| ATF1 yeast |
| ID: | 1503854376 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 525 (442) | ||
| Sequences: | 9683 (8050.5) | ||
| Seq/Len: | 21.907 | ||
| Nf(neff/√len): | 382.9 |
HHblits Results: (2016_02)
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: 21.907).
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 |
| 53_E | 182_W | 3.566 | 1.00 |
| 342_L | 377_T | 3.498 | 1.00 |
| 277_M | 507_S | 3.152 | 1.00 |
| 305_I | 318_F | 3.036 | 1.00 |
| 390_E | 398_H | 3.030 | 1.00 |
| 55_S | 182_W | 2.668 | 1.00 |
| 311_G | 393_W | 2.649 | 1.00 |
| 508_Q | 512_E | 2.649 | 1.00 |
| 324_F | 378_P | 2.637 | 1.00 |
| 289_E | 512_E | 2.597 | 1.00 |
| 330_W | 517_I | 2.584 | 1.00 |
| 297_E | 523_L | 2.471 | 1.00 |
| 498_V | 515_C | 2.442 | 1.00 |
| 80_I | 110_S | 2.432 | 1.00 |
| 69_E | 213_I | 2.413 | 1.00 |
| 326_S | 521_L | 2.393 | 1.00 |
| 202_F | 367_Y | 2.334 | 1.00 |
| 261_F | 402_V | 2.325 | 1.00 |
| 64_T | 68_R | 2.296 | 1.00 |
| 73_K | 205_D | 2.285 | 1.00 |
| 189_S | 194_S | 2.268 | 1.00 |
| 287_V | 502_K | 2.259 | 1.00 |
| 291_I | 496_I | 2.252 | 1.00 |
| 276_R | 510_S | 2.204 | 1.00 |
| 344_D | 375_D | 2.202 | 1.00 |
| 67_L | 171_L | 2.194 | 1.00 |
| 80_I | 166_G | 2.155 | 1.00 |
| 146_Y | 149_K | 2.153 | 1.00 |
| 498_V | 511_L | 2.138 | 1.00 |
| 68_R | 72_L | 2.127 | 1.00 |
| 256_S | 260_G | 2.101 | 1.00 |
| 63_L | 206_L | 2.086 | 1.00 |
| 432_K | 435_C | 2.081 | 1.00 |
| 294_S | 297_E | 2.069 | 1.00 |
| 519_K | 523_L | 2.045 | 1.00 |
| 177_E | 181_K | 2.039 | 1.00 |
| 302_K | 488_S | 2.000 | 1.00 |
| 70_I | 209_E | 1.992 | 1.00 |
| 486_V | 496_I | 1.991 | 1.00 |
| 391_N | 394_P | 1.985 | 1.00 |
| 254_P | 409_N | 1.956 | 1.00 |
| 317_P | 400_H | 1.926 | 1.00 |
| 287_V | 508_Q | 1.919 | 1.00 |
| 484_L | 498_V | 1.918 | 1.00 |
| 301_I | 315_I | 1.904 | 1.00 |
| 301_I | 318_F | 1.878 | 1.00 |
| 303_A | 307_S | 1.877 | 1.00 |
| 41_R | 83_P | 1.865 | 1.00 |
| 168_S | 193_M | 1.857 | 1.00 |
| 60_R | 173_C | 1.853 | 1.00 |
| 70_I | 206_L | 1.852 | 1.00 |
| 342_L | 379_W | 1.848 | 1.00 |
| 401_E | 405_E | 1.848 | 1.00 |
| 69_E | 209_E | 1.842 | 1.00 |
| 204_H | 365_Y | 1.835 | 1.00 |
| 321_V | 395_L | 1.830 | 1.00 |
| 55_S | 467_C | 1.829 | 1.00 |
| 292_N | 493_G | 1.829 | 1.00 |
| 500_S | 511_L | 1.825 | 1.00 |
| 69_E | 72_L | 1.823 | 1.00 |
| 323_W | 484_L | 1.813 | 1.00 |
| 512_E | 516_S | 1.811 | 1.00 |
| 59_T | 62_Q | 1.774 | 1.00 |
| 65_L | 213_I | 1.773 | 1.00 |
| 325_V | 395_L | 1.747 | 1.00 |
| 74_N | 205_D | 1.743 | 1.00 |
| 154_T | 172_I | 1.743 | 1.00 |
| 330_W | 514_L | 1.743 | 1.00 |
| 62_Q | 213_I | 1.734 | 1.00 |
| 311_G | 397_E | 1.692 | 1.00 |
| 322_C | 522_L | 1.692 | 1.00 |
| 283_T | 503_N | 1.683 | 1.00 |
| 76_T | 79_H | 1.665 | 1.00 |
| 315_I | 494_M | 1.662 | 1.00 |
| 160_P | 165_T | 1.642 | 1.00 |
| 328_H | 380_I | 1.639 | 1.00 |
| 291_I | 515_C | 1.615 | 1.00 |
| 57_Y | 181_K | 1.609 | 1.00 |
| 285_D | 503_N | 1.605 | 1.00 |
| 326_S | 518_Y | 1.597 | 1.00 |
| 59_T | 210_L | 1.593 | 1.00 |
| 62_Q | 214_K | 1.590 | 1.00 |
| 325_V | 521_L | 1.589 | 1.00 |
| 149_K | 153_L | 1.583 | 1.00 |
| 292_N | 495_N | 1.547 | 1.00 |
| 175_P | 183_K | 1.541 | 1.00 |
| 289_E | 508_Q | 1.530 | 1.00 |
| 321_V | 399_Y | 1.528 | 1.00 |
| 55_S | 465_S | 1.521 | 1.00 |
| 150_I | 174_L | 1.502 | 1.00 |
| 81_V | 193_M | 1.495 | 1.00 |
| 255_K | 259_S | 1.494 | 1.00 |
| 313_C | 396_I | 1.473 | 1.00 |
| 242_K | 245_D | 1.468 | 1.00 |
| 283_T | 501_T | 1.467 | 1.00 |
| 378_P | 399_Y | 1.458 | 1.00 |
| 424_V | 428_V | 1.450 | 1.00 |
| 174_L | 186_I | 1.450 | 1.00 |
| 209_E | 213_I | 1.447 | 1.00 |
| 298_F | 494_M | 1.445 | 1.00 |
| 81_V | 192_C | 1.443 | 1.00 |
| 162_F | 165_T | 1.438 | 1.00 |
| 294_S | 523_L | 1.437 | 1.00 |
| 507_S | 510_S | 1.431 | 1.00 |
| 289_E | 515_C | 1.430 | 1.00 |
| 29_M | 104_P | 1.411 | 1.00 |
| 307_S | 311_G | 1.405 | 0.99 |
| 63_L | 185_F | 1.403 | 0.99 |
| 287_V | 500_S | 1.391 | 0.99 |
| 219_K | 232_L | 1.391 | 0.99 |
| 436_D | 439_I | 1.389 | 0.99 |
| 381_S | 390_E | 1.385 | 0.99 |
| 375_D | 424_V | 1.377 | 0.99 |
| 198_S | 367_Y | 1.375 | 0.99 |
| 513_E | 517_I | 1.373 | 0.99 |
| 320_H | 345_I | 1.354 | 0.99 |
| 324_F | 345_I | 1.353 | 0.99 |
| 288_T | 499_A | 1.350 | 0.99 |
| 154_T | 188_V | 1.345 | 0.99 |
| 394_P | 397_E | 1.343 | 0.99 |
| 298_F | 302_K | 1.341 | 0.99 |
| 154_T | 157_L | 1.341 | 0.99 |
| 51_Y | 186_I | 1.329 | 0.99 |
| 53_E | 184_K | 1.319 | 0.99 |
| 60_R | 64_T | 1.319 | 0.99 |
| 177_E | 180_E | 1.316 | 0.99 |
| 265_H | 344_D | 1.313 | 0.99 |
| 243_V | 246_F | 1.313 | 0.99 |
| 403_I | 407_L | 1.312 | 0.99 |
| 171_L | 185_F | 1.311 | 0.99 |
| 147_T | 184_K | 1.307 | 0.99 |
| 317_P | 404_S | 1.306 | 0.99 |
| 38_A | 42_Q | 1.305 | 0.99 |
| 194_S | 199_S | 1.305 | 0.99 |
| 204_H | 208_D | 1.299 | 0.99 |
| 297_E | 300_A | 1.282 | 0.99 |
| 254_P | 415_G | 1.275 | 0.99 |
| 53_E | 467_C | 1.273 | 0.99 |
| 58_C | 183_K | 1.270 | 0.99 |
| 257_L | 406_A | 1.249 | 0.99 |
| 144_G | 148_A | 1.246 | 0.98 |
| 259_S | 427_Y | 1.246 | 0.98 |
| 329_K | 517_I | 1.243 | 0.98 |
| 257_L | 261_F | 1.239 | 0.98 |
| 239_P | 242_K | 1.239 | 0.98 |
| 36_Y | 369_A | 1.238 | 0.98 |
| 299_Q | 303_A | 1.238 | 0.98 |
| 62_Q | 210_L | 1.232 | 0.98 |
| 298_F | 315_I | 1.232 | 0.98 |
| 242_K | 246_F | 1.229 | 0.98 |
| 58_C | 63_L | 1.228 | 0.98 |
| 379_W | 390_E | 1.225 | 0.98 |
| 304_N | 311_G | 1.218 | 0.98 |
| 381_S | 389_K | 1.211 | 0.98 |
| 380_I | 390_E | 1.211 | 0.98 |
| 291_I | 516_S | 1.204 | 0.98 |
| 400_H | 404_S | 1.201 | 0.98 |
| 51_Y | 184_K | 1.200 | 0.98 |
| 447_L | 450_N | 1.199 | 0.98 |
| 150_I | 153_L | 1.195 | 0.98 |
| 197_R | 350_D | 1.194 | 0.98 |
| 152_K | 156_T | 1.193 | 0.98 |
| 300_A | 523_L | 1.193 | 0.98 |
| 290_I | 497_V | 1.193 | 0.98 |
| 256_S | 259_S | 1.190 | 0.98 |
| 261_F | 405_E | 1.189 | 0.98 |
| 238_E | 242_K | 1.188 | 0.98 |
| 316_T | 347_I | 1.186 | 0.98 |
| 449_S | 452_G | 1.186 | 0.98 |
| 319_L | 494_M | 1.185 | 0.98 |
| 398_H | 402_V | 1.178 | 0.98 |
| 444_G | 447_L | 1.176 | 0.98 |
| 107_D | 111_V | 1.176 | 0.98 |
| 390_E | 394_P | 1.173 | 0.98 |
| 48_F | 194_S | 1.167 | 0.97 |
| 295_P | 299_Q | 1.166 | 0.97 |
| 171_L | 187_F | 1.164 | 0.97 |
| 173_C | 185_F | 1.164 | 0.97 |
| 326_S | 517_I | 1.162 | 0.97 |
| 109_I | 112_L | 1.161 | 0.97 |
| 290_I | 496_I | 1.158 | 0.97 |
| 104_P | 109_I | 1.158 | 0.97 |
| 80_I | 167_P | 1.154 | 0.97 |
| 240_I | 243_V | 1.152 | 0.97 |
| 320_H | 403_I | 1.143 | 0.97 |
| 255_K | 416_L | 1.142 | 0.97 |
| 323_W | 518_Y | 1.139 | 0.97 |
| 176_E | 184_K | 1.131 | 0.97 |
| 75_P | 239_P | 1.128 | 0.97 |
| 151_F | 186_I | 1.128 | 0.97 |
| 26_A | 84_T | 1.127 | 0.97 |
| 255_K | 427_Y | 1.120 | 0.96 |
| 319_L | 518_Y | 1.117 | 0.96 |
| 29_M | 81_V | 1.117 | 0.96 |
| 49_C | 188_V | 1.115 | 0.96 |
| 84_T | 87_P | 1.114 | 0.96 |
| 75_P | 78_L | 1.114 | 0.96 |
| 34_D | 248_P | 1.112 | 0.96 |
| 291_I | 519_K | 1.107 | 0.96 |
| 331_G | 340_E | 1.106 | 0.96 |
| 148_A | 152_K | 1.106 | 0.96 |
| 104_P | 107_D | 1.106 | 0.96 |
| 379_W | 398_H | 1.105 | 0.96 |
| 194_S | 202_F | 1.097 | 0.96 |
| 23_N | 75_P | 1.096 | 0.96 |
| 446_T | 450_N | 1.093 | 0.96 |
| 297_E | 519_K | 1.085 | 0.96 |
| 381_S | 388_N | 1.083 | 0.96 |
| 62_Q | 66_A | 1.078 | 0.95 |
| 313_C | 318_F | 1.078 | 0.95 |
| 304_N | 307_S | 1.078 | 0.95 |
| 366_R | 370_N | 1.076 | 0.95 |
| 505_V | 511_L | 1.073 | 0.95 |
| 415_G | 418_F | 1.068 | 0.95 |
| 55_S | 181_K | 1.067 | 0.95 |
| 71_C | 169_W | 1.066 | 0.95 |
| 313_C | 317_P | 1.060 | 0.95 |
| 483_S | 499_A | 1.059 | 0.95 |
| 293_I | 519_K | 1.058 | 0.95 |
| 240_I | 247_R | 1.058 | 0.95 |
| 516_S | 519_K | 1.056 | 0.95 |
| 496_I | 515_C | 1.055 | 0.95 |
| 158_T | 170_R | 1.053 | 0.95 |
| 191_H | 196_G | 1.048 | 0.94 |
| 317_P | 396_I | 1.043 | 0.94 |
| 442_R | 445_G | 1.038 | 0.94 |
| 211_N | 462_A | 1.035 | 0.94 |
| 66_A | 209_E | 1.035 | 0.94 |
| 446_T | 452_G | 1.035 | 0.94 |
| 263_Y | 266_L | 1.034 | 0.94 |
| 239_P | 246_F | 1.030 | 0.94 |
| 325_V | 392_F | 1.029 | 0.94 |
| 288_T | 497_V | 1.029 | 0.94 |
| 448_L | 451_V | 1.022 | 0.93 |
| 205_D | 209_E | 1.022 | 0.93 |
| 294_S | 298_F | 1.017 | 0.93 |
| 402_V | 405_E | 1.016 | 0.93 |
| 300_A | 303_A | 1.016 | 0.93 |
| 63_L | 210_L | 1.009 | 0.93 |
| 60_R | 175_P | 1.006 | 0.93 |
| 313_C | 400_H | 1.006 | 0.93 |
| 257_L | 405_E | 1.002 | 0.92 |
| 279_D | 504_V | 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 | |
| 2vsqA | 1 | 0.8038 | 100 | 0.341 | Contact Map |
| 4tx3B | 1 | 0.8019 | 100 | 0.363 | Contact Map |
| 2jgpA | 1 | 0.8076 | 100 | 0.367 | Contact Map |
| 4jn3A | 2 | 0.779 | 100 | 0.377 | Contact Map |
| 1l5aA | 3 | 0.7543 | 100 | 0.38 | Contact Map |
| 4znmA | 2 | 0 | 100 | 0.384 | Contact Map |
| 2xhgA | 1 | 0.8095 | 100 | 0.409 | Contact Map |
| 4hvmA | 4 | 0.7143 | 100 | 0.415 | Contact Map |
| 3fotA | 1 | 0.8552 | 100 | 0.43 | Contact Map |
| 1q9jA | 2 | 0.7238 | 100 | 0.45 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)