| xcc |
| ID: | 1484894865 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 791 (746) | ||
| Sequences: | 13912 (9379.4) | ||
| Seq/Len: | 18.649 | ||
| Nf(neff/√len): | 343.4 |
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: 18.649).
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 |
| 664_V | 691_F | 5.566 | 1.00 |
| 622_A | 645_H | 5.503 | 1.00 |
| 226_G | 310_F | 5.261 | 1.00 |
| 498_Y | 547_N | 5.194 | 1.00 |
| 710_L | 730_T | 5.136 | 1.00 |
| 732_V | 754_F | 4.939 | 1.00 |
| 496_L | 549_L | 4.429 | 1.00 |
| 563_L | 607_L | 4.255 | 1.00 |
| 234_Y | 302_R | 4.159 | 1.00 |
| 228_V | 308_A | 3.928 | 1.00 |
| 569_V | 601_R | 3.789 | 1.00 |
| 489_K | 557_Y | 3.629 | 1.00 |
| 490_L | 557_Y | 3.603 | 1.00 |
| 618_A | 649_L | 3.442 | 1.00 |
| 196_F | 213_G | 3.362 | 1.00 |
| 316_W | 396_R | 3.327 | 1.00 |
| 643_K | 672_A | 3.316 | 1.00 |
| 705_Q | 737_D | 3.240 | 1.00 |
| 188_W | 221_R | 3.202 | 1.00 |
| 571_R | 601_R | 3.148 | 1.00 |
| 712_G | 730_T | 3.132 | 1.00 |
| 498_Y | 549_L | 3.129 | 1.00 |
| 226_G | 308_A | 3.103 | 1.00 |
| 128_R | 152_I | 3.096 | 1.00 |
| 666_W | 691_F | 3.027 | 1.00 |
| 232_G | 302_R | 3.023 | 1.00 |
| 559_I | 565_A | 2.990 | 1.00 |
| 230_V | 306_A | 2.961 | 1.00 |
| 492_I | 555_G | 2.904 | 1.00 |
| 227_Y | 309_W | 2.874 | 1.00 |
| 710_L | 732_V | 2.851 | 1.00 |
| 192_I | 217_A | 2.844 | 1.00 |
| 44_T | 130_E | 2.823 | 1.00 |
| 236_N | 300_I | 2.810 | 1.00 |
| 126_M | 151_F | 2.771 | 1.00 |
| 748_L | 783_T | 2.749 | 1.00 |
| 563_L | 609_W | 2.740 | 1.00 |
| 161_G | 180_Y | 2.718 | 1.00 |
| 405_L | 483_L | 2.701 | 1.00 |
| 232_G | 304_I | 2.691 | 1.00 |
| 746_V | 787_L | 2.676 | 1.00 |
| 657_G | 699_Y | 2.666 | 1.00 |
| 47_A | 51_E | 2.651 | 1.00 |
| 758_G | 778_I | 2.630 | 1.00 |
| 320_D | 392_L | 2.626 | 1.00 |
| 715_E | 725_K | 2.624 | 1.00 |
| 324_I | 388_V | 2.612 | 1.00 |
| 712_G | 728_G | 2.607 | 1.00 |
| 165_V | 176_I | 2.579 | 1.00 |
| 645_H | 668_D | 2.578 | 1.00 |
| 230_V | 304_I | 2.575 | 1.00 |
| 661_N | 696_T | 2.563 | 1.00 |
| 707_G | 735_F | 2.541 | 1.00 |
| 415_R | 475_D | 2.533 | 1.00 |
| 744_L | 789_Y | 2.532 | 1.00 |
| 548_Y | 599_V | 2.527 | 1.00 |
| 491_S | 558_L | 2.500 | 1.00 |
| 161_G | 791_F | 2.496 | 1.00 |
| 565_A | 607_L | 2.489 | 1.00 |
| 616_L | 651_A | 2.467 | 1.00 |
| 318_L | 394_L | 2.457 | 1.00 |
| 182_A | 190_F | 2.440 | 1.00 |
| 734_L | 753_L | 2.433 | 1.00 |
| 747_A | 786_S | 2.416 | 1.00 |
| 190_F | 219_L | 2.413 | 1.00 |
| 490_L | 555_G | 2.376 | 1.00 |
| 605_A | 620_A | 2.353 | 1.00 |
| 748_L | 785_L | 2.331 | 1.00 |
| 130_E | 150_N | 2.304 | 1.00 |
| 662_G | 695_L | 2.298 | 1.00 |
| 500_M | 545_D | 2.297 | 1.00 |
| 194_G | 215_L | 2.292 | 1.00 |
| 658_F | 697_P | 2.280 | 1.00 |
| 706_F | 736_G | 2.266 | 1.00 |
| 708_V | 732_V | 2.210 | 1.00 |
| 708_V | 734_L | 2.192 | 1.00 |
| 410_G | 480_Y | 2.178 | 1.00 |
| 621_F | 667_T | 2.165 | 1.00 |
| 187_H | 221_R | 2.164 | 1.00 |
| 560_N | 563_L | 2.150 | 1.00 |
| 663_G | 694_Q | 2.148 | 1.00 |
| 162_S | 790_D | 2.117 | 1.00 |
| 614_L | 653_Y | 2.114 | 1.00 |
| 320_D | 390_N | 2.113 | 1.00 |
| 737_D | 745_T | 2.112 | 1.00 |
| 745_T | 788_R | 2.110 | 1.00 |
| 740_I | 746_V | 2.103 | 1.00 |
| 622_A | 643_K | 2.102 | 1.00 |
| 46_G | 49_A | 2.092 | 1.00 |
| 188_W | 219_L | 2.086 | 1.00 |
| 660_V | 697_P | 2.081 | 1.00 |
| 192_I | 215_L | 2.066 | 1.00 |
| 198_Q | 211_K | 2.062 | 1.00 |
| 65_I | 131_A | 2.060 | 1.00 |
| 746_V | 785_L | 2.058 | 1.00 |
| 739_R | 745_T | 2.058 | 1.00 |
| 190_F | 194_G | 2.055 | 1.00 |
| 620_A | 645_H | 2.044 | 1.00 |
| 569_V | 603_T | 2.037 | 1.00 |
| 194_G | 213_G | 2.035 | 1.00 |
| 750_V | 783_T | 2.031 | 1.00 |
| 571_R | 599_V | 2.024 | 1.00 |
| 100_E | 153_S | 2.024 | 1.00 |
| 618_A | 647_I | 2.021 | 1.00 |
| 316_W | 394_L | 2.017 | 1.00 |
| 163_V | 789_Y | 2.006 | 1.00 |
| 617_F | 650_E | 1.987 | 1.00 |
| 322_F | 390_N | 1.987 | 1.00 |
| 67_G | 665_T | 1.976 | 1.00 |
| 620_A | 647_I | 1.973 | 1.00 |
| 225_N | 310_F | 1.972 | 1.00 |
| 172_D | 200_D | 1.969 | 1.00 |
| 709_N | 733_N | 1.939 | 1.00 |
| 228_V | 306_A | 1.936 | 1.00 |
| 164_G | 788_R | 1.933 | 1.00 |
| 750_V | 753_L | 1.929 | 1.00 |
| 559_I | 607_L | 1.921 | 1.00 |
| 750_V | 781_R | 1.906 | 1.00 |
| 489_K | 559_I | 1.867 | 1.00 |
| 704_Y | 738_Y | 1.865 | 1.00 |
| 415_R | 473_R | 1.846 | 1.00 |
| 613_G | 653_Y | 1.835 | 1.00 |
| 227_Y | 311_D | 1.829 | 1.00 |
| 556_N | 564_G | 1.825 | 1.00 |
| 599_V | 627_E | 1.818 | 1.00 |
| 744_L | 787_L | 1.816 | 1.00 |
| 163_V | 178_F | 1.812 | 1.00 |
| 655_Y | 697_P | 1.804 | 1.00 |
| 21_L | 24_V | 1.800 | 1.00 |
| 326_D | 386_G | 1.799 | 1.00 |
| 393_S | 480_Y | 1.793 | 1.00 |
| 229_R | 307_E | 1.774 | 1.00 |
| 731_Q | 778_I | 1.773 | 1.00 |
| 397_E | 406_N | 1.769 | 1.00 |
| 165_V | 174_T | 1.747 | 1.00 |
| 413_T | 477_N | 1.742 | 1.00 |
| 57_S | 60_E | 1.739 | 1.00 |
| 566_F | 619_T | 1.736 | 1.00 |
| 167_R | 172_D | 1.731 | 1.00 |
| 658_F | 699_Y | 1.719 | 1.00 |
| 319_S | 393_S | 1.715 | 1.00 |
| 164_G | 177_D | 1.713 | 1.00 |
| 406_N | 484_T | 1.711 | 1.00 |
| 323_R | 389_T | 1.708 | 1.00 |
| 708_V | 753_L | 1.694 | 1.00 |
| 749_N | 784_S | 1.691 | 1.00 |
| 220_T | 227_Y | 1.690 | 1.00 |
| 609_W | 616_L | 1.685 | 1.00 |
| 500_M | 547_N | 1.681 | 1.00 |
| 409_M | 481_V | 1.680 | 1.00 |
| 624_R | 643_K | 1.665 | 1.00 |
| 684_V | 690_D | 1.664 | 1.00 |
| 739_R | 790_D | 1.662 | 1.00 |
| 603_T | 624_R | 1.659 | 1.00 |
| 596_A | 627_E | 1.651 | 1.00 |
| 567_A | 605_A | 1.651 | 1.00 |
| 83_V | 147_G | 1.651 | 1.00 |
| 322_F | 388_V | 1.647 | 1.00 |
| 101_D | 153_S | 1.646 | 1.00 |
| 222_L | 227_Y | 1.644 | 1.00 |
| 554_G | 568_R | 1.626 | 1.00 |
| 84_R | 648_E | 1.625 | 1.00 |
| 693_W | 712_G | 1.620 | 1.00 |
| 486_D | 491_S | 1.615 | 1.00 |
| 225_N | 311_D | 1.609 | 1.00 |
| 621_F | 665_T | 1.609 | 1.00 |
| 162_S | 788_R | 1.606 | 1.00 |
| 411_Y | 477_N | 1.601 | 1.00 |
| 190_F | 217_A | 1.599 | 1.00 |
| 487_S | 490_L | 1.595 | 1.00 |
| 312_L | 318_L | 1.595 | 1.00 |
| 318_L | 392_L | 1.573 | 1.00 |
| 412_Y | 478_A | 1.569 | 1.00 |
| 405_L | 485_F | 1.565 | 1.00 |
| 315_G | 396_R | 1.564 | 1.00 |
| 160_G | 181_G | 1.561 | 1.00 |
| 48_E | 52_Q | 1.558 | 1.00 |
| 37_K | 558_L | 1.556 | 1.00 |
| 696_T | 709_N | 1.552 | 1.00 |
| 607_L | 618_A | 1.550 | 1.00 |
| 66_P | 650_E | 1.536 | 1.00 |
| 196_F | 211_K | 1.531 | 1.00 |
| 234_Y | 300_I | 1.529 | 1.00 |
| 664_V | 693_W | 1.515 | 1.00 |
| 610_R | 615_S | 1.508 | 1.00 |
| 691_F | 714_T | 1.501 | 1.00 |
| 628_Q | 642_Y | 1.497 | 1.00 |
| 647_I | 666_W | 1.489 | 1.00 |
| 309_W | 317_N | 1.486 | 1.00 |
| 50_I | 61_I | 1.476 | 1.00 |
| 745_T | 790_D | 1.472 | 1.00 |
| 731_Q | 758_G | 1.464 | 1.00 |
| 567_A | 603_T | 1.457 | 1.00 |
| 166_S | 175_R | 1.456 | 1.00 |
| 189_Q | 220_T | 1.452 | 1.00 |
| 178_F | 194_G | 1.451 | 1.00 |
| 659_T | 698_S | 1.451 | 1.00 |
| 477_N | 500_M | 1.450 | 1.00 |
| 624_R | 641_S | 1.449 | 1.00 |
| 164_G | 786_S | 1.437 | 1.00 |
| 711_I | 733_N | 1.434 | 1.00 |
| 127_D | 155_T | 1.434 | 1.00 |
| 603_T | 622_A | 1.431 | 1.00 |
| 166_S | 786_S | 1.429 | 1.00 |
| 223_F | 228_V | 1.425 | 1.00 |
| 313_G | 316_W | 1.419 | 1.00 |
| 551_Y | 571_R | 1.419 | 1.00 |
| 317_N | 395_S | 1.417 | 1.00 |
| 494_G | 553_L | 1.413 | 1.00 |
| 753_L | 781_R | 1.413 | 1.00 |
| 659_T | 700_R | 1.412 | 1.00 |
| 162_S | 179_N | 1.410 | 1.00 |
| 159_E | 180_Y | 1.410 | 1.00 |
| 60_E | 63_R | 1.409 | 1.00 |
| 667_T | 688_Q | 1.406 | 0.99 |
| 400_G | 403_R | 1.401 | 0.99 |
| 665_T | 692_V | 1.394 | 0.99 |
| 399_G | 404_T | 1.386 | 0.99 |
| 168_G | 173_N | 1.375 | 0.99 |
| 502_D | 545_D | 1.370 | 0.99 |
| 157_D | 189_Q | 1.369 | 0.99 |
| 130_E | 152_I | 1.366 | 0.99 |
| 785_L | 789_Y | 1.365 | 0.99 |
| 101_D | 231_Y | 1.362 | 0.99 |
| 400_G | 405_L | 1.360 | 0.99 |
| 616_L | 649_L | 1.355 | 0.99 |
| 309_W | 319_S | 1.354 | 0.99 |
| 641_S | 673_R | 1.353 | 0.99 |
| 601_R | 624_R | 1.344 | 0.99 |
| 103_L | 321_K | 1.343 | 0.99 |
| 101_D | 218_N | 1.340 | 0.99 |
| 53_S | 64_N | 1.337 | 0.99 |
| 127_D | 154_K | 1.334 | 0.99 |
| 614_L | 651_A | 1.333 | 0.99 |
| 698_S | 707_G | 1.321 | 0.99 |
| 324_I | 386_G | 1.319 | 0.99 |
| 662_G | 693_W | 1.308 | 0.99 |
| 626_Q | 641_S | 1.306 | 0.99 |
| 488_G | 557_Y | 1.304 | 0.99 |
| 602_Q | 623_A | 1.303 | 0.99 |
| 215_L | 234_Y | 1.300 | 0.99 |
| 734_L | 750_V | 1.296 | 0.99 |
| 478_A | 497_R | 1.294 | 0.99 |
| 133_R | 648_E | 1.292 | 0.99 |
| 666_W | 690_D | 1.291 | 0.99 |
| 599_V | 626_Q | 1.291 | 0.99 |
| 499_D | 550_S | 1.289 | 0.99 |
| 736_G | 750_V | 1.288 | 0.99 |
| 48_E | 51_E | 1.288 | 0.99 |
| 161_G | 178_F | 1.287 | 0.99 |
| 403_R | 485_F | 1.282 | 0.99 |
| 642_Y | 685_P | 1.282 | 0.99 |
| 559_I | 563_L | 1.280 | 0.99 |
| 404_T | 486_D | 1.280 | 0.99 |
| 717_Y | 725_K | 1.279 | 0.99 |
| 478_A | 499_D | 1.277 | 0.99 |
| 491_S | 556_N | 1.273 | 0.99 |
| 163_V | 176_I | 1.272 | 0.99 |
| 20_N | 23_S | 1.272 | 0.99 |
| 572_G | 600_V | 1.267 | 0.99 |
| 408_R | 484_T | 1.265 | 0.99 |
| 411_Y | 479_P | 1.263 | 0.99 |
| 220_T | 229_R | 1.262 | 0.99 |
| 751_N | 782_T | 1.261 | 0.99 |
| 66_P | 663_G | 1.261 | 0.99 |
| 655_Y | 660_V | 1.253 | 0.99 |
| 701_G | 706_F | 1.252 | 0.99 |
| 732_V | 753_L | 1.252 | 0.99 |
| 185_A | 188_W | 1.244 | 0.98 |
| 34_T | 37_K | 1.243 | 0.98 |
| 566_F | 606_G | 1.243 | 0.98 |
| 787_L | 791_F | 1.241 | 0.98 |
| 683_N | 722_N | 1.239 | 0.98 |
| 711_I | 731_Q | 1.238 | 0.98 |
| 704_Y | 736_G | 1.238 | 0.98 |
| 195_F | 214_Q | 1.237 | 0.98 |
| 502_D | 543_D | 1.232 | 0.98 |
| 660_V | 695_L | 1.230 | 0.98 |
| 558_L | 564_G | 1.226 | 0.98 |
| 218_N | 229_R | 1.222 | 0.98 |
| 407_L | 481_V | 1.221 | 0.98 |
| 81_I | 149_I | 1.220 | 0.98 |
| 555_G | 559_I | 1.216 | 0.98 |
| 233_K | 303_T | 1.214 | 0.98 |
| 713_T | 729_Y | 1.211 | 0.98 |
| 632_V | 637_F | 1.207 | 0.98 |
| 479_P | 498_Y | 1.200 | 0.98 |
| 326_D | 384_D | 1.200 | 0.98 |
| 504_R | 543_D | 1.199 | 0.98 |
| 615_S | 652_S | 1.195 | 0.98 |
| 563_L | 567_A | 1.194 | 0.98 |
| 398_F | 407_L | 1.191 | 0.98 |
| 647_I | 664_V | 1.182 | 0.98 |
| 312_L | 394_L | 1.182 | 0.98 |
| 131_A | 149_I | 1.181 | 0.98 |
| 551_Y | 555_G | 1.180 | 0.98 |
| 167_R | 174_T | 1.178 | 0.98 |
| 741_T | 744_L | 1.176 | 0.98 |
| 19_V | 22_D | 1.172 | 0.98 |
| 33_T | 37_K | 1.167 | 0.97 |
| 163_V | 791_F | 1.163 | 0.97 |
| 406_N | 486_D | 1.160 | 0.97 |
| 179_N | 191_N | 1.157 | 0.97 |
| 155_T | 218_N | 1.155 | 0.97 |
| 47_A | 154_K | 1.151 | 0.97 |
| 657_G | 701_G | 1.147 | 0.97 |
| 223_F | 308_A | 1.146 | 0.97 |
| 159_E | 183_P | 1.146 | 0.97 |
| 484_T | 491_S | 1.145 | 0.97 |
| 315_G | 397_E | 1.145 | 0.97 |
| 669_A | 688_Q | 1.143 | 0.97 |
| 719_Q | 723_Q | 1.143 | 0.97 |
| 238_R | 298_H | 1.142 | 0.97 |
| 187_H | 223_F | 1.140 | 0.97 |
| 395_S | 406_N | 1.139 | 0.97 |
| 189_Q | 222_L | 1.137 | 0.97 |
| 408_R | 482_A | 1.137 | 0.97 |
| 180_Y | 192_I | 1.136 | 0.97 |
| 68_I | 83_V | 1.135 | 0.97 |
| 307_E | 321_K | 1.134 | 0.97 |
| 98_L | 149_I | 1.132 | 0.97 |
| 394_L | 409_M | 1.132 | 0.97 |
| 413_T | 475_D | 1.127 | 0.97 |
| 174_T | 198_Q | 1.126 | 0.97 |
| 317_N | 397_E | 1.122 | 0.97 |
| 43_S | 133_R | 1.119 | 0.96 |
| 613_G | 655_Y | 1.119 | 0.96 |
| 733_N | 751_N | 1.116 | 0.96 |
| 103_L | 305_G | 1.109 | 0.96 |
| 735_F | 747_A | 1.108 | 0.96 |
| 310_F | 313_G | 1.107 | 0.96 |
| 138_S | 482_A | 1.104 | 0.96 |
| 154_K | 179_N | 1.102 | 0.96 |
| 611_R | 614_L | 1.102 | 0.96 |
| 747_A | 788_R | 1.098 | 0.96 |
| 170_D | 783_T | 1.095 | 0.96 |
| 566_F | 608_K | 1.090 | 0.96 |
| 740_I | 744_L | 1.088 | 0.96 |
| 574_R | 598_N | 1.088 | 0.96 |
| 49_A | 52_Q | 1.088 | 0.96 |
| 651_A | 662_G | 1.087 | 0.96 |
| 155_T | 220_T | 1.085 | 0.96 |
| 693_W | 697_P | 1.077 | 0.95 |
| 492_I | 553_L | 1.077 | 0.95 |
| 99_Q | 148_I | 1.077 | 0.95 |
| 652_S | 659_T | 1.072 | 0.95 |
| 551_Y | 569_V | 1.071 | 0.95 |
| 565_A | 605_A | 1.066 | 0.95 |
| 311_D | 317_N | 1.065 | 0.95 |
| 652_S | 661_N | 1.063 | 0.95 |
| 83_V | 131_A | 1.061 | 0.95 |
| 484_T | 493_D | 1.056 | 0.95 |
| 43_S | 650_E | 1.054 | 0.95 |
| 700_R | 739_R | 1.053 | 0.95 |
| 624_R | 672_A | 1.051 | 0.94 |
| 716_A | 726_M | 1.046 | 0.94 |
| 161_G | 182_A | 1.044 | 0.94 |
| 751_N | 784_S | 1.035 | 0.94 |
| 729_Y | 758_G | 1.035 | 0.94 |
| 100_E | 105_V | 1.034 | 0.94 |
| 97_Q | 144_A | 1.028 | 0.94 |
| 743_A | 789_Y | 1.027 | 0.94 |
| 727_P | 756_T | 1.027 | 0.94 |
| 224_E | 310_F | 1.022 | 0.93 |
| 755_N | 781_R | 1.016 | 0.93 |
| 184_F | 219_L | 1.013 | 0.93 |
| 691_F | 712_G | 1.011 | 0.93 |
| 734_L | 748_L | 1.011 | 0.93 |
| 700_R | 705_Q | 1.009 | 0.93 |
| 21_L | 25_F | 1.008 | 0.93 |
| 319_S | 395_S | 1.007 | 0.93 |
| 601_R | 626_Q | 1.007 | 0.93 |
| 475_D | 502_D | 1.006 | 0.93 |
| 744_L | 748_L | 1.003 | 0.93 |
| 229_R | 309_W | 1.001 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4cu4A | 1 | 0.847 | 100 | 0.322 | Contact Map |
| 3efmA | 1 | 0.6839 | 100 | 0.34 | Contact Map |
| 1xkwA | 1 | 0.7977 | 100 | 0.351 | Contact Map |
| 1kmoA | 1 | 0.7889 | 100 | 0.357 | Contact Map |
| 3qlbA | 2 | 0.7939 | 100 | 0.361 | Contact Map |
| 2gufA | 1 | 0.6865 | 100 | 0.364 | Contact Map |
| 3fhhA | 1 | 0.7257 | 100 | 0.365 | Contact Map |
| 3v8xA | 1 | 0.8647 | 100 | 0.365 | Contact Map |
| 2hdiA | 1 | 0.6877 | 100 | 0.37 | Contact Map |
| 2w16A | 2 | 0.8205 | 100 | 0.371 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)