| HHAT_HUMAN_8iter |
| ID: | 1415749757 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 493 (418) | ||
| Sequences: | 2761 (2226.3) | ||
| Seq/Len: | 6.605 | ||
| Nf(neff/√len): | 108.9 |
Jackhmmer Results: (2014_04_16)
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: 6.605).
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 |
| 328_M | 333_G | 5.247 | 1.00 |
| 363_G | 366_F | 5.134 | 1.00 |
| 258_A | 302_V | 4.016 | 1.00 |
| 258_A | 298_V | 3.674 | 1.00 |
| 210_Y | 311_M | 3.525 | 1.00 |
| 391_L | 442_S | 3.447 | 1.00 |
| 290_L | 440_I | 3.370 | 1.00 |
| 251_L | 320_A | 3.283 | 1.00 |
| 181_T | 185_L | 3.150 | 1.00 |
| 136_T | 184_S | 3.026 | 1.00 |
| 179_Y | 213_V | 2.966 | 1.00 |
| 298_V | 302_V | 2.954 | 1.00 |
| 221_S | 348_R | 2.919 | 1.00 |
| 395_G | 438_M | 2.885 | 1.00 |
| 373_A | 390_A | 2.701 | 1.00 |
| 329_F | 333_G | 2.661 | 1.00 |
| 73_W | 310_L | 2.656 | 1.00 |
| 81_V | 100_Y | 2.643 | 1.00 |
| 102_M | 121_T | 2.614 | 1.00 |
| 326_S | 443_N | 2.592 | 1.00 |
| 257_L | 261_M | 2.541 | 1.00 |
| 449_G | 452_V | 2.493 | 1.00 |
| 346_L | 371_T | 2.467 | 1.00 |
| 251_L | 308_A | 2.459 | 1.00 |
| 346_L | 375_V | 2.456 | 1.00 |
| 156_K | 383_D | 2.396 | 1.00 |
| 252_L | 303_L | 2.263 | 1.00 |
| 84_M | 96_I | 2.260 | 1.00 |
| 121_T | 205_L | 2.259 | 1.00 |
| 319_P | 341_G | 2.225 | 1.00 |
| 97_L | 206_A | 2.178 | 1.00 |
| 98_M | 205_L | 2.142 | 1.00 |
| 441_L | 457_W | 2.107 | 1.00 |
| 182_S | 207_Y | 2.072 | 1.00 |
| 286_G | 440_I | 2.050 | 1.00 |
| 120_H | 140_S | 2.014 | 1.00 |
| 377_Y | 386_W | 2.007 | 1.00 |
| 366_F | 370_M | 1.994 | 1.00 |
| 392_N | 439_L | 1.980 | 1.00 |
| 387_C | 445_V | 1.950 | 1.00 |
| 94_P | 203_W | 1.933 | 1.00 |
| 88_L | 96_I | 1.914 | 1.00 |
| 352_I | 357_S | 1.902 | 1.00 |
| 180_Y | 208_V | 1.896 | 1.00 |
| 444_L | 460_I | 1.894 | 1.00 |
| 360_G | 364_T | 1.879 | 1.00 |
| 372_F | 375_V | 1.875 | 1.00 |
| 224_E | 344_N | 1.868 | 1.00 |
| 81_V | 314_D | 1.818 | 1.00 |
| 330_S | 399_E | 1.813 | 1.00 |
| 391_L | 395_G | 1.806 | 1.00 |
| 332_T | 400_N | 1.761 | 1.00 |
| 124_S | 136_T | 1.757 | 1.00 |
| 364_T | 400_N | 1.756 | 1.00 |
| 133_Q | 137_W | 1.747 | 1.00 |
| 355_G | 367_S | 1.743 | 1.00 |
| 369_A | 390_A | 1.693 | 1.00 |
| 287_G | 437_S | 1.691 | 1.00 |
| 222_F | 226_I | 1.668 | 1.00 |
| 432_A | 436_T | 1.662 | 1.00 |
| 124_S | 128_A | 1.659 | 1.00 |
| 312_R | 317_T | 1.639 | 1.00 |
| 329_F | 431_L | 1.635 | 1.00 |
| 359_H | 364_T | 1.622 | 1.00 |
| 185_L | 189_W | 1.620 | 1.00 |
| 447_L | 453_G | 1.609 | 1.00 |
| 121_T | 124_S | 1.606 | 1.00 |
| 445_V | 453_G | 1.568 | 0.99 |
| 127_V | 136_T | 1.559 | 0.99 |
| 372_F | 396_V | 1.520 | 0.99 |
| 124_S | 180_Y | 1.519 | 0.99 |
| 384_Y | 447_L | 1.507 | 0.99 |
| 225_F | 229_M | 1.501 | 0.99 |
| 243_V | 312_R | 1.500 | 0.99 |
| 356_G | 367_S | 1.500 | 0.99 |
| 86_T | 313_L | 1.498 | 0.99 |
| 124_S | 140_S | 1.486 | 0.99 |
| 154_E | 158_R | 1.479 | 0.99 |
| 252_L | 313_L | 1.479 | 0.99 |
| 246_L | 312_R | 1.474 | 0.99 |
| 200_S | 203_W | 1.474 | 0.99 |
| 123_I | 139_C | 1.457 | 0.99 |
| 445_V | 454_K | 1.456 | 0.99 |
| 201_F | 205_L | 1.453 | 0.99 |
| 156_K | 159_W | 1.450 | 0.99 |
| 124_S | 127_V | 1.443 | 0.99 |
| 372_F | 392_N | 1.432 | 0.99 |
| 151_G | 166_Y | 1.426 | 0.99 |
| 123_I | 127_V | 1.425 | 0.99 |
| 320_A | 323_R | 1.423 | 0.99 |
| 243_V | 317_T | 1.421 | 0.99 |
| 439_L | 443_N | 1.420 | 0.99 |
| 301_L | 308_A | 1.408 | 0.99 |
| 334_M | 443_N | 1.404 | 0.99 |
| 445_V | 457_W | 1.392 | 0.98 |
| 286_G | 444_L | 1.390 | 0.98 |
| 372_F | 393_W | 1.390 | 0.98 |
| 340_V | 344_N | 1.373 | 0.98 |
| 435_S | 439_L | 1.365 | 0.98 |
| 352_I | 355_G | 1.362 | 0.98 |
| 137_W | 142_L | 1.359 | 0.98 |
| 369_A | 393_W | 1.350 | 0.98 |
| 153_E | 377_Y | 1.340 | 0.98 |
| 203_W | 230_Q | 1.333 | 0.98 |
| 444_L | 453_G | 1.325 | 0.98 |
| 282_C | 456_Y | 1.322 | 0.98 |
| 283_W | 460_I | 1.318 | 0.98 |
| 359_H | 363_G | 1.314 | 0.98 |
| 362_L | 366_F | 1.307 | 0.97 |
| 343_H | 347_I | 1.306 | 0.97 |
| 228_Q | 317_T | 1.304 | 0.97 |
| 352_I | 356_G | 1.303 | 0.97 |
| 125_F | 129_Q | 1.289 | 0.97 |
| 122_T | 201_F | 1.286 | 0.97 |
| 357_S | 360_G | 1.285 | 0.97 |
| 124_S | 184_S | 1.279 | 0.97 |
| 332_T | 399_E | 1.270 | 0.97 |
| 111_T | 115_A | 1.267 | 0.97 |
| 352_I | 367_S | 1.264 | 0.97 |
| 278_E | 281_S | 1.263 | 0.97 |
| 293_V | 443_N | 1.251 | 0.96 |
| 213_V | 220_L | 1.246 | 0.96 |
| 120_H | 124_S | 1.245 | 0.96 |
| 151_G | 154_E | 1.239 | 0.96 |
| 392_N | 442_S | 1.232 | 0.96 |
| 439_L | 442_S | 1.226 | 0.96 |
| 120_H | 143_L | 1.222 | 0.96 |
| 293_V | 326_S | 1.213 | 0.96 |
| 102_M | 209_F | 1.211 | 0.96 |
| 343_H | 371_T | 1.205 | 0.95 |
| 179_Y | 220_L | 1.198 | 0.95 |
| 375_V | 396_V | 1.197 | 0.95 |
| 244_L | 313_L | 1.196 | 0.95 |
| 365_L | 401_G | 1.193 | 0.95 |
| 373_A | 386_W | 1.191 | 0.95 |
| 285_L | 456_Y | 1.188 | 0.95 |
| 271_Y | 447_L | 1.180 | 0.95 |
| 128_A | 187_L | 1.177 | 0.95 |
| 134_L | 138_L | 1.166 | 0.94 |
| 191_Q | 223_S | 1.164 | 0.94 |
| 202_P | 206_A | 1.159 | 0.94 |
| 361_L | 365_L | 1.159 | 0.94 |
| 350_V | 374_F | 1.156 | 0.94 |
| 450_N | 454_K | 1.151 | 0.94 |
| 151_G | 155_V | 1.147 | 0.94 |
| 84_M | 88_L | 1.147 | 0.94 |
| 343_H | 368_T | 1.146 | 0.94 |
| 286_G | 460_I | 1.145 | 0.93 |
| 371_T | 375_V | 1.145 | 0.93 |
| 224_E | 319_P | 1.137 | 0.93 |
| 341_G | 344_N | 1.135 | 0.93 |
| 331_F | 395_G | 1.129 | 0.93 |
| 277_L | 282_C | 1.104 | 0.92 |
| 351_Y | 356_G | 1.101 | 0.92 |
| 334_M | 439_L | 1.097 | 0.91 |
| 180_Y | 204_M | 1.095 | 0.91 |
| 186_E | 349_Y | 1.095 | 0.91 |
| 287_G | 290_L | 1.088 | 0.91 |
| 99_L | 103_W | 1.087 | 0.91 |
| 259_E | 296_F | 1.081 | 0.91 |
| 119_L | 139_C | 1.079 | 0.91 |
| 242_C | 246_L | 1.076 | 0.90 |
| 359_H | 366_F | 1.075 | 0.90 |
| 198_S | 230_Q | 1.071 | 0.90 |
| 146_T | 150_Q | 1.067 | 0.90 |
| 220_L | 319_P | 1.065 | 0.90 |
| 244_L | 247_G | 1.064 | 0.90 |
| 454_K | 458_N | 1.063 | 0.90 |
| 351_Y | 355_G | 1.060 | 0.89 |
| 354_V | 367_S | 1.060 | 0.89 |
| 204_M | 208_V | 1.057 | 0.89 |
| 270_I | 285_L | 1.056 | 0.89 |
| 179_Y | 311_M | 1.055 | 0.89 |
| 458_N | 462_I | 1.055 | 0.89 |
| 102_M | 205_L | 1.054 | 0.89 |
| 82_S | 86_T | 1.054 | 0.89 |
| 146_T | 167_Y | 1.048 | 0.89 |
| 171_F | 215_H | 1.048 | 0.89 |
| 403_R | 407_E | 1.045 | 0.89 |
| 346_L | 372_F | 1.044 | 0.89 |
| 94_P | 316_L | 1.043 | 0.88 |
| 455_T | 459_R | 1.042 | 0.88 |
| 365_L | 400_N | 1.042 | 0.88 |
| 331_F | 439_L | 1.042 | 0.88 |
| 442_S | 445_V | 1.034 | 0.88 |
| 291_A | 436_T | 1.034 | 0.88 |
| 448_G | 452_V | 1.030 | 0.88 |
| 131_R | 190_Q | 1.028 | 0.87 |
| 141_L | 374_F | 1.027 | 0.87 |
| 198_S | 203_W | 1.025 | 0.87 |
| 213_V | 216_N | 1.025 | 0.87 |
| 387_C | 453_G | 1.023 | 0.87 |
| 183_F | 199_Y | 1.018 | 0.87 |
| 326_S | 439_L | 1.015 | 0.87 |
| 368_T | 400_N | 1.008 | 0.86 |
| 358_Q | 367_S | 1.003 | 0.86 |
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 | |
| 1rmkA | 1 | 0.0629 | 19.7 | 0.973 | Contact Map |
| 3si5X | 2 | 0.0264 | 4.9 | 0.979 | Contact Map |
| 1fftB | 2 | 0.1014 | 4.6 | 0.98 | Contact Map |
| 2rddB | 1 | 0.0669 | 2.4 | 0.982 | Contact Map |
| 2i2jA | 1 | 0.0426 | 2.2 | 0.983 | Contact Map |
| 2yevB | 2 | 0.1034 | 1.8 | 0.983 | Contact Map |
| 1v54J | 2 | 0.0669 | 1.7 | 0.984 | Contact Map |
| 2dw3A | 1 | 0.1278 | 1.5 | 0.984 | Contact Map |
| 2nrgA | 1 | 0.1298 | 1.5 | 0.984 | Contact Map |
| 4gntB | 1 | 0.0426 | 1.3 | 0.985 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)