| TbpA2 |
| ID: | 1503953294 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 763 (691) | ||
| Sequences: | 17763 (12402.4) | ||
| Seq/Len: | 25.706 | ||
| Nf(neff/√len): | 471.8 |
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: 25.706).
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 |
| 656_G | 690_F | 5.591 | 1.00 |
| 618_G | 637_W | 5.424 | 1.00 |
| 438_Y | 465_S | 5.357 | 1.00 |
| 545_R | 593_K | 4.866 | 1.00 |
| 481_H | 530_Y | 4.425 | 1.00 |
| 436_G | 467_L | 4.233 | 1.00 |
| 692_V | 714_F | 4.216 | 1.00 |
| 262_H | 306_Y | 4.125 | 1.00 |
| 487_L | 524_L | 3.868 | 1.00 |
| 430_L | 475_Y | 3.525 | 1.00 |
| 489_T | 524_L | 3.484 | 1.00 |
| 143_S | 167_T | 3.411 | 1.00 |
| 658_Y | 690_F | 3.307 | 1.00 |
| 270_D | 298_R | 3.295 | 1.00 |
| 371_H | 422_D | 3.274 | 1.00 |
| 429_T | 475_Y | 3.193 | 1.00 |
| 264_F | 304_Y | 3.171 | 1.00 |
| 707_N | 758_S | 3.150 | 1.00 |
| 262_H | 304_Y | 3.146 | 1.00 |
| 317_L | 359_L | 3.139 | 1.00 |
| 438_Y | 467_L | 3.073 | 1.00 |
| 141_I | 166_F | 3.009 | 1.00 |
| 620_Y | 637_W | 3.005 | 1.00 |
| 615_R | 642_G | 2.999 | 1.00 |
| 376_K | 419_S | 2.956 | 1.00 |
| 541_V | 597_V | 2.947 | 1.00 |
| 477_V | 483_I | 2.937 | 1.00 |
| 656_G | 692_V | 2.904 | 1.00 |
| 268_L | 298_R | 2.851 | 1.00 |
| 651_S | 697_Q | 2.799 | 1.00 |
| 381_D | 414_R | 2.790 | 1.00 |
| 481_H | 532_F | 2.777 | 1.00 |
| 320_A | 356_R | 2.750 | 1.00 |
| 209_F | 256_Y | 2.706 | 1.00 |
| 57_T | 145_K | 2.703 | 1.00 |
| 59_S | 62_Q | 2.634 | 1.00 |
| 653_S | 695_T | 2.625 | 1.00 |
| 483_I | 530_Y | 2.617 | 1.00 |
| 658_Y | 688_S | 2.592 | 1.00 |
| 708_M | 755_F | 2.587 | 1.00 |
| 379_F | 416_F | 2.579 | 1.00 |
| 432_A | 473_L | 2.574 | 1.00 |
| 654_L | 692_V | 2.541 | 1.00 |
| 539_F | 599_G | 2.527 | 1.00 |
| 319_V | 357_G | 2.526 | 1.00 |
| 694_L | 713_L | 2.479 | 1.00 |
| 217_K | 248_T | 2.466 | 1.00 |
| 60_S | 64_R | 2.460 | 1.00 |
| 537_A | 601_V | 2.456 | 1.00 |
| 611_G | 645_Y | 2.430 | 1.00 |
| 603_G | 609_S | 2.408 | 1.00 |
| 317_L | 357_G | 2.397 | 1.00 |
| 321_K | 355_T | 2.395 | 1.00 |
| 259_N | 262_H | 2.355 | 1.00 |
| 215_L | 248_T | 2.338 | 1.00 |
| 704_V | 761_V | 2.324 | 1.00 |
| 616_L | 641_G | 2.321 | 1.00 |
| 266_L | 300_Y | 2.314 | 1.00 |
| 145_K | 165_S | 2.308 | 1.00 |
| 266_L | 302_L | 2.303 | 1.00 |
| 661_A | 685_L | 2.297 | 1.00 |
| 709_G | 756_A | 2.296 | 1.00 |
| 431_K | 476_Q | 2.276 | 1.00 |
| 655_T | 693_D | 2.263 | 1.00 |
| 315_A | 360_S | 2.233 | 1.00 |
| 706_L | 759_V | 2.232 | 1.00 |
| 487_L | 526_H | 2.220 | 1.00 |
| 614_F | 643_I | 2.212 | 1.00 |
| 466_H | 522_T | 2.209 | 1.00 |
| 430_L | 473_L | 2.208 | 1.00 |
| 478_H | 481_H | 2.195 | 1.00 |
| 272_A | 296_P | 2.182 | 1.00 |
| 187_T | 198_Q | 2.174 | 1.00 |
| 593_K | 622_K | 2.158 | 1.00 |
| 710_I | 713_L | 2.153 | 1.00 |
| 268_L | 300_Y | 2.131 | 1.00 |
| 540_S | 598_S | 2.126 | 1.00 |
| 708_M | 757_A | 2.123 | 1.00 |
| 263_R | 305_R | 2.115 | 1.00 |
| 718_Y | 750_A | 2.115 | 1.00 |
| 543_L | 593_K | 2.108 | 1.00 |
| 650_W | 698_V | 2.101 | 1.00 |
| 78_E | 146_V | 2.074 | 1.00 |
| 311_W | 362_Y | 2.074 | 1.00 |
| 522_T | 550_N | 2.063 | 1.00 |
| 264_F | 302_L | 2.060 | 1.00 |
| 70_N | 73_D | 2.049 | 1.00 |
| 545_R | 591_V | 2.040 | 1.00 |
| 265_T | 303_E | 2.034 | 1.00 |
| 700_L | 706_L | 2.024 | 1.00 |
| 208_R | 256_Y | 2.018 | 1.00 |
| 519_Q | 550_N | 2.005 | 1.00 |
| 377_V | 418_L | 1.988 | 1.00 |
| 381_D | 412_K | 1.976 | 1.00 |
| 261_T | 306_Y | 1.958 | 1.00 |
| 211_G | 254_I | 1.955 | 1.00 |
| 371_H | 424_V | 1.941 | 1.00 |
| 489_T | 522_T | 1.931 | 1.00 |
| 652_I | 696_G | 1.919 | 1.00 |
| 541_V | 595_I | 1.914 | 1.00 |
| 109_D | 253_K | 1.912 | 1.00 |
| 378_E | 417_S | 1.905 | 1.00 |
| 96_I | 162_G | 1.901 | 1.00 |
| 704_V | 759_V | 1.899 | 1.00 |
| 699_N | 705_T | 1.894 | 1.00 |
| 209_F | 254_I | 1.889 | 1.00 |
| 321_K | 353_T | 1.883 | 1.00 |
| 657_R | 693_D | 1.878 | 1.00 |
| 528_L | 543_L | 1.877 | 1.00 |
| 440_R | 463_K | 1.875 | 1.00 |
| 547_R | 591_V | 1.868 | 1.00 |
| 257_D | 263_R | 1.865 | 1.00 |
| 710_I | 755_F | 1.848 | 1.00 |
| 474_E | 482_Q | 1.841 | 1.00 |
| 204_F | 211_G | 1.840 | 1.00 |
| 612_L | 645_Y | 1.830 | 1.00 |
| 109_D | 267_F | 1.828 | 1.00 |
| 705_T | 760_E | 1.825 | 1.00 |
| 543_L | 595_I | 1.822 | 1.00 |
| 108_V | 168_T | 1.820 | 1.00 |
| 477_V | 530_Y | 1.819 | 1.00 |
| 654_L | 694_L | 1.794 | 1.00 |
| 379_F | 414_R | 1.794 | 1.00 |
| 372_R | 423_E | 1.781 | 1.00 |
| 377_V | 416_F | 1.766 | 1.00 |
| 697_Q | 705_T | 1.753 | 1.00 |
| 142_S | 169_K | 1.753 | 1.00 |
| 710_I | 753_R | 1.751 | 1.00 |
| 551_F | 590_A | 1.749 | 1.00 |
| 315_A | 359_L | 1.742 | 1.00 |
| 544_F | 619_S | 1.738 | 1.00 |
| 617_K | 640_V | 1.738 | 1.00 |
| 109_D | 168_T | 1.729 | 1.00 |
| 183_F | 202_G | 1.727 | 1.00 |
| 142_S | 170_E | 1.725 | 1.00 |
| 484_G | 529_T | 1.725 | 1.00 |
| 61_E | 64_R | 1.719 | 1.00 |
| 188_G | 758_S | 1.711 | 1.00 |
| 255_G | 263_R | 1.707 | 1.00 |
| 544_F | 594_G | 1.707 | 1.00 |
| 323_K | 353_T | 1.703 | 1.00 |
| 526_H | 547_R | 1.686 | 1.00 |
| 613_T | 644_D | 1.685 | 1.00 |
| 375_S | 420_L | 1.683 | 1.00 |
| 472_G | 486_R | 1.679 | 1.00 |
| 319_V | 355_T | 1.675 | 1.00 |
| 213_A | 252_T | 1.674 | 1.00 |
| 305_R | 316_K | 1.671 | 1.00 |
| 60_S | 169_K | 1.661 | 1.00 |
| 612_L | 643_I | 1.652 | 1.00 |
| 427_T | 430_L | 1.644 | 1.00 |
| 97_R | 596_E | 1.632 | 1.00 |
| 217_K | 246_H | 1.631 | 1.00 |
| 544_F | 621_S | 1.630 | 1.00 |
| 250_W | 270_D | 1.627 | 1.00 |
| 61_E | 65_K | 1.614 | 1.00 |
| 618_G | 639_V | 1.611 | 1.00 |
| 417_S | 439_D | 1.611 | 1.00 |
| 434_I | 471_L | 1.604 | 1.00 |
| 145_K | 167_T | 1.595 | 1.00 |
| 706_L | 757_A | 1.583 | 1.00 |
| 691_V | 750_A | 1.555 | 1.00 |
| 699_N | 762_R | 1.555 | 1.00 |
| 188_G | 197_R | 1.548 | 1.00 |
| 186_K | 199_V | 1.543 | 1.00 |
| 757_A | 761_V | 1.538 | 1.00 |
| 440_R | 465_S | 1.535 | 1.00 |
| 616_L | 639_V | 1.534 | 1.00 |
| 416_F | 440_R | 1.532 | 1.00 |
| 485_Y | 528_L | 1.523 | 1.00 |
| 108_V | 113_Q | 1.516 | 1.00 |
| 186_K | 760_E | 1.515 | 1.00 |
| 429_T | 477_V | 1.513 | 1.00 |
| 538_H | 600_A | 1.497 | 1.00 |
| 485_Y | 526_H | 1.494 | 1.00 |
| 469_W | 489_T | 1.490 | 1.00 |
| 536_Y | 601_V | 1.483 | 1.00 |
| 484_G | 542_G | 1.477 | 1.00 |
| 219_W | 246_H | 1.469 | 1.00 |
| 183_F | 763_F | 1.469 | 1.00 |
| 304_Y | 317_L | 1.467 | 1.00 |
| 258_I | 264_F | 1.463 | 1.00 |
| 303_E | 318_F | 1.456 | 1.00 |
| 537_A | 599_G | 1.452 | 1.00 |
| 642_G | 655_T | 1.451 | 1.00 |
| 210_F | 255_G | 1.446 | 1.00 |
| 530_Y | 541_V | 1.429 | 1.00 |
| 80_G | 619_S | 1.427 | 1.00 |
| 56_S | 148_K | 1.424 | 1.00 |
| 41_L | 44_I | 1.419 | 1.00 |
| 215_L | 250_W | 1.416 | 1.00 |
| 539_F | 597_V | 1.412 | 1.00 |
| 432_A | 471_L | 1.406 | 0.99 |
| 363_P | 372_R | 1.406 | 0.99 |
| 553_Q | 587_E | 1.406 | 0.99 |
| 607_G | 610_D | 1.403 | 0.99 |
| 654_L | 713_L | 1.391 | 0.99 |
| 555_R | 585_V | 1.390 | 0.99 |
| 311_W | 360_S | 1.389 | 0.99 |
| 360_S | 375_S | 1.388 | 0.99 |
| 492_R | 521_E | 1.383 | 0.99 |
| 476_Q | 482_Q | 1.381 | 0.99 |
| 705_T | 762_R | 1.381 | 0.99 |
| 305_R | 314_T | 1.381 | 0.99 |
| 417_S | 437_R | 1.379 | 0.99 |
| 603_G | 614_F | 1.367 | 0.99 |
| 613_T | 646_E | 1.366 | 0.99 |
| 639_V | 658_Y | 1.363 | 0.99 |
| 532_F | 539_F | 1.363 | 0.99 |
| 185_S | 200_I | 1.363 | 0.99 |
| 431_K | 474_E | 1.360 | 0.99 |
| 687_P | 716_R | 1.356 | 0.99 |
| 473_L | 477_V | 1.355 | 0.99 |
| 40_E | 43_E | 1.353 | 0.99 |
| 614_F | 641_G | 1.350 | 0.99 |
| 693_D | 711_F | 1.342 | 0.99 |
| 187_T | 196_W | 1.341 | 0.99 |
| 63_L | 74_L | 1.336 | 0.99 |
| 603_G | 643_I | 1.333 | 0.99 |
| 547_R | 589_K | 1.332 | 0.99 |
| 186_K | 758_S | 1.331 | 0.99 |
| 644_D | 653_S | 1.327 | 0.99 |
| 184_L | 762_R | 1.327 | 0.99 |
| 595_I | 620_Y | 1.325 | 0.99 |
| 713_L | 753_R | 1.323 | 0.99 |
| 213_A | 250_W | 1.323 | 0.99 |
| 490_G | 523_A | 1.320 | 0.99 |
| 691_V | 718_Y | 1.317 | 0.99 |
| 323_K | 351_D | 1.317 | 0.99 |
| 263_R | 307_N | 1.314 | 0.99 |
| 526_H | 545_R | 1.311 | 0.99 |
| 609_S | 612_L | 1.298 | 0.99 |
| 711_F | 754_N | 1.294 | 0.99 |
| 522_T | 549_H | 1.285 | 0.99 |
| 374_S | 423_E | 1.283 | 0.99 |
| 469_W | 487_L | 1.272 | 0.99 |
| 525_N | 546_T | 1.271 | 0.99 |
| 477_V | 481_H | 1.268 | 0.99 |
| 62_Q | 65_K | 1.267 | 0.99 |
| 423_E | 431_K | 1.260 | 0.99 |
| 211_G | 252_T | 1.255 | 0.99 |
| 81_I | 96_I | 1.251 | 0.99 |
| 373_L | 422_D | 1.250 | 0.99 |
| 418_L | 438_Y | 1.242 | 0.98 |
| 695_T | 707_N | 1.239 | 0.98 |
| 308_G | 315_A | 1.238 | 0.98 |
| 657_R | 691_V | 1.236 | 0.98 |
| 637_W | 660_A | 1.230 | 0.98 |
| 523_A | 546_T | 1.221 | 0.98 |
| 94_F | 164_V | 1.220 | 0.98 |
| 661_A | 688_S | 1.219 | 0.98 |
| 148_K | 596_E | 1.218 | 0.98 |
| 310_S | 362_Y | 1.216 | 0.98 |
| 314_T | 361_T | 1.211 | 0.98 |
| 372_R | 425_A | 1.210 | 0.98 |
| 439_D | 468_S | 1.209 | 0.98 |
| 692_V | 713_L | 1.195 | 0.98 |
| 184_L | 760_E | 1.195 | 0.98 |
| 261_T | 307_N | 1.191 | 0.98 |
| 600_A | 615_R | 1.185 | 0.98 |
| 484_G | 531_R | 1.184 | 0.98 |
| 189_Y | 196_W | 1.182 | 0.98 |
| 600_A | 613_T | 1.182 | 0.98 |
| 533_Q | 538_H | 1.181 | 0.98 |
| 318_F | 358_E | 1.180 | 0.98 |
| 707_N | 760_E | 1.178 | 0.98 |
| 650_W | 696_G | 1.176 | 0.98 |
| 524_L | 549_H | 1.174 | 0.98 |
| 39_E | 42_G | 1.174 | 0.98 |
| 591_V | 626_H | 1.172 | 0.98 |
| 759_V | 763_F | 1.166 | 0.97 |
| 270_D | 296_P | 1.165 | 0.97 |
| 696_G | 710_I | 1.163 | 0.97 |
| 630_P | 636_P | 1.162 | 0.97 |
| 425_A | 431_K | 1.161 | 0.97 |
| 111_I | 318_F | 1.160 | 0.97 |
| 41_L | 45_S | 1.158 | 0.97 |
| 303_E | 316_K | 1.156 | 0.97 |
| 111_I | 301_G | 1.154 | 0.97 |
| 529_T | 542_G | 1.154 | 0.97 |
| 170_E | 255_G | 1.153 | 0.97 |
| 620_Y | 636_P | 1.153 | 0.97 |
| 170_E | 253_K | 1.151 | 0.97 |
| 481_H | 485_Y | 1.144 | 0.97 |
| 107_I | 163_A | 1.142 | 0.97 |
| 647_T | 652_I | 1.139 | 0.97 |
| 307_N | 314_T | 1.138 | 0.97 |
| 694_L | 710_I | 1.135 | 0.97 |
| 142_S | 167_T | 1.133 | 0.97 |
| 700_L | 759_V | 1.132 | 0.97 |
| 97_R | 527_E | 1.131 | 0.97 |
| 185_S | 761_V | 1.128 | 0.97 |
| 498_D | 584_F | 1.127 | 0.97 |
| 549_H | 589_K | 1.125 | 0.97 |
| 265_T | 318_F | 1.123 | 0.97 |
| 374_S | 421_L | 1.122 | 0.97 |
| 426_L | 473_L | 1.121 | 0.97 |
| 442_N | 463_K | 1.118 | 0.96 |
| 428_D | 475_Y | 1.117 | 0.96 |
| 316_K | 361_T | 1.116 | 0.96 |
| 255_G | 265_T | 1.111 | 0.96 |
| 469_W | 473_L | 1.105 | 0.96 |
| 107_I | 165_S | 1.105 | 0.96 |
| 308_G | 360_S | 1.096 | 0.96 |
| 621_S | 634_I | 1.092 | 0.96 |
| 524_L | 547_R | 1.091 | 0.96 |
| 423_E | 433_T | 1.090 | 0.96 |
| 60_S | 142_S | 1.089 | 0.96 |
| 473_L | 485_Y | 1.087 | 0.96 |
| 253_K | 265_T | 1.084 | 0.96 |
| 364_L | 373_L | 1.083 | 0.96 |
| 211_G | 215_L | 1.081 | 0.95 |
| 258_I | 262_H | 1.077 | 0.95 |
| 426_L | 432_A | 1.075 | 0.95 |
| 173_D | 210_F | 1.073 | 0.95 |
| 111_I | 320_A | 1.072 | 0.95 |
| 383_F | 412_K | 1.060 | 0.95 |
| 365_A | 370_T | 1.059 | 0.95 |
| 690_F | 716_R | 1.058 | 0.95 |
| 603_G | 611_G | 1.057 | 0.95 |
| 704_V | 708_M | 1.052 | 0.95 |
| 73_D | 76_R | 1.050 | 0.94 |
| 362_Y | 375_S | 1.049 | 0.94 |
| 697_Q | 707_N | 1.042 | 0.94 |
| 660_A | 688_S | 1.040 | 0.94 |
| 604_S | 612_L | 1.038 | 0.94 |
| 66_N | 77_H | 1.035 | 0.94 |
| 595_I | 599_G | 1.033 | 0.94 |
| 711_F | 756_A | 1.032 | 0.94 |
| 153_V | 421_L | 1.032 | 0.94 |
| 442_N | 461_S | 1.028 | 0.94 |
| 36_N | 39_E | 1.028 | 0.94 |
| 552_I | 584_F | 1.023 | 0.93 |
| 208_R | 258_I | 1.023 | 0.93 |
| 146_V | 164_V | 1.022 | 0.93 |
| 269_E | 299_R | 1.021 | 0.93 |
| 105_A | 159_A | 1.019 | 0.93 |
| 106_V | 164_V | 1.019 | 0.93 |
| 695_T | 709_G | 1.017 | 0.93 |
| 160_L | 523_A | 1.017 | 0.93 |
| 659_S | 689_Y | 1.016 | 0.93 |
| 651_S | 699_N | 1.008 | 0.93 |
| 385_E | 410_P | 1.006 | 0.93 |
| 444_A | 461_S | 1.005 | 0.93 |
| 364_L | 371_H | 1.001 | 0.92 |
| 433_T | 472_G | 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 | |
| 3efmA | 1 | 0.6959 | 100 | 0.344 | Contact Map |
| 1xkwA | 1 | 0.7864 | 100 | 0.358 | Contact Map |
| 3v8xA | 1 | 0.8794 | 100 | 0.36 | Contact Map |
| 3qlbA | 2 | 0.7733 | 100 | 0.36 | Contact Map |
| 1kmoA | 1 | 0.8034 | 100 | 0.361 | Contact Map |
| 2hdiA | 1 | 0.7431 | 100 | 0.365 | Contact Map |
| 3fhhA | 1 | 0.7706 | 100 | 0.366 | Contact Map |
| 4cu4A | 1 | 0.8008 | 100 | 0.373 | Contact Map |
| 2w16A | 2 | 0.8585 | 100 | 0.373 | Contact Map |
| 4b7oA | 1 | 0.8087 | 100 | 0.373 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)