| NPP |
| ID: | 1505317066 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 432 (401) | ||
| Sequences: | 3651 (2361.9) | ||
| Seq/Len: | 9.105 | ||
| Nf(neff/√len): | 117.9 |
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: 9.105).
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 | 5.951 | 1.00 |
| 96_T | 106_H | 3.497 | 1.00 |
| 105_H | 413_D | 3.326 | 1.00 |
| 138_E | 146_N | 3.288 | 1.00 |
| 48_L | 401_M | 3.270 | 1.00 |
| 185_D | 236_R | 2.821 | 1.00 |
| 251_N | 382_D | 2.732 | 1.00 |
| 220_S | 223_Y | 2.654 | 1.00 |
| 145_E | 169_S | 2.590 | 1.00 |
| 75_E | 379_Q | 2.395 | 1.00 |
| 188_R | 240_G | 2.354 | 1.00 |
| 234_I | 238_L | 2.317 | 1.00 |
| 138_E | 143_G | 2.272 | 1.00 |
| 210_D | 214_H | 2.251 | 1.00 |
| 192_A | 244_D | 2.210 | 1.00 |
| 72_L | 377_L | 2.209 | 1.00 |
| 314_C | 335_L | 2.207 | 1.00 |
| 49_L | 252_I | 2.181 | 1.00 |
| 71_Q | 242_Q | 2.135 | 1.00 |
| 49_L | 250_T | 2.118 | 1.00 |
| 242_Q | 247_R | 2.114 | 1.00 |
| 323_R | 366_D | 2.077 | 1.00 |
| 52_S | 94_H | 2.077 | 1.00 |
| 50_L | 203_T | 2.033 | 1.00 |
| 70_S | 74_R | 1.988 | 1.00 |
| 69_L | 254_V | 1.939 | 1.00 |
| 83_T | 393_D | 1.900 | 1.00 |
| 144_V | 149_Q | 1.894 | 1.00 |
| 97_L | 397_V | 1.884 | 1.00 |
| 253_I | 401_M | 1.848 | 1.00 |
| 213_G | 260_M | 1.832 | 1.00 |
| 47_A | 200_R | 1.807 | 1.00 |
| 90_T | 94_H | 1.799 | 1.00 |
| 238_L | 252_I | 1.795 | 1.00 |
| 261_A | 371_S | 1.780 | 1.00 |
| 82_M | 374_A | 1.779 | 1.00 |
| 239_A | 243_R | 1.765 | 1.00 |
| 66_T | 70_S | 1.762 | 1.00 |
| 316_R | 319_E | 1.759 | 1.00 |
| 50_L | 255_V | 1.751 | 1.00 |
| 86_Y | 338_Q | 1.749 | 1.00 |
| 68_N | 71_Q | 1.719 | 1.00 |
| 210_D | 363_H | 1.716 | 1.00 |
| 50_L | 201_L | 1.714 | 1.00 |
| 102_R | 395_V | 1.706 | 1.00 |
| 380_G | 383_L | 1.700 | 1.00 |
| 68_N | 238_L | 1.687 | 1.00 |
| 85_S | 96_T | 1.668 | 1.00 |
| 290_G | 333_P | 1.666 | 1.00 |
| 98_V | 203_T | 1.661 | 1.00 |
| 311_H | 340_H | 1.652 | 1.00 |
| 302_E | 335_L | 1.633 | 1.00 |
| 214_H | 257_D | 1.629 | 1.00 |
| 69_L | 234_I | 1.618 | 1.00 |
| 341_E | 371_S | 1.612 | 1.00 |
| 293_P | 334_S | 1.607 | 1.00 |
| 264_A | 267_H | 1.597 | 1.00 |
| 313_D | 340_H | 1.590 | 1.00 |
| 384_A | 387_K | 1.584 | 1.00 |
| 149_Q | 200_R | 1.584 | 1.00 |
| 147_T | 408_P | 1.583 | 1.00 |
| 55_G | 260_M | 1.580 | 1.00 |
| 256_S | 374_A | 1.554 | 1.00 |
| 214_H | 363_H | 1.553 | 1.00 |
| 93_N | 394_N | 1.547 | 1.00 |
| 101_L | 105_H | 1.538 | 1.00 |
| 66_T | 227_V | 1.528 | 1.00 |
| 208_H | 212_A | 1.526 | 1.00 |
| 84_P | 93_N | 1.526 | 1.00 |
| 81_W | 391_G | 1.510 | 1.00 |
| 65_I | 228_R | 1.507 | 1.00 |
| 96_T | 394_N | 1.505 | 1.00 |
| 71_Q | 75_E | 1.498 | 1.00 |
| 393_D | 396_D | 1.493 | 1.00 |
| 210_D | 257_D | 1.493 | 1.00 |
| 219_E | 262_E | 1.478 | 1.00 |
| 53_I | 56_L | 1.472 | 1.00 |
| 251_N | 383_L | 1.469 | 1.00 |
| 101_L | 137_G | 1.465 | 1.00 |
| 399_A | 412_N | 1.464 | 1.00 |
| 339_M | 345_A | 1.459 | 1.00 |
| 67_P | 231_D | 1.452 | 1.00 |
| 94_H | 111_N | 1.441 | 0.99 |
| 85_S | 103_P | 1.438 | 0.99 |
| 102_R | 325_Q | 1.434 | 0.99 |
| 341_E | 369_L | 1.427 | 0.99 |
| 218_P | 361_G | 1.427 | 0.99 |
| 56_L | 227_V | 1.417 | 0.99 |
| 398_Y | 412_N | 1.404 | 0.99 |
| 79_A | 376_F | 1.404 | 0.99 |
| 212_A | 226_A | 1.399 | 0.99 |
| 184_V | 237_L | 1.399 | 0.99 |
| 241_M | 252_I | 1.395 | 0.99 |
| 144_V | 405_L | 1.394 | 0.99 |
| 251_N | 381_P | 1.387 | 0.99 |
| 251_N | 404_L | 1.377 | 0.99 |
| 80_R | 390_P | 1.375 | 0.99 |
| 209_V | 230_V | 1.364 | 0.99 |
| 218_P | 262_E | 1.360 | 0.99 |
| 98_V | 140_V | 1.357 | 0.99 |
| 181_D | 236_R | 1.351 | 0.99 |
| 53_I | 209_V | 1.348 | 0.99 |
| 187_V | 204_L | 1.346 | 0.99 |
| 267_H | 343_W | 1.345 | 0.99 |
| 53_I | 234_I | 1.342 | 0.99 |
| 392_F | 396_D | 1.334 | 0.99 |
| 144_V | 151_A | 1.324 | 0.99 |
| 136_G | 329_H | 1.307 | 0.99 |
| 71_Q | 238_L | 1.303 | 0.99 |
| 51_I | 252_I | 1.294 | 0.99 |
| 56_L | 60_M | 1.286 | 0.99 |
| 62_D | 78_R | 1.276 | 0.98 |
| 66_T | 69_L | 1.273 | 0.98 |
| 216_H | 222_Q | 1.271 | 0.98 |
| 292_E | 333_P | 1.267 | 0.98 |
| 302_E | 316_R | 1.265 | 0.98 |
| 214_H | 258_H | 1.264 | 0.98 |
| 73_A | 78_R | 1.263 | 0.98 |
| 72_L | 379_Q | 1.262 | 0.98 |
| 253_I | 378_A | 1.260 | 0.98 |
| 396_D | 414_G | 1.245 | 0.98 |
| 79_A | 392_F | 1.239 | 0.98 |
| 402_S | 412_N | 1.238 | 0.98 |
| 90_T | 210_D | 1.232 | 0.98 |
| 51_I | 237_L | 1.231 | 0.98 |
| 90_T | 257_D | 1.228 | 0.98 |
| 402_S | 409_A | 1.228 | 0.98 |
| 152_A | 199_N | 1.225 | 0.98 |
| 419_L | 422_A | 1.219 | 0.98 |
| 97_L | 255_V | 1.218 | 0.98 |
| 114_R | 119_G | 1.213 | 0.98 |
| 87_P | 103_P | 1.212 | 0.98 |
| 54_D | 214_H | 1.209 | 0.98 |
| 90_T | 111_N | 1.208 | 0.98 |
| 235_G | 239_A | 1.208 | 0.98 |
| 48_L | 251_N | 1.197 | 0.97 |
| 231_D | 235_G | 1.186 | 0.97 |
| 49_L | 202_V | 1.182 | 0.97 |
| 90_T | 258_H | 1.176 | 0.97 |
| 276_P | 279_I | 1.166 | 0.97 |
| 46_H | 382_D | 1.165 | 0.97 |
| 396_D | 418_T | 1.162 | 0.97 |
| 397_V | 401_M | 1.162 | 0.97 |
| 48_L | 404_L | 1.156 | 0.97 |
| 54_D | 257_D | 1.150 | 0.97 |
| 82_M | 397_V | 1.148 | 0.96 |
| 241_M | 250_T | 1.143 | 0.96 |
| 15_L | 20_S | 1.139 | 0.96 |
| 150_H | 197_Q | 1.138 | 0.96 |
| 376_F | 392_F | 1.138 | 0.96 |
| 111_N | 210_D | 1.138 | 0.96 |
| 221_R | 225_D | 1.131 | 0.96 |
| 144_V | 201_L | 1.128 | 0.96 |
| 137_G | 410_A | 1.112 | 0.96 |
| 314_C | 337_C | 1.104 | 0.95 |
| 142_V | 163_I | 1.098 | 0.95 |
| 181_D | 206_F | 1.093 | 0.95 |
| 149_Q | 405_L | 1.089 | 0.95 |
| 186_A | 190_W | 1.089 | 0.95 |
| 392_F | 419_L | 1.084 | 0.95 |
| 81_W | 373_R | 1.082 | 0.95 |
| 300_A | 304_S | 1.080 | 0.95 |
| 210_D | 258_H | 1.078 | 0.95 |
| 77_V | 383_L | 1.077 | 0.94 |
| 398_Y | 402_S | 1.072 | 0.94 |
| 256_S | 375_V | 1.071 | 0.94 |
| 83_T | 368_A | 1.071 | 0.94 |
| 15_L | 18_A | 1.070 | 0.94 |
| 238_L | 247_R | 1.069 | 0.94 |
| 187_V | 202_V | 1.068 | 0.94 |
| 153_T | 159_S | 1.064 | 0.94 |
| 63_R | 224_A | 1.061 | 0.94 |
| 418_T | 421_P | 1.058 | 0.94 |
| 54_D | 258_H | 1.053 | 0.94 |
| 409_A | 412_N | 1.052 | 0.94 |
| 45_P | 200_R | 1.050 | 0.93 |
| 383_L | 400_L | 1.049 | 0.93 |
| 257_D | 363_H | 1.048 | 0.93 |
| 382_D | 404_L | 1.044 | 0.93 |
| 206_F | 237_L | 1.038 | 0.93 |
| 60_M | 213_G | 1.037 | 0.93 |
| 116_P | 334_S | 1.035 | 0.93 |
| 396_D | 399_A | 1.034 | 0.93 |
| 17_A | 20_S | 1.033 | 0.93 |
| 240_G | 243_R | 1.032 | 0.93 |
| 191_L | 202_V | 1.031 | 0.93 |
| 181_D | 233_A | 1.031 | 0.93 |
| 53_I | 254_V | 1.030 | 0.93 |
| 238_L | 242_Q | 1.029 | 0.93 |
| 16_L | 20_S | 1.021 | 0.92 |
| 88_S | 364_G | 1.021 | 0.92 |
| 139_P | 142_V | 1.015 | 0.92 |
| 72_L | 254_V | 1.009 | 0.92 |
| 51_I | 204_L | 1.009 | 0.92 |
| 65_I | 224_A | 1.007 | 0.91 |
| 53_I | 230_V | 1.004 | 0.91 |
| 153_T | 203_T | 1.004 | 0.91 |
| 204_L | 237_L | 1.003 | 0.91 |
| 184_V | 206_F | 1.003 | 0.91 |
| 82_M | 394_N | 1.000 | 0.91 |
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 | 0.337 | Contact Map |
| 4lr2A | 1 | 0.8704 | 100 | 0.364 | Contact Map |
| 4gtwA | 2 | 0.9398 | 100 | 0.386 | Contact Map |
| 3nkqA | 1 | 0.912 | 100 | 0.386 | Contact Map |
| 3q3qA | 1 | 0.8843 | 100 | 0.456 | Contact Map |
| 3szyA | 1 | 0.8148 | 100 | 0.472 | Contact Map |
| 1ei6A | 4 | 0.8056 | 100 | 0.482 | Contact Map |
| 4fdiA | 2 | 0.6829 | 100 | 0.669 | Contact Map |
| 3b5qA | 2 | 0.6458 | 100 | 0.68 | Contact Map |
| 1fsuA | 1 | 0.6574 | 100 | 0.682 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)