# This file is the result of combining several RDB files, specifically # T0344.t04.dssp-ebghstl.rdb (weight 1.53986) # T0344.t04.stride-ebghtl.rdb (weight 1.24869) # T0344.t04.str2.rdb (weight 1.54758) # T0344.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 T0344.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.6722 # # ============================================ # Comments from T0344.t04.stride-ebghtl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.6722 # # ============================================ # Comments from T0344.t04.str2.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.6722 # # ============================================ # Comments from T0344.t04.alpha.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.6722 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2220 0.0130 0.7650 2 R 0.7419 0.0107 0.2473 3 I 0.8840 0.0087 0.1072 4 V 0.8725 0.0200 0.1075 5 A 0.8426 0.0199 0.1375 6 A 0.6575 0.0700 0.2724 7 D 0.3613 0.0684 0.5704 8 T 0.1667 0.0608 0.7724 9 G 0.1087 0.0727 0.8186 10 G 0.1926 0.1270 0.6804 11 A 0.4054 0.1520 0.4426 12 V 0.5330 0.1532 0.3138 13 L 0.4345 0.1748 0.3907 14 D 0.1999 0.2019 0.5982 15 E 0.0418 0.3575 0.6007 16 T 0.0597 0.2866 0.6536 17 F 0.1263 0.1932 0.6805 18 E 0.1149 0.1317 0.7535 19 P 0.1601 0.2672 0.5727 20 I 0.2226 0.3462 0.4312 21 G 0.4711 0.2326 0.2964 22 L 0.5794 0.2644 0.1562 23 I 0.6215 0.2277 0.1508 24 A 0.6992 0.1293 0.1715 25 T 0.6941 0.1370 0.1689 26 V 0.6819 0.1661 0.1519 27 A 0.6658 0.2293 0.1049 28 V 0.6508 0.2523 0.0969 29 L 0.6626 0.2239 0.1135 30 V 0.6698 0.1478 0.1824 31 E 0.5333 0.1343 0.3324 32 K 0.2323 0.0682 0.6995 33 P 0.1500 0.1046 0.7454 34 Y 0.1403 0.1389 0.7208 35 R 0.1336 0.1446 0.7218 36 S 0.1354 0.1172 0.7474 37 A 0.1069 0.4278 0.4653 38 K 0.1597 0.4148 0.4255 39 E 0.3970 0.3151 0.2879 40 V 0.5764 0.1986 0.2250 41 M 0.6821 0.1603 0.1576 42 V 0.7075 0.1301 0.1624 43 K 0.7034 0.1112 0.1854 44 Y 0.5891 0.0636 0.3473 45 A 0.2971 0.0515 0.6514 46 N 0.1367 0.0166 0.8467 47 P 0.0461 0.1669 0.7870 48 Y 0.0804 0.1470 0.7726 49 D 0.1591 0.1595 0.6814 50 Y 0.2340 0.1361 0.6300 51 D 0.2267 0.1205 0.6527 52 L 0.1075 0.3288 0.5637 53 T 0.0765 0.3617 0.5618 54 G 0.0436 0.4810 0.4755 55 R 0.0614 0.6930 0.2456 56 Q 0.0948 0.7502 0.1550 57 A 0.0902 0.7529 0.1569 58 I 0.0611 0.8030 0.1359 59 R 0.0265 0.8755 0.0980 60 D 0.0150 0.9075 0.0775 61 E 0.0099 0.9412 0.0490 62 V 0.0092 0.9498 0.0410 63 L 0.0078 0.9566 0.0357 64 L 0.0071 0.9575 0.0353 65 A 0.0072 0.9564 0.0365 66 I 0.0102 0.9532 0.0366 67 E 0.0094 0.9512 0.0394 68 L 0.0071 0.9405 0.0524 69 A 0.0085 0.9083 0.0832 70 R 0.0189 0.8344 0.1467 71 K 0.0334 0.6415 0.3251 72 V 0.0905 0.3117 0.5978 73 K 0.0897 0.0425 0.8678 74 P 0.1009 0.0663 0.8328 75 D 0.1643 0.0983 0.7374 76 V 0.7985 0.0301 0.1714 77 I 0.8852 0.0125 0.1023 78 H 0.8719 0.0149 0.1133 79 L 0.6774 0.0362 0.2864 80 D 0.2980 0.0742 0.6278 81 S 0.1359 0.1415 0.7226 82 T 0.1679 0.1807 0.6514 83 L 0.2419 0.1685 0.5895 84 G 0.1693 0.0906 0.7401 85 G 0.2985 0.0882 0.6133 86 I 0.6375 0.0548 0.3077 87 E 0.7628 0.0526 0.1846 88 L 0.7521 0.0679 0.1801 89 R 0.6495 0.0978 0.2528 90 K 0.4789 0.1006 0.4204 91 L 0.1968 0.0879 0.7153 92 D 0.0859 0.0576 0.8565 93 E 0.0577 0.4095 0.5328 94 P 0.0484 0.5311 0.4205 95 T 0.0881 0.5839 0.3281 96 I 0.1071 0.6655 0.2274 97 D 0.1727 0.5762 0.2511 98 A 0.2305 0.5493 0.2203 99 L 0.2662 0.3271 0.4067 100 G 0.2876 0.1206 0.5917 101 I 0.3878 0.0849 0.5272 102 S 0.3137 0.0916 0.5947 103 D 0.1155 0.1738 0.7107 104 K 0.0499 0.1979 0.7521 105 G 0.0472 0.2535 0.6992 106 K 0.0653 0.6093 0.3254 107 E 0.1623 0.7074 0.1304 108 V 0.1087 0.7890 0.1023 109 W 0.0620 0.8395 0.0985 110 K 0.0352 0.8822 0.0826 111 E 0.0323 0.8548 0.1129 112 L 0.0212 0.7969 0.1819 113 S 0.0207 0.7218 0.2575 114 K 0.0095 0.6818 0.3087 115 D 0.0141 0.5970 0.3890 116 L 0.0145 0.7373 0.2482 117 Q 0.0085 0.7929 0.1986 118 P 0.0049 0.9105 0.0846 119 L 0.0050 0.9299 0.0650 120 A 0.0069 0.9269 0.0662 121 R 0.0066 0.9151 0.0783 122 K 0.0084 0.8871 0.1045 123 F 0.0159 0.8660 0.1182 124 W 0.0217 0.8640 0.1143 125 E 0.0272 0.8382 0.1346 126 E 0.0397 0.7475 0.2128 127 T 0.0665 0.3639 0.5695 128 N 0.0996 0.0360 0.8644 129 I 0.3775 0.0109 0.6116 130 E 0.7947 0.0077 0.1976 131 I 0.9140 0.0042 0.0818 132 V 0.9089 0.0076 0.0836 133 A 0.8926 0.0070 0.1005 134 I 0.7879 0.0264 0.1857 135 G 0.4529 0.0225 0.5247 136 K 0.2433 0.0871 0.6696 137 S 0.1743 0.0761 0.7497 138 S 0.2277 0.0890 0.6833 139 V 0.3349 0.0580 0.6071 140 P 0.4655 0.1002 0.4343 141 V 0.5639 0.1860 0.2501 142 R 0.5916 0.2071 0.2012 143 I 0.3981 0.4947 0.1072 144 A 0.3815 0.5297 0.0888 145 E 0.4203 0.4823 0.0974 146 I 0.3813 0.5087 0.1100 147 Y 0.3098 0.5296 0.1607 148 A 0.2095 0.5189 0.2716 149 G 0.1833 0.4698 0.3470 150 I 0.2646 0.5320 0.2034 151 Y 0.2647 0.5625 0.1727 152 S 0.2296 0.5666 0.2038 153 A 0.1272 0.7108 0.1620 154 K 0.1223 0.7493 0.1283 155 W 0.2070 0.6450 0.1480 156 G 0.2835 0.5506 0.1659 157 I 0.2702 0.5621 0.1677 158 E 0.2415 0.5330 0.2255 159 N 0.2569 0.4825 0.2606 160 V 0.3397 0.4063 0.2539 161 E 0.2718 0.4011 0.3271 162 K 0.2457 0.3461 0.4082 163 E 0.0736 0.1164 0.8099 164 G 0.0743 0.0340 0.8917 165 H 0.4292 0.0133 0.5575 166 L 0.8658 0.0044 0.1298 167 I 0.9038 0.0058 0.0904 168 I 0.8398 0.0214 0.1388 169 G 0.6986 0.0173 0.2841 170 L 0.4521 0.0177 0.5302 171 P 0.3707 0.0561 0.5732 172 R 0.4248 0.0893 0.4860 173 Y 0.7234 0.0384 0.2382 174 M 0.8043 0.0130 0.1828 175 E 0.8791 0.0070 0.1139 176 V 0.8876 0.0058 0.1066 177 N 0.8928 0.0049 0.1023 178 I 0.8014 0.0083 0.1904 179 K 0.5411 0.0267 0.4322 180 D 0.1404 0.0511 0.8085 181 G 0.1252 0.0409 0.8338 182 K 0.5824 0.0229 0.3947 183 I 0.8187 0.0097 0.1716 184 I 0.7092 0.0287 0.2621 185 G 0.4811 0.0406 0.4783 186 R 0.4270 0.0479 0.5250 187 S 0.4651 0.0318 0.5031 188 L 0.3756 0.0235 0.6010 189 D 0.2006 0.0120 0.7874 190 P 0.0238 0.2772 0.6989 191 R 0.0296 0.2432 0.7272 192 E 0.0959 0.2237 0.6803 193 G 0.1328 0.0874 0.7798 194 G 0.2590 0.0633 0.6776 195 L 0.5440 0.0522 0.4038 196 Y 0.5668 0.0467 0.3866 197 G 0.5526 0.0258 0.4216 198 S 0.7227 0.0198 0.2576 199 A 0.8183 0.0162 0.1655 200 E 0.8574 0.0133 0.1294 201 V 0.8407 0.0113 0.1479 202 S 0.7407 0.0147 0.2446 203 V 0.3938 0.0173 0.5889 204 P 0.1903 0.0474 0.7623 205 E 0.0729 0.0741 0.8530 206 G 0.1655 0.0430 0.7915 207 V 0.5390 0.0082 0.4527 208 K 0.7983 0.0108 0.1909 209 W 0.8751 0.0089 0.1160 210 E 0.8564 0.0138 0.1298 211 I 0.7996 0.0169 0.1835 212 Y 0.4720 0.0129 0.5151 213 P 0.1667 0.0510 0.7823 214 N 0.1105 0.0615 0.8280 215 P 0.0197 0.5817 0.3986 216 V 0.0355 0.6584 0.3061 217 A 0.0980 0.6789 0.2231 218 R 0.1816 0.6174 0.2010 219 R 0.3084 0.4837 0.2079 220 F 0.4637 0.3457 0.1906 221 M 0.5861 0.2782 0.1358 222 I 0.6510 0.2538 0.0952 223 F 0.6561 0.2479 0.0961 224 E 0.6671 0.2355 0.0974 225 I 0.6180 0.2306 0.1513 226 F 0.4820 0.1711 0.3469 227 S 0.2736 0.1252 0.6013 228 K 0.1262 0.1125 0.7612 229 R 0.0653 0.0443 0.8905