# This file is the result of combining several RDB files, specifically # T0264.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0264.t2k.stride-ebghtl.rdb (weight 1.24869) # T0264.t2k.str2.rdb (weight 1.54758) # T0264.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 T0264.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0264 # 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 T0264.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 367 # # ============================================ # Comments from T0264.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0264 # 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 T0264.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 367 # # ============================================ # Comments from T0264.t2k.str2.rdb # ============================================ # TARGET T0264 # 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 T0264.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 367 # # ============================================ # Comments from T0264.t2k.alpha.rdb # ============================================ # TARGET T0264 # 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 T0264.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 367 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1735 0.1517 0.6748 2 A 0.2497 0.1078 0.6425 3 R 0.1827 0.1091 0.7082 4 G 0.1508 0.0733 0.7759 5 R 0.1332 0.0708 0.7960 6 E 0.1783 0.0521 0.7696 7 A 0.1424 0.0680 0.7895 8 V 0.2674 0.0216 0.7109 9 T 0.7947 0.0051 0.2002 10 L 0.9194 0.0032 0.0774 11 L 0.9282 0.0035 0.0684 12 L 0.9288 0.0033 0.0679 13 V 0.8931 0.0116 0.0953 14 G 0.8152 0.0076 0.1772 15 W 0.5276 0.0208 0.4516 16 G 0.2868 0.0165 0.6967 17 Y 0.0897 0.0682 0.8422 18 A 0.0473 0.0612 0.8915 19 P 0.0427 0.1115 0.8457 20 G 0.0283 0.1357 0.8361 21 M 0.1274 0.1797 0.6929 22 Q 0.2148 0.2926 0.4926 23 T 0.1231 0.4728 0.4041 24 L 0.0075 0.9412 0.0513 25 E 0.0058 0.9498 0.0444 26 A 0.0052 0.9530 0.0418 27 L 0.0053 0.9556 0.0390 28 D 0.0048 0.9539 0.0413 29 A 0.0049 0.9490 0.0462 30 V 0.0063 0.9212 0.0724 31 R 0.0073 0.8032 0.1895 32 R 0.0159 0.3747 0.6094 33 A 0.0832 0.0354 0.8815 34 D 0.0475 0.0600 0.8925 35 V 0.8733 0.0085 0.1182 36 V 0.9290 0.0034 0.0676 37 Y 0.9193 0.0044 0.0763 38 V 0.8439 0.0083 0.1478 39 E 0.3588 0.0717 0.5695 40 S 0.1013 0.1619 0.7369 41 Y 0.1313 0.2347 0.6340 42 T 0.1652 0.2042 0.6306 43 M 0.1245 0.2154 0.6601 44 P 0.0295 0.6723 0.2982 45 G 0.0238 0.7560 0.2202 46 S 0.0227 0.8038 0.1734 47 S 0.0199 0.8243 0.1558 48 W 0.0173 0.8036 0.1791 49 L 0.0170 0.7428 0.2402 50 Y 0.0250 0.6749 0.3001 51 K 0.0163 0.7403 0.2433 52 S 0.0105 0.8161 0.1734 53 V 0.0105 0.8363 0.1532 54 V 0.0219 0.8116 0.1665 55 E 0.0263 0.7659 0.2078 56 A 0.0409 0.6786 0.2804 57 A 0.0787 0.4904 0.4310 58 G 0.1170 0.3033 0.5797 59 E 0.1227 0.1981 0.6792 60 A 0.2053 0.1492 0.6455 61 R 0.3770 0.1148 0.5082 62 V 0.4928 0.1085 0.3987 63 V 0.4368 0.1223 0.4409 64 E 0.3035 0.1431 0.5534 65 A 0.1349 0.1686 0.6965 66 S 0.0777 0.1382 0.7841 67 R 0.0669 0.1724 0.7607 68 R 0.0718 0.2310 0.6972 69 D 0.0678 0.3067 0.6255 70 L 0.0111 0.8163 0.1726 71 E 0.0074 0.8824 0.1102 72 E 0.0071 0.9026 0.0903 73 R 0.0057 0.9155 0.0788 74 S 0.0054 0.9330 0.0616 75 R 0.0049 0.9442 0.0509 76 E 0.0049 0.9454 0.0497 77 I 0.0049 0.9444 0.0506 78 V 0.0055 0.9412 0.0534 79 S 0.0053 0.9260 0.0687 80 R 0.0081 0.8691 0.1228 81 A 0.0250 0.6985 0.2765 82 L 0.0308 0.2736 0.6956 83 D 0.0249 0.0509 0.9242 84 A 0.0787 0.0173 0.9040 85 V 0.2473 0.0104 0.7422 86 V 0.8408 0.0040 0.1552 87 A 0.9124 0.0034 0.0842 88 V 0.9239 0.0033 0.0728 89 V 0.8788 0.0059 0.1153 90 T 0.6605 0.0164 0.3231 91 A 0.2503 0.0429 0.7068 92 G 0.0865 0.0396 0.8739 93 D 0.1004 0.0363 0.8632 94 P 0.0768 0.1787 0.7444 95 M 0.1443 0.1945 0.6613 96 V 0.2043 0.2848 0.5109 97 A 0.1351 0.2594 0.6055 98 T 0.0756 0.3049 0.6195 99 T 0.0272 0.5858 0.3870 100 H 0.0083 0.8699 0.1218 101 S 0.0050 0.9532 0.0419 102 S 0.0048 0.9588 0.0364 103 L 0.0048 0.9590 0.0363 104 A 0.0048 0.9593 0.0359 105 A 0.0050 0.9577 0.0373 106 E 0.0050 0.9581 0.0369 107 A 0.0048 0.9572 0.0380 108 L 0.0052 0.9454 0.0494 109 E 0.0052 0.8898 0.1050 110 A 0.0446 0.3015 0.6539 111 G 0.0428 0.0155 0.9417 112 V 0.0898 0.0082 0.9021 113 A 0.5573 0.0076 0.4352 114 V 0.8676 0.0040 0.1284 115 R 0.9110 0.0038 0.0851 116 Y 0.8935 0.0054 0.1011 117 I 0.6198 0.0107 0.3694 118 P 0.0990 0.0538 0.8473 119 G 0.0380 0.0361 0.9260 120 V 0.0874 0.3444 0.5682 121 S 0.0464 0.6423 0.3113 122 G 0.0172 0.8947 0.0880 123 V 0.0069 0.9332 0.0599 124 Q 0.0064 0.9376 0.0561 125 A 0.0067 0.9423 0.0511 126 A 0.0062 0.9524 0.0415 127 R 0.0058 0.9499 0.0443 128 G 0.0068 0.9353 0.0579 129 A 0.0089 0.8999 0.0912 130 T 0.0458 0.4822 0.4720 131 M 0.0371 0.0445 0.9184 132 L 0.0743 0.0214 0.9042 133 S 0.2450 0.0412 0.7138 134 F 0.3307 0.1265 0.5429 135 Y 0.3114 0.1110 0.5776 136 R 0.2503 0.0943 0.6553 137 F 0.1019 0.1223 0.7758 138 G 0.1431 0.0742 0.7826 139 G 0.4704 0.0279 0.5017 140 T 0.7557 0.0142 0.2301 141 V 0.8485 0.0098 0.1417 142 T 0.8670 0.0097 0.1232 143 L 0.8367 0.0088 0.1545 144 P 0.7609 0.0104 0.2287 145 G 0.6185 0.0205 0.3610 146 P 0.4106 0.0426 0.5468 147 W 0.2058 0.0675 0.7267 148 R 0.0972 0.1535 0.7494 149 G 0.1116 0.1386 0.7499 150 V 0.1463 0.1297 0.7240 151 T 0.1377 0.0736 0.7887 152 P 0.0980 0.1185 0.7835 153 I 0.0565 0.1882 0.7553 154 S 0.0552 0.2555 0.6892 155 V 0.0417 0.6104 0.3479 156 A 0.0221 0.8071 0.1708 157 R 0.0128 0.8905 0.0967 158 R 0.0088 0.9180 0.0733 159 I 0.0075 0.9336 0.0590 160 Y 0.0088 0.9348 0.0565 161 L 0.0083 0.9250 0.0667 162 N 0.0086 0.9094 0.0820 163 L 0.0072 0.8871 0.1056 164 C 0.0072 0.8305 0.1622 165 A 0.0348 0.5913 0.3739 166 G 0.0310 0.2402 0.7288 167 L 0.0543 0.2213 0.7244 168 H 0.1908 0.2597 0.5495 169 T 0.3659 0.2798 0.3543 170 T 0.4015 0.3012 0.2973 171 A 0.3899 0.2901 0.3200 172 L 0.1664 0.5218 0.3117 173 L 0.0738 0.5791 0.3471 174 D 0.0625 0.5810 0.3565 175 V 0.0483 0.6265 0.3253 176 D 0.0496 0.5111 0.4392 177 E 0.0507 0.3628 0.5865 178 R 0.0674 0.1993 0.7333 179 G 0.0689 0.1074 0.8237 180 V 0.1805 0.0978 0.7217 181 Q 0.6775 0.0749 0.2477 182 L 0.8160 0.0606 0.1235 183 S 0.8385 0.0593 0.1023 184 P 0.6729 0.1687 0.1584 185 G 0.3922 0.2594 0.3484 186 Q 0.1443 0.3316 0.5241 187 G 0.1076 0.3670 0.5254 188 V 0.0283 0.7244 0.2473 189 S 0.0204 0.7252 0.2544 190 L 0.0154 0.7614 0.2232 191 L 0.0066 0.9168 0.0766 192 L 0.0051 0.9441 0.0509 193 E 0.0048 0.9510 0.0442 194 A 0.0047 0.9543 0.0410 195 D 0.0047 0.9532 0.0421 196 R 0.0051 0.9446 0.0503 197 E 0.0052 0.9363 0.0585 198 Y 0.0076 0.9108 0.0816 199 A 0.0090 0.8584 0.1326 200 R 0.0102 0.7581 0.2317 201 E 0.0237 0.5445 0.4317 202 A 0.0491 0.2637 0.6872 203 G 0.0398 0.1722 0.7880 204 A 0.0755 0.1711 0.7534 205 P 0.1050 0.2439 0.6512 206 A 0.1048 0.2700 0.6252 207 L 0.1183 0.1855 0.6962 208 L 0.1544 0.1107 0.7349 209 A 0.0917 0.1112 0.7971 210 R 0.0344 0.1619 0.8037 211 L 0.0402 0.0984 0.8615 212 P 0.1309 0.0341 0.8350 213 S 0.3186 0.0273 0.6541 214 V 0.8074 0.0105 0.1821 215 L 0.9101 0.0082 0.0817 216 V 0.9203 0.0078 0.0719 217 E 0.8956 0.0123 0.0921 218 A 0.7949 0.0271 0.1780 219 G 0.6947 0.0398 0.2655 220 A 0.4065 0.0555 0.5380 221 G 0.1757 0.0274 0.7968 222 G 0.1067 0.0296 0.8637 223 G 0.0675 0.1373 0.7951 224 H 0.1030 0.1216 0.7753 225 R 0.4175 0.0595 0.5230 226 V 0.7591 0.0271 0.2138 227 L 0.8434 0.0195 0.1372 228 Y 0.8353 0.0221 0.1426 229 W 0.7972 0.0194 0.1834 230 S 0.6133 0.0153 0.3714 231 S 0.3554 0.0234 0.6211 232 L 0.0096 0.8512 0.1391 233 E 0.0065 0.8776 0.1159 234 R 0.0068 0.8910 0.1022 235 L 0.0088 0.8783 0.1129 236 S 0.0120 0.8573 0.1307 237 T 0.0121 0.8006 0.1873 238 A 0.0181 0.7629 0.2190 239 D 0.0365 0.6456 0.3179 240 V 0.0298 0.4335 0.5367 241 E 0.0355 0.1418 0.8227 242 G 0.0584 0.0623 0.8794 243 G 0.0814 0.0403 0.8784 244 V 0.1246 0.0358 0.8396 245 Y 0.3396 0.0114 0.6490 246 S 0.8406 0.0044 0.1550 247 I 0.9282 0.0034 0.0684 248 V 0.9297 0.0033 0.0670 249 I 0.9200 0.0035 0.0765 250 P 0.7736 0.0196 0.2068 251 A 0.3030 0.0249 0.6721 252 R 0.1670 0.0547 0.7783 253 L 0.1877 0.0950 0.7173 254 S 0.1277 0.1172 0.7551 255 G 0.0822 0.2776 0.6402 256 V 0.0216 0.7144 0.2640 257 E 0.0118 0.8273 0.1609 258 E 0.0092 0.8781 0.1127 259 W 0.0133 0.8838 0.1029 260 L 0.0119 0.9027 0.0854 261 L 0.0138 0.8935 0.0927 262 A 0.0118 0.8845 0.1038 263 A 0.0119 0.8399 0.1482 264 A 0.0190 0.7606 0.2204 265 S 0.0307 0.5867 0.3826 266 G 0.0263 0.4137 0.5600 267 Q 0.0490 0.1942 0.7568 268 R 0.0525 0.2855 0.6620 269 R 0.0676 0.3227 0.6097 270 P 0.0798 0.3343 0.5858 271 L 0.1320 0.3047 0.5632 272 E 0.1721 0.3342 0.4936 273 Y 0.1957 0.3720 0.4323 274 D 0.2482 0.2790 0.4728 275 R 0.3181 0.2696 0.4122 276 S 0.3507 0.2684 0.3809 277 V 0.2939 0.2856 0.4205 278 Y 0.2117 0.2859 0.5024 279 E 0.2398 0.3155 0.4447 280 T 0.3029 0.2765 0.4206 281 V 0.2390 0.2848 0.4762 282 E 0.2061 0.2700 0.5239 283 E 0.1684 0.3354 0.4962 284 N 0.0905 0.3735 0.5359 285 C 0.1361 0.3405 0.5235 286 K 0.1749 0.2917 0.5335 287 K 0.1397 0.1885 0.6718 288 G 0.2120 0.0633 0.7247 289 V 0.5041 0.0288 0.4671 290 Y 0.7818 0.0218 0.1964 291 M 0.7527 0.0132 0.2341 292 E 0.6379 0.0140 0.3481 293 P 0.4958 0.0155 0.4886 294 V 0.0834 0.0295 0.8871