| cpn |
| ID: | 1401301777 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 543 (516) | ||
| Sequences: | 3354 (1445.9) | ||
| Seq/Len: | 6.500 | ||
| Nf(neff/√len): | 63.7 |
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: 6.500).
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 |
| 135_L | 492_L | 4.638 | 1.00 |
| 130_K | 133_E | 4.309 | 1.00 |
| 482_D | 485_E | 4.043 | 1.00 |
| 139_A | 492_L | 3.981 | 1.00 |
| 147_K | 176_E | 3.715 | 1.00 |
| 474_N | 477_T | 3.667 | 1.00 |
| 474_N | 481_E | 3.551 | 1.00 |
| 341_G | 358_E | 3.372 | 1.00 |
| 172_E | 176_E | 3.266 | 1.00 |
| 234_L | 323_A | 3.242 | 1.00 |
| 134_L | 137_T | 3.181 | 1.00 |
| 151_T | 172_E | 3.069 | 1.00 |
| 128_A | 499_I | 3.024 | 1.00 |
| 455_I | 480_V | 2.971 | 1.00 |
| 206_T | 369_I | 2.951 | 1.00 |
| 422_I | 430_V | 2.833 | 1.00 |
| 59_N | 64_I | 2.760 | 1.00 |
| 481_E | 486_N | 2.743 | 1.00 |
| 103_L | 124_Y | 2.696 | 1.00 |
| 126_A | 426_E | 2.672 | 1.00 |
| 408_E | 495_K | 2.593 | 1.00 |
| 106_K | 435_D | 2.572 | 1.00 |
| 147_K | 179_S | 2.503 | 1.00 |
| 124_Y | 503_A | 2.466 | 1.00 |
| 274_A | 278_A | 2.438 | 1.00 |
| 128_A | 503_A | 2.348 | 1.00 |
| 135_L | 407_T | 2.271 | 1.00 |
| 415_L | 430_V | 2.247 | 1.00 |
| 267_K | 271_D | 2.210 | 1.00 |
| 473_L | 478_G | 2.207 | 1.00 |
| 340_A | 356_V | 2.182 | 1.00 |
| 227_V | 230_A | 2.135 | 1.00 |
| 174_I | 384_V | 2.103 | 1.00 |
| 226_K | 342_L | 2.098 | 1.00 |
| 404_G | 483_M | 2.062 | 1.00 |
| 441_P | 459_V | 2.054 | 1.00 |
| 95_T | 498_A | 2.047 | 1.00 |
| 450_L | 473_L | 2.042 | 1.00 |
| 76_K | 79_I | 2.028 | 1.00 |
| 136_K | 496_T | 2.022 | 1.00 |
| 130_K | 418_Y | 1.969 | 1.00 |
| 125_Q | 507_E | 1.952 | 1.00 |
| 133_E | 137_T | 1.951 | 1.00 |
| 470_C | 482_D | 1.936 | 1.00 |
| 400_I | 489_V | 1.930 | 1.00 |
| 234_L | 317_L | 1.913 | 1.00 |
| 102_E | 105_R | 1.909 | 1.00 |
| 103_L | 433_F | 1.880 | 1.00 |
| 433_F | 503_A | 1.877 | 1.00 |
| 29_R | 33_E | 1.864 | 1.00 |
| 438_E | 460_R | 1.855 | 1.00 |
| 197_K | 378_E | 1.844 | 1.00 |
| 173_I | 206_T | 1.834 | 1.00 |
| 104_L | 509_L | 1.807 | 1.00 |
| 180_A | 210_K | 1.801 | 1.00 |
| 155_M | 168_E | 1.799 | 1.00 |
| 133_E | 136_K | 1.795 | 1.00 |
| 382_R | 385_D | 1.793 | 1.00 |
| 132_Q | 136_K | 1.788 | 1.00 |
| 232_I | 340_A | 1.782 | 1.00 |
| 437_L | 499_I | 1.768 | 1.00 |
| 134_L | 414_K | 1.759 | 1.00 |
| 290_I | 305_A | 1.755 | 1.00 |
| 149_I | 152_K | 1.748 | 1.00 |
| 59_N | 382_R | 1.748 | 1.00 |
| 458_K | 461_A | 1.734 | 1.00 |
| 131_A | 411_L | 1.717 | 1.00 |
| 324_N | 336_D | 1.716 | 1.00 |
| 275_E | 278_A | 1.711 | 1.00 |
| 178_V | 395_I | 1.709 | 1.00 |
| 29_R | 101_G | 1.707 | 1.00 |
| 129_Q | 133_E | 1.703 | 1.00 |
| 445_A | 450_L | 1.693 | 1.00 |
| 416_R | 434_A | 1.692 | 1.00 |
| 270_K | 274_A | 1.682 | 1.00 |
| 178_V | 193_I | 1.677 | 1.00 |
| 107_A | 124_Y | 1.674 | 1.00 |
| 86_E | 382_R | 1.666 | 1.00 |
| 146_D | 149_I | 1.659 | 1.00 |
| 229_D | 339_D | 1.637 | 1.00 |
| 474_N | 486_N | 1.637 | 1.00 |
| 32_A | 101_G | 1.635 | 1.00 |
| 121_V | 125_Q | 1.633 | 1.00 |
| 458_K | 479_A | 1.623 | 1.00 |
| 439_V | 443_T | 1.622 | 1.00 |
| 438_E | 442_R | 1.620 | 1.00 |
| 481_E | 488_V | 1.619 | 1.00 |
| 367_M | 384_V | 1.616 | 1.00 |
| 131_A | 437_L | 1.605 | 1.00 |
| 36_R | 101_G | 1.604 | 1.00 |
| 56_V | 382_R | 1.584 | 1.00 |
| 130_K | 414_K | 1.571 | 0.99 |
| 197_K | 381_A | 1.523 | 0.99 |
| 58_T | 379_E | 1.520 | 0.99 |
| 229_D | 281_A | 1.519 | 0.99 |
| 201_A | 205_D | 1.517 | 0.99 |
| 371_G | 377_I | 1.514 | 0.99 |
| 286_C | 317_L | 1.511 | 0.99 |
| 228_T | 342_L | 1.504 | 0.99 |
| 285_F | 356_V | 1.482 | 0.99 |
| 418_Y | 430_V | 1.482 | 0.99 |
| 450_L | 478_G | 1.479 | 0.99 |
| 254_D | 257_K | 1.477 | 0.99 |
| 415_L | 434_A | 1.456 | 0.99 |
| 110_L | 115_V | 1.452 | 0.99 |
| 227_V | 284_L | 1.437 | 0.99 |
| 147_K | 172_E | 1.437 | 0.99 |
| 173_I | 367_M | 1.430 | 0.99 |
| 418_Y | 421_G | 1.427 | 0.99 |
| 124_Y | 433_F | 1.424 | 0.99 |
| 86_E | 389_G | 1.423 | 0.99 |
| 86_E | 385_D | 1.409 | 0.99 |
| 339_D | 360_K | 1.409 | 0.99 |
| 407_T | 411_L | 1.384 | 0.98 |
| 312_S | 315_E | 1.377 | 0.98 |
| 277_K | 303_I | 1.374 | 0.98 |
| 131_A | 415_L | 1.366 | 0.98 |
| 26_L | 30_I | 1.360 | 0.98 |
| 409_V | 460_R | 1.352 | 0.98 |
| 168_E | 172_E | 1.342 | 0.98 |
| 296_H | 300_K | 1.328 | 0.98 |
| 134_L | 138_I | 1.312 | 0.97 |
| 371_G | 510_L | 1.305 | 0.97 |
| 61_G | 94_T | 1.304 | 0.97 |
| 326_I | 332_L | 1.300 | 0.97 |
| 64_I | 382_R | 1.298 | 0.97 |
| 48_L | 516_I | 1.293 | 0.97 |
| 18_R | 22_R | 1.283 | 0.97 |
| 301_E | 305_A | 1.282 | 0.97 |
| 23_M | 26_L | 1.281 | 0.97 |
| 102_E | 439_V | 1.281 | 0.97 |
| 105_R | 439_V | 1.281 | 0.97 |
| 318_A | 325_V | 1.280 | 0.97 |
| 119_I | 426_E | 1.274 | 0.97 |
| 127_A | 433_F | 1.264 | 0.97 |
| 81_V | 96_A | 1.262 | 0.97 |
| 231_K | 339_D | 1.260 | 0.97 |
| 29_R | 105_R | 1.258 | 0.97 |
| 233_A | 332_L | 1.250 | 0.96 |
| 444_L | 475_V | 1.248 | 0.96 |
| 413_M | 417_E | 1.248 | 0.96 |
| 333_S | 336_D | 1.247 | 0.96 |
| 369_I | 377_I | 1.238 | 0.96 |
| 417_E | 420_E | 1.237 | 0.96 |
| 276_I | 279_S | 1.235 | 0.96 |
| 132_Q | 500_Q | 1.235 | 0.96 |
| 410_E | 463_H | 1.226 | 0.96 |
| 423_S | 430_V | 1.224 | 0.96 |
| 25_I | 29_R | 1.221 | 0.96 |
| 60_D | 63_T | 1.221 | 0.96 |
| 135_L | 496_T | 1.213 | 0.95 |
| 122_K | 426_E | 1.213 | 0.95 |
| 137_T | 414_K | 1.209 | 0.95 |
| 130_K | 134_L | 1.206 | 0.95 |
| 110_L | 428_L | 1.202 | 0.95 |
| 406_S | 410_E | 1.199 | 0.95 |
| 25_I | 104_L | 1.198 | 0.95 |
| 340_A | 343_V | 1.197 | 0.95 |
| 130_K | 430_V | 1.196 | 0.95 |
| 263_E | 267_K | 1.195 | 0.95 |
| 229_D | 341_G | 1.194 | 0.95 |
| 410_E | 469_K | 1.189 | 0.95 |
| 106_K | 109_E | 1.183 | 0.95 |
| 95_T | 440_I | 1.180 | 0.95 |
| 134_L | 410_E | 1.178 | 0.94 |
| 346_R | 352_S | 1.178 | 0.94 |
| 230_A | 340_A | 1.172 | 0.94 |
| 306_A | 354_I | 1.171 | 0.94 |
| 58_T | 64_I | 1.166 | 0.94 |
| 106_K | 436_A | 1.165 | 0.94 |
| 8_L | 12_M | 1.163 | 0.94 |
| 341_G | 357_E | 1.153 | 0.94 |
| 176_E | 210_K | 1.152 | 0.94 |
| 397_D | 493_R | 1.149 | 0.93 |
| 298_L | 305_A | 1.142 | 0.93 |
| 207_E | 368_L | 1.138 | 0.93 |
| 60_D | 386_D | 1.136 | 0.93 |
| 445_A | 452_A | 1.135 | 0.93 |
| 396_E | 493_R | 1.135 | 0.93 |
| 28_G | 78_L | 1.128 | 0.93 |
| 347_K | 351_D | 1.128 | 0.93 |
| 341_G | 359_C | 1.123 | 0.92 |
| 401_V | 492_L | 1.120 | 0.92 |
| 126_A | 130_K | 1.118 | 0.92 |
| 483_M | 488_V | 1.117 | 0.92 |
| 402_S | 406_S | 1.115 | 0.92 |
| 234_L | 325_V | 1.110 | 0.92 |
| 414_K | 417_E | 1.106 | 0.92 |
| 496_T | 500_Q | 1.104 | 0.92 |
| 150_L | 154_A | 1.099 | 0.91 |
| 407_T | 492_L | 1.098 | 0.91 |
| 427_Q | 431_R | 1.095 | 0.91 |
| 431_R | 435_D | 1.094 | 0.91 |
| 132_Q | 496_T | 1.087 | 0.91 |
| 384_V | 388_V | 1.080 | 0.90 |
| 123_G | 127_A | 1.078 | 0.90 |
| 409_V | 441_P | 1.078 | 0.90 |
| 288_K | 310_K | 1.078 | 0.90 |
| 59_N | 104_L | 1.076 | 0.90 |
| 467_G | 471_A | 1.075 | 0.90 |
| 394_T | 398_G | 1.075 | 0.90 |
| 111_L | 120_V | 1.075 | 0.90 |
| 230_A | 283_V | 1.073 | 0.90 |
| 212_V | 320_A | 1.073 | 0.90 |
| 139_A | 399_R | 1.070 | 0.90 |
| 147_K | 151_T | 1.070 | 0.90 |
| 432_A | 435_D | 1.068 | 0.90 |
| 153_I | 400_I | 1.067 | 0.90 |
| 382_R | 389_G | 1.065 | 0.90 |
| 93_T | 386_D | 1.065 | 0.90 |
| 412_S | 460_R | 1.064 | 0.89 |
| 293_L | 297_Y | 1.056 | 0.89 |
| 402_S | 484_C | 1.048 | 0.88 |
| 422_I | 426_E | 1.047 | 0.88 |
| 450_L | 475_V | 1.046 | 0.88 |
| 37_S | 46_K | 1.044 | 0.88 |
| 227_V | 283_V | 1.044 | 0.88 |
| 277_K | 280_G | 1.043 | 0.88 |
| 39_L | 95_T | 1.042 | 0.88 |
| 199_S | 204_D | 1.040 | 0.88 |
| 471_A | 480_V | 1.040 | 0.88 |
| 198_K | 377_I | 1.033 | 0.88 |
| 140_C | 484_C | 1.032 | 0.87 |
| 462_A | 471_A | 1.027 | 0.87 |
| 455_I | 473_L | 1.018 | 0.86 |
| 317_L | 356_V | 1.017 | 0.86 |
| 40_G | 43_G | 1.016 | 0.86 |
| 227_V | 282_N | 1.015 | 0.86 |
| 379_E | 382_R | 1.014 | 0.86 |
| 59_N | 159_T | 1.005 | 0.86 |
| 152_K | 487_G | 1.004 | 0.85 |
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 | |
| 3ruvA | 4 | 0.9503 | 100 | 0.028 | Contact Map |
| 3j1bA | 16 | 0.9319 | 100 | 0.059 | Contact Map |
| 1q3qA | 4 | 0.9466 | 100 | 0.069 | Contact Map |
| 1a6dA | 1 | 0.9208 | 100 | 0.075 | Contact Map |
| 1a6dB | 1 | 0.919 | 100 | 0.092 | Contact Map |
| 3ko1A | 9 | 0.9245 | 100 | 0.096 | Contact Map |
| 3p9dG | 2 | 0.9319 | 100 | 0.115 | Contact Map |
| 3p9dF | 2 | 0.9632 | 100 | 0.12 | Contact Map |
| 3p9dD | 2 | 0.9429 | 100 | 0.121 | Contact Map |
| 3p9dC | 2 | 0.9319 | 100 | 0.122 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)