| ling-y |
| ID: | 1419871722 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 442 (436) | ||
| Sequences: | 5521 (4481) | ||
| Seq/Len: | 12.663 | ||
| Nf(neff/√len): | 214.6 |
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: 12.663).
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 |
| 378_N | 382_S | 4.567 | 1.00 |
| 423_F | 432_F | 4.418 | 1.00 |
| 411_K | 415_E | 4.290 | 1.00 |
| 377_E | 431_T | 4.068 | 1.00 |
| 347_I | 413_L | 3.705 | 1.00 |
| 392_F | 421_Y | 3.621 | 1.00 |
| 410_V | 421_Y | 3.530 | 1.00 |
| 419_L | 436_F | 3.462 | 1.00 |
| 359_S | 379_S | 3.414 | 1.00 |
| 251_K | 279_D | 3.375 | 1.00 |
| 254_I | 274_A | 3.332 | 1.00 |
| 388_L | 425_M | 3.172 | 1.00 |
| 359_S | 363_G | 3.117 | 1.00 |
| 414_L | 419_L | 3.104 | 1.00 |
| 414_L | 434_I | 2.962 | 1.00 |
| 413_L | 417_E | 2.953 | 1.00 |
| 390_Q | 393_S | 2.929 | 1.00 |
| 425_M | 430_L | 2.885 | 1.00 |
| 347_I | 414_L | 2.875 | 1.00 |
| 339_L | 344_M | 2.696 | 1.00 |
| 234_E | 238_G | 2.461 | 1.00 |
| 339_L | 417_E | 2.378 | 1.00 |
| 193_S | 198_G | 2.361 | 1.00 |
| 391_S | 423_F | 2.332 | 1.00 |
| 310_T | 348_L | 2.268 | 1.00 |
| 302_E | 341_P | 2.256 | 1.00 |
| 384_E | 387_K | 2.244 | 1.00 |
| 383_E | 391_S | 2.223 | 1.00 |
| 353_S | 357_K | 2.192 | 1.00 |
| 423_F | 430_L | 2.185 | 1.00 |
| 392_F | 432_F | 2.163 | 1.00 |
| 83_G | 87_E | 2.163 | 1.00 |
| 331_S | 368_G | 2.151 | 1.00 |
| 305_D | 308_Q | 2.139 | 1.00 |
| 405_M | 409_V | 2.135 | 1.00 |
| 347_I | 434_I | 2.125 | 1.00 |
| 180_M | 207_L | 2.112 | 1.00 |
| 424_E | 433_F | 2.084 | 1.00 |
| 420_A | 435_D | 2.081 | 1.00 |
| 368_G | 375_F | 2.070 | 1.00 |
| 251_K | 282_N | 2.060 | 1.00 |
| 350_N | 410_V | 2.051 | 1.00 |
| 373_E | 435_D | 2.049 | 1.00 |
| 312_N | 341_P | 2.046 | 1.00 |
| 368_G | 377_E | 2.003 | 1.00 |
| 313_L | 352_I | 2.002 | 1.00 |
| 422_R | 433_F | 1.998 | 1.00 |
| 188_R | 209_Q | 1.994 | 1.00 |
| 235_F | 239_A | 1.994 | 1.00 |
| 304_I | 339_L | 1.969 | 1.00 |
| 388_L | 423_F | 1.943 | 1.00 |
| 343_V | 346_L | 1.934 | 1.00 |
| 424_E | 431_T | 1.917 | 1.00 |
| 363_G | 379_S | 1.911 | 1.00 |
| 314_V | 367_I | 1.907 | 1.00 |
| 179_R | 184_D | 1.891 | 1.00 |
| 414_L | 421_Y | 1.858 | 1.00 |
| 366_R | 377_E | 1.828 | 1.00 |
| 351_L | 432_F | 1.827 | 1.00 |
| 303_T | 336_Q | 1.823 | 1.00 |
| 419_L | 437_P | 1.808 | 1.00 |
| 375_F | 433_F | 1.802 | 1.00 |
| 195_D | 198_G | 1.801 | 1.00 |
| 282_N | 286_L | 1.795 | 1.00 |
| 254_I | 278_V | 1.795 | 1.00 |
| 392_F | 411_K | 1.792 | 1.00 |
| 321_A | 356_I | 1.791 | 1.00 |
| 387_K | 396_A | 1.777 | 1.00 |
| 398_R | 401_K | 1.752 | 1.00 |
| 351_L | 410_V | 1.733 | 1.00 |
| 327_Q | 364_L | 1.715 | 1.00 |
| 312_N | 345_K | 1.712 | 1.00 |
| 378_N | 381_S | 1.711 | 1.00 |
| 391_S | 432_F | 1.696 | 1.00 |
| 304_I | 344_M | 1.689 | 1.00 |
| 375_F | 431_T | 1.686 | 1.00 |
| 329_D | 366_R | 1.686 | 1.00 |
| 274_A | 278_V | 1.682 | 1.00 |
| 414_L | 436_F | 1.678 | 1.00 |
| 364_L | 379_S | 1.653 | 1.00 |
| 387_K | 390_Q | 1.628 | 1.00 |
| 348_L | 374_L | 1.627 | 1.00 |
| 238_G | 394_D | 1.627 | 1.00 |
| 392_F | 423_F | 1.600 | 1.00 |
| 283_H | 342_S | 1.570 | 1.00 |
| 254_I | 271_L | 1.561 | 1.00 |
| 255_E | 275_L | 1.555 | 1.00 |
| 303_T | 338_Y | 1.541 | 1.00 |
| 329_D | 364_L | 1.504 | 1.00 |
| 42_Q | 108_F | 1.497 | 1.00 |
| 177_T | 203_Q | 1.493 | 1.00 |
| 426_E | 429_R | 1.468 | 1.00 |
| 344_M | 417_E | 1.452 | 1.00 |
| 185_S | 188_R | 1.442 | 1.00 |
| 188_R | 208_Y | 1.437 | 1.00 |
| 263_R | 266_D | 1.435 | 1.00 |
| 242_E | 346_L | 1.419 | 1.00 |
| 383_E | 430_L | 1.413 | 1.00 |
| 390_Q | 396_A | 1.411 | 1.00 |
| 388_L | 392_F | 1.403 | 0.99 |
| 258_R | 272_G | 1.398 | 0.99 |
| 247_L | 278_V | 1.387 | 0.99 |
| 415_E | 420_A | 1.386 | 0.99 |
| 305_D | 336_Q | 1.381 | 0.99 |
| 177_T | 204_I | 1.369 | 0.99 |
| 191_V | 202_E | 1.363 | 0.99 |
| 348_L | 352_I | 1.360 | 0.99 |
| 309_M | 313_L | 1.356 | 0.99 |
| 366_R | 379_S | 1.354 | 0.99 |
| 358_H | 381_S | 1.353 | 0.99 |
| 347_I | 410_V | 1.351 | 0.99 |
| 250_L | 278_V | 1.347 | 0.99 |
| 378_N | 430_L | 1.345 | 0.99 |
| 173_I | 201_K | 1.343 | 0.99 |
| 188_R | 212_L | 1.342 | 0.99 |
| 159_A | 163_A | 1.322 | 0.99 |
| 321_A | 365_V | 1.314 | 0.99 |
| 305_D | 334_H | 1.314 | 0.99 |
| 264_Y | 267_R | 1.310 | 0.99 |
| 335_Q | 369_E | 1.309 | 0.99 |
| 352_I | 367_I | 1.298 | 0.99 |
| 343_V | 416_H | 1.292 | 0.99 |
| 204_I | 207_L | 1.287 | 0.99 |
| 194_K | 198_G | 1.285 | 0.99 |
| 180_M | 208_Y | 1.282 | 0.99 |
| 378_N | 429_R | 1.281 | 0.99 |
| 174_K | 199_N | 1.277 | 0.99 |
| 251_K | 275_L | 1.275 | 0.99 |
| 178_R | 199_N | 1.275 | 0.99 |
| 250_L | 274_A | 1.263 | 0.99 |
| 385_Q | 388_L | 1.250 | 0.99 |
| 385_Q | 425_M | 1.246 | 0.98 |
| 340_N | 343_V | 1.244 | 0.98 |
| 316_D | 345_K | 1.243 | 0.98 |
| 173_I | 189_L | 1.243 | 0.98 |
| 7_F | 164_R | 1.235 | 0.98 |
| 347_I | 417_E | 1.232 | 0.98 |
| 89_K | 92_V | 1.219 | 0.98 |
| 331_S | 366_R | 1.217 | 0.98 |
| 326_L | 365_V | 1.210 | 0.98 |
| 351_L | 434_I | 1.199 | 0.98 |
| 357_K | 400_V | 1.195 | 0.98 |
| 186_Q | 212_L | 1.195 | 0.98 |
| 377_E | 426_E | 1.194 | 0.98 |
| 189_L | 205_N | 1.194 | 0.98 |
| 232_K | 236_L | 1.193 | 0.98 |
| 343_V | 347_I | 1.186 | 0.98 |
| 343_V | 413_L | 1.184 | 0.98 |
| 174_K | 203_Q | 1.182 | 0.98 |
| 9_K | 195_D | 1.182 | 0.98 |
| 190_R | 205_N | 1.181 | 0.98 |
| 317_Y | 353_S | 1.163 | 0.97 |
| 177_T | 181_M | 1.162 | 0.97 |
| 421_Y | 432_F | 1.159 | 0.97 |
| 337_A | 436_F | 1.158 | 0.97 |
| 385_Q | 426_E | 1.150 | 0.97 |
| 258_R | 268_D | 1.146 | 0.97 |
| 317_Y | 349_S | 1.136 | 0.97 |
| 287_Q | 403_S | 1.135 | 0.97 |
| 287_Q | 343_V | 1.127 | 0.97 |
| 234_E | 394_D | 1.127 | 0.97 |
| 382_S | 430_L | 1.118 | 0.96 |
| 251_K | 255_E | 1.116 | 0.96 |
| 80_T | 125_Q | 1.113 | 0.96 |
| 170_I | 197_I | 1.112 | 0.96 |
| 314_V | 330_N | 1.111 | 0.96 |
| 235_F | 289_L | 1.110 | 0.96 |
| 376_I | 380_C | 1.108 | 0.96 |
| 310_T | 374_L | 1.106 | 0.96 |
| 211_L | 214_V | 1.102 | 0.96 |
| 391_S | 396_A | 1.100 | 0.96 |
| 262_G | 267_R | 1.100 | 0.96 |
| 235_F | 240_S | 1.099 | 0.96 |
| 249_S | 252_I | 1.088 | 0.96 |
| 422_R | 435_D | 1.088 | 0.96 |
| 309_M | 339_L | 1.088 | 0.96 |
| 235_F | 242_E | 1.087 | 0.96 |
| 273_V | 277_I | 1.087 | 0.96 |
| 397_S | 401_K | 1.082 | 0.96 |
| 374_L | 434_I | 1.080 | 0.95 |
| 410_V | 414_L | 1.075 | 0.95 |
| 307_L | 311_Q | 1.057 | 0.95 |
| 235_F | 395_N | 1.056 | 0.95 |
| 389_A | 411_K | 1.053 | 0.95 |
| 265_K | 268_D | 1.049 | 0.94 |
| 83_G | 86_T | 1.049 | 0.94 |
| 239_A | 288_I | 1.048 | 0.94 |
| 258_R | 275_L | 1.047 | 0.94 |
| 247_L | 282_N | 1.041 | 0.94 |
| 188_R | 205_N | 1.041 | 0.94 |
| 212_L | 216_A | 1.040 | 0.94 |
| 352_I | 376_I | 1.039 | 0.94 |
| 163_A | 167_V | 1.030 | 0.94 |
| 360_V | 363_G | 1.028 | 0.94 |
| 173_I | 204_I | 1.027 | 0.94 |
| 274_A | 277_I | 1.025 | 0.93 |
| 301_R | 418_K | 1.024 | 0.93 |
| 243_L | 281_L | 1.022 | 0.93 |
| 170_I | 200_L | 1.021 | 0.93 |
| 383_E | 425_M | 1.020 | 0.93 |
| 301_R | 417_E | 1.017 | 0.93 |
| 251_K | 278_V | 1.017 | 0.93 |
| 164_R | 171_L | 1.017 | 0.93 |
| 393_S | 411_K | 1.012 | 0.93 |
| 387_K | 391_S | 1.011 | 0.93 |
| 171_L | 174_K | 1.004 | 0.93 |
| 301_R | 338_Y | 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 | |
| 4i5sA | 2 | 0.6222 | 100 | 0.442 | Contact Map |
| 4bixA | 2 | 0.5045 | 100 | 0.495 | Contact Map |
| 4ctiA | 4 | 0.5068 | 100 | 0.537 | Contact Map |
| 4mpcA | 1 | 0.6742 | 100 | 0.546 | Contact Map |
| 1y8oA | 1 | 0.6674 | 100 | 0.547 | Contact Map |
| 2e0aA | 2 | 0.6742 | 100 | 0.549 | Contact Map |
| 2c2aA | 1 | 0.509 | 100 | 0.565 | Contact Map |
| 4ew8A | 2 | 0.5068 | 100 | 0.566 | Contact Map |
| 2q8gA | 1 | 0.6697 | 100 | 0.566 | Contact Map |
| 3jz3A | 2 | 0.3552 | 100 | 0.583 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)