| BFD |
| ID: | 1467248768 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 528 (522) | ||
| Sequences: | 5216 (2989.6) | ||
| Seq/Len: | 9.992 | ||
| Nf(neff/√len): | 130.9 |
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: 9.992).
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 |
| 485_A | 488_K | 5.222 | 1.00 |
| 51_V | 81_A | 4.787 | 1.00 |
| 454_N | 520_E | 4.516 | 1.00 |
| 361_T | 504_K | 4.097 | 1.00 |
| 225_E | 246_H | 3.635 | 1.00 |
| 18_D | 63_K | 3.352 | 1.00 |
| 499_N | 502_Q | 3.318 | 1.00 |
| 498_D | 502_Q | 2.973 | 1.00 |
| 60_A | 417_E | 2.950 | 1.00 |
| 496_K | 522_S | 2.909 | 1.00 |
| 207_L | 220_C | 2.896 | 1.00 |
| 361_T | 364_D | 2.804 | 1.00 |
| 219_D | 319_G | 2.744 | 1.00 |
| 193_L | 296_I | 2.738 | 1.00 |
| 452_I | 518_L | 2.682 | 1.00 |
| 245_R | 390_R | 2.636 | 1.00 |
| 197_L | 271_L | 2.548 | 1.00 |
| 64_P | 147_S | 2.489 | 1.00 |
| 456_G | 480_G | 2.472 | 1.00 |
| 19_T | 40_R | 2.468 | 1.00 |
| 362_L | 425_V | 2.357 | 1.00 |
| 82_L | 94_V | 2.345 | 1.00 |
| 267_H | 270_V | 2.344 | 1.00 |
| 10_E | 14_R | 2.336 | 1.00 |
| 8_T | 139_M | 2.300 | 1.00 |
| 93_I | 143_I | 2.292 | 1.00 |
| 205_I | 224_A | 2.281 | 1.00 |
| 482_D | 485_A | 2.260 | 1.00 |
| 224_A | 231_V | 2.259 | 1.00 |
| 69_L | 78_A | 2.245 | 1.00 |
| 497_A | 506_S | 2.235 | 1.00 |
| 496_K | 520_E | 2.199 | 1.00 |
| 495_L | 509_E | 2.189 | 1.00 |
| 407_L | 426_I | 2.188 | 1.00 |
| 451_V | 519_I | 2.184 | 1.00 |
| 55_D | 84_N | 2.183 | 1.00 |
| 316_A | 321_M | 2.114 | 1.00 |
| 196_A | 312_D | 2.110 | 1.00 |
| 75_T | 96_A | 2.100 | 1.00 |
| 205_I | 271_L | 2.096 | 1.00 |
| 219_D | 323_S | 2.056 | 1.00 |
| 231_V | 242_F | 2.040 | 1.00 |
| 487_A | 518_L | 2.029 | 1.00 |
| 375_E | 426_I | 2.027 | 1.00 |
| 102_A | 161_D | 1.993 | 1.00 |
| 61_S | 416_A | 1.987 | 1.00 |
| 23_N | 78_A | 1.971 | 1.00 |
| 78_A | 94_V | 1.954 | 1.00 |
| 414_Q | 446_I | 1.897 | 1.00 |
| 64_P | 93_I | 1.890 | 1.00 |
| 374_N | 430_S | 1.884 | 1.00 |
| 67_I | 78_A | 1.878 | 1.00 |
| 431_A | 435_I | 1.877 | 1.00 |
| 506_S | 519_I | 1.864 | 1.00 |
| 495_L | 506_S | 1.834 | 1.00 |
| 191_D | 330_E | 1.821 | 1.00 |
| 8_T | 158_V | 1.814 | 1.00 |
| 410_A | 424_A | 1.806 | 1.00 |
| 273_I | 298_V | 1.793 | 1.00 |
| 123_V | 126_S | 1.791 | 1.00 |
| 6_G | 34_D | 1.771 | 1.00 |
| 11_L | 140_S | 1.759 | 1.00 |
| 205_I | 223_L | 1.754 | 1.00 |
| 79_M | 122_L | 1.752 | 1.00 |
| 195_K | 199_S | 1.747 | 1.00 |
| 487_A | 492_V | 1.740 | 1.00 |
| 503_L | 521_V | 1.738 | 1.00 |
| 76_G | 83_S | 1.734 | 1.00 |
| 484_R | 494_A | 1.733 | 1.00 |
| 127_Y | 156_L | 1.721 | 1.00 |
| 200_A | 268_D | 1.709 | 1.00 |
| 375_E | 430_S | 1.704 | 1.00 |
| 498_D | 522_S | 1.702 | 1.00 |
| 131_S | 134_E | 1.691 | 1.00 |
| 510_A | 519_I | 1.690 | 1.00 |
| 273_I | 318_I | 1.685 | 1.00 |
| 486_L | 489_G | 1.671 | 1.00 |
| 32_L | 41_Y | 1.663 | 1.00 |
| 357_T | 503_L | 1.662 | 1.00 |
| 55_D | 59_Q | 1.653 | 1.00 |
| 137_H | 141_R | 1.650 | 1.00 |
| 10_E | 13_R | 1.634 | 1.00 |
| 357_T | 500_L | 1.618 | 1.00 |
| 272_V | 275_A | 1.614 | 1.00 |
| 493_Q | 515_G | 1.610 | 1.00 |
| 118_L | 122_L | 1.601 | 1.00 |
| 495_L | 517_V | 1.598 | 1.00 |
| 203_P | 268_D | 1.593 | 1.00 |
| 218_A | 222_M | 1.593 | 1.00 |
| 503_L | 507_L | 1.586 | 1.00 |
| 497_A | 502_Q | 1.586 | 1.00 |
| 423_I | 511_L | 1.574 | 1.00 |
| 224_A | 242_F | 1.571 | 1.00 |
| 435_I | 486_L | 1.570 | 1.00 |
| 408_P | 437_A | 1.565 | 1.00 |
| 452_I | 483_F | 1.564 | 1.00 |
| 204_A | 267_H | 1.559 | 1.00 |
| 95_T | 158_V | 1.551 | 1.00 |
| 8_T | 95_T | 1.537 | 1.00 |
| 495_L | 519_I | 1.536 | 1.00 |
| 451_V | 521_V | 1.521 | 1.00 |
| 90_S | 405_F | 1.519 | 1.00 |
| 221_V | 225_E | 1.500 | 1.00 |
| 6_G | 10_E | 1.492 | 1.00 |
| 504_K | 508_Q | 1.482 | 1.00 |
| 19_T | 63_K | 1.479 | 1.00 |
| 15_Q | 143_I | 1.475 | 1.00 |
| 200_A | 203_P | 1.468 | 1.00 |
| 125_W | 142_A | 1.467 | 1.00 |
| 51_V | 78_A | 1.464 | 1.00 |
| 127_Y | 138_A | 1.464 | 1.00 |
| 222_M | 226_R | 1.455 | 1.00 |
| 203_P | 229_A | 1.454 | 1.00 |
| 298_V | 321_M | 1.453 | 1.00 |
| 226_R | 328_L | 1.446 | 1.00 |
| 396_Y | 413_V | 1.444 | 1.00 |
| 205_I | 229_A | 1.441 | 1.00 |
| 405_F | 409_A | 1.427 | 1.00 |
| 226_R | 332_S | 1.423 | 1.00 |
| 484_R | 488_K | 1.419 | 1.00 |
| 411_I | 441_A | 1.419 | 1.00 |
| 269_V | 296_I | 1.417 | 1.00 |
| 365_M | 508_Q | 1.416 | 1.00 |
| 431_A | 518_L | 1.416 | 1.00 |
| 69_L | 94_V | 1.406 | 0.99 |
| 197_L | 269_V | 1.403 | 0.99 |
| 424_A | 450_F | 1.390 | 0.99 |
| 505_G | 509_E | 1.386 | 0.99 |
| 239_R | 244_T | 1.384 | 0.99 |
| 233_V | 249_F | 1.382 | 0.99 |
| 194_V | 198_N | 1.378 | 0.99 |
| 451_V | 507_L | 1.375 | 0.99 |
| 114_D | 117_N | 1.371 | 0.99 |
| 93_I | 156_L | 1.359 | 0.99 |
| 221_V | 243_P | 1.356 | 0.99 |
| 374_N | 406_A | 1.347 | 0.99 |
| 359_F | 425_V | 1.344 | 0.99 |
| 7_T | 136_P | 1.336 | 0.99 |
| 186_N | 189_D | 1.336 | 0.99 |
| 12_L | 66_F | 1.331 | 0.99 |
| 104_I | 128_E | 1.327 | 0.99 |
| 93_I | 154_V | 1.320 | 0.99 |
| 441_A | 492_V | 1.320 | 0.99 |
| 35_F | 39_F | 1.319 | 0.99 |
| 484_R | 496_K | 1.316 | 0.99 |
| 442_A | 492_V | 1.314 | 0.99 |
| 93_I | 147_S | 1.313 | 0.99 |
| 406_A | 426_I | 1.309 | 0.99 |
| 125_W | 145_M | 1.304 | 0.99 |
| 371_I | 413_V | 1.303 | 0.99 |
| 82_L | 92_L | 1.302 | 0.99 |
| 79_M | 118_L | 1.300 | 0.99 |
| 357_T | 361_T | 1.297 | 0.99 |
| 502_Q | 505_G | 1.294 | 0.99 |
| 449_I | 510_A | 1.292 | 0.99 |
| 98_Q | 157_S | 1.291 | 0.99 |
| 27_N | 31_F | 1.287 | 0.99 |
| 505_G | 508_Q | 1.285 | 0.99 |
| 124_K | 152_G | 1.280 | 0.99 |
| 492_V | 518_L | 1.278 | 0.99 |
| 58_A | 90_S | 1.276 | 0.99 |
| 212_D | 241_P | 1.276 | 0.99 |
| 306_A | 310_M | 1.271 | 0.99 |
| 358_V | 521_V | 1.271 | 0.99 |
| 202_N | 266_G | 1.255 | 0.99 |
| 53_I | 415_L | 1.251 | 0.99 |
| 31_F | 68_N | 1.247 | 0.99 |
| 101_R | 161_D | 1.247 | 0.99 |
| 11_L | 15_Q | 1.241 | 0.98 |
| 493_Q | 509_E | 1.238 | 0.98 |
| 139_M | 156_L | 1.233 | 0.98 |
| 125_W | 141_R | 1.232 | 0.98 |
| 273_I | 322_A | 1.231 | 0.98 |
| 138_A | 141_R | 1.223 | 0.98 |
| 191_D | 195_K | 1.222 | 0.98 |
| 200_A | 269_V | 1.221 | 0.98 |
| 205_I | 220_C | 1.219 | 0.98 |
| 20_V | 35_F | 1.218 | 0.98 |
| 317_D | 320_A | 1.215 | 0.98 |
| 11_L | 14_R | 1.213 | 0.98 |
| 432_N | 490_Y | 1.210 | 0.98 |
| 42_I | 444_Y | 1.203 | 0.98 |
| 17_I | 66_F | 1.198 | 0.98 |
| 429_G | 458_Y | 1.197 | 0.98 |
| 42_I | 415_L | 1.197 | 0.98 |
| 9_Y | 35_F | 1.190 | 0.98 |
| 146_A | 154_V | 1.187 | 0.98 |
| 22_G | 41_Y | 1.186 | 0.98 |
| 129_P | 135_V | 1.182 | 0.98 |
| 30_P | 164_D | 1.178 | 0.98 |
| 15_Q | 140_S | 1.175 | 0.98 |
| 75_T | 118_L | 1.173 | 0.98 |
| 31_F | 158_V | 1.161 | 0.97 |
| 396_Y | 405_F | 1.154 | 0.97 |
| 3_S | 166_D | 1.152 | 0.97 |
| 431_A | 483_F | 1.150 | 0.97 |
| 75_T | 119_P | 1.145 | 0.97 |
| 79_M | 119_P | 1.141 | 0.97 |
| 127_Y | 141_R | 1.141 | 0.97 |
| 93_I | 146_A | 1.139 | 0.97 |
| 414_Q | 421_Q | 1.137 | 0.97 |
| 7_T | 167_A | 1.135 | 0.97 |
| 451_V | 503_L | 1.131 | 0.97 |
| 415_L | 446_I | 1.129 | 0.97 |
| 432_N | 481_I | 1.124 | 0.97 |
| 204_A | 264_L | 1.124 | 0.97 |
| 466_G | 473_V | 1.123 | 0.97 |
| 488_K | 493_Q | 1.122 | 0.97 |
| 56_G | 412_G | 1.122 | 0.97 |
| 129_P | 158_V | 1.121 | 0.97 |
| 202_N | 268_D | 1.120 | 0.96 |
| 219_D | 322_A | 1.119 | 0.96 |
| 222_M | 332_S | 1.116 | 0.96 |
| 494_A | 518_L | 1.114 | 0.96 |
| 431_A | 438_L | 1.112 | 0.96 |
| 129_P | 159_P | 1.110 | 0.96 |
| 138_A | 142_A | 1.105 | 0.96 |
| 207_L | 231_V | 1.104 | 0.96 |
| 194_V | 325_L | 1.103 | 0.96 |
| 21_F | 57_Y | 1.100 | 0.96 |
| 57_Y | 416_A | 1.100 | 0.96 |
| 77_N | 80_G | 1.098 | 0.96 |
| 391_N | 394_S | 1.098 | 0.96 |
| 456_G | 522_S | 1.098 | 0.96 |
| 411_I | 440_T | 1.096 | 0.96 |
| 492_V | 516_P | 1.095 | 0.96 |
| 414_Q | 447_P | 1.094 | 0.96 |
| 211_V | 220_C | 1.088 | 0.96 |
| 56_G | 60_A | 1.085 | 0.96 |
| 196_A | 294_R | 1.082 | 0.95 |
| 109_L | 403_L | 1.072 | 0.95 |
| 198_N | 332_S | 1.072 | 0.95 |
| 360_D | 364_D | 1.068 | 0.95 |
| 361_T | 365_M | 1.064 | 0.95 |
| 44_A | 50_V | 1.064 | 0.95 |
| 423_I | 449_I | 1.064 | 0.95 |
| 424_A | 430_S | 1.063 | 0.95 |
| 20_V | 66_F | 1.062 | 0.95 |
| 49_C | 437_A | 1.058 | 0.95 |
| 305_A | 315_V | 1.055 | 0.95 |
| 204_A | 270_V | 1.050 | 0.94 |
| 258_A | 262_Q | 1.048 | 0.94 |
| 262_Q | 266_G | 1.046 | 0.94 |
| 501_E | 505_G | 1.045 | 0.94 |
| 159_P | 162_D | 1.038 | 0.94 |
| 20_V | 68_N | 1.037 | 0.94 |
| 85_A | 92_L | 1.032 | 0.94 |
| 113_V | 402_G | 1.031 | 0.94 |
| 361_T | 503_L | 1.031 | 0.94 |
| 209_P | 236_S | 1.030 | 0.94 |
| 207_L | 211_V | 1.029 | 0.94 |
| 435_I | 490_Y | 1.029 | 0.94 |
| 421_Q | 511_L | 1.022 | 0.93 |
| 222_M | 328_L | 1.019 | 0.93 |
| 132_A | 165_K | 1.018 | 0.93 |
| 363_N | 388_N | 1.017 | 0.93 |
| 51_V | 67_I | 1.017 | 0.93 |
| 426_I | 434_S | 1.015 | 0.93 |
| 100_T | 103_M | 1.015 | 0.93 |
| 78_A | 96_A | 1.013 | 0.93 |
| 510_A | 517_V | 1.013 | 0.93 |
| 502_Q | 506_S | 1.012 | 0.93 |
| 431_A | 452_I | 1.012 | 0.93 |
| 19_T | 42_I | 1.010 | 0.93 |
| 192_I | 195_K | 1.008 | 0.93 |
| 58_A | 65_A | 1.006 | 0.93 |
| 115_A | 155_Y | 1.005 | 0.93 |
| 145_M | 150_P | 1.005 | 0.93 |
| 373_L | 384_W | 1.004 | 0.93 |
| 425_V | 451_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 | |
| 1q6zA | 1 | 0.9848 | 100 | 0.138 | Contact Map |
| 4k9qA | 2 | 0.9848 | 100 | 0.16 | Contact Map |
| 4q9dA | 2 | 0 | 100 | 0.161 | Contact Map |
| 1ozhA | 4 | 0.9735 | 100 | 0.181 | Contact Map |
| 2panA | 6 | 0.9886 | 100 | 0.184 | Contact Map |
| 2ihtA | 4 | 0.9811 | 100 | 0.186 | Contact Map |
| 4rjjA | 8 | 0.983 | 100 | 0.187 | Contact Map |
| 2uz1A | 2 | 0.9905 | 100 | 0.188 | Contact Map |
| 1t9bA | 2 | 0.9867 | 100 | 0.188 | Contact Map |
| 1ybhA | 1 | 0.9848 | 100 | 0.19 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)