| 1AJS |
| ID: | 1411588666 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 412 (388) | ||
| Sequences: | 29096 (19226.2) | ||
| Seq/Len: | 74.990 | ||
| Nf(neff/√len): | 976.1 |
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: 74.990).
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 |
| 336_E | 398_D | 4.106 | 1.00 |
| 58_Q | 62_N | 3.953 | 1.00 |
| 377_K | 406_E | 3.845 | 1.00 |
| 174_L | 214_R | 3.790 | 1.00 |
| 340_R | 401_A | 3.561 | 1.00 |
| 332_S | 394_T | 3.341 | 1.00 |
| 82_C | 311_S | 3.017 | 1.00 |
| 399_Y | 403_S | 2.954 | 1.00 |
| 336_E | 394_T | 2.831 | 1.00 |
| 331_L | 335_S | 2.738 | 1.00 |
| 105_S | 111_A | 2.684 | 1.00 |
| 51_P | 55_K | 2.637 | 1.00 |
| 55_K | 59_R | 2.601 | 1.00 |
| 35_L | 400_V | 2.512 | 1.00 |
| 172_G | 176_D | 2.479 | 1.00 |
| 170_L | 207_Q | 2.474 | 1.00 |
| 81_T | 85_R | 2.367 | 1.00 |
| 202_P | 206_K | 2.342 | 1.00 |
| 393_T | 396_N | 2.327 | 1.00 |
| 336_E | 340_R | 2.318 | 1.00 |
| 209_A | 213_K | 2.243 | 1.00 |
| 210_S | 214_R | 2.224 | 1.00 |
| 340_R | 343_A | 2.206 | 1.00 |
| 372_Y | 376_Q | 2.202 | 1.00 |
| 132_P | 153_K | 2.198 | 1.00 |
| 132_P | 183_F | 2.186 | 1.00 |
| 335_S | 339_A | 2.176 | 1.00 |
| 170_L | 211_V | 2.167 | 1.00 |
| 207_Q | 210_S | 2.157 | 1.00 |
| 174_L | 215_R | 2.131 | 1.00 |
| 308_R | 311_S | 2.126 | 1.00 |
| 351_N | 364_G | 2.108 | 1.00 |
| 212_M | 219_P | 2.088 | 1.00 |
| 132_P | 178_E | 2.086 | 1.00 |
| 399_Y | 402_T | 2.076 | 1.00 |
| 329_R | 333_M | 2.068 | 1.00 |
| 188_L | 208_I | 2.063 | 1.00 |
| 340_R | 398_D | 2.059 | 1.00 |
| 340_R | 402_T | 2.054 | 1.00 |
| 132_P | 156_R | 2.023 | 1.00 |
| 186_F | 212_M | 2.014 | 1.00 |
| 185_I | 220_F | 1.969 | 1.00 |
| 373_L | 376_Q | 1.939 | 1.00 |
| 339_A | 343_A | 1.934 | 1.00 |
| 174_L | 207_Q | 1.927 | 1.00 |
| 159_R | 172_G | 1.899 | 1.00 |
| 126_T | 184_S | 1.896 | 1.00 |
| 212_M | 217_L | 1.892 | 1.00 |
| 172_G | 175_S | 1.888 | 1.00 |
| 206_K | 210_S | 1.879 | 1.00 |
| 338_R | 342_E | 1.847 | 1.00 |
| 186_F | 217_L | 1.836 | 1.00 |
| 137_S | 159_R | 1.832 | 1.00 |
| 132_P | 182_E | 1.807 | 1.00 |
| 54_R | 58_Q | 1.791 | 1.00 |
| 379_I | 403_S | 1.784 | 1.00 |
| 52_V | 308_R | 1.776 | 1.00 |
| 211_V | 215_R | 1.762 | 1.00 |
| 216_F | 249_E | 1.747 | 1.00 |
| 254_Q | 269_N | 1.742 | 1.00 |
| 57_E | 61_A | 1.734 | 1.00 |
| 267_V | 306_V | 1.729 | 1.00 |
| 171_Q | 174_L | 1.722 | 1.00 |
| 174_L | 211_V | 1.703 | 1.00 |
| 115_G | 251_F | 1.697 | 1.00 |
| 78_E | 307_A | 1.694 | 1.00 |
| 108_G | 253_A | 1.667 | 1.00 |
| 88_L | 94_A | 1.654 | 1.00 |
| 169_D | 172_G | 1.649 | 1.00 |
| 203_E | 206_K | 1.648 | 1.00 |
| 52_V | 312_D | 1.645 | 1.00 |
| 308_R | 312_D | 1.633 | 1.00 |
| 55_K | 58_Q | 1.619 | 1.00 |
| 174_L | 178_E | 1.603 | 1.00 |
| 209_A | 219_P | 1.585 | 1.00 |
| 171_Q | 207_Q | 1.583 | 1.00 |
| 177_L | 211_V | 1.582 | 1.00 |
| 220_F | 253_A | 1.552 | 1.00 |
| 171_Q | 175_S | 1.552 | 1.00 |
| 340_R | 344_L | 1.542 | 1.00 |
| 377_K | 403_S | 1.539 | 1.00 |
| 394_T | 398_D | 1.539 | 1.00 |
| 77_A | 81_T | 1.538 | 1.00 |
| 82_C | 307_A | 1.513 | 1.00 |
| 147_F | 152_F | 1.508 | 1.00 |
| 379_I | 400_V | 1.508 | 1.00 |
| 78_E | 311_S | 1.494 | 1.00 |
| 340_R | 405_H | 1.487 | 1.00 |
| 402_T | 406_E | 1.478 | 1.00 |
| 115_G | 220_F | 1.466 | 1.00 |
| 81_T | 97_E | 1.426 | 1.00 |
| 177_L | 217_L | 1.420 | 1.00 |
| 223_S | 252_C | 1.415 | 1.00 |
| 373_L | 377_K | 1.413 | 1.00 |
| 187_V | 220_F | 1.405 | 0.99 |
| 224_A | 255_S | 1.402 | 0.99 |
| 387_I | 400_V | 1.398 | 0.99 |
| 100_V | 271_T | 1.391 | 0.99 |
| 106_L | 110_G | 1.389 | 0.99 |
| 374_I | 381_L | 1.387 | 0.99 |
| 137_S | 157_S | 1.379 | 0.99 |
| 161_W | 204_Q | 1.377 | 0.99 |
| 272_V | 280_I | 1.370 | 0.99 |
| 56_V | 308_R | 1.369 | 0.99 |
| 30_P | 378_H | 1.364 | 0.99 |
| 201_T | 204_Q | 1.362 | 0.99 |
| 167_G | 204_Q | 1.350 | 0.99 |
| 80_R | 84_S | 1.332 | 0.99 |
| 83_A | 269_N | 1.327 | 0.99 |
| 337_L | 361_S | 1.325 | 0.99 |
| 337_L | 340_R | 1.325 | 0.99 |
| 111_A | 253_A | 1.311 | 0.99 |
| 133_V | 147_F | 1.305 | 0.99 |
| 299_P | 302_G | 1.301 | 0.99 |
| 325_T | 328_D | 1.296 | 0.99 |
| 83_A | 104_Q | 1.296 | 0.99 |
| 328_D | 332_S | 1.295 | 0.99 |
| 84_S | 97_E | 1.294 | 0.99 |
| 59_R | 63_N | 1.293 | 0.99 |
| 99_R | 277_P | 1.289 | 0.99 |
| 173_F | 208_I | 1.287 | 0.99 |
| 82_C | 85_R | 1.286 | 0.99 |
| 211_V | 217_L | 1.282 | 0.99 |
| 337_L | 387_I | 1.281 | 0.99 |
| 334_R | 338_R | 1.270 | 0.99 |
| 333_M | 394_T | 1.269 | 0.99 |
| 153_K | 156_R | 1.266 | 0.99 |
| 87_A | 271_T | 1.266 | 0.99 |
| 122_W | 152_F | 1.262 | 0.99 |
| 210_S | 213_K | 1.260 | 0.99 |
| 134_Y | 176_D | 1.259 | 0.99 |
| 381_L | 385_G | 1.258 | 0.99 |
| 342_E | 352_H | 1.252 | 0.99 |
| 126_T | 182_E | 1.248 | 0.99 |
| 324_K | 327_A | 1.237 | 0.98 |
| 307_A | 311_S | 1.234 | 0.98 |
| 328_D | 331_L | 1.232 | 0.98 |
| 398_D | 402_T | 1.230 | 0.98 |
| 161_W | 169_D | 1.226 | 0.98 |
| 98_K | 277_P | 1.225 | 0.98 |
| 343_A | 405_H | 1.221 | 0.98 |
| 377_K | 410_K | 1.220 | 0.98 |
| 344_L | 405_H | 1.218 | 0.98 |
| 54_R | 61_A | 1.216 | 0.98 |
| 329_R | 332_S | 1.205 | 0.98 |
| 337_L | 401_A | 1.202 | 0.98 |
| 201_T | 207_Q | 1.193 | 0.98 |
| 373_L | 410_K | 1.186 | 0.98 |
| 256_F | 306_V | 1.185 | 0.98 |
| 405_H | 409_T | 1.180 | 0.98 |
| 54_R | 62_N | 1.173 | 0.98 |
| 369_Q | 373_L | 1.171 | 0.98 |
| 374_I | 404_I | 1.158 | 0.97 |
| 338_R | 354_T | 1.154 | 0.97 |
| 59_R | 308_R | 1.153 | 0.97 |
| 339_A | 342_E | 1.151 | 0.97 |
| 203_E | 207_Q | 1.151 | 0.97 |
| 112_L | 220_F | 1.148 | 0.97 |
| 204_Q | 207_Q | 1.142 | 0.97 |
| 85_R | 311_S | 1.141 | 0.97 |
| 190_A | 226_Q | 1.138 | 0.97 |
| 156_R | 176_D | 1.126 | 0.97 |
| 51_P | 54_R | 1.119 | 0.96 |
| 35_L | 397_L | 1.119 | 0.96 |
| 105_S | 268_G | 1.116 | 0.96 |
| 178_E | 215_R | 1.115 | 0.96 |
| 396_N | 399_Y | 1.114 | 0.96 |
| 329_R | 394_T | 1.113 | 0.96 |
| 372_Y | 375_N | 1.110 | 0.96 |
| 195_P | 225_Y | 1.109 | 0.96 |
| 57_E | 305_I | 1.109 | 0.96 |
| 50_L | 312_D | 1.106 | 0.96 |
| 177_L | 183_F | 1.104 | 0.96 |
| 134_Y | 183_F | 1.101 | 0.96 |
| 140_W | 143_H | 1.101 | 0.96 |
| 332_S | 336_E | 1.098 | 0.96 |
| 175_S | 179_N | 1.098 | 0.96 |
| 324_K | 328_D | 1.096 | 0.96 |
| 338_R | 361_S | 1.088 | 0.96 |
| 363_T | 387_I | 1.073 | 0.95 |
| 134_Y | 186_F | 1.072 | 0.95 |
| 291_V | 295_W | 1.071 | 0.95 |
| 188_L | 205_W | 1.067 | 0.95 |
| 401_A | 405_H | 1.061 | 0.95 |
| 344_L | 401_A | 1.060 | 0.95 |
| 108_G | 224_A | 1.057 | 0.95 |
| 178_E | 182_E | 1.057 | 0.95 |
| 400_V | 403_S | 1.056 | 0.95 |
| 85_R | 89_G | 1.047 | 0.94 |
| 326_M | 330_I | 1.038 | 0.94 |
| 116_A | 187_V | 1.035 | 0.94 |
| 113_R | 117_E | 1.027 | 0.94 |
| 133_V | 185_I | 1.025 | 0.93 |
| 87_A | 269_N | 1.024 | 0.93 |
| 45_C | 48_W | 1.017 | 0.93 |
| 116_A | 147_F | 1.014 | 0.93 |
| 58_Q | 61_A | 1.012 | 0.93 |
| 333_M | 397_L | 1.011 | 0.93 |
| 251_F | 272_V | 1.007 | 0.93 |
| 76_L | 304_R | 1.003 | 0.93 |
| 178_E | 183_F | 1.002 | 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 | |
| 1ajsA | 1 | 0.9854 | 100 | 0.272 | Contact Map |
| 4f4eA | 2 | 0.9539 | 100 | 0.275 | Contact Map |
| 3mebA | 2 | 0.9636 | 100 | 0.286 | Contact Map |
| 2q7wA | 1 | 0.9029 | 100 | 0.29 | Contact Map |
| 3fslA | 6 | 0.9539 | 100 | 0.291 | Contact Map |
| 4eu1A | 2 | 0.9175 | 100 | 0.294 | Contact Map |
| 3k7yA | 1 | 0.9684 | 100 | 0.298 | Contact Map |
| 4h51A | 2 | 0.9612 | 100 | 0.303 | Contact Map |
| 7aatA | 2 | 0.9587 | 100 | 0.303 | Contact Map |
| 2ay1A | 2 | 0.9466 | 100 | 0.303 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)