| dpbp |
| ID: | 1501847237 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 507 (495) | ||
| Sequences: | 14685 (9424.2) | ||
| Seq/Len: | 29.667 | ||
| Nf(neff/√len): | 423.6 |
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: 29.667).
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 |
| 188_Q | 199_K | 4.537 | 1.00 |
| 130_V | 136_Q | 4.153 | 1.00 |
| 131_D | 134_T | 4.012 | 1.00 |
| 330_K | 333_A | 3.981 | 1.00 |
| 128_K | 136_Q | 3.926 | 1.00 |
| 292_D | 296_K | 3.810 | 1.00 |
| 280_K | 337_E | 3.750 | 1.00 |
| 91_V | 95_D | 3.471 | 1.00 |
| 69_K | 133_N | 3.431 | 1.00 |
| 441_D | 445_P | 3.425 | 1.00 |
| 186_Q | 199_K | 3.286 | 1.00 |
| 91_V | 129_K | 3.224 | 1.00 |
| 333_A | 337_E | 2.976 | 1.00 |
| 290_N | 293_A | 2.960 | 1.00 |
| 449_T | 454_K | 2.846 | 1.00 |
| 62_T | 136_Q | 2.840 | 1.00 |
| 85_L | 182_T | 2.837 | 1.00 |
| 287_Y | 330_K | 2.809 | 1.00 |
| 280_K | 283_Q | 2.773 | 1.00 |
| 53_K | 66_H | 2.727 | 1.00 |
| 438_P | 441_D | 2.694 | 1.00 |
| 285_L | 372_W | 2.689 | 1.00 |
| 62_T | 138_V | 2.675 | 1.00 |
| 445_P | 458_L | 2.628 | 1.00 |
| 37_V | 54_W | 2.604 | 1.00 |
| 57_S | 61_K | 2.561 | 1.00 |
| 280_K | 334_L | 2.551 | 1.00 |
| 128_K | 138_V | 2.509 | 1.00 |
| 56_V | 63_Y | 2.487 | 1.00 |
| 88_D | 129_K | 2.474 | 1.00 |
| 88_D | 160_K | 2.472 | 1.00 |
| 77_K | 161_E | 2.467 | 1.00 |
| 454_K | 457_E | 2.439 | 1.00 |
| 197_R | 213_T | 2.434 | 1.00 |
| 279_V | 283_Q | 2.421 | 1.00 |
| 66_H | 134_T | 2.406 | 1.00 |
| 347_D | 380_K | 2.399 | 1.00 |
| 451_D | 454_K | 2.392 | 1.00 |
| 160_K | 164_D | 2.376 | 1.00 |
| 71_V | 85_L | 2.375 | 1.00 |
| 64_T | 136_Q | 2.351 | 1.00 |
| 436_Y | 465_V | 2.343 | 1.00 |
| 434_W | 469_Q | 2.341 | 1.00 |
| 72_K | 203_G | 2.336 | 1.00 |
| 186_Q | 202_D | 2.329 | 1.00 |
| 55_E | 66_H | 2.304 | 1.00 |
| 2_T | 213_T | 2.302 | 1.00 |
| 274_K | 277_D | 2.299 | 1.00 |
| 72_K | 78_E | 2.267 | 1.00 |
| 74_H | 201_F | 2.263 | 1.00 |
| 345_S | 378_Q | 2.224 | 1.00 |
| 94_F | 137_F | 2.184 | 1.00 |
| 422_C | 435_C | 2.177 | 1.00 |
| 269_Y | 473_L | 2.169 | 1.00 |
| 457_E | 461_Q | 2.141 | 1.00 |
| 185_F | 211_I | 2.087 | 1.00 |
| 442_L | 461_Q | 2.082 | 1.00 |
| 422_C | 440_E | 2.056 | 1.00 |
| 228_K | 233_E | 2.047 | 1.00 |
| 373_A | 378_Q | 2.029 | 1.00 |
| 75_D | 159_S | 2.015 | 1.00 |
| 458_L | 461_Q | 2.009 | 1.00 |
| 289_V | 368_I | 2.008 | 1.00 |
| 438_P | 461_Q | 2.000 | 1.00 |
| 283_Q | 330_K | 1.994 | 1.00 |
| 327_D | 330_K | 1.990 | 1.00 |
| 90_V | 135_V | 1.989 | 1.00 |
| 88_D | 91_V | 1.978 | 1.00 |
| 4_V | 215_V | 1.975 | 1.00 |
| 6_C | 234_C | 1.958 | 1.00 |
| 15_N | 96_R | 1.947 | 1.00 |
| 52_E | 66_H | 1.936 | 1.00 |
| 442_L | 458_L | 1.919 | 1.00 |
| 439_F | 462_A | 1.900 | 1.00 |
| 436_Y | 469_Q | 1.890 | 1.00 |
| 332_K | 336_K | 1.887 | 1.00 |
| 189_Q | 197_R | 1.880 | 1.00 |
| 77_K | 159_S | 1.866 | 1.00 |
| 438_P | 465_V | 1.862 | 1.00 |
| 2_T | 215_V | 1.862 | 1.00 |
| 288_A | 375_V | 1.858 | 1.00 |
| 34_N | 49_G | 1.853 | 1.00 |
| 87_A | 129_K | 1.832 | 1.00 |
| 88_D | 132_D | 1.830 | 1.00 |
| 269_Y | 400_T | 1.823 | 1.00 |
| 125_S | 140_T | 1.823 | 1.00 |
| 199_K | 213_T | 1.819 | 1.00 |
| 273_K | 399_Q | 1.818 | 1.00 |
| 37_V | 65_F | 1.811 | 1.00 |
| 197_R | 215_V | 1.808 | 1.00 |
| 57_S | 62_T | 1.798 | 1.00 |
| 64_T | 134_T | 1.798 | 1.00 |
| 219_T | 228_K | 1.797 | 1.00 |
| 89_D | 160_K | 1.791 | 1.00 |
| 435_C | 440_E | 1.789 | 1.00 |
| 200_A | 212_D | 1.787 | 1.00 |
| 195_R | 215_V | 1.783 | 1.00 |
| 40_K | 47_I | 1.765 | 1.00 |
| 369_Q | 373_A | 1.762 | 1.00 |
| 446_A | 459_Y | 1.747 | 1.00 |
| 86_N | 89_D | 1.746 | 1.00 |
| 191_Q | 194_S | 1.739 | 1.00 |
| 306_A | 477_H | 1.731 | 1.00 |
| 385_E | 388_E | 1.722 | 1.00 |
| 464_V | 468_D | 1.712 | 1.00 |
| 52_E | 69_K | 1.711 | 1.00 |
| 71_V | 182_T | 1.710 | 1.00 |
| 392_R | 397_E | 1.698 | 1.00 |
| 281_V | 338_A | 1.695 | 1.00 |
| 54_W | 65_F | 1.673 | 1.00 |
| 126_E | 138_V | 1.659 | 1.00 |
| 188_Q | 213_T | 1.625 | 1.00 |
| 40_K | 45_E | 1.617 | 1.00 |
| 446_A | 458_L | 1.616 | 1.00 |
| 347_D | 382_V | 1.597 | 1.00 |
| 75_D | 161_E | 1.587 | 1.00 |
| 461_Q | 464_V | 1.558 | 1.00 |
| 456_V | 460_K | 1.554 | 1.00 |
| 70_G | 78_E | 1.552 | 1.00 |
| 437_K | 441_D | 1.551 | 1.00 |
| 130_V | 134_T | 1.542 | 1.00 |
| 159_S | 162_Y | 1.537 | 1.00 |
| 334_L | 337_E | 1.536 | 1.00 |
| 292_D | 305_S | 1.530 | 1.00 |
| 362_R | 366_E | 1.528 | 1.00 |
| 66_H | 133_N | 1.526 | 1.00 |
| 279_V | 468_D | 1.524 | 1.00 |
| 198_Y | 216_F | 1.507 | 1.00 |
| 279_V | 469_Q | 1.507 | 1.00 |
| 57_S | 64_T | 1.505 | 1.00 |
| 191_Q | 195_R | 1.498 | 1.00 |
| 454_K | 458_L | 1.488 | 1.00 |
| 189_Q | 195_R | 1.484 | 1.00 |
| 68_R | 71_V | 1.477 | 1.00 |
| 52_E | 68_R | 1.473 | 1.00 |
| 276_L | 346_I | 1.454 | 1.00 |
| 457_E | 460_K | 1.454 | 1.00 |
| 441_D | 444_Q | 1.447 | 1.00 |
| 86_N | 132_D | 1.441 | 1.00 |
| 465_V | 469_Q | 1.439 | 1.00 |
| 281_V | 335_L | 1.435 | 1.00 |
| 329_E | 332_K | 1.429 | 1.00 |
| 286_T | 470_A | 1.427 | 1.00 |
| 74_H | 186_Q | 1.421 | 1.00 |
| 336_K | 341_E | 1.420 | 1.00 |
| 442_L | 465_V | 1.416 | 1.00 |
| 371_D | 374_K | 1.402 | 0.99 |
| 34_N | 182_T | 1.385 | 0.99 |
| 276_L | 285_L | 1.378 | 0.99 |
| 367_M | 371_D | 1.375 | 0.99 |
| 328_P | 332_K | 1.374 | 0.99 |
| 438_P | 442_L | 1.374 | 0.99 |
| 65_F | 137_F | 1.362 | 0.99 |
| 78_E | 133_N | 1.361 | 0.99 |
| 288_A | 372_W | 1.361 | 0.99 |
| 295_I | 305_S | 1.358 | 0.99 |
| 50_L | 90_V | 1.357 | 0.99 |
| 230_Q | 247_R | 1.354 | 0.99 |
| 283_Q | 470_A | 1.354 | 0.99 |
| 50_L | 182_T | 1.345 | 0.99 |
| 445_P | 454_K | 1.336 | 0.99 |
| 442_L | 445_P | 1.318 | 0.99 |
| 283_Q | 334_L | 1.290 | 0.99 |
| 162_Y | 180_I | 1.285 | 0.99 |
| 52_E | 133_N | 1.285 | 0.99 |
| 34_N | 205_W | 1.273 | 0.99 |
| 72_K | 201_F | 1.272 | 0.99 |
| 95_D | 99_N | 1.270 | 0.99 |
| 285_L | 377_V | 1.265 | 0.99 |
| 91_V | 127_V | 1.258 | 0.99 |
| 195_R | 217_S | 1.257 | 0.99 |
| 129_K | 132_D | 1.246 | 0.98 |
| 396_G | 433_K | 1.243 | 0.98 |
| 50_L | 71_V | 1.241 | 0.98 |
| 386_W | 390_L | 1.239 | 0.98 |
| 445_P | 461_Q | 1.238 | 0.98 |
| 293_A | 371_D | 1.236 | 0.98 |
| 295_I | 303_G | 1.234 | 0.98 |
| 421_S | 444_Q | 1.233 | 0.98 |
| 40_K | 43_T | 1.227 | 0.98 |
| 449_T | 458_L | 1.223 | 0.98 |
| 186_Q | 201_F | 1.223 | 0.98 |
| 92_F | 160_K | 1.219 | 0.98 |
| 21_S | 25_Y | 1.210 | 0.98 |
| 228_K | 234_C | 1.210 | 0.98 |
| 188_Q | 197_R | 1.209 | 0.98 |
| 3_L | 488_V | 1.205 | 0.98 |
| 382_V | 392_R | 1.193 | 0.98 |
| 74_H | 203_G | 1.190 | 0.98 |
| 90_V | 157_I | 1.190 | 0.98 |
| 55_E | 64_T | 1.182 | 0.98 |
| 74_H | 180_I | 1.180 | 0.98 |
| 370_A | 373_A | 1.180 | 0.98 |
| 372_W | 379_A | 1.172 | 0.98 |
| 445_P | 449_T | 1.168 | 0.97 |
| 74_H | 181_G | 1.168 | 0.97 |
| 286_T | 473_L | 1.165 | 0.97 |
| 299_Y | 303_G | 1.165 | 0.97 |
| 330_K | 334_L | 1.163 | 0.97 |
| 369_Q | 379_A | 1.160 | 0.97 |
| 125_S | 138_V | 1.157 | 0.97 |
| 296_K | 301_G | 1.157 | 0.97 |
| 333_A | 336_K | 1.153 | 0.97 |
| 293_A | 297_A | 1.152 | 0.97 |
| 329_E | 333_A | 1.148 | 0.97 |
| 87_A | 130_V | 1.145 | 0.97 |
| 141_R | 448_A | 1.142 | 0.97 |
| 370_A | 374_K | 1.140 | 0.97 |
| 312_P | 477_H | 1.131 | 0.97 |
| 116_E | 138_V | 1.129 | 0.97 |
| 411_D | 455_R | 1.127 | 0.97 |
| 34_N | 204_Y | 1.121 | 0.97 |
| 369_Q | 381_I | 1.120 | 0.96 |
| 349_W | 382_V | 1.119 | 0.96 |
| 127_V | 135_V | 1.118 | 0.96 |
| 442_L | 462_A | 1.114 | 0.96 |
| 421_S | 435_C | 1.111 | 0.96 |
| 93_S | 157_I | 1.110 | 0.96 |
| 294_I | 364_M | 1.101 | 0.96 |
| 224_V | 228_K | 1.100 | 0.96 |
| 246_A | 249_K | 1.099 | 0.96 |
| 453_N | 456_V | 1.096 | 0.96 |
| 4_V | 217_S | 1.084 | 0.96 |
| 68_R | 205_W | 1.083 | 0.96 |
| 3_L | 236_V | 1.083 | 0.96 |
| 453_N | 457_E | 1.082 | 0.96 |
| 51_A | 65_F | 1.081 | 0.95 |
| 280_K | 338_A | 1.080 | 0.95 |
| 368_I | 372_W | 1.079 | 0.95 |
| 465_V | 468_D | 1.077 | 0.95 |
| 87_A | 135_V | 1.069 | 0.95 |
| 66_H | 69_K | 1.069 | 0.95 |
| 258_E | 479_T | 1.066 | 0.95 |
| 255_N | 486_K | 1.056 | 0.95 |
| 328_P | 375_V | 1.050 | 0.94 |
| 66_H | 131_D | 1.049 | 0.94 |
| 227_A | 230_Q | 1.048 | 0.94 |
| 57_S | 60_G | 1.046 | 0.94 |
| 365_A | 381_I | 1.045 | 0.94 |
| 91_V | 135_V | 1.039 | 0.94 |
| 235_Q | 485_R | 1.033 | 0.94 |
| 63_Y | 139_L | 1.032 | 0.94 |
| 28_S | 198_Y | 1.032 | 0.94 |
| 446_A | 462_A | 1.030 | 0.94 |
| 85_L | 157_I | 1.026 | 0.94 |
| 299_Y | 476_A | 1.024 | 0.93 |
| 269_Y | 285_L | 1.024 | 0.93 |
| 289_V | 294_I | 1.024 | 0.93 |
| 38_E | 47_I | 1.023 | 0.93 |
| 284_A | 335_L | 1.019 | 0.93 |
| 64_T | 130_V | 1.018 | 0.93 |
| 78_E | 86_N | 1.014 | 0.93 |
| 88_D | 92_F | 1.004 | 0.93 |
| 347_D | 378_Q | 1.003 | 0.93 |
| 200_A | 209_P | 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 | |
| 1dpeA | 1 | 0.9862 | 100 | 0.064 | Contact Map |
| 3m8uA | 1 | 0.9842 | 100 | 0.065 | Contact Map |
| 4qflA | 2 | 0.9862 | 100 | 0.067 | Contact Map |
| 3tpaA | 1 | 0.9842 | 100 | 0.071 | Contact Map |
| 3zs6A | 1 | 0.9586 | 100 | 0.095 | Contact Map |
| 1uqwA | 2 | 0.9408 | 100 | 0.097 | Contact Map |
| 4tozA | 2 | 0 | 100 | 0.099 | Contact Map |
| 1xocA | 1 | 0.9487 | 100 | 0.105 | Contact Map |
| 1jetA | 1 | 0.9586 | 100 | 0.111 | Contact Map |
| 4gl8A | 2 | 0.9546 | 100 | 0.115 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)