# This file is the result of combining several RDB files, specifically # T0355.t06.dssp-ebghstl.rdb (weight 1.53986) # T0355.t06.stride-ebghtl.rdb (weight 1.24869) # T0355.t06.str2.rdb (weight 1.54758) # T0355.t06.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 T0355.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0355 # 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 T0355.t06-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 972 # # ============================================ # Comments from T0355.t06.stride-ebghtl.rdb # ============================================ # TARGET T0355 # Using neural net t06-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 T0355.t06-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 972 # # ============================================ # Comments from T0355.t06.str2.rdb # ============================================ # TARGET T0355 # Using neural net t06-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 T0355.t06-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 972 # # ============================================ # Comments from T0355.t06.alpha.rdb # ============================================ # TARGET T0355 # Using neural net t06-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 T0355.t06-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 972 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0680 0.1961 0.7359 2 Q 0.1271 0.3183 0.5546 3 T 0.1792 0.3507 0.4702 4 I 0.0984 0.4300 0.4716 5 S 0.0596 0.4499 0.4904 6 D 0.0283 0.5489 0.4228 7 N 0.0474 0.4193 0.5332 8 A 0.0213 0.6161 0.3625 9 A 0.0189 0.7434 0.2378 10 N 0.0133 0.8239 0.1628 11 A 0.0085 0.9047 0.0868 12 I 0.0057 0.9322 0.0621 13 Q 0.0067 0.9306 0.0627 14 E 0.0067 0.9227 0.0706 15 I 0.0102 0.8791 0.1107 16 F 0.0370 0.6403 0.3227 17 G 0.0320 0.1685 0.7995 18 R 0.0462 0.1587 0.7951 19 S 0.0767 0.1579 0.7655 20 K 0.1179 0.2175 0.6646 21 A 0.2404 0.1767 0.5828 22 L 0.5030 0.1357 0.3613 23 I 0.5460 0.1031 0.3509 24 G 0.5010 0.0951 0.4039 25 M 0.5762 0.1071 0.3167 26 I 0.5895 0.0886 0.3219 27 H 0.4832 0.0602 0.4566 28 C 0.1630 0.0380 0.7989 29 P 0.0744 0.0742 0.8514 30 A 0.0630 0.1203 0.8167 31 F 0.0729 0.0745 0.8525 32 P 0.0546 0.1236 0.8218 33 G 0.0880 0.1046 0.8074 34 A 0.1340 0.0537 0.8123 35 P 0.1231 0.1201 0.7569 36 R 0.3443 0.1272 0.5286 37 Y 0.4941 0.0832 0.4227 38 R 0.4859 0.0985 0.4156 39 N 0.3631 0.0861 0.5508 40 A 0.2135 0.0512 0.7353 41 S 0.1292 0.0324 0.8385 42 M 0.0104 0.7678 0.2218 43 D 0.0065 0.8566 0.1369 44 A 0.0080 0.8864 0.1056 45 I 0.0106 0.8830 0.1064 46 Y 0.0104 0.8798 0.1098 47 D 0.0084 0.8967 0.0948 48 A 0.0087 0.8851 0.1062 49 C 0.0064 0.9189 0.0747 50 M 0.0048 0.9524 0.0428 51 R 0.0047 0.9575 0.0378 52 D 0.0047 0.9573 0.0380 53 A 0.0047 0.9579 0.0374 54 E 0.0047 0.9587 0.0367 55 R 0.0047 0.9581 0.0372 56 L 0.0048 0.9552 0.0401 57 I 0.0051 0.9429 0.0520 58 E 0.0061 0.8775 0.1163 59 G 0.0416 0.3769 0.5815 60 G 0.0416 0.0277 0.9307 61 M 0.1060 0.0131 0.8809 62 H 0.1194 0.0540 0.8267 63 G 0.8977 0.0074 0.0949 64 L 0.9286 0.0047 0.0667 65 I 0.9270 0.0051 0.0679 66 V 0.8870 0.0113 0.1018 67 E 0.6359 0.0378 0.3262 68 N 0.4235 0.0384 0.5381 69 H 0.2617 0.0586 0.6797 70 G 0.1388 0.0713 0.7899 71 D 0.0932 0.0610 0.8459 72 V 0.1902 0.0302 0.7796 73 P 0.2580 0.0341 0.7079 74 F 0.2032 0.0600 0.7368 75 S 0.1511 0.0452 0.8037 76 K 0.0852 0.0322 0.8827 77 P 0.0585 0.2051 0.7364 78 D 0.0452 0.3759 0.5789 79 D 0.0473 0.3861 0.5665 80 I 0.0658 0.3089 0.6253 81 G 0.0476 0.3072 0.6452 82 P 0.0208 0.8276 0.1515 83 E 0.0249 0.8873 0.0878 84 T 0.0150 0.9251 0.0599 85 S 0.0113 0.9380 0.0508 86 A 0.0096 0.9290 0.0615 87 F 0.0086 0.9313 0.0600 88 M 0.0073 0.9391 0.0536 89 S 0.0072 0.9476 0.0453 90 V 0.0066 0.9438 0.0497 91 V 0.0088 0.9275 0.0637 92 T 0.0121 0.8954 0.0926 93 D 0.0118 0.8191 0.1691 94 R 0.0222 0.6266 0.3511 95 I 0.0547 0.3155 0.6298 96 V 0.1808 0.1349 0.6843 97 R 0.2111 0.1145 0.6744 98 T 0.1206 0.4041 0.4754 99 A 0.0470 0.3162 0.6368 100 G 0.0550 0.2210 0.7240 101 V 0.1210 0.1606 0.7184 102 P 0.1327 0.2918 0.5756 103 V 0.1547 0.5815 0.2638 104 G 0.1674 0.6253 0.2073 105 I 0.0810 0.7989 0.1201 106 N 0.0480 0.8634 0.0887 107 V 0.0538 0.8544 0.0918 108 L 0.0438 0.8151 0.1411 109 A 0.0571 0.6841 0.2588 110 N 0.0262 0.4222 0.5515 111 A 0.0595 0.1080 0.8326 112 P 0.0745 0.1170 0.8085 113 I 0.0842 0.1979 0.7179 114 P 0.1352 0.4111 0.4536 115 A 0.1445 0.6411 0.2145 116 F 0.2644 0.5986 0.1370 117 A 0.2978 0.5982 0.1039 118 I 0.2402 0.6518 0.1080 119 A 0.2203 0.6332 0.1465 120 K 0.1567 0.6239 0.2194 121 A 0.1228 0.5328 0.3444 122 G 0.1469 0.2725 0.5807 123 G 0.1175 0.0927 0.7898 124 A 0.1445 0.1996 0.6560 125 K 0.2143 0.2266 0.5592 126 F 0.3786 0.1694 0.4520 127 I 0.3495 0.1026 0.5479 128 R 0.2270 0.0611 0.7119 129 V 0.0153 0.8823 0.1024 130 N 0.0076 0.9192 0.0732 131 Q 0.0073 0.9261 0.0667 132 W 0.0096 0.9258 0.0646 133 A 0.0099 0.9187 0.0714 134 N 0.0067 0.9311 0.0622 135 A 0.0054 0.9306 0.0640 136 Y 0.0062 0.9224 0.0715 137 V 0.0144 0.9002 0.0854 138 A 0.0190 0.8574 0.1236 139 N 0.0117 0.7564 0.2319 140 E 0.0485 0.4269 0.5246 141 G 0.0526 0.0641 0.8834 142 F 0.1763 0.0631 0.7606 143 M 0.3253 0.0940 0.5807 144 E 0.5462 0.1227 0.3311 145 G 0.6059 0.1381 0.2560 146 R 0.7001 0.1265 0.1734 147 A 0.5762 0.1638 0.2600 148 A 0.3261 0.2485 0.4254 149 E 0.1931 0.3319 0.4750 150 A 0.1205 0.4301 0.4494 151 M 0.0838 0.4280 0.4881 152 R 0.0573 0.4689 0.4738 153 Y 0.0288 0.7082 0.2630 154 R 0.0238 0.7705 0.2057 155 S 0.0134 0.8301 0.1565 156 L 0.0108 0.8851 0.1040 157 L 0.0130 0.8903 0.0967 158 R 0.0102 0.9075 0.0824 159 A 0.0055 0.9467 0.0478 160 E 0.0051 0.9482 0.0467 161 H 0.0057 0.9438 0.0506 162 I 0.0074 0.9357 0.0568 163 K 0.0085 0.9183 0.0731 164 V 0.0263 0.7979 0.1757 165 F 0.0477 0.5104 0.4419 166 A 0.1107 0.3563 0.5330 167 D 0.1547 0.2492 0.5961 168 S 0.2129 0.3015 0.4856 169 H 0.3786 0.2505 0.3709 170 V 0.6018 0.1638 0.2343 171 K 0.6142 0.1408 0.2450 172 H 0.4500 0.1271 0.4229 173 G 0.2142 0.0642 0.7216 174 A 0.1197 0.1285 0.7518 175 H 0.1574 0.1689 0.6737 176 A 0.1535 0.1826 0.6639 177 I 0.1148 0.1149 0.7703 178 T 0.0951 0.0634 0.8415 179 A 0.0496 0.2789 0.6715 180 D 0.0157 0.7981 0.1862 181 R 0.0126 0.8457 0.1417 182 S 0.0091 0.9048 0.0861 183 I 0.0049 0.9468 0.0483 184 D 0.0047 0.9553 0.0400 185 E 0.0047 0.9532 0.0421 186 L 0.0049 0.9473 0.0478 187 T 0.0052 0.9384 0.0565 188 R 0.0058 0.8835 0.1106 189 D 0.0086 0.7725 0.2189 190 L 0.0424 0.6126 0.3450 191 A 0.0407 0.4826 0.4766 192 F 0.1335 0.4327 0.4338 193 F 0.2942 0.2550 0.4508 194 D 0.3858 0.1230 0.4912 195 A 0.3264 0.0928 0.5808 196 D 0.2413 0.0794 0.6793 197 G 0.4149 0.0601 0.5250 198 V 0.6299 0.0441 0.3261 199 I 0.6710 0.0429 0.2861 200 A 0.5523 0.0579 0.3898 201 T 0.3937 0.0719 0.5344 202 G 0.2099 0.0869 0.7032 203 Q 0.1604 0.1615 0.6782 204 R 0.1622 0.1726 0.6652 205 T 0.1023 0.1443 0.7534 206 G 0.0615 0.0739 0.8646 207 N 0.0947 0.0553 0.8500 208 S 0.1211 0.0928 0.7861 209 A 0.1165 0.0841 0.7994 210 S 0.0863 0.0704 0.8432 211 L 0.0055 0.9302 0.0643 212 E 0.0048 0.9495 0.0457 213 E 0.0052 0.9469 0.0480 214 I 0.0050 0.9532 0.0418 215 E 0.0048 0.9570 0.0382 216 E 0.0052 0.9516 0.0432 217 I 0.0057 0.9422 0.0521 218 G 0.0076 0.9280 0.0644 219 A 0.0078 0.8776 0.1146 220 A 0.0156 0.6985 0.2859 221 T 0.0789 0.2997 0.6214 222 H 0.0471 0.0738 0.8791 223 L 0.1149 0.0125 0.8726 224 P 0.3399 0.0096 0.6504 225 L 0.8985 0.0060 0.0955 226 L 0.9190 0.0055 0.0755 227 V 0.8797 0.0214 0.0989 228 G 0.7283 0.0232 0.2485 229 S 0.2997 0.0475 0.6528 230 G 0.1353 0.0262 0.8385 231 V 0.1210 0.0145 0.8644 232 N 0.0695 0.0101 0.9205 233 E 0.0050 0.9059 0.0890 234 G 0.0048 0.9100 0.0852 235 N 0.0051 0.9325 0.0624 236 I 0.0047 0.9580 0.0373 237 V 0.0047 0.9598 0.0355 238 E 0.0047 0.9589 0.0365 239 I 0.0049 0.9517 0.0434 240 L 0.0049 0.9462 0.0489 241 K 0.0063 0.8723 0.1214 242 R 0.0100 0.6122 0.3778 243 T 0.0833 0.1511 0.7656 244 S 0.0362 0.0839 0.8799 245 G 0.7369 0.0314 0.2317 246 V 0.8957 0.0208 0.0835 247 I 0.9020 0.0265 0.0716 248 V 0.8359 0.0624 0.1017 249 A 0.4985 0.1811 0.3204 250 S 0.2899 0.3915 0.3185 251 S 0.3159 0.4461 0.2380 252 L 0.3150 0.5068 0.1782 253 K 0.3217 0.4552 0.2231 254 E 0.2054 0.3319 0.4626 255 G 0.0912 0.1556 0.7532 256 G 0.0571 0.2270 0.7158 257 V 0.0814 0.3177 0.6009 258 W 0.1220 0.2726 0.6054 259 W 0.1094 0.1218 0.7688 260 N 0.0793 0.0726 0.8481 261 P 0.0080 0.8576 0.1344 262 V 0.0086 0.9015 0.0900 263 E 0.0074 0.9183 0.0744 264 L 0.0051 0.9511 0.0438 265 A 0.0048 0.9523 0.0429 266 R 0.0048 0.9487 0.0465 267 V 0.0048 0.9517 0.0436 268 R 0.0047 0.9592 0.0362 269 S 0.0047 0.9581 0.0372 270 F 0.0047 0.9574 0.0379 271 V 0.0047 0.9568 0.0384 272 A 0.0052 0.9352 0.0596 273 A 0.0058 0.8465 0.1477 274 A 0.0096 0.7611 0.2292 275 R 0.0105 0.7414 0.2482 276 P 0.0064 0.7489 0.2447 277 G 0.0091 0.7804 0.2105 278 L 0.0136 0.8125 0.1739 279 E 0.0092 0.8482 0.1426 280 A 0.0095 0.8527 0.1378 281 L 0.0274 0.7860 0.1866 282 E 0.0358 0.7063 0.2579 283 H 0.0391 0.5868 0.3741 284 H 0.0515 0.4041 0.5443 285 H 0.0867 0.2470 0.6663 286 H 0.1170 0.1810 0.7020 287 H 0.0929 0.1018 0.8053 288 H 0.0544 0.0344 0.9112