# This file is the result of combining several RDB files, specifically # T0336.t06.dssp-ebghstl.rdb (weight 1.53986) # T0336.t06.stride-ebghtl.rdb (weight 1.24869) # T0336.t06.str2.rdb (weight 1.54758) # T0336.t06.alpha.rdb (weight 0.659012) # 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) # T0336.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0336.t2k.stride-ebghtl.rdb (weight 1.24869) # T0336.t2k.str2.rdb (weight 1.54758) # T0336.t2k.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.t06.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.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 35.1964 # # ============================================ # Comments from T0336.t06.stride-ebghtl.rdb # ============================================ # TARGET T0336 # 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 T0336.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 35.1964 # # ============================================ # Comments from T0336.t06.str2.rdb # ============================================ # TARGET T0336 # 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 T0336.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 35.1964 # # ============================================ # Comments from T0336.t06.alpha.rdb # ============================================ # TARGET T0336 # 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 T0336.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 35.1964 # # ============================================ # 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 # # ============================================ # Comments from T0336.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0336 # 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 T0336.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 215 # # ============================================ # Comments from T0336.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0336 # 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 T0336.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 215 # # ============================================ # Comments from T0336.t2k.str2.rdb # ============================================ # TARGET T0336 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0336.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 215 # # ============================================ # Comments from T0336.t2k.alpha.rdb # ============================================ # TARGET T0336 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0336.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 215 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0493 0.0974 0.8533 2 S 0.0663 0.1941 0.7396 3 M 0.0519 0.2483 0.6998 4 E 0.0136 0.7970 0.1895 5 E 0.0104 0.8767 0.1129 6 E 0.0071 0.9237 0.0692 7 E 0.0066 0.9438 0.0496 8 F 0.0055 0.9518 0.0427 9 D 0.0052 0.9527 0.0421 10 I 0.0048 0.9563 0.0390 11 R 0.0047 0.9572 0.0381 12 E 0.0047 0.9528 0.0424 13 A 0.0048 0.9489 0.0463 14 L 0.0048 0.9435 0.0517 15 A 0.0050 0.9251 0.0699 16 N 0.0059 0.8782 0.1159 17 G 0.0077 0.8580 0.1343 18 E 0.0079 0.8311 0.1610 19 H 0.0112 0.7209 0.2679 20 L 0.0205 0.6715 0.3080 21 E 0.0313 0.7191 0.2497 22 K 0.0212 0.7986 0.1802 23 I 0.0236 0.8298 0.1466 24 L 0.0323 0.8360 0.1317 25 I 0.0408 0.7866 0.1725 26 M 0.0650 0.6060 0.3289 27 A 0.1236 0.4860 0.3903 28 K 0.1581 0.3969 0.4450 29 Y 0.1052 0.3289 0.5659 30 D 0.0598 0.3247 0.6155 31 E 0.0211 0.5496 0.4293 32 S 0.0179 0.5218 0.4602 33 V 0.0242 0.6883 0.2875 34 L 0.0115 0.8705 0.1180 35 K 0.0056 0.9352 0.0592 36 K 0.0050 0.9440 0.0510 37 L 0.0053 0.9425 0.0522 38 I 0.0053 0.9400 0.0548 39 E 0.0052 0.9062 0.0886 40 L 0.0069 0.8495 0.1436 41 L 0.0316 0.6388 0.3295 42 D 0.0232 0.4198 0.5570 43 D 0.0656 0.1995 0.7349 44 D 0.0240 0.2238 0.7522 45 L 0.0612 0.2095 0.7294 46 W 0.0071 0.8482 0.1447 47 T 0.0062 0.9066 0.0872 48 V 0.0066 0.9282 0.0652 49 V 0.0048 0.9497 0.0455 50 K 0.0047 0.9580 0.0373 51 N 0.0047 0.9575 0.0378 52 A 0.0047 0.9586 0.0367 53 I 0.0047 0.9602 0.0351 54 S 0.0047 0.9596 0.0357 55 I 0.0047 0.9583 0.0370 56 I 0.0047 0.9555 0.0398 57 M 0.0048 0.9526 0.0426 58 V 0.0052 0.9342 0.0606 59 I 0.0060 0.8930 0.1009 60 A 0.0133 0.7845 0.2022 61 K 0.0148 0.5169 0.4683 62 T 0.0325 0.2298 0.7377 63 R 0.0602 0.1056 0.8342 64 E 0.0087 0.7320 0.2594 65 D 0.0076 0.7752 0.2172 66 L 0.0112 0.7910 0.1978 67 Y 0.0152 0.7839 0.2009 68 E 0.0146 0.8147 0.1708 69 P 0.0108 0.8522 0.1370 70 M 0.0160 0.8213 0.1627 71 L 0.0179 0.7902 0.1918 72 K 0.0141 0.8255 0.1604 73 K 0.0091 0.8822 0.1087 74 L 0.0076 0.9011 0.0913 75 F 0.0073 0.9082 0.0845 76 S 0.0066 0.8994 0.0940 77 L 0.0070 0.8712 0.1218 78 L 0.0112 0.7951 0.1937 79 K 0.0269 0.5991 0.3740 80 K 0.0248 0.4401 0.5351 81 S 0.0578 0.2746 0.6676 82 E 0.0238 0.3221 0.6541 83 A 0.0322 0.4417 0.5261 84 I 0.0128 0.8404 0.1468 85 P 0.0066 0.9095 0.0839 86 L 0.0055 0.9360 0.0585 87 T 0.0047 0.9544 0.0409 88 Q 0.0047 0.9590 0.0363 89 E 0.0047 0.9591 0.0362 90 I 0.0047 0.9589 0.0364 91 A 0.0047 0.9596 0.0357 92 K 0.0048 0.9565 0.0387 93 A 0.0048 0.9514 0.0437 94 F 0.0049 0.9420 0.0531 95 G 0.0051 0.9283 0.0666 96 Q 0.0058 0.8997 0.0945 97 M 0.0076 0.8592 0.1332 98 A 0.0119 0.7760 0.2121 99 K 0.0111 0.6417 0.3472 100 E 0.0234 0.4473 0.5293 101 K 0.0453 0.1992 0.7555 102 P 0.0231 0.5606 0.4163 103 E 0.0115 0.6916 0.2969 104 L 0.0154 0.7363 0.2483 105 V 0.0150 0.7894 0.1956 106 K 0.0092 0.8319 0.1589 107 S 0.0101 0.8289 0.1609 108 M 0.0142 0.8461 0.1398 109 I 0.0072 0.9152 0.0776 110 P 0.0048 0.9395 0.0556 111 V 0.0048 0.9460 0.0492 112 L 0.0048 0.9467 0.0485 113 F 0.0049 0.9416 0.0535 114 A 0.0053 0.9104 0.0843 115 N 0.0071 0.8523 0.1405 116 Y 0.0331 0.6322 0.3348 117 R 0.0330 0.3489 0.6180 118 I 0.0723 0.1349 0.7928 119 G 0.0241 0.1861 0.7898 120 D 0.0483 0.2460 0.7056 121 E 0.0061 0.8970 0.0969 122 K 0.0057 0.9307 0.0636 123 T 0.0052 0.9465 0.0483 124 K 0.0047 0.9572 0.0381 125 I 0.0047 0.9591 0.0362 126 N 0.0047 0.9587 0.0367 127 V 0.0047 0.9585 0.0368 128 S 0.0047 0.9599 0.0354 129 Y 0.0047 0.9589 0.0364 130 A 0.0047 0.9585 0.0369 131 L 0.0047 0.9557 0.0396 132 E 0.0048 0.9528 0.0425 133 E 0.0051 0.9361 0.0588 134 I 0.0061 0.8962 0.0977 135 A 0.0086 0.8061 0.1853 136 K 0.0140 0.5745 0.4115 137 A 0.0360 0.2755 0.6885 138 N 0.0531 0.1454 0.8015 139 P 0.0143 0.7224 0.2633 140 M 0.0087 0.8104 0.1808 141 L 0.0087 0.8495 0.1418 142 M 0.0059 0.9188 0.0753 143 A 0.0056 0.9310 0.0634 144 S 0.0053 0.9330 0.0617 145 I 0.0052 0.9345 0.0604 146 V 0.0051 0.9415 0.0534 147 R 0.0048 0.9414 0.0538 148 D 0.0049 0.9357 0.0594 149 F 0.0050 0.9287 0.0664 150 M 0.0055 0.9137 0.0808 151 S 0.0063 0.8656 0.1281 152 M 0.0088 0.8037 0.1875 153 L 0.0352 0.6055 0.3593 154 S 0.0294 0.3815 0.5891 155 S 0.0678 0.2306 0.7017 156 K 0.0269 0.2882 0.6849 157 N 0.0464 0.3290 0.6246 158 R 0.0112 0.8071 0.1817 159 E 0.0094 0.8562 0.1344 160 D 0.0104 0.8939 0.0957 161 K 0.0068 0.9218 0.0714 162 L 0.0057 0.9429 0.0515 163 T 0.0048 0.9491 0.0462 164 A 0.0048 0.9512 0.0441 165 L 0.0047 0.9539 0.0414 166 N 0.0048 0.9524 0.0429 167 F 0.0048 0.9504 0.0448 168 I 0.0051 0.9402 0.0547 169 E 0.0054 0.9262 0.0684 170 A 0.0062 0.8943 0.0995 171 M 0.0139 0.8226 0.1635 172 G 0.0164 0.7382 0.2454 173 E 0.0145 0.6700 0.3155 174 N 0.0254 0.5463 0.4283 175 S 0.0474 0.4374 0.5152 176 F 0.0136 0.7328 0.2536 177 K 0.0101 0.7738 0.2161 178 Y 0.0140 0.7672 0.2189 179 V 0.0157 0.7961 0.1882 180 N 0.0125 0.8220 0.1656 181 P 0.0100 0.8020 0.1880 182 F 0.0139 0.8198 0.1662 183 L 0.0091 0.8985 0.0924 184 P 0.0051 0.9386 0.0563 185 R 0.0049 0.9452 0.0499 186 I 0.0052 0.9472 0.0477 187 I 0.0049 0.9427 0.0524 188 N 0.0053 0.9071 0.0877 189 L 0.0072 0.8619 0.1309 190 L 0.0274 0.6273 0.3452 191 H 0.0260 0.3540 0.6200 192 D 0.0656 0.1133 0.8212 193 G 0.0233 0.1581 0.8185 194 D 0.0518 0.1745 0.7737 195 E 0.0067 0.9012 0.0922 196 I 0.0057 0.9384 0.0559 197 V 0.0053 0.9479 0.0468 198 R 0.0047 0.9566 0.0387 199 A 0.0047 0.9597 0.0356 200 S 0.0047 0.9591 0.0362 201 A 0.0047 0.9586 0.0367 202 V 0.0047 0.9595 0.0358 203 E 0.0047 0.9575 0.0378 204 A 0.0047 0.9546 0.0406 205 L 0.0048 0.9491 0.0461 206 V 0.0049 0.9423 0.0528 207 H 0.0055 0.9067 0.0878 208 L 0.0087 0.8217 0.1695 209 A 0.0245 0.6225 0.3530 210 T 0.0311 0.3512 0.6178 211 L 0.0386 0.1472 0.8142 212 N 0.0614 0.1163 0.8223 213 D 0.0074 0.8269 0.1657 214 K 0.0069 0.8902 0.1029 215 L 0.0088 0.9150 0.0762 216 R 0.0101 0.9313 0.0586 217 K 0.0104 0.9359 0.0537 218 V 0.0121 0.9380 0.0499 219 V 0.0076 0.9450 0.0474 220 I 0.0059 0.9511 0.0430 221 K 0.0048 0.9547 0.0405 222 R 0.0049 0.9524 0.0427 223 L 0.0051 0.9446 0.0503 224 E 0.0055 0.9245 0.0699 225 E 0.0088 0.8428 0.1484 226 L 0.0515 0.5067 0.4418 227 N 0.0550 0.1374 0.8076 228 D 0.0815 0.0482 0.8703 229 T 0.0227 0.2153 0.7621 230 S 0.0244 0.2031 0.7725 231 S 0.0540 0.2727 0.6733 232 L 0.0748 0.5975 0.3277 233 V 0.0722 0.7371 0.1907 234 N 0.0875 0.7764 0.1361 235 K 0.0607 0.8347 0.1046 236 T 0.0726 0.8311 0.0963 237 V 0.0363 0.9019 0.0618 238 K 0.0200 0.9241 0.0559 239 E 0.0178 0.9014 0.0808 240 G 0.0177 0.8193 0.1631 241 I 0.0248 0.8098 0.1654 242 S 0.0225 0.8075 0.1700 243 R 0.0149 0.7950 0.1901 244 L 0.0245 0.6770 0.2985 245 L 0.0484 0.4789 0.4727 246 L 0.0671 0.2529 0.6800 247 L 0.0646 0.1086 0.8269 248 E 0.0778 0.1132 0.8090 249 G 0.1095 0.1842 0.7064 250 H 0.1216 0.1608 0.7176 251 S 0.1067 0.1341 0.7592 252 S 0.0729 0.1275 0.7996 253 S 0.0413 0.0798 0.8789