| GcCGT |
| ID: | 1704863466 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 483 (466) | ||
| Sequences: | 4533 (2868.8) | ||
| Seq/Len: | 9.727 | ||
| Nf(neff/√len): | 132.9 |
HHblits Results: (2016_02)
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 |
| 225_F | 449_A | 4.839 | 1.00 |
| 361_A | 429_I | 4.625 | 1.00 |
| 107_P | 138_S | 4.116 | 1.00 |
| 364_T | 381_V | 4.089 | 1.00 |
| 306_L | 337_K | 4.031 | 1.00 |
| 14_L | 30_G | 3.875 | 1.00 |
| 441_N | 444_K | 3.509 | 1.00 |
| 277_R | 311_S | 3.463 | 1.00 |
| 125_L | 132_V | 3.297 | 1.00 |
| 397_L | 404_G | 3.189 | 1.00 |
| 304_G | 426_L | 3.156 | 1.00 |
| 423_E | 427_R | 2.974 | 1.00 |
| 221_L | 466_F | 2.939 | 1.00 |
| 382_I | 429_I | 2.840 | 1.00 |
| 304_G | 422_V | 2.817 | 1.00 |
| 375_I | 403_V | 2.804 | 1.00 |
| 285_V | 305_I | 2.760 | 1.00 |
| 283_V | 361_A | 2.620 | 1.00 |
| 447_K | 451_E | 2.518 | 1.00 |
| 307_N | 423_E | 2.517 | 1.00 |
| 279_P | 357_P | 2.460 | 1.00 |
| 144_A | 219_C | 2.403 | 1.00 |
| 300_E | 419_R | 2.308 | 1.00 |
| 226_Y | 234_D | 2.296 | 1.00 |
| 151_C | 229_E | 2.275 | 1.00 |
| 153_S | 389_D | 2.220 | 1.00 |
| 44_A | 49_G | 2.218 | 1.00 |
| 402_K | 441_N | 2.210 | 1.00 |
| 43_S | 109_M | 2.197 | 1.00 |
| 440_E | 444_K | 2.157 | 1.00 |
| 303_Y | 419_R | 2.152 | 1.00 |
| 11_H | 41_T | 2.142 | 1.00 |
| 375_I | 442_A | 2.132 | 1.00 |
| 21_G | 25_P | 2.123 | 1.00 |
| 224_T | 233_I | 2.117 | 1.00 |
| 334_F | 338_A | 2.116 | 1.00 |
| 374_A | 381_V | 2.111 | 1.00 |
| 390_Q | 393_N | 2.077 | 1.00 |
| 144_A | 466_F | 2.049 | 1.00 |
| 125_L | 143_C | 2.047 | 1.00 |
| 186_K | 189_E | 1.965 | 1.00 |
| 313_L | 353_V | 1.959 | 1.00 |
| 375_I | 445_W | 1.947 | 1.00 |
| 347_W | 350_Q | 1.902 | 1.00 |
| 132_V | 143_C | 1.870 | 1.00 |
| 382_I | 425_A | 1.821 | 1.00 |
| 366_C | 383_T | 1.814 | 1.00 |
| 443_L | 446_K | 1.791 | 1.00 |
| 310_V | 431_S | 1.751 | 1.00 |
| 298_V | 316_L | 1.740 | 1.00 |
| 43_S | 106_L | 1.739 | 1.00 |
| 283_V | 363_L | 1.726 | 1.00 |
| 405_V | 429_I | 1.714 | 1.00 |
| 383_T | 394_A | 1.694 | 1.00 |
| 244_P | 462_N | 1.688 | 1.00 |
| 310_V | 427_R | 1.680 | 1.00 |
| 280_S | 439_K | 1.678 | 1.00 |
| 291_V | 386_Q | 1.657 | 1.00 |
| 227_E | 451_E | 1.651 | 1.00 |
| 270_C | 349_P | 1.625 | 1.00 |
| 444_K | 448_A | 1.620 | 1.00 |
| 21_G | 369_N | 1.619 | 1.00 |
| 464_V | 468_E | 1.615 | 1.00 |
| 355_A | 377_S | 1.602 | 1.00 |
| 15_V | 132_V | 1.589 | 1.00 |
| 448_A | 451_E | 1.586 | 1.00 |
| 424_R | 428_E | 1.583 | 1.00 |
| 452_T | 458_N | 1.573 | 1.00 |
| 428_E | 434_K | 1.572 | 1.00 |
| 272_E | 275_D | 1.561 | 1.00 |
| 243_K | 469_E | 1.537 | 1.00 |
| 333_E | 336_E | 1.536 | 1.00 |
| 13_F | 43_S | 1.533 | 1.00 |
| 123_L | 136_A | 1.532 | 1.00 |
| 110_L | 123_L | 1.525 | 1.00 |
| 227_E | 448_A | 1.524 | 1.00 |
| 306_L | 333_E | 1.511 | 1.00 |
| 285_V | 304_G | 1.506 | 1.00 |
| 362_F | 370_S | 1.494 | 1.00 |
| 275_D | 356_H | 1.492 | 1.00 |
| 371_T | 397_L | 1.481 | 1.00 |
| 302_A | 331_P | 1.475 | 1.00 |
| 295_Q | 299_T | 1.471 | 1.00 |
| 29_L | 221_L | 1.471 | 1.00 |
| 137_D | 216_K | 1.456 | 1.00 |
| 148_V | 390_Q | 1.449 | 1.00 |
| 226_Y | 237_T | 1.445 | 1.00 |
| 304_G | 308_S | 1.439 | 1.00 |
| 28_R | 351_E | 1.437 | 1.00 |
| 421_E | 424_R | 1.435 | 1.00 |
| 302_A | 314_W | 1.428 | 1.00 |
| 36_K | 464_V | 1.398 | 0.99 |
| 427_R | 431_S | 1.397 | 0.99 |
| 297_Q | 384_F | 1.396 | 0.99 |
| 137_D | 218_F | 1.389 | 0.99 |
| 304_G | 419_R | 1.378 | 0.99 |
| 370_S | 373_E | 1.371 | 0.99 |
| 12_I | 122_C | 1.371 | 0.99 |
| 14_L | 26_M | 1.370 | 0.99 |
| 302_A | 334_F | 1.366 | 0.99 |
| 334_F | 337_K | 1.360 | 0.99 |
| 151_C | 224_T | 1.354 | 0.99 |
| 136_A | 143_C | 1.353 | 0.99 |
| 108_I | 112_K | 1.344 | 0.99 |
| 19_G | 290_V | 1.322 | 0.99 |
| 333_E | 337_K | 1.317 | 0.99 |
| 395_K | 399_E | 1.307 | 0.99 |
| 345_V | 348_S | 1.305 | 0.99 |
| 363_L | 382_I | 1.296 | 0.99 |
| 465_E | 468_E | 1.287 | 0.99 |
| 331_P | 334_F | 1.282 | 0.99 |
| 421_E | 425_A | 1.275 | 0.99 |
| 308_S | 312_F | 1.275 | 0.99 |
| 350_Q | 354_L | 1.269 | 0.99 |
| 146_L | 248_L | 1.259 | 0.99 |
| 449_A | 459_S | 1.246 | 0.98 |
| 371_T | 381_V | 1.246 | 0.98 |
| 287_V | 363_L | 1.244 | 0.98 |
| 153_S | 157_Y | 1.242 | 0.98 |
| 463_L | 467_I | 1.235 | 0.98 |
| 224_T | 229_E | 1.233 | 0.98 |
| 15_V | 106_L | 1.232 | 0.98 |
| 367_G | 370_S | 1.231 | 0.98 |
| 403_V | 445_W | 1.231 | 0.98 |
| 21_G | 24_N | 1.229 | 0.98 |
| 15_V | 129_V | 1.225 | 0.98 |
| 12_I | 40_V | 1.222 | 0.98 |
| 350_Q | 356_H | 1.222 | 0.98 |
| 302_A | 333_E | 1.215 | 0.98 |
| 394_A | 406_R | 1.211 | 0.98 |
| 452_T | 459_S | 1.208 | 0.98 |
| 384_F | 417_I | 1.208 | 0.98 |
| 366_C | 371_T | 1.206 | 0.98 |
| 461_R | 465_E | 1.205 | 0.98 |
| 233_I | 244_P | 1.203 | 0.98 |
| 442_A | 446_K | 1.202 | 0.98 |
| 312_F | 342_G | 1.201 | 0.98 |
| 269_D | 272_E | 1.193 | 0.98 |
| 108_I | 111_K | 1.191 | 0.98 |
| 280_S | 443_L | 1.187 | 0.98 |
| 437_E | 440_E | 1.187 | 0.98 |
| 306_L | 334_F | 1.177 | 0.97 |
| 367_G | 373_E | 1.174 | 0.97 |
| 383_T | 404_G | 1.173 | 0.97 |
| 444_K | 447_K | 1.164 | 0.97 |
| 10_L | 121_S | 1.164 | 0.97 |
| 443_L | 447_K | 1.160 | 0.97 |
| 16_C | 26_M | 1.152 | 0.97 |
| 107_P | 111_K | 1.151 | 0.97 |
| 279_P | 358_A | 1.149 | 0.97 |
| 338_A | 341_R | 1.144 | 0.97 |
| 440_E | 443_L | 1.141 | 0.97 |
| 278_P | 311_S | 1.139 | 0.97 |
| 366_C | 397_L | 1.138 | 0.97 |
| 330_L | 334_F | 1.133 | 0.97 |
| 365_H | 373_E | 1.132 | 0.97 |
| 449_A | 452_T | 1.127 | 0.96 |
| 363_L | 422_V | 1.125 | 0.96 |
| 44_A | 48_V | 1.124 | 0.96 |
| 426_L | 429_I | 1.122 | 0.96 |
| 368_W | 393_N | 1.120 | 0.96 |
| 395_K | 400_E | 1.116 | 0.96 |
| 107_P | 139_L | 1.115 | 0.96 |
| 435_A | 439_K | 1.115 | 0.96 |
| 382_I | 405_V | 1.114 | 0.96 |
| 300_E | 304_G | 1.113 | 0.96 |
| 391_V | 394_A | 1.108 | 0.96 |
| 272_E | 276_T | 1.107 | 0.96 |
| 111_K | 138_S | 1.101 | 0.96 |
| 133_A | 143_C | 1.094 | 0.96 |
| 45_P | 48_V | 1.090 | 0.96 |
| 192_D | 391_V | 1.078 | 0.95 |
| 307_N | 419_R | 1.077 | 0.95 |
| 438_V | 441_N | 1.074 | 0.95 |
| 283_V | 430_T | 1.073 | 0.95 |
| 151_C | 222_M | 1.071 | 0.95 |
| 365_H | 369_N | 1.069 | 0.95 |
| 145_T | 220_I | 1.067 | 0.95 |
| 313_L | 343_K | 1.065 | 0.95 |
| 378_G | 442_A | 1.062 | 0.95 |
| 191_P | 241_P | 1.060 | 0.95 |
| 283_V | 426_L | 1.059 | 0.95 |
| 361_A | 382_I | 1.059 | 0.95 |
| 350_Q | 373_E | 1.056 | 0.94 |
| 106_L | 110_L | 1.055 | 0.94 |
| 403_V | 442_A | 1.053 | 0.94 |
| 287_V | 301_M | 1.047 | 0.94 |
| 226_Y | 244_P | 1.046 | 0.94 |
| 354_L | 373_E | 1.046 | 0.94 |
| 223_D | 372_Q | 1.042 | 0.94 |
| 33_F | 124_I | 1.037 | 0.94 |
| 315_V | 345_V | 1.034 | 0.94 |
| 466_F | 470_V | 1.028 | 0.93 |
| 12_I | 38_L | 1.027 | 0.93 |
| 468_E | 472_R | 1.027 | 0.93 |
| 223_D | 368_W | 1.027 | 0.93 |
| 276_T | 340_D | 1.022 | 0.93 |
| 299_T | 419_R | 1.022 | 0.93 |
| 28_R | 31_K | 1.020 | 0.93 |
| 304_G | 315_V | 1.020 | 0.93 |
| 356_H | 362_F | 1.018 | 0.93 |
| 396_F | 401_F | 1.014 | 0.93 |
| 402_K | 440_E | 1.011 | 0.93 |
| 225_F | 452_T | 1.003 | 0.92 |
| 365_H | 370_S | 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 | |
| 2pq6A | 1 | 0.882 | 100 | 0.329 | Contact Map |
| 2c1xA | 1 | 0.882 | 100 | 0.379 | Contact Map |
| 2vchA | 1 | 0.9151 | 100 | 0.391 | Contact Map |
| 2acvA | 2 | 0.9172 | 100 | 0.418 | Contact Map |
| 3hbfA | 1 | 0.9027 | 100 | 0.421 | Contact Map |
| 4relA | 1 | 0.911 | 100 | 0.465 | Contact Map |
| 2iyaA | 2 | 0.7888 | 100 | 0.561 | Contact Map |
| 2iyfA | 2 | 0.8054 | 100 | 0.588 | Contact Map |
| 3rscA | 2 | 0.8157 | 100 | 0.589 | Contact Map |
| 3ia7A | 2 | 0.8157 | 100 | 0.604 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)