| c4 |
| ID: | 1512535965 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 528 (514) | ||
| Sequences: | 3415 (1520.6) | ||
| Seq/Len: | 6.644 | ||
| Nf(neff/√len): | 67.1 |
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: 6.644).
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_R | 133_D | 4.553 | 1.00 |
| 297_V | 312_V | 3.761 | 1.00 |
| 491_N | 494_E | 3.733 | 1.00 |
| 348_D | 365_G | 3.710 | 1.00 |
| 135_L | 501_V | 3.379 | 1.00 |
| 151_V | 172_P | 3.108 | 1.00 |
| 207_T | 379_I | 3.079 | 1.00 |
| 418_E | 504_S | 3.008 | 1.00 |
| 228_R | 349_L | 3.005 | 1.00 |
| 103_L | 124_F | 2.986 | 1.00 |
| 147_R | 176_D | 2.975 | 1.00 |
| 414_G | 492_T | 2.949 | 1.00 |
| 128_A | 508_I | 2.942 | 1.00 |
| 139_C | 501_V | 2.812 | 1.00 |
| 106_A | 445_S | 2.792 | 1.00 |
| 59_N | 64_I | 2.694 | 1.00 |
| 102_A | 105_G | 2.651 | 1.00 |
| 269_A | 273_N | 2.606 | 1.00 |
| 324_L | 363_V | 2.545 | 1.00 |
| 279_K | 310_I | 2.515 | 1.00 |
| 128_A | 512_S | 2.488 | 1.00 |
| 432_M | 440_W | 2.477 | 1.00 |
| 236_L | 330_C | 2.395 | 1.00 |
| 147_R | 179_L | 2.388 | 1.00 |
| 107_A | 124_F | 2.369 | 1.00 |
| 347_A | 363_V | 2.345 | 1.00 |
| 126_S | 436_Q | 2.339 | 1.00 |
| 174_A | 394_L | 2.287 | 1.00 |
| 443_F | 512_S | 2.286 | 1.00 |
| 276_K | 280_K | 2.262 | 1.00 |
| 136_L | 505_T | 2.229 | 1.00 |
| 32_A | 101_G | 2.214 | 1.00 |
| 172_P | 176_D | 2.199 | 1.00 |
| 134_I | 424_R | 2.175 | 1.00 |
| 235_G | 339_F | 2.092 | 1.00 |
| 95_S | 507_A | 2.090 | 1.00 |
| 379_I | 387_I | 2.076 | 1.00 |
| 483_S | 490_T | 2.069 | 1.00 |
| 229_K | 232_A | 2.059 | 1.00 |
| 173_L | 207_T | 2.051 | 1.00 |
| 202_G | 206_D | 2.011 | 1.00 |
| 124_F | 512_S | 2.006 | 1.00 |
| 272_L | 276_K | 1.998 | 1.00 |
| 135_L | 417_P | 1.942 | 1.00 |
| 103_L | 443_F | 1.925 | 1.00 |
| 287_L | 363_V | 1.916 | 1.00 |
| 130_R | 440_W | 1.914 | 1.00 |
| 425_L | 440_W | 1.904 | 1.00 |
| 448_E | 470_R | 1.897 | 1.00 |
| 483_S | 486_R | 1.888 | 1.00 |
| 124_F | 443_F | 1.880 | 1.00 |
| 447_L | 508_I | 1.868 | 1.00 |
| 451_P | 469_L | 1.856 | 1.00 |
| 131_S | 421_I | 1.840 | 1.00 |
| 449_V | 453_T | 1.837 | 1.00 |
| 412_A | 416_A | 1.834 | 1.00 |
| 106_A | 109_R | 1.819 | 1.00 |
| 135_L | 505_T | 1.785 | 1.00 |
| 417_P | 421_I | 1.782 | 1.00 |
| 233_K | 346_S | 1.768 | 1.00 |
| 313_V | 361_V | 1.721 | 1.00 |
| 155_S | 168_S | 1.716 | 1.00 |
| 428_E | 440_W | 1.704 | 1.00 |
| 130_R | 134_I | 1.703 | 1.00 |
| 130_R | 428_E | 1.701 | 1.00 |
| 410_L | 498_L | 1.686 | 1.00 |
| 479_N | 491_N | 1.672 | 1.00 |
| 176_D | 211_D | 1.666 | 1.00 |
| 102_A | 449_V | 1.636 | 1.00 |
| 39_L | 98_I | 1.623 | 1.00 |
| 261_D | 265_K | 1.610 | 1.00 |
| 287_L | 316_I | 1.593 | 1.00 |
| 325_S | 332_P | 1.593 | 1.00 |
| 132_V | 136_L | 1.591 | 1.00 |
| 236_L | 325_S | 1.589 | 1.00 |
| 472_K | 480_D | 1.589 | 1.00 |
| 76_R | 79_V | 1.563 | 0.99 |
| 29_R | 105_G | 1.560 | 0.99 |
| 122_D | 436_Q | 1.557 | 0.99 |
| 420_E | 473_H | 1.540 | 0.99 |
| 389_E | 392_R | 1.532 | 0.99 |
| 379_I | 390_T | 1.523 | 0.99 |
| 198_K | 388_D | 1.522 | 0.99 |
| 230_E | 349_L | 1.522 | 0.99 |
| 235_G | 344_L | 1.510 | 0.99 |
| 483_S | 495_E | 1.509 | 0.99 |
| 394_L | 398_L | 1.508 | 0.99 |
| 265_K | 269_A | 1.507 | 0.99 |
| 125_Q | 516_K | 1.487 | 0.99 |
| 130_R | 424_R | 1.486 | 0.99 |
| 60_D | 396_D | 1.473 | 0.99 |
| 233_K | 282_K | 1.463 | 0.99 |
| 503_V | 507_A | 1.451 | 0.99 |
| 256_D | 259_Q | 1.426 | 0.99 |
| 311_M | 352_E | 1.413 | 0.99 |
| 134_I | 137_E | 1.413 | 0.99 |
| 305_L | 312_V | 1.406 | 0.99 |
| 124_F | 127_A | 1.405 | 0.99 |
| 180_K | 211_D | 1.393 | 0.99 |
| 242_S | 291_S | 1.391 | 0.99 |
| 395_H | 399_C | 1.386 | 0.98 |
| 59_N | 392_R | 1.376 | 0.98 |
| 95_S | 450_I | 1.376 | 0.98 |
| 490_T | 495_E | 1.370 | 0.98 |
| 441_Q | 445_S | 1.365 | 0.98 |
| 236_L | 324_L | 1.365 | 0.98 |
| 229_K | 284_N | 1.358 | 0.98 |
| 61_G | 94_T | 1.344 | 0.98 |
| 174_A | 397_A | 1.344 | 0.98 |
| 279_K | 308_L | 1.334 | 0.98 |
| 460_L | 465_V | 1.334 | 0.98 |
| 177_S | 181_I | 1.333 | 0.98 |
| 123_S | 127_A | 1.328 | 0.98 |
| 327_G | 366_I | 1.323 | 0.98 |
| 134_I | 420_E | 1.322 | 0.98 |
| 262_K | 265_K | 1.310 | 0.98 |
| 81_V | 96_V | 1.308 | 0.98 |
| 153_A | 410_L | 1.295 | 0.97 |
| 60_D | 63_T | 1.293 | 0.97 |
| 234_I | 328_L | 1.290 | 0.97 |
| 234_I | 347_A | 1.289 | 0.97 |
| 106_A | 446_A | 1.285 | 0.97 |
| 127_A | 440_W | 1.277 | 0.97 |
| 176_D | 179_L | 1.273 | 0.97 |
| 241_I | 278_I | 1.273 | 0.97 |
| 329_G | 345_G | 1.272 | 0.97 |
| 94_T | 396_D | 1.271 | 0.97 |
| 14_K | 523_D | 1.267 | 0.97 |
| 460_L | 484_V | 1.264 | 0.97 |
| 32_A | 36_R | 1.261 | 0.97 |
| 229_K | 286_L | 1.258 | 0.97 |
| 381_G | 387_I | 1.257 | 0.97 |
| 286_L | 305_L | 1.257 | 0.97 |
| 132_V | 505_T | 1.254 | 0.97 |
| 204_I | 390_T | 1.248 | 0.96 |
| 213_V | 327_G | 1.237 | 0.96 |
| 140_H | 493_Y | 1.233 | 0.96 |
| 448_E | 452_T | 1.232 | 0.96 |
| 353_I | 364_T | 1.227 | 0.96 |
| 93_T | 396_D | 1.223 | 0.96 |
| 37_T | 46_K | 1.217 | 0.96 |
| 152_R | 496_H | 1.216 | 0.96 |
| 154_A | 175_V | 1.203 | 0.95 |
| 411_I | 501_V | 1.197 | 0.95 |
| 434_G | 437_A | 1.189 | 0.95 |
| 416_A | 420_E | 1.178 | 0.95 |
| 423_R | 427_K | 1.174 | 0.95 |
| 29_R | 101_G | 1.172 | 0.94 |
| 482_I | 487_S | 1.172 | 0.94 |
| 505_T | 509_T | 1.172 | 0.94 |
| 500_P | 503_V | 1.171 | 0.94 |
| 252_I | 263_I | 1.164 | 0.94 |
| 303_H | 307_K | 1.164 | 0.94 |
| 133_D | 136_L | 1.164 | 0.94 |
| 134_I | 138_M | 1.157 | 0.94 |
| 77_M | 514_C | 1.157 | 0.94 |
| 129_K | 133_D | 1.156 | 0.94 |
| 259_Q | 262_K | 1.154 | 0.94 |
| 86_D | 93_T | 1.150 | 0.94 |
| 219_A | 311_M | 1.146 | 0.94 |
| 168_S | 172_P | 1.144 | 0.94 |
| 480_D | 489_T | 1.144 | 0.94 |
| 127_A | 443_F | 1.137 | 0.93 |
| 73_P | 524_I | 1.136 | 0.93 |
| 123_S | 439_I | 1.134 | 0.93 |
| 177_S | 209_M | 1.131 | 0.93 |
| 278_I | 286_L | 1.130 | 0.93 |
| 128_A | 443_F | 1.129 | 0.93 |
| 132_V | 509_T | 1.126 | 0.93 |
| 198_K | 391_E | 1.126 | 0.93 |
| 377_V | 394_L | 1.123 | 0.93 |
| 28_A | 104_L | 1.123 | 0.93 |
| 14_K | 17_P | 1.122 | 0.93 |
| 291_S | 314_K | 1.121 | 0.93 |
| 40_G | 43_G | 1.120 | 0.93 |
| 352_E | 359_K | 1.118 | 0.92 |
| 210_I | 214_V | 1.116 | 0.92 |
| 492_T | 497_I | 1.114 | 0.92 |
| 62_H | 66_K | 1.110 | 0.92 |
| 420_E | 423_R | 1.109 | 0.92 |
| 134_I | 421_I | 1.109 | 0.92 |
| 442_E | 445_S | 1.102 | 0.92 |
| 427_K | 430_R | 1.100 | 0.92 |
| 278_I | 283_C | 1.095 | 0.91 |
| 426_S | 448_E | 1.089 | 0.91 |
| 406_K | 502_L | 1.089 | 0.91 |
| 275_C | 301_A | 1.087 | 0.91 |
| 275_C | 304_F | 1.087 | 0.91 |
| 154_A | 401_I | 1.087 | 0.91 |
| 228_R | 351_E | 1.082 | 0.91 |
| 114_G | 117_P | 1.082 | 0.91 |
| 235_G | 278_I | 1.081 | 0.91 |
| 277_K | 280_K | 1.081 | 0.91 |
| 455_A | 460_L | 1.080 | 0.91 |
| 208_E | 378_V | 1.072 | 0.90 |
| 460_L | 482_I | 1.070 | 0.90 |
| 36_R | 453_T | 1.064 | 0.90 |
| 411_I | 498_L | 1.064 | 0.90 |
| 465_V | 489_T | 1.063 | 0.90 |
| 86_D | 396_D | 1.063 | 0.90 |
| 160_S | 393_S | 1.060 | 0.90 |
| 211_D | 365_G | 1.057 | 0.89 |
| 119_I | 436_Q | 1.056 | 0.89 |
| 426_S | 441_Q | 1.056 | 0.89 |
| 67_Q | 225_G | 1.055 | 0.89 |
| 61_G | 93_T | 1.048 | 0.89 |
| 506_S | 510_L | 1.047 | 0.89 |
| 99_L | 511_A | 1.046 | 0.89 |
| 180_K | 375_V | 1.034 | 0.88 |
| 115_I | 120_I | 1.033 | 0.88 |
| 150_L | 154_A | 1.032 | 0.88 |
| 421_I | 447_L | 1.032 | 0.88 |
| 499_Q | 504_S | 1.029 | 0.88 |
| 128_A | 132_V | 1.028 | 0.88 |
| 147_R | 151_V | 1.027 | 0.88 |
| 271_L | 300_L | 1.027 | 0.88 |
| 333_I | 339_F | 1.026 | 0.87 |
| 398_L | 402_R | 1.023 | 0.87 |
| 321_I | 324_L | 1.020 | 0.87 |
| 422_S | 426_S | 1.017 | 0.87 |
| 465_V | 482_I | 1.012 | 0.86 |
| 33_D | 36_R | 1.011 | 0.86 |
| 392_R | 399_C | 1.010 | 0.86 |
| 147_R | 172_P | 1.004 | 0.86 |
| 45_D | 59_N | 1.004 | 0.86 |
| 430_R | 441_Q | 1.003 | 0.86 |
| 420_E | 424_R | 1.001 | 0.86 |
| 29_R | 108_E | 1.001 | 0.86 |
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 | |
| 3p9dD | 2 | 0.9886 | 100 | 0.02 | Contact Map |
| 3j1bA | 16 | 0.9602 | 100 | 0.037 | Contact Map |
| 3iygD | 1 | 0.9773 | 100 | 0.041 | Contact Map |
| 1q3qA | 4 | 0.9716 | 100 | 0.044 | Contact Map |
| 1a6dB | 1 | 0.947 | 100 | 0.044 | Contact Map |
| 3ko1A | 9 | 0.9508 | 100 | 0.045 | Contact Map |
| 3iygA | 1 | 0.9659 | 100 | 0.048 | Contact Map |
| 3p9dA | 2 | 0.9659 | 100 | 0.05 | Contact Map |
| 1a6dA | 1 | 0.9489 | 100 | 0.051 | Contact Map |
| 3p9dH | 2 | 0.947 | 100 | 0.053 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)