| VO |
| ID: | 1419606941 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 502 (464) | ||
| Sequences: | 15720 (12173.3) | ||
| Seq/Len: | 33.879 | ||
| Nf(neff/√len): | 565.1 |
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: 33.879).
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 |
| 407_D | 410_N | 4.540 | 1.00 |
| 354_L | 417_E | 4.362 | 1.00 |
| 407_D | 412_K | 3.815 | 1.00 |
| 323_I | 351_Y | 3.420 | 1.00 |
| 313_A | 454_L | 3.353 | 1.00 |
| 329_A | 333_E | 3.342 | 1.00 |
| 252_K | 288_N | 3.341 | 1.00 |
| 327_A | 355_V | 3.240 | 1.00 |
| 377_E | 387_V | 3.238 | 1.00 |
| 325_A | 329_A | 3.177 | 1.00 |
| 313_A | 359_T | 3.092 | 1.00 |
| 251_H | 268_D | 3.079 | 1.00 |
| 339_E | 345_D | 2.837 | 1.00 |
| 327_A | 458_L | 2.836 | 1.00 |
| 400_R | 409_D | 2.772 | 1.00 |
| 326_K | 351_Y | 2.754 | 1.00 |
| 326_K | 414_E | 2.748 | 1.00 |
| 316_Q | 363_H | 2.730 | 1.00 |
| 328_Q | 332_R | 2.642 | 1.00 |
| 374_C | 385_I | 2.626 | 1.00 |
| 328_Q | 497_Y | 2.596 | 1.00 |
| 457_L | 463_W | 2.584 | 1.00 |
| 44_S | 48_M | 2.540 | 1.00 |
| 97_F | 378_T | 2.539 | 1.00 |
| 462_D | 495_T | 2.497 | 1.00 |
| 353_K | 451_Y | 2.473 | 1.00 |
| 379_E | 382_G | 2.459 | 1.00 |
| 177_F | 453_P | 2.437 | 1.00 |
| 377_E | 384_T | 2.390 | 1.00 |
| 328_Q | 462_D | 2.371 | 1.00 |
| 402_P | 408_A | 2.366 | 1.00 |
| 245_E | 292_K | 2.306 | 1.00 |
| 313_A | 317_M | 2.302 | 1.00 |
| 324_L | 462_D | 2.276 | 1.00 |
| 325_A | 462_D | 2.261 | 1.00 |
| 161_R | 460_H | 2.209 | 1.00 |
| 351_Y | 414_E | 2.205 | 1.00 |
| 309_T | 450_V | 2.203 | 1.00 |
| 464_K | 495_T | 2.194 | 1.00 |
| 174_L | 310_L | 2.160 | 1.00 |
| 379_E | 384_T | 2.151 | 1.00 |
| 174_L | 314_M | 2.143 | 1.00 |
| 40_P | 43_G | 2.139 | 1.00 |
| 80_V | 89_V | 2.102 | 1.00 |
| 327_A | 352_L | 2.098 | 1.00 |
| 161_R | 461_F | 2.093 | 1.00 |
| 355_V | 411_F | 2.076 | 1.00 |
| 318_M | 324_L | 2.027 | 1.00 |
| 464_K | 493_V | 2.022 | 1.00 |
| 58_R | 62_K | 1.992 | 1.00 |
| 356_I | 450_V | 1.991 | 1.00 |
| 386_P | 389_T | 1.967 | 1.00 |
| 331_V | 455_A | 1.965 | 1.00 |
| 362_L | 400_R | 1.962 | 1.00 |
| 313_A | 355_V | 1.961 | 1.00 |
| 39_L | 42_L | 1.960 | 1.00 |
| 38_K | 44_S | 1.943 | 1.00 |
| 42_L | 47_H | 1.940 | 1.00 |
| 154_L | 456_Q | 1.917 | 1.00 |
| 249_N | 253_K | 1.895 | 1.00 |
| 332_R | 497_Y | 1.895 | 1.00 |
| 96_A | 376_E | 1.892 | 1.00 |
| 325_A | 328_Q | 1.885 | 1.00 |
| 151_D | 184_R | 1.864 | 1.00 |
| 78_V | 389_T | 1.854 | 1.00 |
| 354_L | 414_E | 1.832 | 1.00 |
| 249_N | 288_N | 1.826 | 1.00 |
| 71_Q | 76_S | 1.814 | 1.00 |
| 86_A | 398_L | 1.800 | 1.00 |
| 66_P | 82_S | 1.785 | 1.00 |
| 56_V | 59_D | 1.777 | 1.00 |
| 324_L | 328_Q | 1.774 | 1.00 |
| 67_L | 80_V | 1.764 | 1.00 |
| 463_W | 494_A | 1.763 | 1.00 |
| 35_G | 44_S | 1.760 | 1.00 |
| 331_V | 349_L | 1.749 | 1.00 |
| 446_G | 450_V | 1.749 | 1.00 |
| 316_Q | 320_N | 1.743 | 1.00 |
| 69_H | 76_S | 1.734 | 1.00 |
| 35_G | 64_Y | 1.728 | 1.00 |
| 59_D | 63_K | 1.723 | 1.00 |
| 68_M | 79_V | 1.719 | 1.00 |
| 334_A | 349_L | 1.688 | 1.00 |
| 238_H | 242_A | 1.683 | 1.00 |
| 85_M | 381_N | 1.679 | 1.00 |
| 323_I | 355_V | 1.659 | 1.00 |
| 33_P | 78_V | 1.653 | 1.00 |
| 402_P | 409_D | 1.652 | 1.00 |
| 287_T | 290_N | 1.648 | 1.00 |
| 189_K | 250_E | 1.633 | 1.00 |
| 203_E | 232_K | 1.626 | 1.00 |
| 399_G | 432_P | 1.618 | 1.00 |
| 196_T | 239_K | 1.618 | 1.00 |
| 314_M | 457_L | 1.616 | 1.00 |
| 355_V | 359_T | 1.605 | 1.00 |
| 59_D | 62_K | 1.593 | 1.00 |
| 396_W | 400_R | 1.589 | 1.00 |
| 316_Q | 362_L | 1.581 | 1.00 |
| 310_L | 453_P | 1.580 | 1.00 |
| 231_G | 235_K | 1.579 | 1.00 |
| 246_D | 250_E | 1.567 | 1.00 |
| 185_S | 445_F | 1.556 | 1.00 |
| 317_M | 323_I | 1.543 | 1.00 |
| 153_V | 157_V | 1.535 | 1.00 |
| 317_M | 327_A | 1.527 | 1.00 |
| 309_T | 365_P | 1.522 | 1.00 |
| 330_E | 349_L | 1.520 | 1.00 |
| 357_K | 430_Y | 1.499 | 1.00 |
| 161_R | 496_P | 1.491 | 1.00 |
| 153_V | 177_F | 1.485 | 1.00 |
| 152_E | 184_R | 1.448 | 1.00 |
| 245_E | 288_N | 1.434 | 1.00 |
| 245_E | 249_N | 1.431 | 1.00 |
| 328_Q | 458_L | 1.430 | 1.00 |
| 82_S | 85_M | 1.424 | 1.00 |
| 376_E | 387_V | 1.421 | 1.00 |
| 200_L | 239_K | 1.413 | 1.00 |
| 128_M | 294_I | 1.405 | 0.99 |
| 127_Q | 290_N | 1.402 | 0.99 |
| 39_L | 47_H | 1.391 | 0.99 |
| 156_L | 177_F | 1.389 | 0.99 |
| 183_C | 191_F | 1.386 | 0.99 |
| 160_V | 494_A | 1.384 | 0.99 |
| 169_N | 172_E | 1.381 | 0.99 |
| 241_D | 292_K | 1.380 | 0.99 |
| 177_F | 181_M | 1.368 | 0.99 |
| 152_E | 180_S | 1.351 | 0.99 |
| 93_H | 378_T | 1.345 | 0.99 |
| 67_L | 85_M | 1.344 | 0.99 |
| 314_M | 454_L | 1.343 | 0.99 |
| 439_I | 443_I | 1.339 | 0.99 |
| 353_K | 357_K | 1.335 | 0.99 |
| 242_A | 246_D | 1.335 | 0.99 |
| 56_V | 60_L | 1.329 | 0.99 |
| 402_P | 406_D | 1.327 | 0.99 |
| 373_E | 388_K | 1.324 | 0.99 |
| 160_V | 173_R | 1.316 | 0.99 |
| 286_I | 290_N | 1.299 | 0.99 |
| 152_E | 190_V | 1.298 | 0.99 |
| 320_N | 323_I | 1.293 | 0.99 |
| 142_V | 448_A | 1.287 | 0.99 |
| 80_V | 86_A | 1.285 | 0.99 |
| 66_P | 403_K | 1.280 | 0.99 |
| 78_V | 385_I | 1.272 | 0.99 |
| 374_C | 388_K | 1.258 | 0.99 |
| 322_T | 326_K | 1.242 | 0.98 |
| 314_M | 492_L | 1.240 | 0.98 |
| 342_D | 345_D | 1.239 | 0.98 |
| 182_T | 302_G | 1.237 | 0.98 |
| 332_R | 459_Y | 1.235 | 0.98 |
| 84_D | 381_N | 1.232 | 0.98 |
| 248_I | 270_I | 1.230 | 0.98 |
| 62_K | 402_P | 1.219 | 0.98 |
| 251_H | 271_D | 1.215 | 0.98 |
| 271_D | 275_R | 1.211 | 0.98 |
| 313_A | 356_I | 1.201 | 0.98 |
| 199_Q | 203_E | 1.198 | 0.98 |
| 157_V | 461_F | 1.196 | 0.98 |
| 235_K | 239_K | 1.195 | 0.98 |
| 150_R | 456_Q | 1.193 | 0.98 |
| 345_D | 348_E | 1.179 | 0.98 |
| 149_R | 445_F | 1.178 | 0.98 |
| 152_E | 155_R | 1.174 | 0.98 |
| 331_V | 352_L | 1.174 | 0.98 |
| 122_G | 125_W | 1.160 | 0.97 |
| 352_L | 355_V | 1.152 | 0.97 |
| 358_E | 361_R | 1.152 | 0.97 |
| 351_Y | 355_V | 1.146 | 0.97 |
| 346_V | 451_Y | 1.144 | 0.97 |
| 58_R | 397_A | 1.144 | 0.97 |
| 374_C | 377_E | 1.139 | 0.97 |
| 399_G | 430_Y | 1.131 | 0.97 |
| 407_D | 415_R | 1.129 | 0.97 |
| 250_E | 254_N | 1.127 | 0.97 |
| 317_M | 458_L | 1.124 | 0.97 |
| 170_F | 314_M | 1.122 | 0.97 |
| 249_N | 252_K | 1.120 | 0.96 |
| 81_T | 394_N | 1.117 | 0.96 |
| 313_A | 411_F | 1.116 | 0.96 |
| 310_L | 450_V | 1.115 | 0.96 |
| 395_V | 431_L | 1.115 | 0.96 |
| 323_I | 414_E | 1.108 | 0.96 |
| 352_L | 451_Y | 1.107 | 0.96 |
| 327_A | 331_V | 1.094 | 0.96 |
| 426_N | 429_E | 1.091 | 0.96 |
| 34_P | 383_Y | 1.076 | 0.95 |
| 314_M | 458_L | 1.074 | 0.95 |
| 179_S | 303_T | 1.071 | 0.95 |
| 377_E | 386_P | 1.065 | 0.95 |
| 60_L | 68_M | 1.064 | 0.95 |
| 157_V | 456_Q | 1.061 | 0.95 |
| 309_T | 359_T | 1.060 | 0.95 |
| 182_T | 186_A | 1.060 | 0.95 |
| 317_M | 454_L | 1.058 | 0.95 |
| 184_R | 190_V | 1.057 | 0.95 |
| 318_M | 492_L | 1.056 | 0.95 |
| 316_Q | 319_R | 1.055 | 0.95 |
| 316_Q | 359_T | 1.047 | 0.94 |
| 406_D | 412_K | 1.046 | 0.94 |
| 174_L | 311_V | 1.044 | 0.94 |
| 203_E | 236_A | 1.041 | 0.94 |
| 385_I | 391_V | 1.035 | 0.94 |
| 157_V | 460_H | 1.035 | 0.94 |
| 325_A | 332_R | 1.035 | 0.94 |
| 178_T | 307_S | 1.033 | 0.94 |
| 237_H | 241_D | 1.033 | 0.94 |
| 125_W | 129_R | 1.030 | 0.94 |
| 360_L | 430_Y | 1.022 | 0.93 |
| 302_G | 305_T | 1.022 | 0.93 |
| 123_D | 126_R | 1.021 | 0.93 |
| 360_L | 432_P | 1.018 | 0.93 |
| 156_L | 457_L | 1.014 | 0.93 |
| 494_A | 497_Y | 1.014 | 0.93 |
| 321_P | 325_A | 1.012 | 0.93 |
| 384_T | 387_V | 1.009 | 0.93 |
| 331_V | 459_Y | 1.009 | 0.93 |
| 350_K | 354_L | 1.007 | 0.93 |
| 37_W | 44_S | 1.002 | 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 | |
| 3swzA | 4 | 0.9064 | 100 | 0.22 | Contact Map |
| 3pm0A | 1 | 0.8765 | 100 | 0.23 | Contact Map |
| 2hi4A | 1 | 0.9163 | 100 | 0.232 | Contact Map |
| 3tbgA | 4 | 0.9044 | 100 | 0.239 | Contact Map |
| 3czhA | 2 | 0.9044 | 100 | 0.239 | Contact Map |
| 3e6iA | 2 | 0.8944 | 100 | 0.247 | Contact Map |
| 1r9oA | 1 | 0.8805 | 100 | 0.247 | Contact Map |
| 3nxuA | 2 | 0.8904 | 100 | 0.249 | Contact Map |
| 4lxjA | 1 | 0.9502 | 100 | 0.251 | Contact Map |
| 1po5A | 1 | 0.9004 | 100 | 0.251 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)