| Lisa N Kinch |
| ID: | 1483642969 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 575 (428) | ||
| Sequences: | 1209 (827.1) | ||
| Seq/Len: | 2.825 | ||
| Nf(neff/√len): | 40.0 |
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: 2.825).
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 |
| 527_L | 532_L | 3.449 | 1.00 |
| 316_I | 322_L | 3.285 | 1.00 |
| 358_R | 362_D | 3.221 | 1.00 |
| 386_R | 424_T | 3.095 | 1.00 |
| 285_A | 302_I | 2.728 | 1.00 |
| 315_E | 323_R | 2.715 | 1.00 |
| 413_V | 499_F | 2.639 | 1.00 |
| 265_K | 280_A | 2.544 | 1.00 |
| 321_H | 326_D | 2.410 | 1.00 |
| 312_K | 322_L | 2.376 | 1.00 |
| 383_F | 476_V | 2.321 | 1.00 |
| 262_V | 329_S | 2.320 | 1.00 |
| 532_L | 563_L | 2.268 | 1.00 |
| 402_A | 454_E | 2.046 | 1.00 |
| 492_I | 530_H | 1.976 | 1.00 |
| 364_R | 381_S | 1.968 | 0.99 |
| 570_P | 573_R | 1.965 | 0.99 |
| 519_L | 523_K | 1.945 | 0.99 |
| 557_K | 561_R | 1.941 | 0.99 |
| 387_M | 392_A | 1.923 | 0.99 |
| 568_R | 572_E | 1.914 | 0.99 |
| 314_I | 318_E | 1.876 | 0.99 |
| 444_F | 473_Y | 1.860 | 0.99 |
| 338_F | 357_F | 1.859 | 0.99 |
| 364_R | 377_L | 1.847 | 0.99 |
| 429_D | 490_D | 1.829 | 0.99 |
| 270_Q | 331_S | 1.828 | 0.99 |
| 277_L | 281_K | 1.828 | 0.99 |
| 341_I | 344_A | 1.814 | 0.99 |
| 359_S | 362_D | 1.807 | 0.99 |
| 279_Y | 312_K | 1.790 | 0.99 |
| 513_N | 517_R | 1.786 | 0.99 |
| 268_S | 280_A | 1.729 | 0.98 |
| 263_L | 324_K | 1.715 | 0.98 |
| 500_A | 553_T | 1.696 | 0.98 |
| 501_C | 553_T | 1.690 | 0.98 |
| 490_D | 517_R | 1.672 | 0.98 |
| 516_M | 560_F | 1.623 | 0.97 |
| 427_D | 490_D | 1.622 | 0.97 |
| 272_D | 275_R | 1.617 | 0.97 |
| 364_R | 368_S | 1.609 | 0.97 |
| 527_L | 563_L | 1.604 | 0.97 |
| 504_L | 560_F | 1.598 | 0.97 |
| 273_K | 277_L | 1.565 | 0.96 |
| 560_F | 567_Y | 1.561 | 0.96 |
| 492_I | 529_E | 1.555 | 0.96 |
| 526_S | 533_S | 1.551 | 0.96 |
| 512_F | 560_F | 1.547 | 0.96 |
| 261_E | 287_K | 1.543 | 0.96 |
| 525_M | 532_L | 1.534 | 0.96 |
| 518_A | 522_T | 1.515 | 0.95 |
| 334_V | 353_Y | 1.512 | 0.95 |
| 504_L | 516_M | 1.502 | 0.95 |
| 65_I | 70_G | 1.501 | 0.95 |
| 396_E | 414_A | 1.489 | 0.95 |
| 506_F | 517_R | 1.486 | 0.95 |
| 298_E | 301_S | 1.480 | 0.95 |
| 556_E | 573_R | 1.445 | 0.94 |
| 259_K | 316_I | 1.444 | 0.94 |
| 555_T | 558_D | 1.442 | 0.94 |
| 550_V | 553_T | 1.438 | 0.94 |
| 390_E | 394_E | 1.438 | 0.94 |
| 506_F | 513_N | 1.434 | 0.93 |
| 260_L | 286_L | 1.401 | 0.92 |
| 532_L | 559_V | 1.400 | 0.92 |
| 447_L | 491_I | 1.393 | 0.92 |
| 344_A | 349_A | 1.369 | 0.91 |
| 308_R | 312_K | 1.360 | 0.91 |
| 472_K | 492_I | 1.359 | 0.91 |
| 353_Y | 358_R | 1.356 | 0.91 |
| 490_D | 506_F | 1.339 | 0.90 |
| 457_L | 477_C | 1.336 | 0.90 |
| 427_D | 517_R | 1.335 | 0.90 |
| 556_E | 570_P | 1.331 | 0.90 |
| 392_A | 425_C | 1.324 | 0.89 |
| 326_D | 329_S | 1.324 | 0.89 |
| 400_Q | 412_C | 1.323 | 0.89 |
| 369_L | 373_Q | 1.317 | 0.89 |
| 415_C | 431_L | 1.313 | 0.89 |
| 344_A | 352_W | 1.299 | 0.88 |
| 260_L | 309_M | 1.285 | 0.87 |
| 391_E | 487_R | 1.284 | 0.87 |
| 253_N | 500_A | 1.283 | 0.87 |
| 257_T | 283_I | 1.279 | 0.87 |
| 334_V | 337_L | 1.272 | 0.86 |
| 376_G | 380_Y | 1.269 | 0.86 |
| 559_V | 563_L | 1.269 | 0.86 |
| 341_I | 376_G | 1.268 | 0.86 |
| 348_T | 351_M | 1.259 | 0.86 |
| 534_T | 549_R | 1.258 | 0.86 |
| 492_I | 506_F | 1.254 | 0.85 |
| 492_I | 505_Y | 1.243 | 0.85 |
| 432_I | 491_I | 1.243 | 0.85 |
| 386_R | 426_G | 1.242 | 0.85 |
| 553_T | 559_V | 1.241 | 0.85 |
| 531_A | 550_V | 1.241 | 0.85 |
| 393_T | 397_Q | 1.239 | 0.84 |
| 338_F | 341_I | 1.237 | 0.84 |
| 340_N | 384_L | 1.225 | 0.84 |
| 272_D | 276_A | 1.225 | 0.84 |
| 338_F | 349_A | 1.225 | 0.84 |
| 521_K | 526_S | 1.224 | 0.83 |
| 118_C | 125_V | 1.224 | 0.83 |
| 552_P | 555_T | 1.222 | 0.83 |
| 505_Y | 513_N | 1.221 | 0.83 |
| 389_R | 418_Y | 1.204 | 0.82 |
| 349_A | 356_G | 1.202 | 0.82 |
| 462_V | 472_K | 1.199 | 0.82 |
| 275_R | 305_I | 1.197 | 0.82 |
| 414_A | 418_Y | 1.196 | 0.82 |
| 494_V | 502_A | 1.196 | 0.82 |
| 502_A | 553_T | 1.195 | 0.81 |
| 418_Y | 428_V | 1.189 | 0.81 |
| 393_T | 421_G | 1.186 | 0.81 |
| 417_S | 427_D | 1.184 | 0.81 |
| 417_S | 513_N | 1.179 | 0.80 |
| 252_H | 255_H | 1.179 | 0.80 |
| 505_Y | 528_S | 1.176 | 0.80 |
| 385_E | 485_R | 1.173 | 0.80 |
| 417_S | 429_D | 1.173 | 0.80 |
| 494_V | 529_E | 1.172 | 0.80 |
| 275_R | 308_R | 1.170 | 0.80 |
| 388_P | 391_E | 1.170 | 0.80 |
| 355_Q | 366_Q | 1.163 | 0.79 |
| 418_Y | 421_G | 1.161 | 0.79 |
| 532_L | 562_L | 1.160 | 0.79 |
| 393_T | 418_Y | 1.157 | 0.78 |
| 400_Q | 404_Q | 1.155 | 0.78 |
| 300_C | 307_K | 1.155 | 0.78 |
| 285_A | 305_I | 1.151 | 0.78 |
| 553_T | 558_D | 1.150 | 0.78 |
| 533_S | 553_T | 1.142 | 0.77 |
| 396_E | 418_Y | 1.140 | 0.77 |
| 556_E | 560_F | 1.140 | 0.77 |
| 256_I | 316_I | 1.137 | 0.77 |
| 417_S | 506_F | 1.136 | 0.77 |
| 556_E | 563_L | 1.135 | 0.77 |
| 386_R | 417_S | 1.134 | 0.76 |
| 498_E | 530_H | 1.134 | 0.76 |
| 426_G | 429_D | 1.133 | 0.76 |
| 461_L | 488_R | 1.133 | 0.76 |
| 253_N | 501_C | 1.129 | 0.76 |
| 344_A | 348_T | 1.127 | 0.76 |
| 414_A | 528_S | 1.126 | 0.76 |
| 433_T | 499_F | 1.123 | 0.76 |
| 399_V | 428_V | 1.117 | 0.75 |
| 457_L | 473_Y | 1.116 | 0.75 |
| 554_P | 558_D | 1.114 | 0.75 |
| 490_D | 513_N | 1.113 | 0.75 |
| 325_L | 329_S | 1.110 | 0.74 |
| 532_L | 553_T | 1.108 | 0.74 |
| 516_M | 563_L | 1.108 | 0.74 |
| 429_D | 517_R | 1.107 | 0.74 |
| 447_L | 473_Y | 1.106 | 0.74 |
| 502_A | 528_S | 1.104 | 0.74 |
| 452_R | 460_D | 1.101 | 0.73 |
| 337_L | 360_L | 1.096 | 0.73 |
| 338_F | 352_W | 1.096 | 0.73 |
| 64_Q | 67_Q | 1.095 | 0.73 |
| 552_P | 558_D | 1.094 | 0.73 |
| 376_G | 379_H | 1.083 | 0.72 |
| 504_L | 567_Y | 1.080 | 0.71 |
| 417_S | 426_G | 1.079 | 0.71 |
| 298_E | 418_Y | 1.073 | 0.71 |
| 370_T | 373_Q | 1.070 | 0.70 |
| 352_W | 363_I | 1.066 | 0.70 |
| 471_Q | 492_I | 1.064 | 0.70 |
| 387_M | 391_E | 1.063 | 0.70 |
| 515_S | 518_A | 1.063 | 0.70 |
| 525_M | 534_T | 1.063 | 0.70 |
| 263_L | 322_L | 1.061 | 0.69 |
| 240_V | 243_Q | 1.061 | 0.69 |
| 452_R | 457_L | 1.059 | 0.69 |
| 388_P | 425_C | 1.056 | 0.69 |
| 252_H | 316_I | 1.052 | 0.69 |
| 533_S | 550_V | 1.052 | 0.69 |
| 476_V | 486_H | 1.048 | 0.68 |
| 472_K | 529_E | 1.046 | 0.68 |
| 382_D | 391_E | 1.045 | 0.68 |
| 387_M | 487_R | 1.044 | 0.68 |
| 559_V | 562_L | 1.040 | 0.67 |
| 410_L | 496_Y | 1.039 | 0.67 |
| 551_L | 562_L | 1.038 | 0.67 |
| 289_F | 293_V | 1.037 | 0.67 |
| 307_K | 311_E | 1.035 | 0.67 |
| 79_G | 109_L | 1.032 | 0.66 |
| 417_S | 505_Y | 1.032 | 0.66 |
| 556_E | 559_V | 1.032 | 0.66 |
| 299_A | 310_A | 1.030 | 0.66 |
| 528_S | 531_A | 1.029 | 0.66 |
| 319_S | 322_L | 1.025 | 0.66 |
| 506_F | 529_E | 1.025 | 0.66 |
| 458_T | 486_H | 1.021 | 0.65 |
| 528_S | 533_S | 1.018 | 0.65 |
| 558_D | 562_L | 1.018 | 0.65 |
| 397_Q | 400_Q | 1.014 | 0.64 |
| 392_A | 418_Y | 1.012 | 0.64 |
| 278_G | 304_G | 1.010 | 0.64 |
| 359_S | 378_K | 1.008 | 0.64 |
| 506_F | 514_R | 1.008 | 0.64 |
| 305_I | 310_A | 1.006 | 0.63 |
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 | |
| 4i2aA | 1 | 0.5722 | 100 | 0.37 | Contact Map |
| 2bcqA | 1 | 0.5635 | 100 | 0.372 | Contact Map |
| 4lzgA | 1 | 0.5565 | 100 | 0.376 | Contact Map |
| 4kliA | 1 | 0.5461 | 100 | 0.395 | Contact Map |
| 4p4mA | 1 | 0.4191 | 100 | 0.45 | Contact Map |
| 3b0xA | 1 | 0.513 | 100 | 0.502 | Contact Map |
| 2w9mA | 2 | 0.4922 | 100 | 0.57 | Contact Map |
| 1jajA | 1 | 0.2991 | 100 | 0.657 | Contact Map |
| 2dunA | 1 | 0.2209 | 99.8 | 0.869 | Contact Map |
| 2jw5A | 1 | 0.1843 | 99.7 | 0.877 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)