# This file is the result of combining several RDB files, specifically # YGR017W.t2k.dssp-ebghstl.rdb (weight 1.53986) # YGR017W.t2k.stride-ebghtl.rdb (weight 1.24869) # YGR017W.t2k.str2.rdb (weight 1.54758) # YGR017W.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 YGR017W.t2k.dssp-ebghstl.rdb # ============================================ # TARGET YGR017W # 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 YGR017W.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 8 # # ============================================ # Comments from YGR017W.t2k.stride-ebghtl.rdb # ============================================ # TARGET YGR017W # 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 YGR017W.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 8 # # ============================================ # Comments from YGR017W.t2k.str2.rdb # ============================================ # TARGET YGR017W # 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 YGR017W.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 8 # # ============================================ # Comments from YGR017W.t2k.alpha.rdb # ============================================ # TARGET YGR017W # 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 YGR017W.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 8 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0531 0.0920 0.8549 2 S 0.0759 0.2066 0.7175 3 H 0.0638 0.2542 0.6820 4 Q 0.0710 0.2506 0.6784 5 M 0.0695 0.2314 0.6991 6 A 0.0430 0.4429 0.5140 7 P 0.0247 0.6961 0.2793 8 W 0.0123 0.8143 0.1734 9 I 0.0074 0.8958 0.0968 10 P 0.0050 0.9399 0.0551 11 M 0.0048 0.9472 0.0480 12 F 0.0048 0.9499 0.0453 13 I 0.0048 0.9501 0.0452 14 Q 0.0049 0.9361 0.0589 15 S 0.0059 0.8975 0.0965 16 C 0.0148 0.8143 0.1708 17 K 0.0189 0.6169 0.3642 18 N 0.0340 0.3287 0.6373 19 N 0.0548 0.1014 0.8438 20 T 0.0720 0.0625 0.8655 21 E 0.0962 0.0411 0.8627 22 P 0.1186 0.0694 0.8120 23 F 0.2020 0.0829 0.7151 24 V 0.3990 0.0776 0.5234 25 S 0.6396 0.0488 0.3116 26 F 0.7361 0.0297 0.2342 27 Q 0.8095 0.0291 0.1613 28 F 0.8247 0.0238 0.1516 29 A 0.7975 0.0196 0.1830 30 T 0.7718 0.0148 0.2134 31 V 0.6841 0.0200 0.2960 32 D 0.5272 0.0413 0.4315 33 E 0.1747 0.1387 0.6866 34 L 0.0594 0.1703 0.7703 35 T 0.0531 0.0800 0.8670 36 N 0.0445 0.0408 0.9147 37 K 0.1385 0.0174 0.8441 38 P 0.3781 0.0269 0.5950 39 R 0.4440 0.0553 0.5008 40 C 0.5518 0.0350 0.4132 41 R 0.6504 0.0308 0.3188 42 T 0.8196 0.0247 0.1557 43 V 0.8836 0.0220 0.0945 44 V 0.8718 0.0335 0.0947 45 F 0.8088 0.0569 0.1343 46 R 0.6350 0.1047 0.2603 47 D 0.4192 0.1804 0.4004 48 F 0.3738 0.2614 0.3648 49 L 0.3446 0.3240 0.3314 50 F 0.2313 0.2885 0.4802 51 H 0.1475 0.1750 0.6775 52 D 0.0696 0.2172 0.7131 53 K 0.0412 0.2433 0.7155 54 R 0.0904 0.1888 0.7208 55 T 0.1067 0.0867 0.8067 56 N 0.1106 0.0575 0.8319 57 V 0.6813 0.0191 0.2996 58 L 0.8667 0.0064 0.1269 59 T 0.8775 0.0088 0.1137 60 F 0.8588 0.0107 0.1305 61 N 0.6830 0.0243 0.2927 62 T 0.4140 0.0442 0.5419 63 D 0.1982 0.0752 0.7267 64 M 0.0453 0.3154 0.6393 65 R 0.0372 0.3120 0.6508 66 S 0.0750 0.4441 0.4809 67 S 0.0580 0.5479 0.3941 68 K 0.0856 0.5867 0.3277 69 I 0.1076 0.5870 0.3054 70 T 0.1079 0.5869 0.3052 71 E 0.1721 0.5124 0.3155 72 S 0.2101 0.3716 0.4183 73 F 0.2778 0.1711 0.5510 74 I 0.3047 0.0751 0.6203 75 T 0.1440 0.0461 0.8099 76 P 0.0369 0.1378 0.8253 77 N 0.0525 0.0874 0.8601 78 S 0.0932 0.0883 0.8185 79 N 0.1223 0.0908 0.7869 80 N 0.2048 0.0901 0.7051 81 S 0.1651 0.1036 0.7313 82 S 0.1525 0.1294 0.7180 83 D 0.1078 0.1653 0.7269 84 S 0.1071 0.1473 0.7456 85 K 0.0807 0.1799 0.7395 86 R 0.1125 0.1441 0.7434 87 C 0.1577 0.1066 0.7357 88 E 0.1113 0.0931 0.7956 89 T 0.1036 0.1291 0.7674 90 P 0.1009 0.3127 0.5865 91 F 0.2389 0.3301 0.4311 92 F 0.4158 0.2811 0.3031 93 E 0.5148 0.2534 0.2318 94 A 0.5936 0.2117 0.1947 95 C 0.6875 0.1431 0.1694 96 F 0.6877 0.1227 0.1896 97 Y 0.6597 0.0577 0.2826 98 F 0.3750 0.0331 0.5919 99 P 0.0862 0.1174 0.7963 100 E 0.0507 0.1192 0.8301 101 T 0.1964 0.0796 0.7239 102 W 0.2220 0.3213 0.4567 103 E 0.4593 0.2728 0.2679 104 Q 0.6559 0.1654 0.1788 105 Y 0.7863 0.0681 0.1457 106 R 0.8231 0.0459 0.1310 107 F 0.7582 0.0619 0.1799 108 S 0.3718 0.0780 0.5502 109 G 0.3079 0.0470 0.6451 110 Q 0.6593 0.0351 0.3056 111 C 0.8116 0.0224 0.1660 112 F 0.8049 0.0292 0.1659 113 T 0.7441 0.0469 0.2091 114 I 0.4527 0.0910 0.4563 115 S 0.1649 0.1712 0.6639 116 K 0.0523 0.5482 0.3994 117 Q 0.0421 0.5446 0.4133 118 F 0.0515 0.6163 0.3322 119 K 0.0506 0.4983 0.4511 120 K 0.0760 0.3544 0.5696 121 I 0.1422 0.1572 0.7007 122 P 0.1558 0.1088 0.7354 123 A 0.1004 0.4487 0.4509 124 E 0.1194 0.5210 0.3596 125 I 0.1799 0.4465 0.3736 126 V 0.2705 0.1894 0.5401 127 T 0.2346 0.1507 0.6146 128 K 0.1834 0.2637 0.5529 129 Y 0.2053 0.2296 0.5650 130 D 0.2039 0.1739 0.6221 131 I 0.1911 0.2000 0.6089 132 F 0.2086 0.1374 0.6540 133 S 0.1509 0.0860 0.7631 134 P 0.0886 0.2973 0.6141 135 R 0.1072 0.3326 0.5602 136 F 0.1140 0.3775 0.5085 137 S 0.0953 0.3114 0.5934 138 E 0.0765 0.2929 0.6306 139 T 0.0649 0.2181 0.7171 140 N 0.0878 0.1227 0.7895 141 D 0.1012 0.1287 0.7700 142 D 0.1004 0.1119 0.7877 143 S 0.0638 0.2535 0.6827 144 T 0.0561 0.3085 0.6355 145 D 0.0821 0.3433 0.5745 146 E 0.0705 0.4331 0.4964 147 E 0.1109 0.3761 0.5130 148 I 0.1468 0.2417 0.6115 149 D 0.1606 0.1367 0.7027 150 T 0.1462 0.0864 0.7674 151 P 0.1513 0.0680 0.7807 152 I 0.1676 0.1037 0.7288 153 N 0.1287 0.0829 0.7884 154 D 0.1173 0.0963 0.7864 155 D 0.0988 0.1108 0.7904 156 D 0.0877 0.1158 0.7965 157 D 0.0669 0.1304 0.8028 158 D 0.0733 0.1336 0.7931 159 D 0.0835 0.1322 0.7843 160 K 0.0770 0.1557 0.7674 161 N 0.0980 0.1101 0.7919 162 N 0.1152 0.0929 0.7919 163 D 0.1362 0.1375 0.7263 164 A 0.1128 0.1639 0.7233 165 D 0.1103 0.1489 0.7409 166 N 0.0985 0.1065 0.7950 167 N 0.1075 0.1713 0.7213 168 D 0.2067 0.1439 0.6494 169 I 0.1769 0.2128 0.6103 170 N 0.1169 0.1926 0.6904 171 E 0.0355 0.3774 0.5872 172 D 0.0443 0.3683 0.5873 173 N 0.0429 0.5092 0.4480 174 K 0.0641 0.5956 0.3402 175 L 0.1178 0.6473 0.2348 176 I 0.1235 0.6650 0.2115 177 E 0.1097 0.6586 0.2317 178 S 0.1122 0.5828 0.3050 179 I 0.0987 0.5501 0.3512 180 E 0.0896 0.4027 0.5076 181 N 0.0784 0.2593 0.6624 182 D 0.0923 0.1697 0.7380 183 E 0.0677 0.2486 0.6837 184 H 0.0815 0.2154 0.7032 185 H 0.1040 0.1256 0.7704 186 E 0.2183 0.1000 0.6816 187 D 0.1225 0.0602 0.8173 188 E 0.0246 0.1452 0.8301 189 D 0.0518 0.0755 0.8727 190 D 0.0475 0.0830 0.8695 191 Y 0.1237 0.0867 0.7895 192 Y 0.2247 0.0813 0.6940 193 P 0.1295 0.0946 0.7759 194 Q 0.0943 0.1166 0.7892 195 P 0.0709 0.2266 0.7025 196 Q 0.0425 0.3857 0.5717 197 E 0.0433 0.4799 0.4768 198 W 0.0225 0.6162 0.3613 199 E 0.0117 0.7895 0.1988 200 A 0.0084 0.8835 0.1081 201 E 0.0076 0.8988 0.0935 202 L 0.0064 0.9103 0.0833 203 L 0.0071 0.9142 0.0787 204 R 0.0071 0.9087 0.0843 205 Q 0.0070 0.8929 0.1002 206 W 0.0083 0.8702 0.1215 207 S 0.0073 0.8468 0.1459 208 S 0.0081 0.7318 0.2601 209 L 0.0213 0.5522 0.4266 210 S 0.0550 0.2761 0.6689 211 R 0.0074 0.7794 0.2132 212 H 0.0106 0.7584 0.2310 213 T 0.0297 0.7338 0.2365 214 K 0.0607 0.6728 0.2665 215 S 0.1316 0.5390 0.3294 216 L 0.1769 0.4499 0.3731 217 Y 0.2830 0.1951 0.5219 218 R 0.2646 0.0885 0.6469 219 K 0.2075 0.0372 0.7553 220 P 0.1504 0.0364 0.8131 221 A 0.1125 0.0327 0.8548 222 P 0.0516 0.0863 0.8621 223 G 0.0360 0.0735 0.8905 224 Q 0.1093 0.0906 0.8000 225 K 0.1920 0.1317 0.6763 226 L 0.1781 0.1606 0.6613 227 T 0.1447 0.1729 0.6824 228 S 0.0866 0.3537 0.5597 229 E 0.0940 0.4582 0.4478 230 T 0.0965 0.5465 0.3570 231 S 0.0883 0.5491 0.3627 232 K 0.0732 0.5855 0.3414 233 Q 0.0726 0.5488 0.3786 234 L 0.0795 0.4033 0.5172 235 D 0.0603 0.3688 0.5709 236 K 0.0587 0.3220 0.6193 237 L 0.0895 0.2681 0.6425 238 H 0.1162 0.1358 0.7479 239 R 0.0501 0.2738 0.6761 240 G 0.0556 0.2147 0.7297 241 V 0.0989 0.1868 0.7142 242 D 0.0992 0.1542 0.7466 243 G 0.0751 0.1959 0.7290 244 A 0.0501 0.3278 0.6221 245 K 0.0447 0.3979 0.5574 246 E 0.0494 0.4407 0.5099 247 D 0.0624 0.3660 0.5716 248 A 0.0805 0.2152 0.7042 249 G 0.0841 0.1236 0.7923 250 L 0.0976 0.1329 0.7695 251 E 0.0661 0.1634 0.7705 252 N 0.1022 0.1179 0.7798 253 F 0.4942 0.0149 0.4909 254 G 0.8078 0.0059 0.1863 255 I 0.9243 0.0032 0.0725 256 V 0.9224 0.0036 0.0740 257 C 0.9207 0.0033 0.0760 258 L 0.8710 0.0065 0.1225 259 C 0.6875 0.0053 0.3072 260 V 0.4157 0.1079 0.4764 261 D 0.2412 0.1589 0.6000 262 S 0.3787 0.1788 0.4424 263 V 0.4967 0.1088 0.3945 264 D 0.4318 0.1375 0.4307 265 F 0.5387 0.1615 0.2998 266 L 0.5145 0.1481 0.3374 267 N 0.6054 0.0688 0.3258 268 L 0.4112 0.0454 0.5435 269 K 0.2989 0.0502 0.6508 270 E 0.1970 0.0538 0.7491 271 G 0.0967 0.0462 0.8570 272 R 0.0637 0.1105 0.8258 273 G 0.0755 0.0818 0.8428 274 G 0.2107 0.0710 0.7183 275 E 0.5993 0.0341 0.3667 276 R 0.7870 0.0249 0.1880 277 W 0.8370 0.0237 0.1392 278 I 0.8013 0.0347 0.1640 279 F 0.7029 0.0481 0.2490 280 Q 0.5300 0.0854 0.3846 281 K 0.3665 0.0890 0.5445 282 T 0.2360 0.0900 0.6740 283 D 0.1136 0.0572 0.8292 284 G 0.0832 0.0735 0.8433 285 K 0.1021 0.1111 0.7869 286 D 0.1368 0.1111 0.7521 287 E 0.0832 0.3611 0.5556 288 D 0.1295 0.3857 0.4848 289 L 0.2311 0.3772 0.3917 290 W 0.3247 0.2609 0.4144 291 E 0.4089 0.2140 0.3771 292 E 0.5294 0.1534 0.3172 293 Q 0.5569 0.1102 0.3330 294 E 0.5562 0.0734 0.3703 295 V 0.3307 0.0511 0.6182 296 C 0.1198 0.0195 0.8608 297 P 0.0391 0.0428 0.9181