| pafa |
| ID: | 1505351539 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 546 (541) | ||
| Sequences: | 1171 (838.9) | ||
| Seq/Len: | 2.165 | ||
| Nf(neff/√len): | 36.1 |
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: 2.165).
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 |
| 147_G | 175_T | 5.161 | 1.00 |
| 276_L | 301_L | 4.654 | 1.00 |
| 329_L | 333_F | 4.354 | 1.00 |
| 158_G | 170_A | 3.615 | 1.00 |
| 414_L | 419_V | 3.574 | 1.00 |
| 284_D | 339_K | 3.482 | 1.00 |
| 143_T | 296_F | 3.188 | 1.00 |
| 518_D | 537_G | 2.945 | 1.00 |
| 84_T | 137_L | 2.849 | 1.00 |
| 67_L | 540_I | 2.835 | 1.00 |
| 436_V | 467_I | 2.829 | 1.00 |
| 280_D | 331_D | 2.744 | 1.00 |
| 237_W | 364_A | 2.673 | 1.00 |
| 244_K | 251_Y | 2.652 | 1.00 |
| 433_V | 469_I | 2.558 | 1.00 |
| 55_G | 330_A | 2.553 | 1.00 |
| 512_Q | 542_E | 2.499 | 1.00 |
| 142_V | 524_S | 2.463 | 1.00 |
| 196_E | 202_N | 2.400 | 1.00 |
| 35_L | 347_V | 2.382 | 1.00 |
| 281_A | 285_G | 2.379 | 1.00 |
| 301_L | 332_F | 2.375 | 1.00 |
| 221_L | 323_L | 2.227 | 1.00 |
| 346_L | 526_L | 2.203 | 1.00 |
| 139_S | 534_G | 2.177 | 1.00 |
| 388_F | 422_Y | 2.134 | 1.00 |
| 51_K | 222_L | 2.124 | 1.00 |
| 283_I | 335_K | 2.090 | 0.99 |
| 307_V | 321_T | 2.069 | 0.99 |
| 51_K | 229_E | 2.047 | 0.99 |
| 85_S | 95_H | 2.045 | 0.99 |
| 222_L | 226_Q | 2.013 | 0.99 |
| 118_T | 135_R | 1.973 | 0.99 |
| 86_I | 350_S | 1.966 | 0.99 |
| 94_I | 534_G | 1.953 | 0.99 |
| 234_N | 247_P | 1.945 | 0.99 |
| 336_L | 345_Y | 1.945 | 0.99 |
| 55_G | 334_N | 1.941 | 0.99 |
| 154_S | 291_D | 1.937 | 0.99 |
| 276_L | 332_F | 1.931 | 0.99 |
| 57_F | 329_L | 1.921 | 0.99 |
| 290_A | 339_K | 1.916 | 0.99 |
| 370_G | 475_Y | 1.909 | 0.99 |
| 333_F | 347_V | 1.905 | 0.99 |
| 273_T | 328_D | 1.891 | 0.99 |
| 211_A | 262_K | 1.855 | 0.98 |
| 346_L | 504_G | 1.848 | 0.98 |
| 383_K | 426_E | 1.832 | 0.98 |
| 109_K | 115_S | 1.830 | 0.98 |
| 280_D | 335_K | 1.810 | 0.98 |
| 424_M | 467_I | 1.806 | 0.98 |
| 409_L | 414_L | 1.778 | 0.98 |
| 33_V | 336_L | 1.776 | 0.98 |
| 239_G | 482_K | 1.766 | 0.98 |
| 408_V | 412_S | 1.760 | 0.97 |
| 140_T | 145_Q | 1.760 | 0.97 |
| 287_Q | 290_A | 1.758 | 0.97 |
| 387_K | 422_Y | 1.756 | 0.97 |
| 54_E | 58_K | 1.751 | 0.97 |
| 76_P | 458_G | 1.742 | 0.97 |
| 420_R | 438_S | 1.725 | 0.97 |
| 404_F | 419_V | 1.719 | 0.97 |
| 160_S | 187_F | 1.707 | 0.97 |
| 59_R | 337_D | 1.692 | 0.97 |
| 87_F | 298_T | 1.683 | 0.96 |
| 121_P | 124_T | 1.679 | 0.96 |
| 39_Q | 308_G | 1.672 | 0.96 |
| 59_R | 333_F | 1.658 | 0.96 |
| 406_R | 416_L | 1.655 | 0.96 |
| 75_V | 489_W | 1.654 | 0.96 |
| 315_S | 318_V | 1.648 | 0.96 |
| 34_G | 348_F | 1.636 | 0.96 |
| 199_K | 203_D | 1.628 | 0.95 |
| 201_V | 278_M | 1.627 | 0.95 |
| 85_S | 516_M | 1.600 | 0.95 |
| 157_V | 282_A | 1.595 | 0.95 |
| 63_T | 501_M | 1.581 | 0.94 |
| 330_A | 334_N | 1.577 | 0.94 |
| 70_V | 498_L | 1.559 | 0.94 |
| 390_A | 393_I | 1.558 | 0.94 |
| 60_M | 499_L | 1.556 | 0.94 |
| 142_V | 296_F | 1.555 | 0.94 |
| 67_L | 514_Y | 1.541 | 0.93 |
| 415_K | 418_D | 1.540 | 0.93 |
| 70_V | 514_Y | 1.537 | 0.93 |
| 284_D | 335_K | 1.532 | 0.93 |
| 287_Q | 291_D | 1.525 | 0.93 |
| 277_Q | 280_D | 1.520 | 0.93 |
| 86_I | 519_I | 1.519 | 0.93 |
| 51_K | 319_E | 1.514 | 0.93 |
| 51_K | 226_Q | 1.509 | 0.92 |
| 71_H | 494_S | 1.508 | 0.92 |
| 88_T | 141_T | 1.504 | 0.92 |
| 170_A | 177_A | 1.503 | 0.92 |
| 157_V | 286_N | 1.496 | 0.92 |
| 331_D | 335_K | 1.470 | 0.91 |
| 55_G | 329_L | 1.464 | 0.91 |
| 108_G | 395_A | 1.460 | 0.91 |
| 289_G | 295_D | 1.448 | 0.90 |
| 305_D | 309_H | 1.445 | 0.90 |
| 79_T | 352_D | 1.444 | 0.90 |
| 409_L | 419_V | 1.442 | 0.90 |
| 138_W | 460_N | 1.437 | 0.90 |
| 254_L | 268_T | 1.437 | 0.90 |
| 432_S | 475_Y | 1.422 | 0.89 |
| 52_Y | 57_F | 1.417 | 0.89 |
| 337_D | 345_Y | 1.415 | 0.89 |
| 309_H | 486_H | 1.394 | 0.88 |
| 147_G | 156_V | 1.389 | 0.88 |
| 51_K | 323_L | 1.386 | 0.88 |
| 362_M | 367_M | 1.385 | 0.87 |
| 40_M | 322_Y | 1.383 | 0.87 |
| 60_M | 333_F | 1.382 | 0.87 |
| 173_N | 367_M | 1.372 | 0.87 |
| 271_G | 303_S | 1.368 | 0.87 |
| 336_L | 347_V | 1.367 | 0.87 |
| 277_Q | 331_D | 1.361 | 0.86 |
| 178_F | 286_N | 1.354 | 0.86 |
| 134_P | 294_T | 1.347 | 0.85 |
| 385_K | 391_D | 1.343 | 0.85 |
| 157_V | 178_F | 1.337 | 0.85 |
| 176_G | 194_T | 1.333 | 0.85 |
| 329_L | 332_F | 1.329 | 0.84 |
| 438_S | 441_E | 1.325 | 0.84 |
| 72_I | 496_I | 1.319 | 0.84 |
| 36_V | 86_I | 1.301 | 0.83 |
| 233_D | 238_E | 1.298 | 0.82 |
| 37_V | 349_L | 1.297 | 0.82 |
| 376_M | 427_L | 1.296 | 0.82 |
| 79_T | 305_D | 1.294 | 0.82 |
| 90_S | 94_I | 1.293 | 0.82 |
| 382_V | 386_Q | 1.292 | 0.82 |
| 320_D | 324_R | 1.291 | 0.82 |
| 174_P | 177_A | 1.281 | 0.81 |
| 305_D | 486_H | 1.279 | 0.81 |
| 124_T | 127_N | 1.269 | 0.80 |
| 155_K | 291_D | 1.264 | 0.80 |
| 372_F | 471_S | 1.255 | 0.79 |
| 208_N | 211_A | 1.254 | 0.79 |
| 72_I | 516_M | 1.254 | 0.79 |
| 162_K | 309_H | 1.254 | 0.79 |
| 342_K | 345_Y | 1.250 | 0.79 |
| 420_R | 424_M | 1.247 | 0.79 |
| 391_D | 408_V | 1.246 | 0.79 |
| 222_L | 327_R | 1.246 | 0.79 |
| 360_G | 371_F | 1.245 | 0.79 |
| 146_L | 296_F | 1.244 | 0.79 |
| 145_Q | 530_Q | 1.242 | 0.78 |
| 79_T | 309_H | 1.240 | 0.78 |
| 65_Y | 510_S | 1.235 | 0.78 |
| 189_T | 194_T | 1.232 | 0.78 |
| 498_L | 514_Y | 1.230 | 0.77 |
| 83_H | 309_H | 1.227 | 0.77 |
| 276_L | 280_D | 1.226 | 0.77 |
| 404_F | 423_V | 1.225 | 0.77 |
| 424_M | 441_E | 1.224 | 0.77 |
| 234_N | 248_T | 1.221 | 0.77 |
| 79_T | 100_N | 1.220 | 0.77 |
| 79_T | 353_H | 1.219 | 0.77 |
| 427_L | 469_I | 1.209 | 0.76 |
| 521_P | 535_A | 1.207 | 0.76 |
| 424_M | 428_K | 1.206 | 0.76 |
| 190_S | 193_Y | 1.201 | 0.75 |
| 498_L | 540_I | 1.187 | 0.74 |
| 473_D | 533_S | 1.184 | 0.74 |
| 220_T | 224_I | 1.181 | 0.73 |
| 79_T | 83_H | 1.179 | 0.73 |
| 132_H | 167_I | 1.172 | 0.73 |
| 335_K | 339_K | 1.172 | 0.73 |
| 500_F | 543_V | 1.171 | 0.72 |
| 154_S | 293_I | 1.169 | 0.72 |
| 160_S | 275_T | 1.166 | 0.72 |
| 309_H | 352_D | 1.164 | 0.72 |
| 333_F | 337_D | 1.161 | 0.72 |
| 112_Y | 163_D | 1.160 | 0.71 |
| 502_G | 505_I | 1.159 | 0.71 |
| 423_V | 467_I | 1.158 | 0.71 |
| 44_Y | 48_Y | 1.149 | 0.70 |
| 59_R | 347_V | 1.147 | 0.70 |
| 60_M | 64_G | 1.146 | 0.70 |
| 427_L | 436_V | 1.141 | 0.70 |
| 153_T | 228_T | 1.140 | 0.70 |
| 37_V | 325_L | 1.136 | 0.69 |
| 87_F | 348_F | 1.132 | 0.69 |
| 78_V | 81_I | 1.131 | 0.69 |
| 58_K | 62_N | 1.130 | 0.69 |
| 393_I | 414_L | 1.129 | 0.68 |
| 441_E | 444_E | 1.126 | 0.68 |
| 40_M | 44_Y | 1.126 | 0.68 |
| 83_H | 100_N | 1.125 | 0.68 |
| 313_P | 355_A | 1.125 | 0.68 |
| 410_A | 413_K | 1.125 | 0.68 |
| 165_A | 300_N | 1.124 | 0.68 |
| 90_S | 95_H | 1.123 | 0.68 |
| 100_N | 486_H | 1.123 | 0.68 |
| 105_K | 466_D | 1.119 | 0.67 |
| 304_T | 321_T | 1.119 | 0.67 |
| 266_R | 306_Y | 1.118 | 0.67 |
| 83_H | 162_K | 1.118 | 0.67 |
| 524_S | 529_I | 1.109 | 0.66 |
| 143_T | 156_V | 1.107 | 0.66 |
| 334_N | 338_K | 1.106 | 0.66 |
| 276_L | 328_D | 1.103 | 0.66 |
| 220_T | 316_I | 1.101 | 0.66 |
| 337_D | 341_G | 1.099 | 0.65 |
| 42_W | 66_S | 1.098 | 0.65 |
| 309_H | 353_H | 1.095 | 0.65 |
| 105_K | 403_Y | 1.089 | 0.64 |
| 380_M | 426_E | 1.088 | 0.64 |
| 103_Y | 107_L | 1.087 | 0.64 |
| 100_N | 309_H | 1.085 | 0.64 |
| 31_L | 295_D | 1.085 | 0.64 |
| 504_G | 526_L | 1.081 | 0.64 |
| 353_H | 486_H | 1.080 | 0.63 |
| 234_N | 246_T | 1.079 | 0.63 |
| 281_A | 284_D | 1.078 | 0.63 |
| 273_T | 277_Q | 1.077 | 0.63 |
| 244_K | 255_A | 1.074 | 0.63 |
| 33_V | 347_V | 1.073 | 0.63 |
| 51_K | 228_T | 1.065 | 0.62 |
| 406_R | 466_D | 1.064 | 0.62 |
| 252_T | 256_K | 1.059 | 0.61 |
| 160_S | 300_N | 1.057 | 0.61 |
| 114_T | 132_H | 1.054 | 0.61 |
| 420_R | 439_T | 1.054 | 0.61 |
| 401_Q | 465_G | 1.052 | 0.60 |
| 66_S | 499_L | 1.051 | 0.60 |
| 56_G | 330_A | 1.050 | 0.60 |
| 12_L | 18_L | 1.050 | 0.60 |
| 162_K | 486_H | 1.047 | 0.60 |
| 158_G | 167_I | 1.046 | 0.60 |
| 100_N | 305_D | 1.045 | 0.60 |
| 167_I | 170_A | 1.044 | 0.60 |
| 65_Y | 508_G | 1.042 | 0.59 |
| 416_L | 420_R | 1.041 | 0.59 |
| 341_G | 344_N | 1.037 | 0.59 |
| 240_L | 482_K | 1.037 | 0.59 |
| 353_H | 493_D | 1.036 | 0.59 |
| 231_S | 235_V | 1.033 | 0.58 |
| 276_L | 331_D | 1.033 | 0.58 |
| 164_R | 486_H | 1.032 | 0.58 |
| 447_I | 456_I | 1.030 | 0.58 |
| 38_D | 100_N | 1.028 | 0.58 |
| 93_S | 435_Y | 1.026 | 0.58 |
| 420_R | 440_E | 1.025 | 0.57 |
| 514_Y | 540_I | 1.024 | 0.57 |
| 524_S | 535_A | 1.022 | 0.57 |
| 235_V | 364_A | 1.021 | 0.57 |
| 434_L | 472_K | 1.019 | 0.57 |
| 49_Y | 58_K | 1.019 | 0.57 |
| 104_D | 111_V | 1.017 | 0.57 |
| 79_T | 162_K | 1.013 | 0.56 |
| 217_G | 255_A | 1.012 | 0.56 |
| 112_Y | 170_A | 1.012 | 0.56 |
| 79_T | 164_R | 1.008 | 0.56 |
| 510_S | 514_Y | 1.008 | 0.56 |
| 164_R | 309_H | 1.007 | 0.55 |
| 77_T | 487_S | 1.006 | 0.55 |
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 | |
| 3q3qA | 1 | 0.9103 | 100 | 0.442 | Contact Map |
| 3szyA | 1 | 0.7088 | 100 | 0.63 | Contact Map |
| 1ei6A | 4 | 0.6923 | 100 | 0.648 | Contact Map |
| 2gsoA | 2 | 0.6777 | 100 | 0.657 | Contact Map |
| 3nkqA | 1 | 0.6978 | 100 | 0.659 | Contact Map |
| 4gtwA | 2 | 0.7271 | 100 | 0.666 | Contact Map |
| 4lr2A | 1 | 0.674 | 100 | 0.674 | Contact Map |
| 2qzuA | 1 | 0.6062 | 100 | 0.771 | Contact Map |
| 2w5vA | 2 | 0.6026 | 100 | 0.776 | Contact Map |
| 3b5qA | 2 | 0.5238 | 100 | 0.781 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)