| 1occ-A |
| ID: | 1408346088 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 514 (510) | ||
| Sequences: | 3212 (1226.8) | ||
| Seq/Len: | 6.298 | ||
| Nf(neff/√len): | 54.3 |
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: 6.298).
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 |
| 428_Q | 454_S | 4.098 | 1.00 |
| 257_I | 391_G | 3.674 | 1.00 |
| 336_P | 410_A | 3.668 | 1.00 |
| 22_F | 102_F | 3.600 | 1.00 |
| 23_G | 73_I | 3.343 | 1.00 |
| 250_G | 388_A | 3.138 | 1.00 |
| 336_P | 407_D | 3.018 | 1.00 |
| 397_F | 475_A | 2.878 | 1.00 |
| 270_Y | 274_V | 2.860 | 1.00 |
| 33_L | 57_V | 2.621 | 1.00 |
| 83_V | 168_I | 2.617 | 1.00 |
| 253_M | 392_G | 2.592 | 1.00 |
| 358_L | 373_V | 2.592 | 1.00 |
| 178_Q | 181_T | 2.560 | 1.00 |
| 177_S | 180_Q | 2.555 | 1.00 |
| 416_I | 464_A | 2.539 | 1.00 |
| 262_S | 327_L | 2.536 | 1.00 |
| 423_M | 457_G | 2.504 | 1.00 |
| 168_I | 189_M | 2.487 | 1.00 |
| 26_A | 109_F | 2.478 | 1.00 |
| 190_I | 281_G | 2.326 | 1.00 |
| 258_V | 345_I | 2.280 | 1.00 |
| 124_T | 143_V | 2.215 | 1.00 |
| 17_T | 81_W | 2.194 | 1.00 |
| 128_V | 231_Y | 2.179 | 1.00 |
| 183_L | 267_P | 2.167 | 1.00 |
| 379_Y | 422_N | 2.163 | 1.00 |
| 63_F | 128_V | 2.100 | 1.00 |
| 327_L | 338_M | 2.081 | 1.00 |
| 187_S | 277_M | 2.064 | 1.00 |
| 394_V | 413_H | 2.037 | 1.00 |
| 5_R | 14_D | 2.001 | 1.00 |
| 261_Y | 395_H | 2.000 | 1.00 |
| 390_M | 468_M | 1.938 | 1.00 |
| 238_F | 242_E | 1.922 | 1.00 |
| 423_M | 453_I | 1.861 | 1.00 |
| 413_H | 417_M | 1.844 | 1.00 |
| 45_G | 442_D | 1.834 | 1.00 |
| 169_I | 178_Q | 1.831 | 1.00 |
| 340_W | 413_H | 1.820 | 1.00 |
| 257_I | 392_G | 1.811 | 1.00 |
| 420_G | 460_I | 1.787 | 1.00 |
| 409_W | 470_F | 1.784 | 1.00 |
| 408_T | 412_I | 1.734 | 1.00 |
| 416_I | 467_L | 1.723 | 1.00 |
| 406_N | 474_E | 1.703 | 1.00 |
| 75_I | 161_A | 1.703 | 1.00 |
| 150_L | 206_I | 1.699 | 1.00 |
| 456_M | 460_I | 1.679 | 1.00 |
| 69_M | 386_V | 1.660 | 1.00 |
| 327_L | 342_L | 1.656 | 1.00 |
| 422_N | 426_F | 1.648 | 1.00 |
| 294_T | 368_H | 1.644 | 1.00 |
| 394_V | 410_A | 1.636 | 1.00 |
| 341_A | 391_G | 1.625 | 1.00 |
| 49_G | 57_V | 1.616 | 1.00 |
| 393_F | 468_M | 1.589 | 0.99 |
| 176_M | 182_P | 1.576 | 0.99 |
| 474_E | 480_R | 1.571 | 0.99 |
| 175_A | 180_Q | 1.556 | 0.99 |
| 257_I | 341_A | 1.556 | 0.99 |
| 426_F | 430_F | 1.553 | 0.99 |
| 448_T | 452_T | 1.539 | 0.99 |
| 63_F | 231_Y | 1.539 | 0.99 |
| 496_N | 504_T | 1.538 | 0.99 |
| 169_I | 189_M | 1.533 | 0.99 |
| 144_D | 213_R | 1.532 | 0.99 |
| 412_I | 467_L | 1.528 | 0.99 |
| 343_G | 418_F | 1.521 | 0.99 |
| 239_G | 242_E | 1.520 | 0.99 |
| 251_F | 316_T | 1.512 | 0.99 |
| 261_Y | 337_A | 1.512 | 0.99 |
| 260_Y | 395_H | 1.509 | 0.99 |
| 190_I | 278_M | 1.501 | 0.99 |
| 161_A | 196_L | 1.492 | 0.99 |
| 54_Y | 59_T | 1.485 | 0.99 |
| 9_S | 14_D | 1.481 | 0.99 |
| 176_M | 181_T | 1.480 | 0.99 |
| 195_L | 199_L | 1.479 | 0.99 |
| 255_S | 323_W | 1.479 | 0.99 |
| 343_G | 414_F | 1.469 | 0.99 |
| 169_I | 193_V | 1.467 | 0.99 |
| 63_F | 146_T | 1.456 | 0.99 |
| 332_I | 338_M | 1.456 | 0.99 |
| 29_V | 64_V | 1.453 | 0.99 |
| 379_Y | 426_F | 1.447 | 0.99 |
| 403_Y | 475_A | 1.443 | 0.99 |
| 198_S | 285_F | 1.441 | 0.99 |
| 407_D | 411_K | 1.440 | 0.99 |
| 22_F | 106_P | 1.434 | 0.99 |
| 22_F | 105_L | 1.430 | 0.99 |
| 399_L | 498_C | 1.428 | 0.99 |
| 409_W | 412_I | 1.427 | 0.99 |
| 363_L | 367_L | 1.426 | 0.99 |
| 356_I | 359_A | 1.417 | 0.99 |
| 313_A | 356_I | 1.410 | 0.98 |
| 39_A | 459_F | 1.406 | 0.98 |
| 163_N | 167_T | 1.404 | 0.98 |
| 390_M | 413_H | 1.399 | 0.98 |
| 51_D | 441_S | 1.380 | 0.98 |
| 383_M | 421_V | 1.378 | 0.98 |
| 68_F | 153_A | 1.374 | 0.98 |
| 97_M | 159_L | 1.373 | 0.98 |
| 474_E | 478_S | 1.369 | 0.98 |
| 172_K | 180_Q | 1.358 | 0.98 |
| 413_H | 465_V | 1.352 | 0.98 |
| 122_A | 146_T | 1.350 | 0.98 |
| 470_F | 474_E | 1.344 | 0.98 |
| 420_G | 457_G | 1.338 | 0.98 |
| 112_L | 149_S | 1.331 | 0.98 |
| 28_M | 32_A | 1.329 | 0.98 |
| 247_I | 251_F | 1.327 | 0.98 |
| 283_L | 312_I | 1.320 | 0.97 |
| 413_H | 468_M | 1.314 | 0.97 |
| 353_L | 356_I | 1.304 | 0.97 |
| 282_F | 286_I | 1.298 | 0.97 |
| 52_Q | 56_V | 1.298 | 0.97 |
| 340_W | 394_V | 1.296 | 0.97 |
| 40_E | 45_G | 1.295 | 0.97 |
| 102_F | 106_P | 1.291 | 0.97 |
| 413_H | 464_A | 1.291 | 0.97 |
| 497_G | 501_P | 1.289 | 0.97 |
| 496_N | 505_F | 1.287 | 0.97 |
| 44_P | 448_T | 1.274 | 0.97 |
| 232_Q | 369_D | 1.274 | 0.97 |
| 274_V | 277_M | 1.269 | 0.97 |
| 500_P | 505_F | 1.268 | 0.97 |
| 80_N | 163_N | 1.268 | 0.97 |
| 236_W | 239_G | 1.267 | 0.96 |
| 497_G | 500_P | 1.263 | 0.96 |
| 35_L | 462_L | 1.261 | 0.96 |
| 86_M | 185_V | 1.259 | 0.96 |
| 124_T | 133_A | 1.258 | 0.96 |
| 273_M | 276_A | 1.257 | 0.96 |
| 244_Y | 249_P | 1.240 | 0.96 |
| 503_H | 506_E | 1.240 | 0.96 |
| 172_K | 175_A | 1.239 | 0.96 |
| 185_V | 189_M | 1.238 | 0.96 |
| 161_A | 192_A | 1.238 | 0.96 |
| 280_I | 319_K | 1.226 | 0.96 |
| 403_Y | 479_K | 1.218 | 0.95 |
| 99_N | 103_W | 1.213 | 0.95 |
| 357_V | 372_Y | 1.204 | 0.95 |
| 127_T | 368_H | 1.197 | 0.95 |
| 498_C | 501_P | 1.194 | 0.95 |
| 432_G | 439_R | 1.191 | 0.95 |
| 254_I | 341_A | 1.190 | 0.95 |
| 82_L | 395_H | 1.188 | 0.94 |
| 242_E | 246_L | 1.177 | 0.94 |
| 193_V | 278_M | 1.177 | 0.94 |
| 212_D | 217_T | 1.176 | 0.94 |
| 459_F | 463_T | 1.175 | 0.94 |
| 197_L | 285_F | 1.175 | 0.94 |
| 432_G | 435_G | 1.174 | 0.94 |
| 375_A | 429_H | 1.170 | 0.94 |
| 409_W | 467_L | 1.169 | 0.94 |
| 261_Y | 338_M | 1.164 | 0.94 |
| 11_N | 14_D | 1.158 | 0.93 |
| 388_A | 391_G | 1.158 | 0.93 |
| 428_Q | 431_L | 1.158 | 0.93 |
| 253_M | 257_I | 1.154 | 0.93 |
| 397_F | 401_S | 1.149 | 0.93 |
| 431_L | 450_W | 1.143 | 0.93 |
| 114_A | 145_L | 1.134 | 0.92 |
| 36_L | 57_V | 1.129 | 0.92 |
| 111_L | 145_L | 1.124 | 0.92 |
| 165_I | 189_M | 1.124 | 0.92 |
| 241_P | 244_Y | 1.121 | 0.92 |
| 127_T | 235_F | 1.115 | 0.92 |
| 470_F | 473_W | 1.113 | 0.92 |
| 37_I | 57_V | 1.112 | 0.91 |
| 416_I | 463_T | 1.107 | 0.91 |
| 173_P | 176_M | 1.107 | 0.91 |
| 151_H | 207_T | 1.102 | 0.91 |
| 337_A | 395_H | 1.101 | 0.91 |
| 124_T | 128_V | 1.100 | 0.91 |
| 306_T | 361_S | 1.098 | 0.91 |
| 190_I | 193_V | 1.098 | 0.91 |
| 41_L | 371_Y | 1.096 | 0.91 |
| 53_I | 57_V | 1.096 | 0.91 |
| 451_N | 455_S | 1.096 | 0.91 |
| 340_W | 390_M | 1.095 | 0.91 |
| 82_L | 400_F | 1.094 | 0.91 |
| 254_I | 344_F | 1.092 | 0.90 |
| 261_Y | 335_S | 1.091 | 0.90 |
| 205_G | 231_Y | 1.091 | 0.90 |
| 314_I | 318_V | 1.090 | 0.90 |
| 198_S | 245_I | 1.090 | 0.90 |
| 35_L | 455_S | 1.088 | 0.90 |
| 36_L | 49_G | 1.084 | 0.90 |
| 460_I | 466_M | 1.083 | 0.90 |
| 410_A | 471_I | 1.081 | 0.90 |
| 31_T | 34_S | 1.075 | 0.90 |
| 273_M | 322_S | 1.075 | 0.90 |
| 211_T | 217_T | 1.071 | 0.89 |
| 240_H | 290_H | 1.068 | 0.89 |
| 473_W | 477_A | 1.067 | 0.89 |
| 359_A | 401_S | 1.065 | 0.89 |
| 240_H | 243_V | 1.065 | 0.89 |
| 485_V | 489_T | 1.062 | 0.89 |
| 82_L | 86_M | 1.059 | 0.89 |
| 241_P | 249_P | 1.059 | 0.89 |
| 347_L | 422_N | 1.053 | 0.88 |
| 336_P | 411_K | 1.051 | 0.88 |
| 496_N | 500_P | 1.050 | 0.88 |
| 83_V | 185_V | 1.048 | 0.88 |
| 339_M | 414_F | 1.046 | 0.88 |
| 179_Y | 275_W | 1.045 | 0.88 |
| 273_M | 277_M | 1.044 | 0.88 |
| 339_M | 411_K | 1.040 | 0.87 |
| 492_L | 509_T | 1.039 | 0.87 |
| 38_R | 41_L | 1.039 | 0.87 |
| 449_M | 453_I | 1.038 | 0.87 |
| 263_G | 333_K | 1.038 | 0.87 |
| 466_M | 470_F | 1.038 | 0.87 |
| 424_T | 458_S | 1.036 | 0.87 |
| 316_T | 319_K | 1.035 | 0.87 |
| 486_D | 489_T | 1.034 | 0.87 |
| 417_M | 464_A | 1.032 | 0.87 |
| 397_F | 403_Y | 1.030 | 0.87 |
| 27_G | 34_S | 1.028 | 0.87 |
| 190_I | 274_V | 1.028 | 0.87 |
| 5_R | 9_S | 1.027 | 0.87 |
| 454_S | 457_G | 1.026 | 0.86 |
| 73_I | 389_I | 1.025 | 0.86 |
| 412_I | 416_I | 1.025 | 0.86 |
| 496_N | 501_P | 1.024 | 0.86 |
| 215_L | 500_P | 1.021 | 0.86 |
| 94_F | 166_T | 1.020 | 0.86 |
| 172_K | 211_T | 1.017 | 0.86 |
| 75_I | 81_W | 1.017 | 0.86 |
| 223_A | 227_D | 1.016 | 0.86 |
| 6_W | 18_L | 1.014 | 0.86 |
| 22_F | 26_A | 1.013 | 0.85 |
| 404_T | 482_V | 1.012 | 0.85 |
| 247_I | 385_A | 1.011 | 0.85 |
| 349_T | 384_G | 1.010 | 0.85 |
| 327_L | 330_G | 1.010 | 0.85 |
| 58_V | 63_F | 1.010 | 0.85 |
| 130_P | 231_Y | 1.009 | 0.85 |
| 74_M | 250_G | 1.009 | 0.85 |
| 403_Y | 476_F | 1.005 | 0.85 |
| 482_V | 498_C | 1.005 | 0.85 |
| 240_H | 376_H | 1.004 | 0.85 |
| 259_T | 267_P | 1.004 | 0.85 |
| 12_H | 16_G | 1.003 | 0.85 |
| 358_L | 367_L | 1.003 | 0.85 |
| 18_L | 102_F | 1.003 | 0.85 |
| 437_P | 440_Y | 1.000 | 0.84 |
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 | |
| 1v54A | 2 | 0.9981 | 100 | 0.036 | Contact Map |
| 1fftA | 2 | 0.9611 | 100 | 0.043 | Contact Map |
| 2yevA | 2 | 0.9922 | 100 | 0.054 | Contact Map |
| 2gsmA | 2 | 0.9728 | 100 | 0.065 | Contact Map |
| 3s8fA | 1 | 0.9475 | 100 | 0.265 | Contact Map |
| 3ayfA | 1 | 0.8755 | 100 | 0.323 | Contact Map |
| 3wfdB | 1 | 0.8191 | 100 | 0.328 | Contact Map |
| 3mk7A | 4 | 0.8677 | 100 | 0.336 | Contact Map |
| 2laqA | 1 | 0.0467 | 10.5 | 0.981 | Contact Map |
| 2l0nA | 1 | 0.0584 | 7.9 | 0.982 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)