# This file is the result of combining several RDB files, specifically # T0172.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0172.t2k.stride-ebghtl.rdb (weight 1.24869) # T0172.t2k.str.rdb (weight 1.53983) # T0172.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 T0172.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0172 # 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 T0172.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 258 # # ============================================ # Comments from T0172.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0172 # 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 T0172.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 258 # # ============================================ # Comments from T0172.t2k.str.rdb # ============================================ # TARGET T0172 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0172.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 258 # # ============================================ # Comments from T0172.t2k.alpha.rdb # ============================================ # TARGET T0172 # 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 T0172.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 258 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0864 0.0412 0.8724 2 R 0.2362 0.0668 0.6969 3 K 0.3591 0.0781 0.5627 4 Y 0.3268 0.0806 0.5927 5 S 0.2494 0.1107 0.6399 6 Q 0.1478 0.2478 0.6044 7 R 0.1050 0.2799 0.6150 8 H 0.0969 0.3767 0.5265 9 I 0.0968 0.5179 0.3852 10 P 0.0325 0.8251 0.1424 11 V 0.0112 0.9249 0.0640 12 M 0.0093 0.9401 0.0507 13 V 0.0053 0.9537 0.0410 14 R 0.0045 0.9568 0.0387 15 E 0.0045 0.9551 0.0403 16 V 0.0047 0.9511 0.0442 17 I 0.0053 0.9402 0.0546 18 E 0.0062 0.9016 0.0921 19 F 0.0090 0.8089 0.1821 20 L 0.0727 0.4004 0.5269 21 K 0.0781 0.0781 0.8438 22 P 0.0913 0.0460 0.8628 23 E 0.0718 0.0352 0.8929 24 D 0.0348 0.1102 0.8550 25 E 0.0383 0.0608 0.9008 26 K 0.2455 0.0262 0.7283 27 I 0.8221 0.0041 0.1738 28 I 0.9098 0.0046 0.0856 29 L 0.9084 0.0050 0.0866 30 D 0.8862 0.0049 0.1089 31 C 0.6486 0.0346 0.3168 32 T 0.4169 0.0362 0.5469 33 V 0.1765 0.0622 0.7612 34 G 0.0917 0.0782 0.8300 35 E 0.0553 0.2261 0.7186 36 G 0.0328 0.4324 0.5348 37 G 0.0118 0.8894 0.0987 38 H 0.0059 0.9387 0.0553 39 S 0.0047 0.9535 0.0419 40 R 0.0047 0.9574 0.0379 41 A 0.0045 0.9559 0.0396 42 I 0.0046 0.9494 0.0460 43 L 0.0050 0.9379 0.0571 44 E 0.0058 0.8712 0.1231 45 H 0.0148 0.6893 0.2959 46 C 0.0818 0.0888 0.8295 47 P 0.0216 0.1011 0.8773 48 G 0.0250 0.0475 0.9275 49 C 0.2734 0.0147 0.7118 50 R 0.8374 0.0058 0.1567 51 I 0.9233 0.0034 0.0733 52 I 0.9059 0.0087 0.0854 53 G 0.9078 0.0056 0.0866 54 I 0.8474 0.0072 0.1454 55 D 0.5677 0.0079 0.4244 56 V 0.0919 0.0321 0.8760 57 D 0.0819 0.0174 0.9008 58 S 0.0050 0.8793 0.1157 59 E 0.0047 0.9278 0.0675 60 V 0.0046 0.9505 0.0449 61 L 0.0044 0.9597 0.0360 62 R 0.0044 0.9592 0.0364 63 I 0.0044 0.9576 0.0380 64 A 0.0046 0.9527 0.0427 65 E 0.0046 0.9507 0.0448 66 E 0.0054 0.9368 0.0578 67 K 0.0081 0.8947 0.0972 68 L 0.0151 0.8562 0.1286 69 K 0.0082 0.8088 0.1831 70 E 0.0109 0.6681 0.3209 71 F 0.0478 0.3426 0.6096 72 S 0.0438 0.0844 0.8718 73 D 0.0617 0.0944 0.8439 74 R 0.2813 0.0435 0.6752 75 V 0.6515 0.0107 0.3378 76 S 0.8544 0.0101 0.1355 77 L 0.8864 0.0091 0.1045 78 F 0.8421 0.0187 0.1392 79 K 0.7431 0.0272 0.2297 80 V 0.3285 0.0608 0.6107 81 S 0.2015 0.0551 0.7434 82 Y 0.0332 0.5741 0.3927 83 R 0.0242 0.5932 0.3826 84 E 0.0295 0.5810 0.3895 85 A 0.0463 0.4348 0.5188 86 D 0.0411 0.4914 0.4675 87 F 0.0374 0.5603 0.4023 88 L 0.0360 0.5499 0.4141 89 L 0.0307 0.5557 0.4135 90 K 0.0225 0.5712 0.4063 91 T 0.0254 0.5570 0.4177 92 L 0.0522 0.3597 0.5881 93 G 0.0431 0.1926 0.7643 94 I 0.0824 0.1602 0.7574 95 E 0.0925 0.0959 0.8116 96 K 0.1298 0.0688 0.8014 97 V 0.3256 0.0145 0.6599 98 D 0.3833 0.0377 0.5790 99 G 0.9118 0.0051 0.0831 100 I 0.9283 0.0040 0.0677 101 L 0.9206 0.0057 0.0737 102 M 0.8725 0.0092 0.1183 103 D 0.4227 0.0175 0.5597 104 L 0.1199 0.0627 0.8173 105 G 0.1012 0.1006 0.7983 106 V 0.1243 0.1585 0.7172 107 S 0.0964 0.1499 0.7537 108 T 0.0936 0.2317 0.6748 109 Y 0.1072 0.2136 0.6792 110 Q 0.1374 0.1906 0.6720 111 L 0.1543 0.1742 0.6716 112 K 0.1023 0.1509 0.7468 113 G 0.0639 0.2821 0.6540 114 E 0.0468 0.3974 0.5559 115 N 0.0713 0.3931 0.5355 116 R 0.1153 0.2261 0.6586 117 G 0.1331 0.0951 0.7718 118 F 0.2752 0.0670 0.6578 119 T 0.3869 0.0771 0.5360 120 F 0.3162 0.1573 0.5265 121 E 0.2078 0.1542 0.6381 122 R 0.1194 0.1295 0.7511 123 E 0.0880 0.0901 0.8219 124 E 0.0914 0.0494 0.8592 125 P 0.1329 0.1099 0.7572 126 L 0.1957 0.1709 0.6333 127 D 0.2394 0.1856 0.5750 128 M 0.2590 0.1946 0.5464 129 R 0.2666 0.1423 0.5911 130 M 0.3016 0.0705 0.6279 131 D 0.1196 0.0432 0.8373 132 L 0.0206 0.1806 0.7988 133 E 0.0304 0.1276 0.8421 134 S 0.0501 0.1218 0.8281 135 E 0.0823 0.0671 0.8506 136 V 0.1830 0.0564 0.7606 137 T 0.1506 0.0425 0.8069 138 A 0.0081 0.8995 0.0925 139 Q 0.0065 0.9200 0.0736 140 K 0.0070 0.9218 0.0712 141 V 0.0090 0.9073 0.0838 142 L 0.0169 0.7638 0.2192 143 N 0.0207 0.4736 0.5058 144 E 0.0328 0.2620 0.7053 145 L 0.0821 0.0968 0.8211 146 P 0.0679 0.1004 0.8317 147 E 0.0057 0.9108 0.0835 148 E 0.0050 0.9152 0.0798 149 E 0.0050 0.9174 0.0776 150 L 0.0052 0.9326 0.0622 151 A 0.0053 0.9335 0.0612 152 R 0.0058 0.9253 0.0689 153 I 0.0049 0.9226 0.0725 154 I 0.0101 0.9012 0.0887 155 F 0.0082 0.8583 0.1335 156 E 0.0101 0.7825 0.2074 157 Y 0.0341 0.5910 0.3749 158 G 0.0347 0.2711 0.6942 159 E 0.0306 0.4215 0.5479 160 E 0.0253 0.5519 0.4228 161 K 0.0172 0.7256 0.2573 162 R 0.0129 0.7714 0.2157 163 F 0.0154 0.7896 0.1950 164 A 0.0083 0.8382 0.1535 165 R 0.0065 0.8960 0.0976 166 R 0.0054 0.9076 0.0869 167 I 0.0051 0.9332 0.0618 168 A 0.0057 0.9360 0.0584 169 R 0.0060 0.9409 0.0531 170 K 0.0060 0.9383 0.0556 171 I 0.0059 0.9332 0.0609 172 V 0.0082 0.9066 0.0852 173 E 0.0108 0.8119 0.1773 174 N 0.0228 0.6333 0.3440 175 R 0.0554 0.1475 0.7971 176 P 0.0485 0.1473 0.8042 177 L 0.0597 0.2580 0.6823 178 N 0.0438 0.3352 0.6210 179 T 0.0632 0.4171 0.5198 180 T 0.0126 0.8500 0.1373 181 L 0.0054 0.9264 0.0682 182 D 0.0053 0.9259 0.0688 183 L 0.0062 0.9418 0.0520 184 V 0.0049 0.9546 0.0406 185 K 0.0049 0.9555 0.0396 186 A 0.0044 0.9560 0.0396 187 V 0.0045 0.9490 0.0465 188 R 0.0049 0.9291 0.0660 189 E 0.0065 0.8577 0.1358 190 A 0.0186 0.7486 0.2328 191 L 0.0617 0.3458 0.5925 192 P 0.0520 0.2179 0.7301 193 S 0.0419 0.3734 0.5847 194 Y 0.0325 0.5008 0.4667 195 E 0.0343 0.5697 0.3960 196 I 0.0420 0.5283 0.4297 197 R 0.0478 0.4981 0.4541 198 R 0.0529 0.3916 0.5555 199 R 0.0521 0.2579 0.6901 200 K 0.0577 0.1322 0.8101 201 R 0.0639 0.0939 0.8422 202 H 0.0885 0.0718 0.8397 203 F 0.0260 0.6295 0.3446 204 A 0.0183 0.7315 0.2502 205 T 0.0146 0.8324 0.1530 206 K 0.0162 0.8676 0.1161 207 T 0.0157 0.8922 0.0922 208 F 0.0204 0.9194 0.0602 209 Q 0.0248 0.9259 0.0493 210 A 0.0249 0.9275 0.0476 211 I 0.0267 0.9253 0.0480 212 R 0.0262 0.9188 0.0550 213 I 0.0358 0.8893 0.0749 214 Y 0.0362 0.8391 0.1246 215 V 0.0300 0.7481 0.2219 216 N 0.0246 0.6137 0.3617 217 R 0.0246 0.4429 0.5325 218 E 0.0307 0.4249 0.5444 219 L 0.0242 0.5987 0.3771 220 E 0.0115 0.7225 0.2660 221 N 0.0115 0.7838 0.2046 222 L 0.0048 0.9096 0.0855 223 K 0.0046 0.9364 0.0590 224 E 0.0046 0.9454 0.0500 225 F 0.0046 0.9484 0.0471 226 L 0.0045 0.9542 0.0413 227 K 0.0045 0.9528 0.0427 228 K 0.0047 0.9457 0.0496 229 A 0.0046 0.9409 0.0545 230 E 0.0054 0.9243 0.0704 231 D 0.0078 0.8482 0.1440 232 L 0.0203 0.6114 0.3683 233 L 0.1411 0.2494 0.6095 234 N 0.1352 0.0318 0.8330 235 P 0.1956 0.0748 0.7296 236 G 0.1638 0.0361 0.8001 237 G 0.4732 0.0111 0.5157 238 R 0.7992 0.0041 0.1967 239 I 0.9241 0.0035 0.0724 240 V 0.9252 0.0036 0.0711 241 V 0.9238 0.0036 0.0726 242 I 0.8701 0.0058 0.1242 243 S 0.7397 0.0074 0.2528 244 F 0.3742 0.0187 0.6071 245 H 0.1404 0.0269 0.8326 246 S 0.0671 0.0628 0.8702 247 L 0.0157 0.4757 0.5087 248 E 0.0166 0.5479 0.4355 249 D 0.0181 0.7459 0.2361 250 R 0.0101 0.8669 0.1230 251 I 0.0107 0.9120 0.0773 252 V 0.0089 0.9356 0.0555 253 K 0.0071 0.9470 0.0458 254 E 0.0059 0.9493 0.0448 255 T 0.0050 0.9440 0.0510 256 F 0.0057 0.9295 0.0648 257 R 0.0056 0.8709 0.1234 258 N 0.0117 0.6642 0.3242 259 S 0.0604 0.2717 0.6679 260 K 0.0330 0.2670 0.7000 261 K 0.0444 0.3355 0.6201 262 L 0.1300 0.3013 0.5687 263 R 0.2885 0.2171 0.4944 264 I 0.4553 0.1665 0.3782 265 L 0.4261 0.1547 0.4191 266 T 0.3691 0.1260 0.5049 267 E 0.2777 0.0932 0.6291 268 K 0.2113 0.0337 0.7550 269 P 0.2336 0.0203 0.7461 270 V 0.3079 0.0247 0.6674 271 R 0.1895 0.0126 0.7979 272 P 0.0891 0.0252 0.8857 273 S 0.0632 0.0274 0.9094 274 E 0.0049 0.9183 0.0768 275 E 0.0045 0.9421 0.0534 276 E 0.0052 0.9330 0.0618 277 I 0.0055 0.9351 0.0594 278 R 0.0086 0.8992 0.0923 279 E 0.0149 0.7803 0.2048 280 N 0.0631 0.2408 0.6961 281 P 0.0176 0.3335 0.6489 282 R 0.0243 0.3177 0.6580 283 A 0.0588 0.2752 0.6660 284 R 0.0553 0.3471 0.5976 285 S 0.1171 0.3767 0.5062 286 G 0.1720 0.4642 0.3638 287 R 0.2798 0.5205 0.1997 288 L 0.3894 0.4522 0.1584 289 R 0.3724 0.4935 0.1341 290 A 0.4091 0.4752 0.1158 291 A 0.3802 0.4844 0.1353 292 E 0.3633 0.4737 0.1630 293 R 0.3305 0.4094 0.2601 294 I 0.1979 0.3433 0.4587 295 E 0.0951 0.1835 0.7214 296 E 0.0754 0.0829 0.8417 297 G 0.0639 0.0865 0.8496 298 G 0.0550 0.0598 0.8853 299 D 0.0492 0.0291 0.9217