| Andrew Yang |
| ID: | 1490332662 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 595 (556) | ||
| Sequences: | 1161 (627.2) | ||
| Seq/Len: | 2.088 | ||
| Nf(neff/√len): | 26.6 |
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: 2.088).
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 |
| 257_D | 314_Y | 5.204 | 1.00 |
| 251_Y | 358_G | 3.612 | 1.00 |
| 507_R | 529_E | 3.346 | 1.00 |
| 397_E | 400_K | 3.331 | 1.00 |
| 488_V | 493_I | 3.289 | 1.00 |
| 393_S | 462_D | 3.002 | 1.00 |
| 154_V | 198_P | 2.990 | 1.00 |
| 183_E | 200_E | 2.877 | 1.00 |
| 343_A | 347_D | 2.767 | 1.00 |
| 97_F | 181_G | 2.600 | 1.00 |
| 368_K | 382_E | 2.561 | 1.00 |
| 338_F | 348_L | 2.454 | 1.00 |
| 319_Q | 335_T | 2.423 | 1.00 |
| 154_V | 182_V | 2.328 | 1.00 |
| 125_K | 183_E | 2.281 | 1.00 |
| 475_R | 482_E | 2.248 | 1.00 |
| 474_H | 482_E | 2.238 | 1.00 |
| 340_M | 343_A | 2.186 | 1.00 |
| 259_L | 354_K | 2.182 | 1.00 |
| 306_V | 542_T | 2.177 | 1.00 |
| 393_S | 396_E | 2.175 | 1.00 |
| 187_G | 197_I | 2.149 | 1.00 |
| 389_F | 486_L | 2.103 | 0.99 |
| 372_H | 558_D | 2.101 | 0.99 |
| 130_I | 174_L | 2.077 | 0.99 |
| 357_S | 387_P | 2.070 | 0.99 |
| 452_V | 490_K | 2.022 | 0.99 |
| 368_K | 384_D | 1.969 | 0.99 |
| 144_D | 151_K | 1.964 | 0.99 |
| 256_L | 355_M | 1.962 | 0.99 |
| 284_Y | 289_D | 1.960 | 0.99 |
| 370_T | 380_A | 1.938 | 0.99 |
| 399_E | 405_K | 1.936 | 0.99 |
| 505_R | 508_Q | 1.931 | 0.99 |
| 284_Y | 291_N | 1.918 | 0.99 |
| 30_K | 37_A | 1.916 | 0.99 |
| 28_A | 32_L | 1.914 | 0.99 |
| 36_E | 40_K | 1.884 | 0.98 |
| 298_P | 319_Q | 1.873 | 0.98 |
| 83_Q | 87_V | 1.864 | 0.98 |
| 401_A | 453_T | 1.857 | 0.98 |
| 507_R | 532_C | 1.789 | 0.98 |
| 367_Y | 386_T | 1.786 | 0.98 |
| 279_K | 522_D | 1.776 | 0.97 |
| 462_D | 474_H | 1.769 | 0.97 |
| 241_K | 559_S | 1.766 | 0.97 |
| 231_D | 235_N | 1.759 | 0.97 |
| 242_F | 567_L | 1.741 | 0.97 |
| 250_T | 254_S | 1.740 | 0.97 |
| 254_S | 258_E | 1.721 | 0.97 |
| 529_E | 532_C | 1.715 | 0.97 |
| 357_S | 367_Y | 1.712 | 0.97 |
| 397_E | 401_A | 1.710 | 0.97 |
| 350_E | 354_K | 1.701 | 0.96 |
| 512_E | 515_K | 1.698 | 0.96 |
| 340_M | 351_I | 1.692 | 0.96 |
| 505_R | 509_L | 1.682 | 0.96 |
| 126_V | 152_L | 1.680 | 0.96 |
| 253_R | 263_E | 1.677 | 0.96 |
| 443_D | 467_M | 1.676 | 0.96 |
| 336_C | 545_W | 1.672 | 0.96 |
| 471_A | 497_Y | 1.668 | 0.96 |
| 443_D | 447_G | 1.662 | 0.96 |
| 312_R | 340_M | 1.658 | 0.96 |
| 17_L | 20_N | 1.647 | 0.96 |
| 252_I | 355_M | 1.646 | 0.96 |
| 254_S | 257_D | 1.641 | 0.95 |
| 357_S | 386_T | 1.634 | 0.95 |
| 244_V | 557_T | 1.612 | 0.95 |
| 298_P | 301_Y | 1.607 | 0.95 |
| 152_L | 196_I | 1.602 | 0.95 |
| 419_K | 423_D | 1.597 | 0.94 |
| 140_L | 155_M | 1.591 | 0.94 |
| 124_L | 196_I | 1.589 | 0.94 |
| 307_V | 535_L | 1.586 | 0.94 |
| 21_E | 25_R | 1.576 | 0.94 |
| 306_V | 539_L | 1.565 | 0.94 |
| 404_V | 427_A | 1.549 | 0.93 |
| 155_M | 189_T | 1.548 | 0.93 |
| 251_Y | 359_M | 1.540 | 0.93 |
| 109_E | 122_V | 1.538 | 0.93 |
| 539_L | 542_T | 1.523 | 0.92 |
| 507_R | 511_E | 1.523 | 0.92 |
| 251_Y | 362_S | 1.522 | 0.92 |
| 95_H | 498_T | 1.520 | 0.92 |
| 282_I | 293_Y | 1.516 | 0.92 |
| 110_Y | 122_V | 1.504 | 0.92 |
| 353_E | 391_R | 1.497 | 0.92 |
| 472_K | 501_N | 1.490 | 0.91 |
| 236_D | 240_Q | 1.486 | 0.91 |
| 360_V | 385_F | 1.482 | 0.91 |
| 512_E | 516_A | 1.482 | 0.91 |
| 268_M | 317_G | 1.479 | 0.91 |
| 250_T | 257_D | 1.476 | 0.91 |
| 304_M | 530_N | 1.460 | 0.90 |
| 75_Y | 79_S | 1.456 | 0.90 |
| 438_T | 466_I | 1.452 | 0.90 |
| 130_I | 143_Y | 1.441 | 0.89 |
| 348_L | 543_A | 1.426 | 0.89 |
| 349_M | 391_R | 1.413 | 0.88 |
| 298_P | 335_T | 1.411 | 0.88 |
| 265_E | 318_R | 1.410 | 0.88 |
| 353_E | 388_P | 1.404 | 0.88 |
| 145_L | 182_V | 1.402 | 0.88 |
| 476_S | 479_G | 1.396 | 0.87 |
| 114_Q | 117_D | 1.395 | 0.87 |
| 209_H | 536_E | 1.390 | 0.87 |
| 520_G | 523_E | 1.389 | 0.87 |
| 79_S | 504_V | 1.381 | 0.87 |
| 423_D | 427_A | 1.377 | 0.86 |
| 260_G | 312_R | 1.361 | 0.86 |
| 100_D | 125_K | 1.356 | 0.85 |
| 179_I | 342_Y | 1.350 | 0.85 |
| 346_H | 350_E | 1.348 | 0.85 |
| 224_R | 231_D | 1.341 | 0.84 |
| 273_P | 526_F | 1.334 | 0.84 |
| 484_F | 496_A | 1.333 | 0.84 |
| 520_G | 524_A | 1.333 | 0.84 |
| 392_I | 397_E | 1.333 | 0.84 |
| 446_V | 460_I | 1.328 | 0.84 |
| 514_A | 518_A | 1.323 | 0.83 |
| 392_I | 458_T | 1.321 | 0.83 |
| 415_E | 418_R | 1.321 | 0.83 |
| 174_L | 203_L | 1.320 | 0.83 |
| 84_Q | 87_V | 1.319 | 0.83 |
| 181_G | 204_L | 1.314 | 0.83 |
| 383_V | 489_M | 1.306 | 0.82 |
| 425_C | 441_L | 1.299 | 0.82 |
| 69_L | 73_Q | 1.298 | 0.82 |
| 394_M | 446_V | 1.296 | 0.81 |
| 261_F | 340_M | 1.292 | 0.81 |
| 105_Q | 109_E | 1.289 | 0.81 |
| 521_D | 524_A | 1.289 | 0.81 |
| 255_F | 354_K | 1.278 | 0.80 |
| 352_T | 545_W | 1.277 | 0.80 |
| 29_E | 32_L | 1.272 | 0.80 |
| 473_W | 505_R | 1.270 | 0.80 |
| 500_L | 509_L | 1.264 | 0.79 |
| 186_P | 196_I | 1.263 | 0.79 |
| 397_E | 450_L | 1.259 | 0.79 |
| 345_Y | 462_D | 1.258 | 0.79 |
| 548_G | 551_R | 1.251 | 0.78 |
| 123_T | 183_E | 1.250 | 0.78 |
| 227_Q | 533_T | 1.250 | 0.78 |
| 465_Q | 473_W | 1.247 | 0.78 |
| 392_I | 453_T | 1.245 | 0.78 |
| 218_L | 223_T | 1.245 | 0.78 |
| 446_V | 487_F | 1.243 | 0.78 |
| 489_M | 555_F | 1.241 | 0.77 |
| 325_I | 563_K | 1.236 | 0.77 |
| 356_L | 486_L | 1.230 | 0.77 |
| 17_L | 29_E | 1.221 | 0.76 |
| 252_I | 256_L | 1.220 | 0.76 |
| 221_K | 225_Y | 1.216 | 0.75 |
| 394_M | 460_I | 1.216 | 0.75 |
| 230_L | 537_Y | 1.213 | 0.75 |
| 229_Y | 537_Y | 1.206 | 0.75 |
| 566_L | 570_A | 1.206 | 0.75 |
| 361_K | 367_Y | 1.206 | 0.75 |
| 397_E | 453_T | 1.205 | 0.74 |
| 507_R | 536_E | 1.199 | 0.74 |
| 296_I | 304_M | 1.197 | 0.74 |
| 182_V | 196_I | 1.192 | 0.73 |
| 29_E | 36_E | 1.188 | 0.73 |
| 106_F | 186_P | 1.187 | 0.73 |
| 379_Q | 558_D | 1.187 | 0.73 |
| 554_M | 562_I | 1.186 | 0.73 |
| 273_P | 293_Y | 1.181 | 0.72 |
| 396_E | 477_K | 1.180 | 0.72 |
| 128_G | 145_L | 1.179 | 0.72 |
| 272_I | 293_Y | 1.167 | 0.71 |
| 102_S | 105_Q | 1.166 | 0.71 |
| 80_Q | 83_Q | 1.163 | 0.71 |
| 390_R | 400_K | 1.163 | 0.71 |
| 491_K | 555_F | 1.163 | 0.71 |
| 424_I | 428_K | 1.159 | 0.70 |
| 36_E | 39_Q | 1.153 | 0.70 |
| 370_T | 382_E | 1.149 | 0.69 |
| 152_L | 180_I | 1.147 | 0.69 |
| 422_D | 436_R | 1.145 | 0.69 |
| 552_L | 557_T | 1.144 | 0.69 |
| 547_M | 552_L | 1.144 | 0.69 |
| 143_Y | 154_V | 1.143 | 0.69 |
| 268_M | 298_P | 1.143 | 0.69 |
| 338_F | 545_W | 1.138 | 0.68 |
| 222_E | 226_R | 1.137 | 0.68 |
| 26_L | 29_E | 1.131 | 0.68 |
| 246_S | 314_Y | 1.130 | 0.68 |
| 101_I | 109_E | 1.130 | 0.68 |
| 24_R | 31_K | 1.123 | 0.67 |
| 412_F | 417_T | 1.123 | 0.67 |
| 264_I | 302_H | 1.121 | 0.67 |
| 425_C | 430_V | 1.119 | 0.66 |
| 463_H | 467_M | 1.118 | 0.66 |
| 126_V | 196_I | 1.114 | 0.66 |
| 252_I | 549_I | 1.114 | 0.66 |
| 547_M | 557_T | 1.111 | 0.66 |
| 345_Y | 474_H | 1.109 | 0.65 |
| 396_E | 399_E | 1.107 | 0.65 |
| 423_D | 549_I | 1.101 | 0.65 |
| 569_P | 573_P | 1.097 | 0.64 |
| 179_I | 242_F | 1.095 | 0.64 |
| 345_Y | 482_E | 1.095 | 0.64 |
| 61_G | 64_A | 1.094 | 0.64 |
| 328_T | 491_K | 1.093 | 0.64 |
| 440_R | 443_D | 1.088 | 0.63 |
| 49_Q | 53_A | 1.087 | 0.63 |
| 66_E | 175_R | 1.084 | 0.63 |
| 330_N | 566_L | 1.084 | 0.63 |
| 485_E | 495_N | 1.082 | 0.63 |
| 136_S | 140_L | 1.079 | 0.62 |
| 32_L | 39_Q | 1.076 | 0.62 |
| 268_M | 301_Y | 1.075 | 0.62 |
| 428_K | 449_F | 1.075 | 0.62 |
| 462_D | 482_E | 1.075 | 0.62 |
| 514_A | 527_I | 1.070 | 0.61 |
| 288_L | 325_I | 1.066 | 0.61 |
| 418_R | 422_D | 1.066 | 0.61 |
| 213_H | 216_F | 1.065 | 0.61 |
| 17_L | 32_L | 1.064 | 0.61 |
| 86_K | 91_D | 1.064 | 0.61 |
| 285_H | 288_L | 1.060 | 0.60 |
| 21_E | 24_R | 1.057 | 0.60 |
| 344_D | 388_P | 1.055 | 0.60 |
| 93_Y | 504_V | 1.054 | 0.60 |
| 146_R | 151_K | 1.054 | 0.60 |
| 259_L | 340_M | 1.053 | 0.59 |
| 14_E | 18_S | 1.050 | 0.59 |
| 459_F | 486_L | 1.045 | 0.59 |
| 240_Q | 244_V | 1.045 | 0.59 |
| 147_G | 150_V | 1.044 | 0.58 |
| 156_A | 201_I | 1.043 | 0.58 |
| 213_H | 217_G | 1.042 | 0.58 |
| 189_T | 193_E | 1.042 | 0.58 |
| 155_M | 187_G | 1.040 | 0.58 |
| 79_S | 230_L | 1.037 | 0.58 |
| 569_P | 572_K | 1.037 | 0.58 |
| 447_G | 451_E | 1.035 | 0.57 |
| 262_L | 310_I | 1.033 | 0.57 |
| 76_K | 80_Q | 1.030 | 0.57 |
| 495_N | 501_N | 1.030 | 0.57 |
| 174_L | 201_I | 1.021 | 0.56 |
| 237_F | 240_Q | 1.021 | 0.56 |
| 370_T | 558_D | 1.020 | 0.56 |
| 16_K | 29_E | 1.017 | 0.55 |
| 22_L | 25_R | 1.016 | 0.55 |
| 17_L | 30_K | 1.015 | 0.55 |
| 507_R | 527_I | 1.015 | 0.55 |
| 247_K | 250_T | 1.015 | 0.55 |
| 317_G | 335_T | 1.012 | 0.55 |
| 222_E | 537_Y | 1.011 | 0.55 |
| 179_I | 233_I | 1.007 | 0.54 |
| 359_M | 363_I | 1.006 | 0.54 |
| 454_C | 458_T | 1.004 | 0.54 |
| 511_E | 514_A | 1.004 | 0.54 |
| 568_F | 572_K | 1.003 | 0.54 |
| 396_E | 400_K | 1.002 | 0.54 |
| 422_D | 426_V | 1.001 | 0.54 |
| 224_R | 235_N | 1.000 | 0.54 |
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 | |
| 4ycuA | 2 | 0 | 100 | 0.335 | Contact Map |
| 4up7A | 1 | 0.8723 | 100 | 0.337 | Contact Map |
| 4pg3A | 4 | 0.8118 | 100 | 0.343 | Contact Map |
| 4ex5A | 2 | 0.8084 | 100 | 0.359 | Contact Map |
| 1e1oA | 1 | 0.8118 | 100 | 0.388 | Contact Map |
| 3a74A | 4 | 0.8118 | 100 | 0.404 | Contact Map |
| 1l0wA | 2 | 0.7681 | 100 | 0.496 | Contact Map |
| 1eovA | 1 | 0.7647 | 100 | 0.508 | Contact Map |
| 1c0aA | 1 | 0.7664 | 100 | 0.512 | Contact Map |
| 3i7fA | 2 | 0.7496 | 100 | 0.516 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)