| test |
| ID: | 1382729628 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 671 (590) | ||
| Sequences: | 1789 (1092.1) | ||
| Seq/Len: | 3.032 | ||
| Nf(neff/√len): | 45.0 |
HHblits Results: (2013_03)
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: 3.032).
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 |
| 137_Y | 184_E | 5.386 | 1.00 |
| 141_K | 160_H | 4.536 | 1.00 |
| 383_R | 416_D | 4.152 | 1.00 |
| 352_A | 519_I | 3.916 | 1.00 |
| 28_Q | 73_K | 3.907 | 1.00 |
| 308_R | 316_E | 3.691 | 1.00 |
| 447_G | 460_T | 3.611 | 1.00 |
| 387_M | 397_C | 3.608 | 1.00 |
| 295_D | 320_R | 3.457 | 1.00 |
| 476_S | 479_A | 3.375 | 1.00 |
| 68_K | 660_F | 3.334 | 1.00 |
| 436_Q | 459_Q | 3.277 | 1.00 |
| 178_T | 203_C | 3.099 | 1.00 |
| 173_D | 176_E | 3.011 | 1.00 |
| 350_D | 354_N | 2.924 | 1.00 |
| 154_I | 185_L | 2.877 | 1.00 |
| 23_L | 92_G | 2.859 | 1.00 |
| 352_A | 485_I | 2.857 | 1.00 |
| 204_D | 274_L | 2.684 | 1.00 |
| 247_P | 297_A | 2.648 | 1.00 |
| 520_K | 524_K | 2.614 | 1.00 |
| 204_D | 297_A | 2.606 | 1.00 |
| 521_Q | 611_E | 2.596 | 1.00 |
| 143_H | 160_H | 2.594 | 1.00 |
| 158_F | 181_V | 2.568 | 1.00 |
| 198_Y | 201_E | 2.566 | 1.00 |
| 526_E | 649_W | 2.546 | 1.00 |
| 65_T | 75_K | 2.528 | 1.00 |
| 143_H | 159_K | 2.497 | 1.00 |
| 107_E | 148_E | 2.428 | 1.00 |
| 355_T | 466_I | 2.302 | 1.00 |
| 122_V | 151_T | 2.294 | 1.00 |
| 421_F | 435_L | 2.244 | 1.00 |
| 287_K | 324_T | 2.219 | 1.00 |
| 422_V | 487_L | 2.210 | 1.00 |
| 305_R | 317_S | 2.184 | 1.00 |
| 119_E | 197_H | 2.149 | 1.00 |
| 383_R | 414_F | 2.130 | 1.00 |
| 201_E | 298_H | 2.119 | 1.00 |
| 158_F | 193_V | 2.106 | 1.00 |
| 519_I | 641_I | 2.062 | 1.00 |
| 504_R | 507_E | 2.058 | 1.00 |
| 404_F | 491_A | 2.053 | 1.00 |
| 192_L | 202_V | 2.042 | 1.00 |
| 397_C | 422_V | 2.028 | 1.00 |
| 175_N | 307_H | 2.025 | 1.00 |
| 480_Y | 554_T | 2.010 | 1.00 |
| 135_R | 139_L | 2.005 | 1.00 |
| 154_I | 191_L | 2.003 | 1.00 |
| 161_F | 184_E | 1.992 | 1.00 |
| 158_F | 178_T | 1.974 | 1.00 |
| 404_F | 494_L | 1.972 | 1.00 |
| 25_E | 283_Q | 1.966 | 1.00 |
| 17_G | 271_E | 1.957 | 1.00 |
| 70_K | 74_Q | 1.950 | 1.00 |
| 263_E | 289_L | 1.944 | 1.00 |
| 521_Q | 524_K | 1.941 | 1.00 |
| 122_V | 155_A | 1.925 | 0.99 |
| 538_N | 653_N | 1.919 | 0.99 |
| 346_F | 526_E | 1.906 | 0.99 |
| 65_T | 106_T | 1.900 | 0.99 |
| 382_C | 418_T | 1.899 | 0.99 |
| 559_A | 570_S | 1.894 | 0.99 |
| 24_I | 40_I | 1.885 | 0.99 |
| 627_V | 639_N | 1.872 | 0.99 |
| 114_S | 117_K | 1.860 | 0.99 |
| 556_L | 572_G | 1.852 | 0.99 |
| 492_L | 508_I | 1.837 | 0.99 |
| 178_T | 193_V | 1.830 | 0.99 |
| 310_S | 316_E | 1.823 | 0.99 |
| 612_G | 626_E | 1.821 | 0.99 |
| 247_P | 304_L | 1.810 | 0.99 |
| 339_H | 648_Y | 1.806 | 0.99 |
| 119_E | 196_Y | 1.799 | 0.99 |
| 466_I | 482_S | 1.798 | 0.99 |
| 186_E | 603_P | 1.780 | 0.99 |
| 515_I | 637_L | 1.768 | 0.99 |
| 143_H | 156_K | 1.765 | 0.99 |
| 652_V | 658_V | 1.764 | 0.99 |
| 193_V | 203_C | 1.757 | 0.99 |
| 161_F | 180_Q | 1.733 | 0.99 |
| 25_E | 28_Q | 1.712 | 0.98 |
| 536_S | 622_H | 1.698 | 0.98 |
| 522_V | 638_L | 1.698 | 0.98 |
| 23_L | 94_A | 1.695 | 0.98 |
| 337_Y | 346_F | 1.692 | 0.98 |
| 71_V | 74_Q | 1.691 | 0.98 |
| 115_D | 143_H | 1.676 | 0.98 |
| 593_I | 646_I | 1.667 | 0.98 |
| 263_E | 304_L | 1.654 | 0.98 |
| 575_A | 605_V | 1.644 | 0.98 |
| 131_Y | 135_R | 1.644 | 0.98 |
| 174_L | 203_C | 1.639 | 0.98 |
| 64_K | 106_T | 1.638 | 0.98 |
| 272_F | 304_L | 1.637 | 0.98 |
| 133_A | 186_E | 1.636 | 0.98 |
| 66_T | 105_K | 1.620 | 0.98 |
| 175_N | 298_H | 1.617 | 0.98 |
| 413_V | 443_A | 1.616 | 0.98 |
| 120_F | 162_Y | 1.603 | 0.97 |
| 204_D | 247_P | 1.602 | 0.97 |
| 558_G | 643_L | 1.600 | 0.97 |
| 272_F | 303_E | 1.597 | 0.97 |
| 527_N | 530_K | 1.595 | 0.97 |
| 66_T | 104_P | 1.588 | 0.97 |
| 306_I | 320_R | 1.585 | 0.97 |
| 20_I | 40_I | 1.582 | 0.97 |
| 594_A | 609_I | 1.580 | 0.97 |
| 182_L | 185_L | 1.577 | 0.97 |
| 289_L | 304_L | 1.571 | 0.97 |
| 493_S | 497_D | 1.544 | 0.97 |
| 385_I | 420_V | 1.540 | 0.96 |
| 161_F | 181_V | 1.534 | 0.96 |
| 60_S | 121_I | 1.533 | 0.96 |
| 602_F | 613_D | 1.527 | 0.96 |
| 114_S | 143_H | 1.522 | 0.96 |
| 176_E | 179_K | 1.516 | 0.96 |
| 419_C | 438_C | 1.498 | 0.96 |
| 120_F | 195_S | 1.498 | 0.96 |
| 75_K | 106_T | 1.492 | 0.96 |
| 115_D | 159_K | 1.491 | 0.96 |
| 423_S | 456_M | 1.489 | 0.96 |
| 406_E | 410_R | 1.488 | 0.95 |
| 511_G | 518_Q | 1.478 | 0.95 |
| 445_T | 460_T | 1.465 | 0.95 |
| 291_L | 297_A | 1.462 | 0.95 |
| 42_V | 89_N | 1.456 | 0.95 |
| 649_W | 653_N | 1.443 | 0.94 |
| 361_D | 364_N | 1.442 | 0.94 |
| 292_E | 320_R | 1.441 | 0.94 |
| 437_Y | 440_E | 1.441 | 0.94 |
| 43_D | 194_K | 1.430 | 0.94 |
| 496_N | 505_H | 1.429 | 0.94 |
| 448_I | 490_F | 1.428 | 0.94 |
| 612_G | 629_E | 1.411 | 0.94 |
| 414_F | 417_D | 1.411 | 0.94 |
| 181_V | 185_L | 1.410 | 0.93 |
| 327_M | 332_I | 1.410 | 0.93 |
| 298_H | 305_R | 1.409 | 0.93 |
| 91_V | 200_G | 1.408 | 0.93 |
| 287_K | 322_I | 1.406 | 0.93 |
| 546_L | 594_A | 1.405 | 0.93 |
| 195_S | 198_Y | 1.391 | 0.93 |
| 174_L | 195_S | 1.384 | 0.93 |
| 8_V | 91_V | 1.381 | 0.93 |
| 429_A | 433_L | 1.374 | 0.92 |
| 162_Y | 195_S | 1.370 | 0.92 |
| 543_L | 593_I | 1.360 | 0.92 |
| 351_S | 482_S | 1.359 | 0.92 |
| 177_L | 181_V | 1.355 | 0.92 |
| 192_L | 274_L | 1.353 | 0.92 |
| 200_G | 301_D | 1.352 | 0.91 |
| 175_N | 179_K | 1.344 | 0.91 |
| 419_C | 443_A | 1.343 | 0.91 |
| 17_G | 273_F | 1.342 | 0.91 |
| 517_E | 520_K | 1.342 | 0.91 |
| 552_F | 556_L | 1.340 | 0.91 |
| 63_V | 75_K | 1.340 | 0.91 |
| 447_G | 456_M | 1.319 | 0.90 |
| 41_A | 62_I | 1.317 | 0.90 |
| 525_L | 528_K | 1.311 | 0.90 |
| 278_P | 290_F | 1.311 | 0.90 |
| 630_T | 638_L | 1.307 | 0.90 |
| 162_Y | 197_H | 1.302 | 0.89 |
| 541_K | 654_R | 1.300 | 0.89 |
| 122_V | 154_I | 1.299 | 0.89 |
| 289_L | 306_I | 1.294 | 0.89 |
| 263_E | 272_F | 1.286 | 0.89 |
| 286_K | 324_T | 1.281 | 0.88 |
| 334_K | 660_F | 1.271 | 0.88 |
| 378_T | 444_L | 1.270 | 0.88 |
| 66_T | 103_Q | 1.267 | 0.88 |
| 447_G | 463_G | 1.265 | 0.87 |
| 268_M | 271_E | 1.265 | 0.87 |
| 137_Y | 160_H | 1.258 | 0.87 |
| 24_I | 76_I | 1.249 | 0.87 |
| 449_V | 457_S | 1.249 | 0.87 |
| 194_K | 202_V | 1.247 | 0.86 |
| 300_Y | 303_E | 1.246 | 0.86 |
| 394_Y | 398_L | 1.241 | 0.86 |
| 514_K | 518_Q | 1.233 | 0.86 |
| 274_L | 297_A | 1.233 | 0.86 |
| 466_I | 483_Q | 1.233 | 0.86 |
| 534_N | 653_N | 1.232 | 0.86 |
| 7_Y | 19_I | 1.220 | 0.85 |
| 7_Y | 15_S | 1.210 | 0.84 |
| 531_D | 534_N | 1.210 | 0.84 |
| 518_Q | 638_L | 1.208 | 0.84 |
| 586_V | 592_I | 1.203 | 0.84 |
| 49_D | 58_M | 1.202 | 0.84 |
| 201_E | 300_Y | 1.201 | 0.83 |
| 278_P | 282_V | 1.200 | 0.83 |
| 136_K | 140_S | 1.199 | 0.83 |
| 492_L | 495_S | 1.197 | 0.83 |
| 176_E | 180_Q | 1.197 | 0.83 |
| 405_E | 409_R | 1.196 | 0.83 |
| 15_S | 19_I | 1.191 | 0.83 |
| 43_D | 91_V | 1.188 | 0.83 |
| 262_S | 285_T | 1.186 | 0.82 |
| 41_A | 121_I | 1.183 | 0.82 |
| 546_L | 555_A | 1.175 | 0.82 |
| 359_R | 489_M | 1.171 | 0.81 |
| 70_K | 73_K | 1.171 | 0.81 |
| 382_C | 417_D | 1.167 | 0.81 |
| 279_A | 282_V | 1.160 | 0.80 |
| 551_Q | 595_F | 1.160 | 0.80 |
| 537_L | 646_I | 1.158 | 0.80 |
| 342_Q | 346_F | 1.143 | 0.79 |
| 439_L | 461_H | 1.139 | 0.79 |
| 179_K | 307_H | 1.137 | 0.79 |
| 307_H | 317_S | 1.136 | 0.79 |
| 350_D | 520_K | 1.136 | 0.79 |
| 614_A | 617_S | 1.134 | 0.78 |
| 274_L | 299_I | 1.131 | 0.78 |
| 24_I | 73_K | 1.126 | 0.78 |
| 407_L | 633_C | 1.124 | 0.77 |
| 537_L | 622_H | 1.124 | 0.77 |
| 103_Q | 148_E | 1.121 | 0.77 |
| 511_G | 631_V | 1.115 | 0.77 |
| 182_L | 205_K | 1.115 | 0.77 |
| 554_T | 640_V | 1.111 | 0.76 |
| 7_Y | 22_N | 1.104 | 0.76 |
| 138_L | 145_F | 1.100 | 0.75 |
| 175_N | 296_I | 1.092 | 0.75 |
| 113_K | 121_I | 1.086 | 0.74 |
| 348_Q | 481_T | 1.086 | 0.74 |
| 646_I | 650_L | 1.086 | 0.74 |
| 457_S | 463_G | 1.085 | 0.74 |
| 525_L | 625_L | 1.083 | 0.74 |
| 578_L | 583_L | 1.082 | 0.74 |
| 392_T | 476_S | 1.082 | 0.74 |
| 515_I | 638_L | 1.079 | 0.73 |
| 139_L | 148_E | 1.079 | 0.73 |
| 385_I | 418_T | 1.078 | 0.73 |
| 604_K | 671_E | 1.077 | 0.73 |
| 452_V | 465_H | 1.077 | 0.73 |
| 68_K | 657_D | 1.076 | 0.73 |
| 645_L | 649_W | 1.075 | 0.73 |
| 20_I | 89_N | 1.066 | 0.72 |
| 68_K | 334_K | 1.064 | 0.72 |
| 129_T | 604_K | 1.063 | 0.72 |
| 275_S | 280_S | 1.061 | 0.72 |
| 492_L | 505_H | 1.053 | 0.71 |
| 376_L | 380_R | 1.052 | 0.71 |
| 420_V | 490_F | 1.050 | 0.70 |
| 138_L | 157_L | 1.047 | 0.70 |
| 400_T | 487_L | 1.045 | 0.70 |
| 554_T | 638_L | 1.044 | 0.70 |
| 6_G | 274_L | 1.039 | 0.69 |
| 8_V | 301_D | 1.037 | 0.69 |
| 421_F | 460_T | 1.036 | 0.69 |
| 514_K | 517_E | 1.034 | 0.69 |
| 485_I | 512_L | 1.032 | 0.69 |
| 400_T | 403_I | 1.031 | 0.68 |
| 64_K | 113_K | 1.030 | 0.68 |
| 542_S | 590_L | 1.030 | 0.68 |
| 179_K | 296_I | 1.028 | 0.68 |
| 91_V | 202_V | 1.027 | 0.68 |
| 544_L | 590_L | 1.026 | 0.68 |
| 448_I | 487_L | 1.025 | 0.68 |
| 403_I | 488_V | 1.020 | 0.67 |
| 493_S | 496_N | 1.019 | 0.67 |
| 518_Q | 630_T | 1.018 | 0.67 |
| 507_E | 631_V | 1.017 | 0.67 |
| 66_T | 106_T | 1.016 | 0.67 |
| 297_A | 304_L | 1.013 | 0.66 |
| 1_M | 4_I | 1.012 | 0.66 |
| 528_K | 531_D | 1.012 | 0.66 |
| 545_L | 562_I | 1.012 | 0.66 |
| 457_S | 465_H | 1.010 | 0.66 |
| 448_I | 466_I | 1.010 | 0.66 |
| 353_F | 520_K | 1.007 | 0.66 |
| 281_V | 288_V | 1.007 | 0.66 |
| 511_G | 514_K | 1.006 | 0.66 |
| 342_Q | 526_E | 1.003 | 0.65 |
| 63_V | 86_I | 1.002 | 0.65 |
| 387_M | 420_V | 1.001 | 0.65 |
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 | |
| 2bplA | 3 | 0.8614 | 100 | 0.409 | Contact Map |
| 2zj3A | 1 | 0.5022 | 100 | 0.636 | Contact Map |
| 2pocA | 4 | 0.4829 | 100 | 0.638 | Contact Map |
| 3tbfA | 8 | 0.4873 | 100 | 0.641 | Contact Map |
| 1moqA | 1 | 0.5007 | 100 | 0.642 | Contact Map |
| 3fj1A | 4 | 0.4575 | 100 | 0.693 | Contact Map |
| 3knzA | 6 | 0.4396 | 100 | 0.693 | Contact Map |
| 1j5xA | 1 | 0.4441 | 100 | 0.693 | Contact Map |
| 2e5fA | 2 | 0.4441 | 100 | 0.7 | Contact Map |
| 2amlA | 2 | 0.4888 | 100 | 0.702 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)