| NS3 proteasehelicase |
| ID: | 1414523943 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 618 (309) | ||
| Sequences: | 25795 (15096.1) | ||
| Seq/Len: | 83.479 | ||
| Nf(neff/√len): | 858.8 |
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: 83.479).
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 |
| 396_K | 401_D | 4.087 | 1.00 |
| 204_L | 235_L | 3.280 | 1.00 |
| 383_I | 402_W | 2.968 | 1.00 |
| 365_I | 388_K | 2.921 | 1.00 |
| 222_A | 231_M | 2.886 | 1.00 |
| 266_T | 276_P | 2.873 | 1.00 |
| 207_I | 218_T | 2.865 | 1.00 |
| 362_V | 368_G | 2.852 | 1.00 |
| 182_I | 312_I | 2.843 | 1.00 |
| 375_L | 406_V | 2.780 | 1.00 |
| 251_H | 256_I | 2.777 | 1.00 |
| 381_K | 403_D | 2.733 | 1.00 |
| 395_V | 399_T | 2.620 | 1.00 |
| 362_V | 406_V | 2.526 | 1.00 |
| 380_K | 404_F | 2.508 | 1.00 |
| 372_A | 406_V | 2.456 | 1.00 |
| 259_L | 264_T | 2.421 | 1.00 |
| 362_V | 371_I | 2.389 | 1.00 |
| 358_T | 421_R | 2.307 | 1.00 |
| 287_H | 413_M | 2.178 | 1.00 |
| 258_D | 262_H | 2.161 | 1.00 |
| 411_S | 415_A | 2.110 | 1.00 |
| 392_S | 396_K | 2.103 | 1.00 |
| 372_A | 376_R | 2.067 | 1.00 |
| 193_L | 197_A | 2.017 | 1.00 |
| 232_E | 236_R | 1.973 | 1.00 |
| 383_I | 393_E | 1.968 | 1.00 |
| 372_A | 382_V | 1.958 | 1.00 |
| 227_V | 230_E | 1.941 | 1.00 |
| 217_R | 279_N | 1.922 | 1.00 |
| 371_I | 406_V | 1.919 | 1.00 |
| 458_R | 471_Q | 1.866 | 1.00 |
| 368_G | 384_Q | 1.857 | 1.00 |
| 287_H | 456_Q | 1.816 | 1.00 |
| 191_M | 314_M | 1.809 | 1.00 |
| 294_I | 298_G | 1.809 | 1.00 |
| 397_T | 405_V | 1.808 | 1.00 |
| 393_E | 402_W | 1.787 | 1.00 |
| 424_D | 458_R | 1.773 | 1.00 |
| 203_Y | 314_M | 1.766 | 1.00 |
| 207_I | 282_I | 1.754 | 1.00 |
| 369_N | 384_Q | 1.752 | 1.00 |
| 372_A | 384_Q | 1.737 | 1.00 |
| 383_I | 396_K | 1.719 | 1.00 |
| 227_V | 414_G | 1.714 | 1.00 |
| 344_W | 347_G | 1.706 | 1.00 |
| 447_M | 473_I | 1.691 | 1.00 |
| 460_R | 463_R | 1.673 | 1.00 |
| 421_R | 472_Y | 1.643 | 1.00 |
| 407_T | 411_S | 1.636 | 1.00 |
| 219_L | 278_Y | 1.622 | 1.00 |
| 185_K | 310_A | 1.620 | 1.00 |
| 391_D | 395_V | 1.617 | 1.00 |
| 337_R | 341_E | 1.616 | 1.00 |
| 367_A | 446_P | 1.598 | 1.00 |
| 258_D | 261_C | 1.585 | 1.00 |
| 367_A | 370_D | 1.551 | 1.00 |
| 459_G | 463_R | 1.525 | 1.00 |
| 281_I | 311_G | 1.520 | 1.00 |
| 205_P | 208_V | 1.514 | 1.00 |
| 424_D | 473_I | 1.511 | 1.00 |
| 374_C | 378_N | 1.511 | 1.00 |
| 229_A | 391_D | 1.504 | 1.00 |
| 368_G | 406_V | 1.483 | 1.00 |
| 364_S | 367_A | 1.454 | 1.00 |
| 413_M | 456_Q | 1.417 | 1.00 |
| 261_C | 264_T | 1.416 | 1.00 |
| 275_V | 278_Y | 1.408 | 1.00 |
| 219_L | 281_I | 1.381 | 0.99 |
| 157_R | 167_Q | 1.379 | 0.99 |
| 186_R | 332_I | 1.378 | 0.99 |
| 396_K | 402_W | 1.375 | 0.99 |
| 360_W | 404_F | 1.367 | 0.99 |
| 220_I | 235_L | 1.364 | 0.99 |
| 392_S | 395_V | 1.340 | 0.99 |
| 295_A | 299_Y | 1.339 | 0.99 |
| 450_T | 453_S | 1.328 | 0.99 |
| 229_A | 233_E | 1.321 | 0.99 |
| 389_T | 393_E | 1.319 | 0.99 |
| 357_K | 403_D | 1.318 | 0.99 |
| 218_T | 280_L | 1.313 | 0.99 |
| 167_Q | 170_K | 1.310 | 0.99 |
| 200_T | 231_M | 1.302 | 0.99 |
| 181_D | 188_L | 1.297 | 0.99 |
| 368_G | 386_S | 1.293 | 0.99 |
| 356_G | 420_E | 1.291 | 0.99 |
| 205_P | 210_E | 1.289 | 0.99 |
| 224_T | 413_M | 1.289 | 0.99 |
| 222_A | 228_A | 1.289 | 0.99 |
| 203_Y | 231_M | 1.276 | 0.99 |
| 400_N | 403_D | 1.275 | 0.99 |
| 412_E | 453_S | 1.255 | 0.99 |
| 393_E | 405_V | 1.244 | 0.98 |
| 369_N | 386_S | 1.244 | 0.98 |
| 181_D | 184_R | 1.236 | 0.98 |
| 201_K | 234_A | 1.212 | 0.98 |
| 218_T | 282_I | 1.210 | 0.98 |
| 317_T | 456_Q | 1.207 | 0.98 |
| 281_I | 301_S | 1.200 | 0.98 |
| 230_E | 234_A | 1.199 | 0.98 |
| 234_A | 416_N | 1.193 | 0.98 |
| 206_A | 209_R | 1.187 | 0.98 |
| 295_A | 298_G | 1.186 | 0.98 |
| 358_T | 404_F | 1.156 | 0.97 |
| 205_P | 209_R | 1.151 | 0.97 |
| 230_E | 416_N | 1.147 | 0.97 |
| 294_I | 297_R | 1.139 | 0.97 |
| 361_F | 411_S | 1.134 | 0.97 |
| 412_E | 457_R | 1.118 | 0.96 |
| 233_E | 236_R | 1.112 | 0.96 |
| 252_T | 255_E | 1.112 | 0.96 |
| 288_F | 413_M | 1.108 | 0.96 |
| 163_S | 167_Q | 1.103 | 0.96 |
| 408_T | 462_G | 1.093 | 0.96 |
| 359_V | 407_T | 1.092 | 0.96 |
| 373_A | 377_K | 1.089 | 0.96 |
| 188_L | 191_M | 1.086 | 0.96 |
| 291_P | 294_I | 1.083 | 0.96 |
| 357_K | 420_E | 1.079 | 0.95 |
| 251_H | 265_F | 1.077 | 0.95 |
| 349_E | 353_D | 1.072 | 0.95 |
| 251_H | 254_R | 1.068 | 0.95 |
| 157_R | 163_S | 1.064 | 0.95 |
| 424_D | 457_R | 1.062 | 0.95 |
| 298_G | 301_S | 1.054 | 0.95 |
| 187_R | 331_P | 1.045 | 0.94 |
| 180_D | 183_F | 1.041 | 0.94 |
| 154_V | 163_S | 1.041 | 0.94 |
| 154_V | 201_K | 1.033 | 0.94 |
| 226_V | 230_E | 1.031 | 0.94 |
| 484_D | 487_H | 1.027 | 0.94 |
| 191_M | 312_I | 1.021 | 0.93 |
| 376_R | 382_V | 1.019 | 0.93 |
| 301_S | 304_V | 1.017 | 0.93 |
| 357_K | 419_A | 1.016 | 0.93 |
| 216_L | 279_N | 1.014 | 0.93 |
| 154_V | 157_R | 1.012 | 0.93 |
| 259_L | 263_A | 1.011 | 0.93 |
| 206_A | 210_E | 1.010 | 0.93 |
| 448_P | 454_A | 1.010 | 0.93 |
| 368_G | 372_A | 1.005 | 0.93 |
| 196_G | 317_T | 1.003 | 0.93 |
| 365_I | 387_R | 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 | |
| 2whxA | 1 | 0.9369 | 100 | 0.149 | Contact Map |
| 2wv9A | 1 | 0.9353 | 100 | 0.188 | Contact Map |
| 2jlqA | 1 | 0.7282 | 100 | 0.485 | Contact Map |
| 1yksA | 1 | 0.6958 | 100 | 0.488 | Contact Map |
| 2z83A | 1 | 0.6893 | 100 | 0.5 | Contact Map |
| 2v6iA | 1 | 0.6812 | 100 | 0.528 | Contact Map |
| 3o8bA | 2 | 0.9078 | 100 | 0.586 | Contact Map |
| 4m9kA | 1 | 0.2476 | 100 | 0.628 | Contact Map |
| 3e90B | 2 | 0.2783 | 100 | 0.63 | Contact Map |
| 2ggvB | 1 | 0.2735 | 100 | 0.64 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)