| A1_main |
| ID: | 1438563522 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 1000 (571) | ||
| Sequences: | 15810 (12069.9) | ||
| Seq/Len: | 27.688 | ||
| Nf(neff/√len): | 505.1 |
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: 27.688).
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 |
| 278_E | 307_D | 2.879 | 1.00 |
| 311_R | 340_D | 2.796 | 1.00 |
| 382_C | 411_S | 2.578 | 1.00 |
| 208_A | 237_E | 2.507 | 1.00 |
| 293_A | 325_I | 2.502 | 1.00 |
| 223_I | 255_I | 2.436 | 1.00 |
| 451_M | 479_D | 2.333 | 1.00 |
| 517_N | 545_N | 2.304 | 1.00 |
| 134_N | 163_N | 2.293 | 1.00 |
| 241_C | 274_D | 2.246 | 1.00 |
| 483_W | 513_D | 2.245 | 1.00 |
| 498_M | 531_A | 2.201 | 1.00 |
| 430_C | 465_V | 2.201 | 1.00 |
| 282_H | 313_P | 2.124 | 1.00 |
| 256_V | 292_L | 2.122 | 1.00 |
| 47_M | 81_S | 2.108 | 1.00 |
| 167_C | 204_N | 2.079 | 1.00 |
| 115_M | 148_A | 2.061 | 1.00 |
| 67_N | 96_N | 2.052 | 1.00 |
| 415_K | 447_D | 2.007 | 1.00 |
| 288_D | 322_S | 1.995 | 1.00 |
| 82_V | 114_V | 1.987 | 1.00 |
| 100_M | 130_G | 1.928 | 1.00 |
| 212_H | 243_A | 1.914 | 1.00 |
| 219_D | 222_M | 1.900 | 1.00 |
| 386_H | 417_P | 1.870 | 1.00 |
| 447_D | 451_M | 1.858 | 1.00 |
| 43_Q | 46_L | 1.819 | 1.00 |
| 182_M | 222_M | 1.799 | 1.00 |
| 295_Y | 299_V | 1.798 | 1.00 |
| 455_H | 485_A | 1.784 | 1.00 |
| 397_V | 429_T | 1.783 | 1.00 |
| 71_H | 102_P | 1.765 | 1.00 |
| 411_S | 415_K | 1.746 | 1.00 |
| 77_N | 111_N | 1.742 | 1.00 |
| 251_G | 289_H | 1.742 | 1.00 |
| 419_H | 453_P | 1.740 | 1.00 |
| 314_L | 326_V | 1.738 | 1.00 |
| 245_H | 280_M | 1.733 | 1.00 |
| 315_I | 346_F | 1.708 | 1.00 |
| 215_V | 218_G | 1.704 | 1.00 |
| 307_D | 311_R | 1.695 | 1.00 |
| 218_G | 252_A | 1.691 | 1.00 |
| 322_S | 325_I | 1.682 | 1.00 |
| 74_V | 77_N | 1.675 | 1.00 |
| 110_M | 145_N | 1.667 | 1.00 |
| 311_R | 319_A | 1.662 | 1.00 |
| 318_T | 321_A | 1.646 | 1.00 |
| 466_V | 497_T | 1.629 | 1.00 |
| 479_D | 483_W | 1.628 | 1.00 |
| 521_H | 551_F | 1.620 | 1.00 |
| 149_L | 181_C | 1.618 | 1.00 |
| 119_L | 151_I | 1.614 | 1.00 |
| 328_L | 332_K | 1.599 | 1.00 |
| 399_N | 403_F | 1.595 | 1.00 |
| 86_L | 117_V | 1.584 | 1.00 |
| 225_M | 229_N | 1.582 | 1.00 |
| 253_T | 295_Y | 1.577 | 1.00 |
| 137_V | 149_L | 1.575 | 1.00 |
| 487_H | 519_A | 1.572 | 1.00 |
| 145_N | 148_A | 1.570 | 1.00 |
| 78_Q | 81_S | 1.569 | 1.00 |
| 104_H | 136_A | 1.569 | 1.00 |
| 285_S | 288_D | 1.568 | 1.00 |
| 513_D | 517_N | 1.565 | 1.00 |
| 138_I | 169_P | 1.563 | 1.00 |
| 454_L | 466_V | 1.558 | 1.00 |
| 248_A | 251_G | 1.557 | 1.00 |
| 458_A | 461_G | 1.557 | 1.00 |
| 237_E | 241_C | 1.556 | 1.00 |
| 244_I | 256_V | 1.547 | 1.00 |
| 153_L | 159_P | 1.545 | 1.00 |
| 340_D | 344_R | 1.538 | 1.00 |
| 211_L | 223_I | 1.524 | 1.00 |
| 327_N | 331_S | 1.523 | 1.00 |
| 32_T | 63_D | 1.521 | 1.00 |
| 79_I | 117_V | 1.506 | 1.00 |
| 227_L | 258_L | 1.503 | 1.00 |
| 468_L | 472_K | 1.496 | 1.00 |
| 178_S | 181_C | 1.495 | 1.00 |
| 297_I | 328_L | 1.494 | 1.00 |
| 393_G | 396_S | 1.489 | 1.00 |
| 274_D | 278_E | 1.488 | 1.00 |
| 151_I | 155_K | 1.488 | 1.00 |
| 317_A | 326_V | 1.482 | 1.00 |
| 171_H | 210_P | 1.481 | 1.00 |
| 106_A | 115_M | 1.480 | 1.00 |
| 107_V | 110_M | 1.480 | 1.00 |
| 144_N | 178_S | 1.474 | 1.00 |
| 252_A | 255_I | 1.465 | 1.00 |
| 96_N | 105_I | 1.465 | 1.00 |
| 330_L | 336_V | 1.463 | 1.00 |
| 42_G | 78_Q | 1.462 | 1.00 |
| 253_T | 257_K | 1.459 | 1.00 |
| 294_D | 328_L | 1.457 | 1.00 |
| 457_A | 466_V | 1.456 | 1.00 |
| 486_L | 498_M | 1.455 | 1.00 |
| 141_C | 144_N | 1.455 | 1.00 |
| 344_R | 378_D | 1.453 | 1.00 |
| 70_L | 82_V | 1.451 | 1.00 |
| 418_L | 430_C | 1.448 | 1.00 |
| 290_H | 328_L | 1.443 | 1.00 |
| 278_E | 286_L | 1.443 | 1.00 |
| 220_L | 258_L | 1.439 | 1.00 |
| 425_G | 462_H | 1.431 | 1.00 |
| 220_L | 254_E | 1.411 | 1.00 |
| 553_H | 556_L | 1.410 | 1.00 |
| 36_H | 69_P | 1.403 | 0.99 |
| 323_W | 327_N | 1.398 | 0.99 |
| 260_I | 295_Y | 1.397 | 0.99 |
| 426_R | 429_T | 1.393 | 0.99 |
| 111_N | 114_V | 1.389 | 0.99 |
| 220_L | 224_K | 1.384 | 0.99 |
| 174_A | 177_G | 1.383 | 0.99 |
| 177_G | 219_D | 1.381 | 0.99 |
| 204_N | 208_A | 1.378 | 0.99 |
| 39_A | 42_G | 1.374 | 0.99 |
| 524_A | 527_G | 1.373 | 0.99 |
| 422_A | 425_G | 1.373 | 0.99 |
| 297_I | 332_K | 1.370 | 0.99 |
| 285_S | 325_I | 1.370 | 0.99 |
| 394_P | 398_N | 1.369 | 0.99 |
| 467_Q | 471_K | 1.366 | 0.99 |
| 100_M | 108_Q | 1.365 | 0.99 |
| 306_I | 338_I | 1.356 | 0.99 |
| 130_G | 134_N | 1.356 | 0.99 |
| 378_D | 382_C | 1.354 | 0.99 |
| 494_Y | 497_T | 1.352 | 0.99 |
| 84_F | 88_R | 1.350 | 0.99 |
| 96_N | 100_M | 1.347 | 0.99 |
| 208_A | 216_Q | 1.341 | 0.99 |
| 290_H | 294_D | 1.341 | 0.99 |
| 461_G | 494_Y | 1.340 | 0.99 |
| 103_L | 115_M | 1.337 | 0.99 |
| 281_L | 293_A | 1.336 | 0.99 |
| 285_S | 293_A | 1.332 | 0.99 |
| 318_T | 326_V | 1.327 | 0.99 |
| 455_H | 487_H | 1.324 | 0.99 |
| 289_H | 292_L | 1.319 | 0.99 |
| 215_V | 223_I | 1.314 | 0.99 |
| 237_E | 246_F | 1.313 | 0.99 |
| 297_I | 303_I | 1.313 | 0.99 |
| 253_T | 291_E | 1.312 | 0.99 |
| 117_V | 121_H | 1.310 | 0.99 |
| 517_N | 525_R | 1.310 | 0.99 |
| 298_S | 332_K | 1.309 | 0.99 |
| 307_D | 316_L | 1.304 | 0.99 |
| 134_N | 142_T | 1.303 | 0.99 |
| 493_G | 528_H | 1.302 | 0.99 |
| 73_A | 82_V | 1.302 | 0.99 |
| 290_H | 325_I | 1.301 | 0.99 |
| 215_V | 255_I | 1.297 | 0.99 |
| 392_G | 426_R | 1.294 | 0.99 |
| 83_K | 87_S | 1.293 | 0.99 |
| 130_G | 139_I | 1.289 | 0.99 |
| 140_A | 149_L | 1.289 | 0.99 |
| 214_A | 223_I | 1.288 | 0.99 |
| 451_M | 459_K | 1.288 | 0.99 |
| 502_L | 534_L | 1.286 | 0.99 |
| 163_N | 167_C | 1.284 | 0.99 |
| 385_L | 397_V | 1.283 | 0.99 |
| 150_Q | 154_K | 1.279 | 0.99 |
| 63_D | 67_N | 1.279 | 0.99 |
| 258_L | 262_S | 1.277 | 0.99 |
| 247_A | 256_V | 1.274 | 0.99 |
| 35_L | 47_M | 1.273 | 0.99 |
| 434_L | 468_L | 1.273 | 0.99 |
| 294_D | 298_S | 1.268 | 0.99 |
| 463_D | 467_Q | 1.267 | 0.99 |
| 189_G | 198_L | 1.265 | 0.99 |
| 415_K | 423_S | 1.264 | 0.99 |
| 179_K | 183_E | 1.259 | 0.99 |
| 248_A | 292_L | 1.254 | 0.99 |
| 224_K | 258_L | 1.250 | 0.99 |
| 257_K | 295_Y | 1.250 | 0.99 |
| 483_W | 491_M | 1.248 | 0.99 |
| 185_I | 189_G | 1.247 | 0.99 |
| 107_V | 148_A | 1.247 | 0.99 |
| 49_K | 53_D | 1.242 | 0.98 |
| 290_H | 324_N | 1.240 | 0.98 |
| 398_N | 432_R | 1.233 | 0.98 |
| 490_S | 493_G | 1.230 | 0.98 |
| 513_D | 522_F | 1.225 | 0.98 |
| 79_I | 113_E | 1.222 | 0.98 |
| 224_K | 228_D | 1.220 | 0.98 |
| 421_A | 430_C | 1.215 | 0.98 |
| 163_N | 172_Q | 1.214 | 0.98 |
| 533_A | 537_S | 1.204 | 0.98 |
| 241_C | 249_T | 1.201 | 0.98 |
| 79_I | 83_K | 1.200 | 0.98 |
| 184_I | 188_F | 1.199 | 0.98 |
| 520_L | 532_V | 1.199 | 0.98 |
| 282_H | 315_I | 1.194 | 0.98 |
| 74_V | 114_V | 1.194 | 0.98 |
| 38_A | 47_M | 1.193 | 0.98 |
| 112_N | 116_K | 1.188 | 0.98 |
| 116_K | 151_I | 1.187 | 0.98 |
| 112_N | 147_E | 1.186 | 0.98 |
| 274_D | 283_R | 1.181 | 0.98 |
| 532_V | 563_V | 1.180 | 0.98 |
| 427_I | 431_Q | 1.177 | 0.98 |
| 431_Q | 435_Q | 1.173 | 0.98 |
| 51_T | 84_F | 1.172 | 0.98 |
| 220_L | 255_I | 1.169 | 0.97 |
| 212_H | 246_F | 1.166 | 0.97 |
| 382_C | 390_R | 1.161 | 0.97 |
| 209_T | 212_H | 1.161 | 0.97 |
| 253_T | 292_L | 1.161 | 0.97 |
| 86_L | 92_P | 1.158 | 0.97 |
| 427_I | 468_L | 1.157 | 0.97 |
| 39_A | 81_S | 1.156 | 0.97 |
| 545_N | 549_A | 1.156 | 0.97 |
| 523_A | 532_V | 1.153 | 0.97 |
| 146_S | 150_Q | 1.151 | 0.97 |
| 112_N | 151_I | 1.150 | 0.97 |
| 419_H | 455_H | 1.148 | 0.97 |
| 67_N | 75_E | 1.147 | 0.97 |
| 490_S | 531_A | 1.146 | 0.97 |
| 273_T | 305_K | 1.143 | 0.97 |
| 386_H | 419_H | 1.143 | 0.97 |
| 167_C | 175_F | 1.141 | 0.97 |
| 44_I | 48_E | 1.140 | 0.97 |
| 227_L | 233_I | 1.139 | 0.97 |
| 340_D | 349_L | 1.138 | 0.97 |
| 215_V | 252_A | 1.137 | 0.97 |
| 63_D | 72_C | 1.134 | 0.97 |
| 534_L | 538_H | 1.130 | 0.97 |
| 470_L | 500_V | 1.130 | 0.97 |
| 435_Q | 472_K | 1.128 | 0.97 |
| 389_C | 429_T | 1.125 | 0.97 |
| 528_H | 531_A | 1.121 | 0.97 |
| 447_D | 456_L | 1.120 | 0.96 |
| 284_A | 293_A | 1.120 | 0.96 |
| 389_C | 392_G | 1.120 | 0.96 |
| 83_K | 117_V | 1.119 | 0.96 |
| 524_A | 532_V | 1.119 | 0.96 |
| 479_D | 488_H | 1.118 | 0.96 |
| 521_H | 524_A | 1.112 | 0.96 |
| 431_Q | 468_L | 1.110 | 0.96 |
| 204_N | 213_L | 1.110 | 0.96 |
| 348_H | 384_P | 1.107 | 0.96 |
| 411_S | 420_F | 1.104 | 0.96 |
| 370_I | 373_L | 1.101 | 0.96 |
| 401_L | 432_R | 1.101 | 0.96 |
| 556_L | 559_K | 1.096 | 0.96 |
| 360_L | 364_F | 1.095 | 0.96 |
| 248_A | 256_V | 1.095 | 0.96 |
| 463_D | 500_V | 1.093 | 0.96 |
| 348_H | 351_V | 1.093 | 0.96 |
| 458_A | 497_T | 1.092 | 0.96 |
| 237_E | 240_R | 1.087 | 0.96 |
| 242_T | 245_H | 1.083 | 0.96 |
| 245_H | 282_H | 1.083 | 0.96 |
| 406_S | 409_S | 1.082 | 0.96 |
| 312_S | 315_I | 1.080 | 0.95 |
| 304_N | 334_A | 1.079 | 0.95 |
| 499_K | 503_D | 1.079 | 0.95 |
| 545_N | 554_L | 1.077 | 0.95 |
| 170_I | 182_M | 1.075 | 0.95 |
| 302_D | 305_K | 1.073 | 0.95 |
| 463_D | 497_T | 1.069 | 0.95 |
| 495_T | 534_L | 1.069 | 0.95 |
| 400_L | 405_V | 1.069 | 0.95 |
| 388_A | 397_V | 1.067 | 0.95 |
| 281_L | 297_I | 1.065 | 0.95 |
| 46_L | 49_K | 1.065 | 0.95 |
| 455_H | 458_A | 1.062 | 0.95 |
| 153_L | 184_I | 1.055 | 0.95 |
| 346_F | 350_T | 1.052 | 0.95 |
| 485_A | 501_I | 1.052 | 0.95 |
| 500_V | 504_T | 1.052 | 0.95 |
| 462_H | 465_V | 1.050 | 0.94 |
| 458_A | 466_V | 1.049 | 0.94 |
| 427_I | 465_V | 1.049 | 0.94 |
| 527_G | 560_R | 1.049 | 0.94 |
| 107_V | 115_M | 1.048 | 0.94 |
| 279_T | 282_H | 1.046 | 0.94 |
| 304_N | 338_I | 1.044 | 0.94 |
| 361_R | 364_F | 1.042 | 0.94 |
| 386_H | 455_H | 1.042 | 0.94 |
| 158_K | 161_K | 1.040 | 0.94 |
| 212_H | 245_H | 1.038 | 0.94 |
| 232_Q | 235_P | 1.037 | 0.94 |
| 487_H | 521_H | 1.036 | 0.94 |
| 422_A | 465_V | 1.034 | 0.94 |
| 203_M | 235_P | 1.033 | 0.94 |
| 209_T | 231_A | 1.033 | 0.94 |
| 228_D | 262_S | 1.031 | 0.94 |
| 419_H | 456_L | 1.030 | 0.94 |
| 211_L | 227_L | 1.030 | 0.94 |
| 394_P | 432_R | 1.029 | 0.94 |
| 401_L | 407_I | 1.024 | 0.93 |
| 398_N | 402_G | 1.024 | 0.93 |
| 304_N | 335_Q | 1.022 | 0.93 |
| 48_E | 52_R | 1.019 | 0.93 |
| 11_S | 14_G | 1.018 | 0.93 |
| 85_L | 90_A | 1.018 | 0.93 |
| 324_N | 327_N | 1.017 | 0.93 |
| 364_F | 368_Q | 1.016 | 0.93 |
| 107_V | 145_N | 1.014 | 0.93 |
| 282_H | 316_L | 1.014 | 0.93 |
| 101_A | 104_H | 1.013 | 0.93 |
| 261_S | 299_V | 1.013 | 0.93 |
| 141_C | 149_L | 1.011 | 0.93 |
| 549_A | 557_H | 1.007 | 0.93 |
| 454_L | 470_L | 1.006 | 0.93 |
| 501_I | 506_L | 1.005 | 0.93 |
| 119_L | 122_R | 1.003 | 0.93 |
| 394_P | 429_T | 1.003 | 0.93 |
| 329_L | 334_A | 1.001 | 0.92 |
| 368_Q | 373_L | 1.000 | 0.92 |
| 71_H | 104_H | 1.000 | 0.92 |
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 | |
| 4rlvA | 1 | 0.579 | 100 | 0.534 | Contact Map |
| 4cj9A | 2 | 0.578 | 100 | 0.553 | Contact Map |
| 3j5pB | 4 | 0.544 | 100 | 0.616 | Contact Map |
| 1n11A | 1 | 0.404 | 100 | 0.661 | Contact Map |
| 3ljnA | 1 | 0.271 | 100 | 0.752 | Contact Map |
| 3utmA | 2 | 0.317 | 100 | 0.754 | Contact Map |
| 4rlyA | 1 | 0.3 | 100 | 0.757 | Contact Map |
| 4oavB | 2 | 0.616 | 100 | 0.76 | Contact Map |
| 4ot9A | 1 | 0.282 | 100 | 0.774 | Contact Map |
| 1wdyA | 1 | 0.278 | 100 | 0.782 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)