| ling-y |
| ID: | 1419864716 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 442 (436) | ||
| Sequences: | 5514 (4475.4) | ||
| Seq/Len: | 12.647 | ||
| Nf(neff/√len): | 214.3 |
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: 12.647).
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 | 4.546 | 1.00 |
| 423_F | 432_F | 4.391 | 1.00 |
| 411_K | 415_E | 4.337 | 1.00 |
| 377_E | 431_T | 4.109 | 1.00 |
| 347_I | 413_L | 3.709 | 1.00 |
| 392_F | 421_Y | 3.610 | 1.00 |
| 410_V | 421_Y | 3.543 | 1.00 |
| 359_S | 379_S | 3.448 | 1.00 |
| 251_K | 279_D | 3.401 | 1.00 |
| 419_L | 436_F | 3.397 | 1.00 |
| 254_I | 274_A | 3.336 | 1.00 |
| 388_L | 425_M | 3.176 | 1.00 |
| 359_S | 363_G | 3.099 | 1.00 |
| 414_L | 419_L | 3.088 | 1.00 |
| 414_L | 434_I | 2.965 | 1.00 |
| 413_L | 417_E | 2.928 | 1.00 |
| 390_Q | 393_S | 2.927 | 1.00 |
| 347_I | 414_L | 2.893 | 1.00 |
| 425_M | 430_L | 2.855 | 1.00 |
| 339_L | 344_M | 2.691 | 1.00 |
| 234_E | 238_G | 2.460 | 1.00 |
| 193_S | 198_G | 2.382 | 1.00 |
| 339_L | 417_E | 2.378 | 1.00 |
| 391_S | 423_F | 2.325 | 1.00 |
| 302_E | 341_P | 2.282 | 1.00 |
| 310_T | 348_L | 2.266 | 1.00 |
| 384_E | 387_K | 2.257 | 1.00 |
| 383_E | 391_S | 2.236 | 1.00 |
| 353_S | 357_K | 2.198 | 1.00 |
| 423_F | 430_L | 2.177 | 1.00 |
| 331_S | 368_G | 2.161 | 1.00 |
| 83_G | 87_E | 2.153 | 1.00 |
| 305_D | 308_Q | 2.153 | 1.00 |
| 392_F | 432_F | 2.137 | 1.00 |
| 405_M | 409_V | 2.127 | 1.00 |
| 424_E | 433_F | 2.126 | 1.00 |
| 347_I | 434_I | 2.123 | 1.00 |
| 420_A | 435_D | 2.108 | 1.00 |
| 180_M | 207_L | 2.096 | 1.00 |
| 350_N | 410_V | 2.084 | 1.00 |
| 251_K | 282_N | 2.084 | 1.00 |
| 368_G | 375_F | 2.060 | 1.00 |
| 373_E | 435_D | 2.055 | 1.00 |
| 368_G | 377_E | 2.024 | 1.00 |
| 312_N | 341_P | 2.017 | 1.00 |
| 188_R | 209_Q | 2.010 | 1.00 |
| 422_R | 433_F | 2.003 | 1.00 |
| 304_I | 339_L | 1.989 | 1.00 |
| 313_L | 352_I | 1.983 | 1.00 |
| 235_F | 239_A | 1.972 | 1.00 |
| 424_E | 431_T | 1.949 | 1.00 |
| 343_V | 346_L | 1.926 | 1.00 |
| 388_L | 423_F | 1.925 | 1.00 |
| 179_R | 184_D | 1.889 | 1.00 |
| 314_V | 367_I | 1.889 | 1.00 |
| 363_G | 379_S | 1.886 | 1.00 |
| 366_R | 377_E | 1.877 | 1.00 |
| 419_L | 437_P | 1.840 | 1.00 |
| 303_T | 336_Q | 1.826 | 1.00 |
| 375_F | 433_F | 1.825 | 1.00 |
| 351_L | 432_F | 1.824 | 1.00 |
| 414_L | 421_Y | 1.815 | 1.00 |
| 321_A | 356_I | 1.812 | 1.00 |
| 282_N | 286_L | 1.811 | 1.00 |
| 392_F | 411_K | 1.799 | 1.00 |
| 254_I | 278_V | 1.798 | 1.00 |
| 195_D | 198_G | 1.792 | 1.00 |
| 387_K | 396_A | 1.769 | 1.00 |
| 398_R | 401_K | 1.763 | 1.00 |
| 351_L | 410_V | 1.731 | 1.00 |
| 327_Q | 364_L | 1.721 | 1.00 |
| 312_N | 345_K | 1.692 | 1.00 |
| 329_D | 366_R | 1.688 | 1.00 |
| 391_S | 432_F | 1.673 | 1.00 |
| 274_A | 278_V | 1.671 | 1.00 |
| 304_I | 344_M | 1.667 | 1.00 |
| 375_F | 431_T | 1.667 | 1.00 |
| 378_N | 381_S | 1.661 | 1.00 |
| 348_L | 374_L | 1.651 | 1.00 |
| 414_L | 436_F | 1.648 | 1.00 |
| 387_K | 390_Q | 1.639 | 1.00 |
| 364_L | 379_S | 1.634 | 1.00 |
| 238_G | 394_D | 1.613 | 1.00 |
| 283_H | 342_S | 1.597 | 1.00 |
| 392_F | 423_F | 1.589 | 1.00 |
| 254_I | 271_L | 1.579 | 1.00 |
| 303_T | 338_Y | 1.561 | 1.00 |
| 255_E | 275_L | 1.533 | 1.00 |
| 329_D | 364_L | 1.533 | 1.00 |
| 42_Q | 108_F | 1.508 | 1.00 |
| 177_T | 203_Q | 1.500 | 1.00 |
| 426_E | 429_R | 1.464 | 1.00 |
| 344_M | 417_E | 1.460 | 1.00 |
| 188_R | 208_Y | 1.451 | 1.00 |
| 185_S | 188_R | 1.435 | 1.00 |
| 390_Q | 396_A | 1.429 | 1.00 |
| 263_R | 266_D | 1.429 | 1.00 |
| 242_E | 346_L | 1.412 | 1.00 |
| 388_L | 392_F | 1.412 | 1.00 |
| 415_E | 420_A | 1.410 | 1.00 |
| 383_E | 430_L | 1.409 | 1.00 |
| 258_R | 272_G | 1.389 | 0.99 |
| 247_L | 278_V | 1.382 | 0.99 |
| 177_T | 204_I | 1.382 | 0.99 |
| 366_R | 379_S | 1.381 | 0.99 |
| 305_D | 336_Q | 1.375 | 0.99 |
| 191_V | 202_E | 1.370 | 0.99 |
| 378_N | 430_L | 1.355 | 0.99 |
| 250_L | 278_V | 1.355 | 0.99 |
| 188_R | 212_L | 1.354 | 0.99 |
| 347_I | 410_V | 1.353 | 0.99 |
| 173_I | 201_K | 1.348 | 0.99 |
| 348_L | 352_I | 1.346 | 0.99 |
| 358_H | 381_S | 1.326 | 0.99 |
| 305_D | 334_H | 1.324 | 0.99 |
| 309_M | 313_L | 1.324 | 0.99 |
| 159_A | 163_A | 1.322 | 0.99 |
| 264_Y | 267_R | 1.319 | 0.99 |
| 321_A | 365_V | 1.312 | 0.99 |
| 335_Q | 369_E | 1.307 | 0.99 |
| 194_K | 198_G | 1.301 | 0.99 |
| 343_V | 416_H | 1.295 | 0.99 |
| 174_K | 199_N | 1.292 | 0.99 |
| 180_M | 208_Y | 1.289 | 0.99 |
| 378_N | 429_R | 1.281 | 0.99 |
| 178_R | 199_N | 1.278 | 0.99 |
| 251_K | 275_L | 1.276 | 0.99 |
| 204_I | 207_L | 1.276 | 0.99 |
| 250_L | 274_A | 1.262 | 0.99 |
| 173_I | 189_L | 1.260 | 0.99 |
| 316_D | 345_K | 1.245 | 0.98 |
| 340_N | 343_V | 1.245 | 0.98 |
| 385_Q | 425_M | 1.240 | 0.98 |
| 385_Q | 388_L | 1.238 | 0.98 |
| 7_F | 164_R | 1.233 | 0.98 |
| 89_K | 92_V | 1.233 | 0.98 |
| 331_S | 366_R | 1.225 | 0.98 |
| 352_I | 367_I | 1.213 | 0.98 |
| 377_E | 426_E | 1.212 | 0.98 |
| 186_Q | 212_L | 1.210 | 0.98 |
| 347_I | 417_E | 1.208 | 0.98 |
| 326_L | 365_V | 1.203 | 0.98 |
| 357_K | 400_V | 1.200 | 0.98 |
| 351_L | 434_I | 1.197 | 0.98 |
| 9_K | 195_D | 1.192 | 0.98 |
| 190_R | 205_N | 1.191 | 0.98 |
| 189_L | 205_N | 1.191 | 0.98 |
| 174_K | 203_Q | 1.190 | 0.98 |
| 343_V | 347_I | 1.190 | 0.98 |
| 343_V | 413_L | 1.186 | 0.98 |
| 232_K | 236_L | 1.183 | 0.98 |
| 385_Q | 426_E | 1.175 | 0.98 |
| 317_Y | 353_S | 1.166 | 0.97 |
| 258_R | 268_D | 1.157 | 0.97 |
| 177_T | 181_M | 1.148 | 0.97 |
| 421_Y | 432_F | 1.148 | 0.97 |
| 317_Y | 349_S | 1.139 | 0.97 |
| 251_K | 255_E | 1.131 | 0.97 |
| 234_E | 394_D | 1.126 | 0.97 |
| 170_I | 197_I | 1.126 | 0.97 |
| 314_V | 330_N | 1.125 | 0.97 |
| 287_Q | 403_S | 1.124 | 0.97 |
| 382_S | 430_L | 1.118 | 0.96 |
| 337_A | 436_F | 1.118 | 0.96 |
| 287_Q | 343_V | 1.113 | 0.96 |
| 80_T | 125_Q | 1.112 | 0.96 |
| 235_F | 289_L | 1.108 | 0.96 |
| 422_R | 435_D | 1.106 | 0.96 |
| 262_G | 267_R | 1.105 | 0.96 |
| 211_L | 214_V | 1.101 | 0.96 |
| 309_M | 339_L | 1.099 | 0.96 |
| 273_V | 277_I | 1.098 | 0.96 |
| 391_S | 396_A | 1.095 | 0.96 |
| 376_I | 380_C | 1.095 | 0.96 |
| 235_F | 240_S | 1.085 | 0.96 |
| 307_L | 311_Q | 1.084 | 0.96 |
| 249_S | 252_I | 1.083 | 0.96 |
| 265_K | 268_D | 1.080 | 0.95 |
| 397_S | 401_K | 1.080 | 0.95 |
| 410_V | 414_L | 1.078 | 0.95 |
| 235_F | 242_E | 1.075 | 0.95 |
| 310_T | 374_L | 1.075 | 0.95 |
| 374_L | 434_I | 1.072 | 0.95 |
| 389_A | 411_K | 1.062 | 0.95 |
| 258_R | 275_L | 1.058 | 0.95 |
| 212_L | 216_A | 1.056 | 0.95 |
| 83_G | 86_T | 1.053 | 0.95 |
| 247_L | 282_N | 1.051 | 0.94 |
| 239_A | 288_I | 1.045 | 0.94 |
| 188_R | 205_N | 1.042 | 0.94 |
| 235_F | 395_N | 1.040 | 0.94 |
| 393_S | 411_K | 1.039 | 0.94 |
| 360_V | 363_G | 1.032 | 0.94 |
| 301_R | 418_K | 1.031 | 0.94 |
| 325_E | 361_P | 1.028 | 0.94 |
| 171_L | 174_K | 1.027 | 0.94 |
| 301_R | 417_E | 1.025 | 0.93 |
| 163_A | 167_V | 1.025 | 0.93 |
| 352_I | 376_I | 1.024 | 0.93 |
| 243_L | 281_L | 1.024 | 0.93 |
| 387_K | 391_S | 1.024 | 0.93 |
| 251_K | 278_V | 1.024 | 0.93 |
| 173_I | 204_I | 1.022 | 0.93 |
| 274_A | 277_I | 1.021 | 0.93 |
| 170_I | 200_L | 1.016 | 0.93 |
| 301_R | 338_Y | 1.002 | 0.92 |
| 383_E | 425_M | 1.002 | 0.92 |
| 138_Q | 142_Q | 1.001 | 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 | 0.444 | Contact Map |
| 4bixA | 2 | 0.5045 | 100 | 0.496 | Contact Map |
| 4ctiA | 4 | 0.5068 | 100 | 0.539 | Contact Map |
| 4mpcA | 1 | 0.6742 | 100 | 0.545 | Contact Map |
| 1y8oA | 1 | 0.6674 | 100 | 0.547 | Contact Map |
| 2e0aA | 2 | 0.6742 | 100 | 0.55 | 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 | 0.568 | Contact Map |
| 3jz3A | 2 | 0.3552 | 100 | 0.581 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)