| aaa |
| ID: | 1411117488 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 445 (422) | ||
| Sequences: | 11728 (7782.8) | ||
| Seq/Len: | 27.791 | ||
| Nf(neff/√len): | 378.9 |
HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 27.791).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 313_I | 325_A | 3.869 | 1.00 |
| 305_A | 315_A | 3.652 | 1.00 |
| 137_V | 331_G | 3.550 | 1.00 |
| 169_G | 245_A | 3.263 | 1.00 |
| 222_R | 226_I | 3.157 | 1.00 |
| 50_I | 236_A | 2.974 | 1.00 |
| 316_R | 325_A | 2.698 | 1.00 |
| 74_Y | 307_D | 2.669 | 1.00 |
| 11_G | 218_K | 2.643 | 1.00 |
| 215_G | 306_D | 2.640 | 1.00 |
| 374_L | 378_G | 2.638 | 1.00 |
| 328_I | 332_I | 2.555 | 1.00 |
| 90_N | 304_A | 2.552 | 1.00 |
| 219_N | 222_R | 2.513 | 1.00 |
| 217_V | 223_N | 2.492 | 1.00 |
| 273_T | 277_I | 2.419 | 1.00 |
| 308_G | 312_P | 2.347 | 1.00 |
| 130_V | 339_L | 2.327 | 1.00 |
| 366_L | 395_F | 2.316 | 1.00 |
| 62_K | 376_G | 2.301 | 1.00 |
| 216_V | 299_Q | 2.290 | 1.00 |
| 59_V | 369_C | 2.286 | 1.00 |
| 302_K | 306_D | 2.274 | 1.00 |
| 78_R | 86_G | 2.273 | 1.00 |
| 369_C | 394_A | 2.235 | 1.00 |
| 12_L | 230_G | 2.216 | 1.00 |
| 16_T | 230_G | 2.150 | 1.00 |
| 12_L | 223_N | 2.034 | 1.00 |
| 313_I | 316_R | 2.023 | 1.00 |
| 314_F | 329_I | 2.008 | 1.00 |
| 12_L | 16_T | 2.006 | 1.00 |
| 11_G | 14_P | 1.987 | 1.00 |
| 78_R | 83_P | 1.980 | 1.00 |
| 254_A | 268_M | 1.972 | 1.00 |
| 167_V | 171_F | 1.969 | 1.00 |
| 94_W | 330_V | 1.968 | 1.00 |
| 129_C | 338_Q | 1.919 | 1.00 |
| 318_N | 324_V | 1.915 | 1.00 |
| 137_V | 327_L | 1.892 | 1.00 |
| 10_V | 14_P | 1.879 | 1.00 |
| 130_V | 335_T | 1.859 | 1.00 |
| 141_I | 324_V | 1.854 | 1.00 |
| 15_V | 217_V | 1.853 | 1.00 |
| 140_N | 291_G | 1.833 | 1.00 |
| 51_I | 393_I | 1.823 | 1.00 |
| 134_W | 335_T | 1.819 | 1.00 |
| 145_K | 149_R | 1.815 | 1.00 |
| 51_I | 55_G | 1.810 | 1.00 |
| 81_F | 374_L | 1.807 | 1.00 |
| 81_F | 370_A | 1.796 | 1.00 |
| 219_N | 226_I | 1.787 | 1.00 |
| 374_L | 377_H | 1.756 | 1.00 |
| 159_L | 163_V | 1.750 | 1.00 |
| 82_G | 85_L | 1.731 | 1.00 |
| 141_I | 328_I | 1.724 | 1.00 |
| 251_P | 254_A | 1.713 | 1.00 |
| 226_I | 230_G | 1.691 | 1.00 |
| 220_P | 225_P | 1.649 | 1.00 |
| 392_T | 396_L | 1.634 | 1.00 |
| 138_L | 142_V | 1.630 | 1.00 |
| 89_T | 367_Y | 1.624 | 1.00 |
| 229_I | 233_L | 1.614 | 1.00 |
| 318_N | 322_T | 1.610 | 1.00 |
| 213_A | 295_L | 1.607 | 1.00 |
| 301_A | 310_F | 1.601 | 1.00 |
| 62_K | 65_F | 1.596 | 1.00 |
| 77_A | 89_T | 1.595 | 1.00 |
| 45_G | 196_T | 1.575 | 1.00 |
| 14_P | 152_A | 1.573 | 1.00 |
| 105_V | 290_L | 1.535 | 1.00 |
| 57_S | 232_V | 1.513 | 1.00 |
| 301_A | 326_G | 1.492 | 1.00 |
| 141_I | 322_T | 1.475 | 1.00 |
| 264_D | 268_M | 1.459 | 1.00 |
| 325_A | 329_I | 1.453 | 1.00 |
| 219_N | 223_N | 1.452 | 1.00 |
| 126_T | 130_V | 1.447 | 1.00 |
| 19_V | 231_G | 1.446 | 1.00 |
| 156_V | 160_I | 1.436 | 1.00 |
| 297_A | 330_V | 1.432 | 1.00 |
| 130_V | 134_W | 1.408 | 1.00 |
| 101_N | 334_M | 1.404 | 0.99 |
| 10_V | 15_V | 1.403 | 0.99 |
| 16_T | 234_I | 1.403 | 0.99 |
| 264_D | 267_R | 1.399 | 0.99 |
| 298_G | 327_L | 1.395 | 0.99 |
| 70_P | 215_G | 1.391 | 0.99 |
| 56_L | 369_C | 1.386 | 0.99 |
| 416_T | 420_I | 1.382 | 0.99 |
| 81_F | 85_L | 1.379 | 0.99 |
| 389_A | 393_I | 1.366 | 0.99 |
| 366_L | 370_A | 1.362 | 0.99 |
| 233_L | 237_V | 1.356 | 0.99 |
| 133_L | 334_M | 1.353 | 0.99 |
| 271_G | 274_A | 1.353 | 0.99 |
| 77_A | 367_Y | 1.353 | 0.99 |
| 104_M | 107_I | 1.345 | 0.99 |
| 13_I | 149_R | 1.338 | 0.99 |
| 136_F | 290_L | 1.337 | 0.99 |
| 49_T | 200_T | 1.333 | 0.99 |
| 57_S | 228_T | 1.327 | 0.99 |
| 134_W | 331_G | 1.326 | 0.99 |
| 258_S | 264_D | 1.325 | 0.99 |
| 74_Y | 303_A | 1.319 | 0.99 |
| 87_Y | 91_V | 1.317 | 0.99 |
| 223_N | 226_I | 1.299 | 0.99 |
| 312_P | 315_A | 1.295 | 0.99 |
| 20_S | 234_I | 1.289 | 0.99 |
| 12_L | 226_I | 1.289 | 0.99 |
| 64_S | 76_Y | 1.288 | 0.99 |
| 214_A | 224_V | 1.286 | 0.99 |
| 205_I | 361_T | 1.285 | 0.99 |
| 332_I | 336_I | 1.283 | 0.99 |
| 112_L | 128_T | 1.280 | 0.99 |
| 59_V | 391_T | 1.279 | 0.99 |
| 55_G | 393_I | 1.276 | 0.99 |
| 302_K | 317_V | 1.271 | 0.99 |
| 160_I | 164_G | 1.270 | 0.99 |
| 398_C | 401_A | 1.269 | 0.99 |
| 50_I | 204_F | 1.265 | 0.99 |
| 137_V | 328_I | 1.263 | 0.99 |
| 165_I | 266_A | 1.257 | 0.99 |
| 133_L | 331_G | 1.243 | 0.98 |
| 121_D | 124_V | 1.243 | 0.98 |
| 47_L | 51_I | 1.237 | 0.98 |
| 80_C | 371_A | 1.237 | 0.98 |
| 312_P | 316_R | 1.235 | 0.98 |
| 370_A | 374_L | 1.233 | 0.98 |
| 23_I | 235_A | 1.231 | 0.98 |
| 317_V | 321_G | 1.230 | 0.98 |
| 137_V | 141_I | 1.225 | 0.98 |
| 144_P | 295_L | 1.222 | 0.98 |
| 320_A | 324_V | 1.219 | 0.98 |
| 44_Y | 193_I | 1.215 | 0.98 |
| 270_L | 274_A | 1.213 | 0.98 |
| 396_L | 400_W | 1.208 | 0.98 |
| 142_V | 320_A | 1.205 | 0.98 |
| 47_L | 240_V | 1.203 | 0.98 |
| 91_V | 310_F | 1.203 | 0.98 |
| 127_I | 131_V | 1.201 | 0.98 |
| 71_G | 74_Y | 1.190 | 0.98 |
| 376_G | 380_F | 1.189 | 0.98 |
| 169_G | 249_M | 1.179 | 0.98 |
| 13_I | 17_L | 1.177 | 0.98 |
| 10_V | 148_T | 1.174 | 0.98 |
| 75_A | 79_R | 1.165 | 0.97 |
| 208_E | 212_V | 1.164 | 0.97 |
| 318_N | 321_G | 1.163 | 0.97 |
| 161_P | 281_C | 1.162 | 0.97 |
| 41_I | 193_I | 1.161 | 0.97 |
| 6_D | 317_V | 1.158 | 0.97 |
| 15_V | 227_A | 1.157 | 0.97 |
| 316_R | 324_V | 1.151 | 0.97 |
| 67_D | 79_R | 1.149 | 0.97 |
| 69_S | 75_A | 1.149 | 0.97 |
| 58_M | 229_I | 1.147 | 0.97 |
| 163_V | 167_V | 1.128 | 0.97 |
| 60_Y | 73_S | 1.128 | 0.97 |
| 61_A | 65_F | 1.124 | 0.97 |
| 108_G | 283_A | 1.123 | 0.97 |
| 151_Q | 291_G | 1.123 | 0.97 |
| 102_I | 105_V | 1.114 | 0.96 |
| 373_L | 392_T | 1.108 | 0.96 |
| 141_I | 318_N | 1.104 | 0.96 |
| 14_P | 149_R | 1.103 | 0.96 |
| 170_W | 245_A | 1.102 | 0.96 |
| 325_A | 328_I | 1.101 | 0.96 |
| 139_L | 150_V | 1.098 | 0.96 |
| 276_A | 280_F | 1.096 | 0.96 |
| 251_P | 268_M | 1.093 | 0.96 |
| 150_V | 154_A | 1.089 | 0.96 |
| 173_F | 248_G | 1.083 | 0.96 |
| 54_L | 58_M | 1.081 | 0.95 |
| 294_T | 298_G | 1.080 | 0.95 |
| 414_F | 418_M | 1.077 | 0.95 |
| 164_G | 168_F | 1.077 | 0.95 |
| 54_L | 229_I | 1.073 | 0.95 |
| 415_V | 419_V | 1.072 | 0.95 |
| 77_A | 371_A | 1.070 | 0.95 |
| 12_L | 227_A | 1.070 | 0.95 |
| 55_G | 59_V | 1.068 | 0.95 |
| 124_V | 127_I | 1.067 | 0.95 |
| 23_I | 231_G | 1.064 | 0.95 |
| 74_Y | 90_N | 1.052 | 0.95 |
| 298_G | 326_G | 1.051 | 0.94 |
| 294_T | 331_G | 1.050 | 0.94 |
| 105_V | 133_L | 1.045 | 0.94 |
| 370_A | 395_F | 1.044 | 0.94 |
| 18_M | 213_A | 1.041 | 0.94 |
| 267_R | 275_G | 1.041 | 0.94 |
| 395_F | 398_C | 1.039 | 0.94 |
| 148_T | 291_G | 1.036 | 0.94 |
| 79_R | 379_H | 1.034 | 0.94 |
| 93_Y | 97_C | 1.034 | 0.94 |
| 391_T | 395_F | 1.030 | 0.94 |
| 60_Y | 368_T | 1.029 | 0.94 |
| 267_R | 272_D | 1.026 | 0.94 |
| 236_A | 240_V | 1.024 | 0.93 |
| 9_K | 145_K | 1.022 | 0.93 |
| 245_A | 248_G | 1.022 | 0.93 |
| 219_N | 225_P | 1.020 | 0.93 |
| 43_I | 244_T | 1.019 | 0.93 |
| 299_Q | 302_K | 1.015 | 0.93 |
| 96_A | 361_T | 1.013 | 0.93 |
| 388_L | 392_T | 1.013 | 0.93 |
| 123_L | 127_I | 1.012 | 0.93 |
| 94_W | 301_A | 1.011 | 0.93 |
| 63_M | 372_L | 1.007 | 0.93 |
| 149_R | 153_V | 1.007 | 0.93 |
| 113_S | 116_F | 1.006 | 0.93 |
| 306_D | 315_A | 1.006 | 0.93 |
| 140_N | 327_L | 1.005 | 0.93 |
| 383_A | 386_A | 1.002 | 0.92 |
| 372_L | 376_G | 1.001 | 0.92 |
| 360_F | 364_P | 1.000 | 0.92 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 3l1lA | 1 | 0.9506 | 100 | 0.194 | Contact Map |
| 3giaA | 1 | 0.9438 | 100 | 0.347 | Contact Map |
| 4djkA | 2 | 0.9258 | 100 | 0.376 | Contact Map |
| 2jlnA | 1 | 0.9056 | 99.7 | 0.792 | Contact Map |
| 3dh4A | 4 | 0.9303 | 98.8 | 0.873 | Contact Map |
| 2xq2A | 1 | 0.9348 | 98.7 | 0.874 | Contact Map |
| 2a65A | 1 | 0.9146 | 94.1 | 0.933 | Contact Map |
| 4c7rA | 3 | 0.9034 | 93.9 | 0.934 | Contact Map |
| 4m48A | 1 | 0.9371 | 91.3 | 0.939 | Contact Map |
| 2wswA | 1 | 0.8022 | 85.5 | 0.945 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)