0047 0.9587 0.0366 210 C 0.0048 0.9563 0.0388 211 T 0.0056 0.9433 0.0512 212 L 0.0063 0.9199 0.0737 213 V 0.0181 0.8261 0.1558 214 G 0.0175 0.4972 0.4853 215 N 0.0346 0.2321 0.7332 216 K 0.0752 0.0381 0.8866 217 P 0.0415 0.0670 0.8915 218 S 0.0579 0.0458 0.8962 219 L 0.0048 0.9523 0.0430 220 Q 0.0047 0.9594 0.0359 221 L 0.0047 0.9594 0.0360 222 Q 0.0046 0.9604 0.0349 223 A 0.0046 0.9607 0.0347 224 E 0.0046 0.9610 0.0343 225 L 0.0047 0.9608 0.0346 226 R 0.0047 0.9611 0.0343 227 Q 0.0046 0.9616 0.0338 228 A 0.0047 0.9605 0.0349 229 V 0.0047 0.9594 0.0359 230 T 0.0047 0.9607 0.0346 231 K 0.0048 0.9595 0.0357 232 S 0.0047 0.9594 0.0359 233 Y 0.0049 0.9586 0.0366 234 D 0.0047 0.9611 0.0343 235 Y 0.0046 0.9610 0.0343 236 M 0.0047 0.9600 0.0353 237 Y 0.0047 0.9605 0.0349 238 L 0.0047 0.9567 0.0386 239 F 0.0047 0.9490 0.0463 240 L 0.0047 0.9524 0.0429 241 E 0.0047 0.9528 0.0425 242 R 0.0048 0.9472 0.0479 243 C 0.0051 0.9175 0.0774 244 I 0.0073 0.8593 0.1335 245 Q 0.0103 0.7551 0.2345 246 L 0.0225 0.6646 0.3129 247 D 0.0367 0.5020 0.4613 248 K 0.0555 0.4030 0.5415 249 V 0.1022 0.1618 0.7360 250 K 0.1019 0.1017 0.7963 251 S 0.0873 0.0457 0.8670 252 P 0.0726 0.0654 0.8620 253 R 0.0509 0.2450 0.7041 254 G 0.0705 0.2184 0.7111 255 R 0.2095 0.1862 0.6043 256 V 0.3713 0.1516 0.4771 257 A 0.4383 0.1518 0.4099 258 A 0.4059 0.1497 0.4444 259 L 0.2777 0.1725 0.5499 260 E 0.1819 0.1077 0.7104 261 M 0.0720 0.0597 0.8684