| c2 |
| ID: | 1512535898 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 527 (519) | ||
| Sequences: | 3213 (1479.7) | ||
| Seq/Len: | 6.191 | ||
| Nf(neff/√len): | 65.0 |
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: 6.191).
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 |
| 130_A | 133_D | 4.514 | 1.00 |
| 341_D | 358_G | 3.894 | 1.00 |
| 290_I | 305_S | 3.703 | 1.00 |
| 206_S | 369_L | 3.698 | 1.00 |
| 150_R | 179_N | 3.330 | 1.00 |
| 481_D | 484_Q | 3.288 | 1.00 |
| 154_I | 175_E | 3.267 | 1.00 |
| 128_S | 498_V | 3.172 | 1.00 |
| 408_E | 494_K | 3.141 | 1.00 |
| 404_G | 482_M | 3.077 | 1.00 |
| 135_L | 491_Y | 3.021 | 1.00 |
| 225_R | 342_V | 2.988 | 1.00 |
| 102_L | 124_Y | 2.949 | 1.00 |
| 105_E | 435_R | 2.934 | 1.00 |
| 277_S | 303_I | 2.808 | 1.00 |
| 101_E | 104_R | 2.804 | 1.00 |
| 267_E | 271_N | 2.727 | 1.00 |
| 233_I | 323_G | 2.613 | 1.00 |
| 340_C | 356_F | 2.577 | 1.00 |
| 317_L | 356_F | 2.509 | 1.00 |
| 274_A | 278_K | 2.461 | 1.00 |
| 175_E | 179_N | 2.431 | 1.00 |
| 106_A | 124_Y | 2.431 | 1.00 |
| 177_A | 384_L | 2.418 | 1.00 |
| 128_S | 502_S | 2.414 | 1.00 |
| 150_R | 182_L | 2.414 | 1.00 |
| 136_T | 495_R | 2.399 | 1.00 |
| 139_A | 491_Y | 2.366 | 1.00 |
| 422_I | 430_V | 2.343 | 1.00 |
| 134_A | 414_A | 2.319 | 1.00 |
| 226_I | 229_A | 2.308 | 1.00 |
| 30_G | 100_A | 2.287 | 1.00 |
| 433_F | 502_S | 2.251 | 1.00 |
| 369_L | 377_L | 2.228 | 1.00 |
| 232_L | 332_P | 2.202 | 1.00 |
| 473_D | 476_N | 2.193 | 1.00 |
| 201_G | 205_D | 2.188 | 1.00 |
| 437_L | 498_V | 2.164 | 1.00 |
| 439_Q | 443_I | 2.135 | 1.00 |
| 94_S | 497_V | 2.134 | 1.00 |
| 285_I | 356_F | 2.115 | 1.00 |
| 270_K | 274_A | 2.104 | 1.00 |
| 58_N | 63_I | 2.089 | 1.00 |
| 176_L | 206_S | 2.022 | 1.00 |
| 158_K | 171_D | 1.978 | 1.00 |
| 135_L | 407_A | 1.927 | 1.00 |
| 402_L | 406_C | 1.912 | 1.00 |
| 418_E | 430_V | 1.891 | 1.00 |
| 285_I | 309_A | 1.888 | 1.00 |
| 101_E | 439_Q | 1.861 | 1.00 |
| 179_N | 210_E | 1.852 | 1.00 |
| 37_L | 97_V | 1.837 | 1.00 |
| 407_A | 411_M | 1.833 | 1.00 |
| 130_A | 430_V | 1.828 | 1.00 |
| 469_T | 481_D | 1.825 | 1.00 |
| 124_Y | 433_F | 1.823 | 1.00 |
| 126_L | 426_K | 1.783 | 1.00 |
| 135_L | 495_R | 1.755 | 1.00 |
| 400_T | 488_V | 1.754 | 1.00 |
| 105_E | 108_K | 1.741 | 1.00 |
| 102_L | 433_F | 1.734 | 1.00 |
| 238_L | 276_I | 1.715 | 1.00 |
| 230_K | 339_E | 1.711 | 1.00 |
| 233_I | 318_A | 1.688 | 1.00 |
| 131_A | 411_M | 1.678 | 1.00 |
| 130_A | 414_A | 1.672 | 1.00 |
| 232_L | 337_L | 1.665 | 1.00 |
| 130_A | 418_E | 1.662 | 1.00 |
| 415_V | 430_V | 1.654 | 1.00 |
| 230_K | 280_G | 1.635 | 1.00 |
| 124_Y | 502_S | 1.622 | 1.00 |
| 306_I | 354_L | 1.618 | 1.00 |
| 458_K | 478_T | 1.615 | 1.00 |
| 197_K | 378_D | 1.615 | 1.00 |
| 132_L | 136_T | 1.608 | 1.00 |
| 318_A | 325_V | 1.608 | 1.00 |
| 227_E | 342_V | 1.586 | 0.99 |
| 239_D | 289_L | 1.584 | 0.99 |
| 379_E | 382_R | 1.582 | 0.99 |
| 122_E | 426_K | 1.581 | 0.99 |
| 263_K | 267_E | 1.579 | 0.99 |
| 130_A | 134_A | 1.574 | 0.99 |
| 369_L | 380_A | 1.554 | 0.99 |
| 410_V | 463_I | 1.547 | 0.99 |
| 473_D | 480_A | 1.533 | 0.99 |
| 277_S | 301_L | 1.527 | 0.99 |
| 59_D | 386_D | 1.524 | 0.99 |
| 203_L | 380_A | 1.513 | 0.99 |
| 462_S | 470_S | 1.501 | 0.99 |
| 105_E | 436_A | 1.496 | 0.99 |
| 385_H | 389_S | 1.491 | 0.99 |
| 298_F | 305_S | 1.482 | 0.99 |
| 124_Y | 127_A | 1.470 | 0.99 |
| 384_L | 388_L | 1.441 | 0.99 |
| 284_F | 298_F | 1.424 | 0.99 |
| 180_A | 208_L | 1.412 | 0.98 |
| 231_I | 340_C | 1.411 | 0.98 |
| 493_L | 497_V | 1.410 | 0.98 |
| 259_A | 263_K | 1.407 | 0.98 |
| 134_A | 410_V | 1.401 | 0.98 |
| 150_R | 175_E | 1.399 | 0.98 |
| 367_I | 384_L | 1.393 | 0.98 |
| 416_D | 438_R | 1.389 | 0.98 |
| 94_S | 440_L | 1.385 | 0.98 |
| 177_A | 387_A | 1.378 | 0.98 |
| 157_A | 391_L | 1.368 | 0.98 |
| 140_V | 483_R | 1.364 | 0.98 |
| 438_R | 460_R | 1.364 | 0.98 |
| 450_F | 474_L | 1.362 | 0.98 |
| 298_F | 303_I | 1.361 | 0.98 |
| 155_H | 486_G | 1.359 | 0.98 |
| 431_E | 435_R | 1.358 | 0.98 |
| 132_L | 495_R | 1.355 | 0.98 |
| 35_S | 44_K | 1.352 | 0.98 |
| 93_T | 386_D | 1.342 | 0.98 |
| 473_D | 485_L | 1.334 | 0.98 |
| 218_F | 345_E | 1.333 | 0.98 |
| 413_K | 417_T | 1.333 | 0.98 |
| 320_V | 359_C | 1.329 | 0.97 |
| 123_G | 127_A | 1.322 | 0.97 |
| 346_I | 357_S | 1.318 | 0.97 |
| 183_R | 210_E | 1.318 | 0.97 |
| 134_A | 137_K | 1.299 | 0.97 |
| 171_D | 175_E | 1.298 | 0.97 |
| 60_G | 93_T | 1.294 | 0.97 |
| 404_G | 487_I | 1.279 | 0.97 |
| 490_S | 493_L | 1.275 | 0.97 |
| 156_I | 400_T | 1.274 | 0.97 |
| 92_T | 386_D | 1.273 | 0.96 |
| 125_R | 506_E | 1.270 | 0.96 |
| 231_I | 321_T | 1.268 | 0.96 |
| 296_Q | 300_D | 1.263 | 0.96 |
| 450_F | 455_L | 1.262 | 0.96 |
| 154_I | 158_K | 1.259 | 0.96 |
| 157_A | 178_T | 1.249 | 0.96 |
| 254_S | 257_K | 1.248 | 0.96 |
| 432_A | 435_R | 1.248 | 0.96 |
| 75_K | 78_V | 1.246 | 0.96 |
| 176_L | 367_I | 1.245 | 0.96 |
| 218_F | 304_N | 1.243 | 0.96 |
| 345_E | 352_P | 1.240 | 0.96 |
| 133_D | 136_T | 1.240 | 0.96 |
| 27_I | 104_R | 1.239 | 0.96 |
| 30_G | 34_K | 1.239 | 0.96 |
| 80_I | 95_V | 1.234 | 0.96 |
| 58_N | 382_R | 1.232 | 0.96 |
| 482_M | 487_I | 1.224 | 0.95 |
| 232_L | 276_I | 1.219 | 0.95 |
| 207_F | 368_V | 1.204 | 0.95 |
| 269_M | 293_Y | 1.203 | 0.95 |
| 85_D | 92_T | 1.201 | 0.95 |
| 489_E | 494_K | 1.201 | 0.95 |
| 288_Q | 310_D | 1.200 | 0.95 |
| 401_V | 491_Y | 1.191 | 0.94 |
| 441_P | 459_L | 1.185 | 0.94 |
| 359_C | 362_G | 1.175 | 0.94 |
| 226_I | 283_T | 1.174 | 0.94 |
| 179_N | 182_L | 1.174 | 0.94 |
| 288_Q | 308_H | 1.173 | 0.94 |
| 412_S | 416_D | 1.172 | 0.94 |
| 34_K | 446_D | 1.171 | 0.94 |
| 232_L | 269_M | 1.167 | 0.94 |
| 127_A | 430_V | 1.162 | 0.93 |
| 276_I | 281_I | 1.159 | 0.93 |
| 43_D | 58_N | 1.155 | 0.93 |
| 339_E | 360_K | 1.152 | 0.93 |
| 85_D | 386_D | 1.151 | 0.93 |
| 180_A | 184_L | 1.150 | 0.93 |
| 225_R | 344_E | 1.149 | 0.93 |
| 183_R | 365_C | 1.138 | 0.92 |
| 314_V | 317_L | 1.137 | 0.92 |
| 417_T | 420_Q | 1.136 | 0.92 |
| 12_E | 513_N | 1.135 | 0.92 |
| 218_F | 354_L | 1.131 | 0.92 |
| 233_I | 317_L | 1.130 | 0.92 |
| 154_I | 171_D | 1.127 | 0.92 |
| 38_G | 41_G | 1.125 | 0.92 |
| 134_A | 411_M | 1.123 | 0.92 |
| 129_A | 133_D | 1.120 | 0.92 |
| 410_V | 413_K | 1.117 | 0.91 |
| 210_E | 358_G | 1.116 | 0.91 |
| 59_D | 62_T | 1.115 | 0.91 |
| 157_A | 174_A | 1.112 | 0.91 |
| 273_I | 294_P | 1.111 | 0.91 |
| 153_L | 391_L | 1.110 | 0.91 |
| 109_L | 429_A | 1.109 | 0.91 |
| 274_A | 301_L | 1.108 | 0.91 |
| 229_A | 283_T | 1.105 | 0.91 |
| 163_S | 383_S | 1.102 | 0.91 |
| 289_L | 308_H | 1.099 | 0.91 |
| 293_Y | 297_L | 1.095 | 0.90 |
| 239_D | 294_P | 1.090 | 0.90 |
| 322_G | 338_G | 1.088 | 0.90 |
| 233_I | 325_V | 1.087 | 0.90 |
| 98_L | 501_A | 1.085 | 0.90 |
| 7_G | 10_V | 1.085 | 0.90 |
| 401_V | 488_V | 1.082 | 0.90 |
| 470_S | 479_I | 1.082 | 0.90 |
| 123_G | 429_A | 1.079 | 0.90 |
| 253_D | 257_K | 1.079 | 0.90 |
| 27_I | 107_E | 1.078 | 0.89 |
| 491_Y | 495_R | 1.078 | 0.89 |
| 273_I | 297_L | 1.073 | 0.89 |
| 126_L | 130_A | 1.070 | 0.89 |
| 99_S | 501_A | 1.069 | 0.89 |
| 415_V | 434_A | 1.064 | 0.89 |
| 37_L | 440_L | 1.061 | 0.88 |
| 409_M | 438_R | 1.058 | 0.88 |
| 250_F | 261_L | 1.055 | 0.88 |
| 21_S | 24_V | 1.055 | 0.88 |
| 371_G | 377_L | 1.051 | 0.88 |
| 411_M | 437_L | 1.051 | 0.88 |
| 433_F | 437_L | 1.049 | 0.88 |
| 420_Q | 431_E | 1.043 | 0.87 |
| 229_A | 343_I | 1.043 | 0.87 |
| 416_D | 431_E | 1.041 | 0.87 |
| 455_L | 472_L | 1.041 | 0.87 |
| 396_K | 492_K | 1.035 | 0.87 |
| 163_S | 167_S | 1.030 | 0.86 |
| 311_F | 315_E | 1.030 | 0.86 |
| 326_V | 332_P | 1.028 | 0.86 |
| 101_E | 443_I | 1.028 | 0.86 |
| 106_A | 123_G | 1.026 | 0.86 |
| 445_A | 450_F | 1.025 | 0.86 |
| 285_I | 314_V | 1.021 | 0.86 |
| 226_I | 282_N | 1.019 | 0.86 |
| 153_L | 157_A | 1.017 | 0.85 |
| 228_N | 501_A | 1.015 | 0.85 |
| 401_V | 407_A | 1.012 | 0.85 |
| 324_E | 336_K | 1.006 | 0.85 |
| 283_T | 343_I | 1.005 | 0.85 |
| 12_E | 15_A | 1.001 | 0.84 |
| 109_L | 123_G | 1.000 | 0.84 |
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 | |
| 3p9dB | 2 | 0.9715 | 100 | 0.031 | Contact Map |
| 1q3qA | 4 | 0.9696 | 100 | 0.038 | Contact Map |
| 3iygB | 1 | 0.9696 | 100 | 0.04 | Contact Map |
| 3j1bA | 16 | 0.9583 | 100 | 0.042 | Contact Map |
| 1a6dA | 1 | 0.9412 | 100 | 0.043 | Contact Map |
| 1a6dB | 1 | 0.9393 | 100 | 0.045 | Contact Map |
| 3ko1A | 9 | 0.9431 | 100 | 0.045 | Contact Map |
| 3p9dA | 2 | 0.9791 | 100 | 0.048 | Contact Map |
| 3p9dG | 2 | 0.9564 | 100 | 0.048 | Contact Map |
| 3iygH | 1 | 0.9677 | 100 | 0.05 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)