| npp |
| ID: | 1505351744 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 432 (389) | ||
| Sequences: | 3074 (2154.1) | ||
| Seq/Len: | 7.902 | ||
| Nf(neff/√len): | 109.2 |
HHblits Results: (2016_02)
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: 7.902).
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 |
| 68_N | 235_G | 6.268 | 1.00 |
| 96_T | 106_H | 4.093 | 1.00 |
| 138_E | 146_N | 3.582 | 1.00 |
| 48_L | 401_M | 3.120 | 1.00 |
| 251_N | 382_D | 2.839 | 1.00 |
| 220_S | 223_Y | 2.830 | 1.00 |
| 105_H | 413_D | 2.603 | 1.00 |
| 234_I | 238_L | 2.494 | 1.00 |
| 138_E | 143_G | 2.451 | 1.00 |
| 145_E | 169_S | 2.403 | 1.00 |
| 302_E | 335_L | 2.281 | 1.00 |
| 253_I | 401_M | 2.267 | 1.00 |
| 210_D | 214_H | 2.262 | 1.00 |
| 69_L | 254_V | 2.226 | 1.00 |
| 314_C | 335_L | 2.219 | 1.00 |
| 70_S | 74_R | 2.159 | 1.00 |
| 185_D | 236_R | 2.156 | 1.00 |
| 52_S | 94_H | 2.096 | 1.00 |
| 75_E | 379_Q | 2.019 | 1.00 |
| 188_R | 240_G | 1.983 | 1.00 |
| 50_L | 201_L | 1.960 | 1.00 |
| 83_T | 393_D | 1.898 | 1.00 |
| 85_S | 96_T | 1.893 | 1.00 |
| 47_A | 200_R | 1.880 | 1.00 |
| 323_R | 366_D | 1.877 | 1.00 |
| 72_L | 377_L | 1.870 | 1.00 |
| 316_R | 319_E | 1.863 | 1.00 |
| 144_V | 149_Q | 1.863 | 1.00 |
| 50_L | 203_T | 1.841 | 1.00 |
| 242_Q | 247_R | 1.828 | 1.00 |
| 264_A | 267_H | 1.827 | 1.00 |
| 380_G | 383_L | 1.826 | 1.00 |
| 90_T | 94_H | 1.825 | 1.00 |
| 86_Y | 338_Q | 1.821 | 1.00 |
| 69_L | 234_I | 1.815 | 1.00 |
| 49_L | 250_T | 1.802 | 1.00 |
| 192_A | 244_D | 1.800 | 1.00 |
| 49_L | 252_I | 1.798 | 1.00 |
| 213_G | 260_M | 1.787 | 1.00 |
| 210_D | 363_H | 1.780 | 1.00 |
| 97_L | 397_V | 1.772 | 1.00 |
| 238_L | 252_I | 1.760 | 1.00 |
| 68_N | 238_L | 1.755 | 1.00 |
| 149_Q | 200_R | 1.753 | 1.00 |
| 50_L | 255_V | 1.741 | 1.00 |
| 102_R | 395_V | 1.728 | 1.00 |
| 261_A | 371_S | 1.720 | 1.00 |
| 311_H | 340_H | 1.712 | 1.00 |
| 101_L | 105_H | 1.694 | 1.00 |
| 239_A | 243_R | 1.691 | 1.00 |
| 98_V | 203_T | 1.690 | 1.00 |
| 71_Q | 75_E | 1.688 | 1.00 |
| 102_R | 325_Q | 1.688 | 1.00 |
| 82_M | 374_A | 1.678 | 1.00 |
| 293_P | 334_S | 1.664 | 1.00 |
| 214_H | 257_D | 1.651 | 1.00 |
| 341_E | 371_S | 1.649 | 1.00 |
| 68_N | 71_Q | 1.646 | 1.00 |
| 214_H | 363_H | 1.639 | 1.00 |
| 66_T | 70_S | 1.633 | 1.00 |
| 219_E | 262_E | 1.626 | 1.00 |
| 55_G | 260_M | 1.605 | 1.00 |
| 210_D | 257_D | 1.594 | 1.00 |
| 302_E | 306_L | 1.589 | 1.00 |
| 53_I | 234_I | 1.585 | 1.00 |
| 302_E | 316_R | 1.542 | 1.00 |
| 384_A | 387_K | 1.534 | 1.00 |
| 251_N | 383_L | 1.533 | 1.00 |
| 54_D | 214_H | 1.509 | 1.00 |
| 101_L | 137_G | 1.502 | 1.00 |
| 218_P | 262_E | 1.498 | 0.99 |
| 339_M | 345_A | 1.489 | 0.99 |
| 71_Q | 242_Q | 1.486 | 0.99 |
| 84_P | 93_N | 1.486 | 0.99 |
| 290_G | 333_P | 1.485 | 0.99 |
| 216_H | 222_Q | 1.467 | 0.99 |
| 251_N | 381_P | 1.467 | 0.99 |
| 144_V | 151_A | 1.460 | 0.99 |
| 51_I | 252_I | 1.458 | 0.99 |
| 97_L | 255_V | 1.458 | 0.99 |
| 144_V | 405_L | 1.447 | 0.99 |
| 147_T | 408_P | 1.444 | 0.99 |
| 94_H | 111_N | 1.440 | 0.99 |
| 114_R | 119_G | 1.436 | 0.99 |
| 208_H | 212_A | 1.430 | 0.99 |
| 218_P | 361_G | 1.420 | 0.99 |
| 67_P | 231_D | 1.414 | 0.99 |
| 48_L | 251_N | 1.412 | 0.99 |
| 96_T | 394_N | 1.402 | 0.99 |
| 256_S | 374_A | 1.388 | 0.99 |
| 235_G | 239_A | 1.381 | 0.99 |
| 313_D | 340_H | 1.368 | 0.99 |
| 62_D | 78_R | 1.366 | 0.99 |
| 209_V | 230_V | 1.364 | 0.99 |
| 341_E | 369_L | 1.357 | 0.99 |
| 53_I | 209_V | 1.356 | 0.99 |
| 66_T | 227_V | 1.337 | 0.99 |
| 376_F | 392_F | 1.333 | 0.99 |
| 267_H | 343_W | 1.332 | 0.99 |
| 393_D | 396_D | 1.329 | 0.99 |
| 54_D | 257_D | 1.322 | 0.98 |
| 303_A | 306_L | 1.321 | 0.98 |
| 241_M | 252_I | 1.318 | 0.98 |
| 90_T | 257_D | 1.318 | 0.98 |
| 48_L | 405_L | 1.303 | 0.98 |
| 214_H | 258_H | 1.301 | 0.98 |
| 85_S | 103_P | 1.293 | 0.98 |
| 221_R | 225_D | 1.292 | 0.98 |
| 90_T | 111_N | 1.277 | 0.98 |
| 79_A | 376_F | 1.273 | 0.98 |
| 79_A | 392_F | 1.269 | 0.98 |
| 98_V | 140_V | 1.268 | 0.98 |
| 253_I | 378_A | 1.263 | 0.98 |
| 81_W | 391_G | 1.256 | 0.98 |
| 54_D | 258_H | 1.252 | 0.98 |
| 72_L | 379_Q | 1.251 | 0.98 |
| 396_D | 399_A | 1.250 | 0.98 |
| 56_L | 60_M | 1.250 | 0.98 |
| 93_N | 394_N | 1.248 | 0.98 |
| 251_N | 404_L | 1.244 | 0.97 |
| 212_A | 226_A | 1.244 | 0.97 |
| 71_Q | 238_L | 1.235 | 0.97 |
| 66_T | 69_L | 1.235 | 0.97 |
| 90_T | 210_D | 1.234 | 0.97 |
| 206_F | 237_L | 1.229 | 0.97 |
| 149_Q | 405_L | 1.218 | 0.97 |
| 87_P | 103_P | 1.216 | 0.97 |
| 63_R | 224_A | 1.213 | 0.97 |
| 49_L | 202_V | 1.209 | 0.97 |
| 299_A | 316_R | 1.208 | 0.97 |
| 392_F | 419_L | 1.200 | 0.97 |
| 302_E | 314_C | 1.199 | 0.97 |
| 48_L | 253_I | 1.190 | 0.96 |
| 46_H | 382_D | 1.188 | 0.96 |
| 85_S | 93_N | 1.188 | 0.96 |
| 45_P | 200_R | 1.178 | 0.96 |
| 152_A | 199_N | 1.176 | 0.96 |
| 90_T | 258_H | 1.170 | 0.96 |
| 392_F | 396_D | 1.167 | 0.96 |
| 140_V | 401_M | 1.164 | 0.96 |
| 186_A | 189_G | 1.160 | 0.96 |
| 399_A | 412_N | 1.160 | 0.96 |
| 65_I | 228_R | 1.159 | 0.96 |
| 80_R | 390_P | 1.156 | 0.96 |
| 204_L | 237_L | 1.154 | 0.96 |
| 314_C | 337_C | 1.153 | 0.96 |
| 402_S | 409_A | 1.151 | 0.95 |
| 418_T | 421_P | 1.151 | 0.95 |
| 167_R | 171_W | 1.147 | 0.95 |
| 241_M | 250_T | 1.141 | 0.95 |
| 257_D | 363_H | 1.137 | 0.95 |
| 48_L | 404_L | 1.135 | 0.95 |
| 111_N | 210_D | 1.134 | 0.95 |
| 47_A | 198_R | 1.133 | 0.95 |
| 238_L | 247_R | 1.132 | 0.95 |
| 83_T | 368_A | 1.132 | 0.95 |
| 150_H | 197_Q | 1.131 | 0.95 |
| 382_D | 404_L | 1.123 | 0.95 |
| 60_M | 213_G | 1.108 | 0.94 |
| 144_V | 201_L | 1.107 | 0.94 |
| 84_P | 88_S | 1.105 | 0.94 |
| 82_M | 397_V | 1.100 | 0.94 |
| 397_V | 401_M | 1.097 | 0.94 |
| 225_D | 228_R | 1.088 | 0.93 |
| 56_L | 227_V | 1.082 | 0.93 |
| 389_L | 422_A | 1.082 | 0.93 |
| 210_D | 258_H | 1.079 | 0.93 |
| 187_V | 204_L | 1.079 | 0.93 |
| 194_D | 198_R | 1.073 | 0.93 |
| 116_P | 334_S | 1.070 | 0.93 |
| 65_I | 224_A | 1.062 | 0.92 |
| 73_A | 78_R | 1.055 | 0.92 |
| 139_P | 142_V | 1.053 | 0.92 |
| 231_D | 235_G | 1.050 | 0.92 |
| 181_D | 236_R | 1.046 | 0.91 |
| 142_V | 166_V | 1.045 | 0.91 |
| 104_D | 327_G | 1.039 | 0.91 |
| 276_P | 279_I | 1.037 | 0.91 |
| 256_S | 375_V | 1.033 | 0.91 |
| 241_M | 244_D | 1.032 | 0.91 |
| 170_Q | 193_T | 1.023 | 0.90 |
| 88_S | 364_G | 1.022 | 0.90 |
| 258_H | 363_H | 1.022 | 0.90 |
| 99_T | 106_H | 1.022 | 0.90 |
| 47_A | 249_R | 1.022 | 0.90 |
| 209_V | 212_A | 1.022 | 0.90 |
| 419_L | 422_A | 1.021 | 0.90 |
| 53_I | 230_V | 1.021 | 0.90 |
| 105_H | 415_N | 1.019 | 0.90 |
| 54_D | 363_H | 1.017 | 0.90 |
| 77_V | 383_L | 1.017 | 0.90 |
| 385_Q | 424_R | 1.016 | 0.90 |
| 260_M | 361_G | 1.013 | 0.90 |
| 153_T | 159_S | 1.012 | 0.90 |
| 72_L | 76_G | 1.010 | 0.89 |
| 326_Y | 332_I | 1.004 | 0.89 |
| 72_L | 238_L | 1.001 | 0.89 |
| 57_R | 60_M | 1.001 | 0.89 |
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 | |
| 2gsoA | 2 | 0.8843 | 100 | 0.377 | Contact Map |
| 4lr2A | 1 | 0.8704 | 100 | 0.409 | Contact Map |
| 4gtwA | 2 | 0.9352 | 100 | 0.438 | Contact Map |
| 3nkqA | 1 | 0.9421 | 100 | 0.44 | Contact Map |
| 3q3qA | 1 | 0.8889 | 100 | 0.484 | Contact Map |
| 3szyA | 1 | 0.8102 | 100 | 0.496 | Contact Map |
| 1ei6A | 4 | 0.8056 | 100 | 0.51 | Contact Map |
| 4fdiA | 2 | 0.6852 | 100 | 0.699 | Contact Map |
| 3b5qA | 2 | 0.6481 | 100 | 0.701 | Contact Map |
| 3ed4A | 4 | 0.6968 | 100 | 0.705 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)