| test4 |
| ID: | 1435814636 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 563 (537) | ||
| Sequences: | 7003 (4790.8) | ||
| Seq/Len: | 13.041 | ||
| Nf(neff/√len): | 206.7 |
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: 13.041).
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 |
| 497_S | 500_P | 5.519 | 1.00 |
| 55_A | 84_G | 4.262 | 1.00 |
| 236_D | 256_H | 3.992 | 1.00 |
| 470_N | 537_E | 3.802 | 1.00 |
| 373_Q | 519_D | 3.752 | 1.00 |
| 514_T | 517_E | 3.373 | 1.00 |
| 230_E | 327_K | 3.217 | 1.00 |
| 230_E | 331_Q | 3.203 | 1.00 |
| 204_I | 307_V | 2.991 | 1.00 |
| 511_R | 539_M | 2.979 | 1.00 |
| 64_I | 429_A | 2.932 | 1.00 |
| 510_H | 524_D | 2.844 | 1.00 |
| 373_Q | 376_N | 2.822 | 1.00 |
| 218_A | 231_T | 2.801 | 1.00 |
| 513_A | 517_E | 2.754 | 1.00 |
| 202_D | 336_T | 2.699 | 1.00 |
| 309_F | 329_V | 2.679 | 1.00 |
| 510_H | 534_R | 2.648 | 1.00 |
| 377_F | 523_Q | 2.637 | 1.00 |
| 208_D | 283_L | 2.635 | 1.00 |
| 67_M | 157_Y | 2.584 | 1.00 |
| 279_A | 282_I | 2.573 | 1.00 |
| 21_T | 44_R | 2.542 | 1.00 |
| 512_V | 521_L | 2.460 | 1.00 |
| 422_T | 440_L | 2.435 | 1.00 |
| 448_Q | 502_F | 2.420 | 1.00 |
| 72_T | 81_A | 2.415 | 1.00 |
| 96_L | 153_I | 2.363 | 1.00 |
| 148_E | 165_L | 2.330 | 1.00 |
| 510_H | 521_L | 2.281 | 1.00 |
| 376_N | 519_D | 2.263 | 1.00 |
| 511_R | 537_E | 2.227 | 1.00 |
| 494_D | 497_S | 2.217 | 1.00 |
| 498_L | 501_T | 2.192 | 1.00 |
| 8_K | 36_K | 2.187 | 1.00 |
| 447_L | 451_V | 2.176 | 1.00 |
| 505_K | 532_K | 2.157 | 1.00 |
| 85_I | 97_H | 2.149 | 1.00 |
| 15_K | 42_G | 2.097 | 1.00 |
| 12_E | 16_Q | 2.088 | 1.00 |
| 79_L | 83_N | 2.009 | 1.00 |
| 207_L | 281_L | 2.005 | 1.00 |
| 59_D | 63_R | 1.999 | 1.00 |
| 255_Q | 401_P | 1.993 | 1.00 |
| 284_S | 287_A | 1.987 | 1.00 |
| 48_N | 54_A | 1.979 | 1.00 |
| 99_V | 164_Y | 1.970 | 1.00 |
| 374_L | 441_F | 1.961 | 1.00 |
| 67_M | 96_L | 1.951 | 1.00 |
| 127_R | 130_A | 1.946 | 1.00 |
| 206_V | 210_D | 1.935 | 1.00 |
| 426_A | 463_K | 1.929 | 1.00 |
| 235_I | 242_A | 1.929 | 1.00 |
| 458_I | 504_A | 1.927 | 1.00 |
| 519_D | 523_Q | 1.926 | 1.00 |
| 232_K | 236_D | 1.925 | 1.00 |
| 429_A | 436_K | 1.923 | 1.00 |
| 216_I | 283_L | 1.908 | 1.00 |
| 468_V | 535_M | 1.904 | 1.00 |
| 242_A | 252_I | 1.903 | 1.00 |
| 216_I | 235_I | 1.899 | 1.00 |
| 417_F | 421_A | 1.890 | 1.00 |
| 387_E | 442_I | 1.889 | 1.00 |
| 65_K | 428_A | 1.885 | 1.00 |
| 8_K | 39_E | 1.880 | 1.00 |
| 207_L | 305_N | 1.840 | 1.00 |
| 383_V | 425_A | 1.825 | 1.00 |
| 141_D | 144_T | 1.818 | 1.00 |
| 216_I | 240_F | 1.808 | 1.00 |
| 207_L | 324_V | 1.798 | 1.00 |
| 285_V | 309_F | 1.794 | 1.00 |
| 10_L | 149_I | 1.761 | 1.00 |
| 12_E | 15_K | 1.744 | 1.00 |
| 208_D | 281_L | 1.726 | 1.00 |
| 98_V | 167_L | 1.708 | 1.00 |
| 387_E | 446_S | 1.704 | 1.00 |
| 426_A | 437_R | 1.680 | 1.00 |
| 239_Q | 258_R | 1.672 | 1.00 |
| 372_N | 376_N | 1.672 | 1.00 |
| 496_L | 506_D | 1.657 | 1.00 |
| 234_L | 238_T | 1.655 | 1.00 |
| 457_M | 504_A | 1.653 | 1.00 |
| 34_L | 45_W | 1.646 | 1.00 |
| 517_E | 520_K | 1.642 | 1.00 |
| 229_A | 233_K | 1.641 | 1.00 |
| 467_F | 522_T | 1.630 | 1.00 |
| 407_I | 425_A | 1.622 | 1.00 |
| 237_L | 334_L | 1.616 | 1.00 |
| 133_S | 164_Y | 1.614 | 1.00 |
| 85_I | 95_V | 1.614 | 1.00 |
| 467_F | 536_I | 1.614 | 1.00 |
| 147_A | 151_R | 1.605 | 1.00 |
| 139_I | 145_A | 1.602 | 1.00 |
| 205_L | 333_L | 1.590 | 1.00 |
| 215_V | 279_A | 1.590 | 1.00 |
| 233_K | 237_L | 1.584 | 1.00 |
| 373_Q | 377_F | 1.584 | 1.00 |
| 81_A | 97_H | 1.576 | 1.00 |
| 59_D | 87_G | 1.572 | 1.00 |
| 454_I | 504_A | 1.566 | 1.00 |
| 137_A | 165_L | 1.558 | 1.00 |
| 426_A | 462_L | 1.548 | 1.00 |
| 423_L | 457_M | 1.546 | 1.00 |
| 505_K | 524_D | 1.544 | 1.00 |
| 197_E | 200_V | 1.542 | 1.00 |
| 46_A | 427_F | 1.540 | 1.00 |
| 211_A | 214_P | 1.534 | 1.00 |
| 379_Q | 382_D | 1.511 | 1.00 |
| 24_G | 45_W | 1.511 | 1.00 |
| 53_N | 453_E | 1.503 | 1.00 |
| 370_M | 538_V | 1.502 | 1.00 |
| 237_L | 338_A | 1.502 | 1.00 |
| 451_V | 498_L | 1.500 | 1.00 |
| 48_N | 57_A | 1.500 | 1.00 |
| 415_I | 449_L | 1.497 | 1.00 |
| 211_A | 281_L | 1.494 | 1.00 |
| 500_P | 505_K | 1.486 | 1.00 |
| 520_K | 524_D | 1.486 | 1.00 |
| 20_N | 44_R | 1.483 | 1.00 |
| 505_K | 510_H | 1.482 | 1.00 |
| 513_A | 539_M | 1.480 | 1.00 |
| 369_W | 515_T | 1.462 | 1.00 |
| 369_W | 373_Q | 1.460 | 1.00 |
| 440_L | 466_L | 1.452 | 1.00 |
| 44_R | 460_W | 1.442 | 1.00 |
| 457_M | 464_P | 1.439 | 1.00 |
| 200_V | 203_T | 1.436 | 1.00 |
| 10_L | 167_L | 1.431 | 1.00 |
| 149_I | 165_L | 1.424 | 1.00 |
| 142_I | 174_L | 1.420 | 1.00 |
| 21_T | 427_F | 1.419 | 1.00 |
| 375_G | 399_T | 1.415 | 1.00 |
| 378_L | 439_I | 1.404 | 0.99 |
| 13_R | 150_D | 1.398 | 0.99 |
| 260_G | 275_A | 1.396 | 0.99 |
| 281_L | 307_V | 1.395 | 0.99 |
| 55_A | 81_A | 1.394 | 0.99 |
| 233_K | 334_L | 1.394 | 0.99 |
| 203_T | 206_V | 1.374 | 0.99 |
| 505_K | 534_R | 1.370 | 0.99 |
| 244_V | 259_Y | 1.369 | 0.99 |
| 17_V | 150_D | 1.366 | 0.99 |
| 144_T | 147_A | 1.363 | 0.99 |
| 46_A | 460_W | 1.362 | 0.99 |
| 518_W | 538_V | 1.349 | 0.99 |
| 317_R | 322_P | 1.342 | 0.99 |
| 467_F | 538_V | 1.341 | 0.99 |
| 235_I | 252_I | 1.341 | 0.99 |
| 23_F | 61_Y | 1.340 | 0.99 |
| 78_E | 99_V | 1.339 | 0.99 |
| 463_K | 532_K | 1.338 | 0.99 |
| 496_L | 500_P | 1.336 | 0.99 |
| 104_I | 170_N | 1.334 | 0.99 |
| 496_L | 511_R | 1.333 | 0.99 |
| 377_F | 519_D | 1.332 | 0.99 |
| 382_D | 437_R | 1.330 | 0.99 |
| 70_I | 81_A | 1.328 | 0.99 |
| 521_L | 536_I | 1.316 | 0.99 |
| 504_A | 535_M | 1.313 | 0.99 |
| 155_T | 163_V | 1.313 | 0.99 |
| 365_L | 370_M | 1.309 | 0.99 |
| 30_N | 33_L | 1.306 | 0.99 |
| 134_E | 161_R | 1.302 | 0.99 |
| 15_K | 40_V | 1.299 | 0.99 |
| 520_K | 523_Q | 1.294 | 0.99 |
| 53_N | 450_T | 1.293 | 0.99 |
| 249_K | 254_E | 1.292 | 0.99 |
| 231_T | 330_L | 1.289 | 0.99 |
| 216_I | 234_L | 1.288 | 0.99 |
| 17_V | 153_I | 1.287 | 0.99 |
| 8_K | 12_E | 1.286 | 0.99 |
| 9_Y | 146_P | 1.276 | 0.99 |
| 285_V | 330_L | 1.267 | 0.99 |
| 72_T | 97_H | 1.260 | 0.99 |
| 526_S | 536_I | 1.259 | 0.99 |
| 218_A | 222_C | 1.257 | 0.99 |
| 369_W | 518_W | 1.257 | 0.99 |
| 201_I | 336_T | 1.257 | 0.99 |
| 82_L | 128_M | 1.256 | 0.99 |
| 214_P | 280_D | 1.250 | 0.99 |
| 327_K | 331_Q | 1.242 | 0.98 |
| 5_T | 8_K | 1.241 | 0.98 |
| 133_S | 136_T | 1.229 | 0.98 |
| 9_Y | 176_V | 1.228 | 0.98 |
| 455_S | 459_R | 1.225 | 0.98 |
| 518_W | 522_T | 1.224 | 0.98 |
| 232_K | 253_D | 1.219 | 0.98 |
| 96_L | 156_T | 1.219 | 0.98 |
| 222_C | 231_T | 1.218 | 0.98 |
| 198_K | 332_K | 1.212 | 0.98 |
| 196_S | 329_V | 1.211 | 0.98 |
| 454_I | 535_M | 1.210 | 0.98 |
| 510_H | 536_I | 1.203 | 0.98 |
| 383_V | 429_A | 1.201 | 0.98 |
| 89_Y | 162_P | 1.198 | 0.98 |
| 499_L | 535_M | 1.193 | 0.98 |
| 379_Q | 437_R | 1.187 | 0.98 |
| 7_G | 36_K | 1.185 | 0.98 |
| 60_G | 64_I | 1.180 | 0.98 |
| 86_A | 412_W | 1.178 | 0.98 |
| 205_L | 209_K | 1.178 | 0.98 |
| 439_I | 527_F | 1.175 | 0.98 |
| 234_L | 334_L | 1.166 | 0.97 |
| 365_L | 538_V | 1.163 | 0.97 |
| 447_L | 535_M | 1.159 | 0.97 |
| 252_I | 256_H | 1.159 | 0.97 |
| 229_A | 232_K | 1.157 | 0.97 |
| 230_E | 233_K | 1.156 | 0.97 |
| 236_D | 258_R | 1.155 | 0.97 |
| 405_Y | 436_K | 1.154 | 0.97 |
| 55_A | 95_V | 1.153 | 0.97 |
| 137_A | 148_E | 1.150 | 0.97 |
| 472_D | 492_G | 1.148 | 0.97 |
| 427_F | 462_L | 1.144 | 0.97 |
| 55_A | 70_I | 1.137 | 0.97 |
| 385_I | 438_V | 1.134 | 0.97 |
| 5_T | 175_N | 1.132 | 0.97 |
| 230_E | 334_L | 1.130 | 0.97 |
| 328_F | 331_Q | 1.130 | 0.97 |
| 465_Y | 534_R | 1.124 | 0.97 |
| 67_M | 153_I | 1.123 | 0.97 |
| 4_I | 12_E | 1.118 | 0.96 |
| 496_L | 537_E | 1.110 | 0.96 |
| 233_K | 331_Q | 1.109 | 0.96 |
| 235_I | 258_R | 1.108 | 0.96 |
| 418_T | 440_L | 1.106 | 0.96 |
| 274_E | 278_S | 1.105 | 0.96 |
| 468_V | 495_H | 1.103 | 0.96 |
| 437_R | 527_F | 1.102 | 0.96 |
| 499_L | 504_A | 1.096 | 0.96 |
| 19_V | 69_C | 1.095 | 0.96 |
| 61_Y | 428_A | 1.095 | 0.96 |
| 254_E | 259_Y | 1.091 | 0.96 |
| 419_T | 466_L | 1.091 | 0.96 |
| 512_V | 517_E | 1.090 | 0.96 |
| 445_G | 474_Y | 1.085 | 0.96 |
| 82_L | 132_I | 1.081 | 0.95 |
| 451_V | 502_F | 1.080 | 0.95 |
| 13_R | 149_I | 1.079 | 0.95 |
| 62_A | 94_G | 1.078 | 0.95 |
| 252_I | 259_Y | 1.074 | 0.95 |
| 6_L | 142_I | 1.073 | 0.95 |
| 22_V | 37_I | 1.070 | 0.95 |
| 383_V | 438_V | 1.069 | 0.95 |
| 296_S | 299_Y | 1.060 | 0.95 |
| 64_I | 425_A | 1.060 | 0.95 |
| 506_D | 535_M | 1.060 | 0.95 |
| 20_N | 61_Y | 1.058 | 0.95 |
| 233_K | 236_D | 1.058 | 0.95 |
| 463_K | 531_S | 1.054 | 0.95 |
| 499_L | 506_D | 1.053 | 0.95 |
| 168_P | 171_L | 1.052 | 0.95 |
| 216_I | 231_T | 1.047 | 0.94 |
| 64_I | 407_I | 1.046 | 0.94 |
| 137_A | 151_R | 1.044 | 0.94 |
| 426_A | 532_K | 1.041 | 0.94 |
| 426_A | 430_E | 1.040 | 0.94 |
| 211_A | 280_D | 1.040 | 0.94 |
| 215_V | 282_I | 1.039 | 0.94 |
| 278_S | 348_A | 1.039 | 0.94 |
| 523_Q | 529_D | 1.034 | 0.94 |
| 10_L | 98_V | 1.032 | 0.94 |
| 213_N | 278_S | 1.031 | 0.94 |
| 523_Q | 528_N | 1.031 | 0.94 |
| 230_E | 330_L | 1.024 | 0.93 |
| 205_L | 336_T | 1.023 | 0.93 |
| 498_L | 502_F | 1.023 | 0.93 |
| 128_M | 132_I | 1.021 | 0.93 |
| 203_T | 207_L | 1.021 | 0.93 |
| 530_N | 534_R | 1.019 | 0.93 |
| 85_I | 132_I | 1.014 | 0.93 |
| 6_L | 145_A | 1.014 | 0.93 |
| 142_I | 171_L | 1.011 | 0.93 |
| 386_A | 408_S | 1.011 | 0.93 |
| 472_D | 539_M | 1.011 | 0.93 |
| 505_K | 530_N | 1.009 | 0.93 |
| 512_V | 518_W | 1.009 | 0.93 |
| 228_K | 232_K | 1.003 | 0.93 |
| 210_D | 281_L | 1.003 | 0.93 |
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 | |
| 1ovmA | 4 | 0.9432 | 100 | 0.165 | Contact Map |
| 4cokA | 2 | 0.9663 | 100 | 0.18 | Contact Map |
| 2nxwA | 2 | 0.9396 | 100 | 0.194 | Contact Map |
| 2vk8A | 4 | 0.9982 | 100 | 0.201 | Contact Map |
| 2panA | 6 | 0.9591 | 100 | 0.219 | Contact Map |
| 1ozhA | 4 | 0.9378 | 100 | 0.219 | Contact Map |
| 2pgnA | 2 | 0.9485 | 100 | 0.223 | Contact Map |
| 1ybhA | 1 | 0.9591 | 100 | 0.223 | Contact Map |
| 4rjjA | 8 | 0.9503 | 100 | 0.227 | Contact Map |
| 1t9bA | 2 | 0.9609 | 100 | 0.228 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)