| P450fmaniferaewGtoD |
| ID: | 1495652919 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 558 (488) | ||
| Sequences: | 3205 (2309.1) | ||
| Seq/Len: | 6.568 | ||
| Nf(neff/√len): | 104.5 |
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: 6.568).
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 |
| 393_A | 459_L | 5.240 | 1.00 |
| 449_D | 454_R | 4.475 | 1.00 |
| 364_Q | 368_E | 4.129 | 1.00 |
| 362_L | 394_V | 3.898 | 1.00 |
| 449_D | 452_A | 3.661 | 1.00 |
| 351_L | 402_Y | 3.601 | 1.00 |
| 497_T | 503_F | 3.544 | 1.00 |
| 362_L | 498_M | 3.496 | 1.00 |
| 360_K | 364_Q | 3.286 | 1.00 |
| 358_V | 390_Y | 3.171 | 1.00 |
| 274_V | 323_E | 3.135 | 1.00 |
| 348_L | 494_M | 3.099 | 1.00 |
| 361_K | 456_E | 3.053 | 1.00 |
| 502_T | 548_T | 3.020 | 1.00 |
| 394_V | 453_F | 2.980 | 1.00 |
| 344_T | 490_L | 2.955 | 1.00 |
| 348_L | 394_V | 2.856 | 1.00 |
| 414_G | 427_I | 2.773 | 1.00 |
| 273_C | 291_S | 2.771 | 1.00 |
| 362_L | 391_T | 2.761 | 1.00 |
| 363_H | 502_T | 2.753 | 1.00 |
| 348_L | 398_A | 2.712 | 1.00 |
| 504_Q | 546_T | 2.685 | 1.00 |
| 110_M | 440_I | 2.612 | 1.00 |
| 225_D | 261_R | 2.567 | 1.00 |
| 260_S | 264_S | 2.464 | 1.00 |
| 363_H | 550_K | 2.458 | 1.00 |
| 181_D | 500_K | 2.429 | 1.00 |
| 104_I | 113_S | 2.415 | 1.00 |
| 56_H | 59_V | 2.391 | 1.00 |
| 444_A | 450_P | 2.237 | 1.00 |
| 361_K | 390_Y | 2.234 | 1.00 |
| 271_N | 323_E | 2.227 | 1.00 |
| 207_A | 485_M | 2.215 | 1.00 |
| 392_E | 491_K | 2.154 | 1.00 |
| 352_L | 362_L | 2.135 | 1.00 |
| 411_A | 425_L | 2.116 | 1.00 |
| 395_V | 490_L | 2.111 | 1.00 |
| 267_R | 327_F | 2.106 | 1.00 |
| 390_Y | 456_E | 2.098 | 1.00 |
| 47_G | 56_H | 2.069 | 1.00 |
| 196_V | 349_F | 2.030 | 1.00 |
| 199_P | 493_V | 2.018 | 1.00 |
| 180_L | 195_L | 1.973 | 1.00 |
| 181_D | 501_Y | 1.953 | 1.00 |
| 401_L | 442_Y | 1.938 | 1.00 |
| 54_F | 58_K | 1.935 | 1.00 |
| 359_V | 502_T | 1.925 | 1.00 |
| 181_D | 549_Q | 1.915 | 1.00 |
| 349_F | 545_M | 1.874 | 1.00 |
| 169_M | 485_M | 1.858 | 1.00 |
| 366_H | 391_T | 1.842 | 1.00 |
| 360_K | 502_T | 1.836 | 1.00 |
| 95_W | 98_A | 1.802 | 1.00 |
| 271_N | 275_E | 1.797 | 1.00 |
| 504_Q | 548_T | 1.792 | 1.00 |
| 52_W | 55_G | 1.785 | 1.00 |
| 345_L | 493_V | 1.780 | 1.00 |
| 189_I | 506_A | 1.755 | 1.00 |
| 351_L | 398_A | 1.740 | 1.00 |
| 90_F | 105_I | 1.728 | 1.00 |
| 353_S | 359_V | 1.726 | 1.00 |
| 51_S | 54_F | 1.709 | 1.00 |
| 264_S | 268_R | 1.706 | 1.00 |
| 110_M | 435_V | 1.699 | 1.00 |
| 47_G | 84_Y | 1.684 | 1.00 |
| 369_Q | 388_L | 1.662 | 1.00 |
| 48_P | 56_H | 1.662 | 1.00 |
| 359_V | 363_H | 1.647 | 1.00 |
| 228_D | 258_I | 1.640 | 1.00 |
| 392_E | 487_M | 1.635 | 1.00 |
| 366_H | 495_V | 1.619 | 1.00 |
| 357_D | 361_K | 1.614 | 1.00 |
| 414_G | 424_R | 1.610 | 1.00 |
| 191_S | 542_G | 1.609 | 1.00 |
| 179_K | 195_L | 1.594 | 1.00 |
| 444_A | 451_A | 1.584 | 1.00 |
| 410_Q | 430_G | 1.576 | 1.00 |
| 442_Y | 451_A | 1.575 | 0.99 |
| 349_F | 497_T | 1.567 | 0.99 |
| 172_E | 212_P | 1.567 | 0.99 |
| 360_K | 363_H | 1.566 | 0.99 |
| 396_K | 470_F | 1.566 | 0.99 |
| 341_S | 489_T | 1.555 | 0.99 |
| 363_H | 367_I | 1.548 | 0.99 |
| 174_L | 496_M | 1.536 | 0.99 |
| 268_R | 272_K | 1.536 | 0.99 |
| 426_P | 431_L | 1.527 | 0.99 |
| 427_I | 430_G | 1.523 | 0.99 |
| 393_A | 456_E | 1.517 | 0.99 |
| 267_R | 324_E | 1.496 | 0.99 |
| 48_P | 84_Y | 1.495 | 0.99 |
| 416_T | 424_R | 1.494 | 0.99 |
| 102_V | 431_L | 1.492 | 0.99 |
| 345_L | 490_L | 1.491 | 0.99 |
| 344_T | 398_A | 1.490 | 0.99 |
| 149_M | 329_N | 1.479 | 0.99 |
| 137_T | 332_T | 1.473 | 0.99 |
| 90_F | 103_V | 1.466 | 0.99 |
| 189_I | 544_M | 1.466 | 0.99 |
| 411_A | 427_I | 1.461 | 0.99 |
| 351_L | 355_A | 1.460 | 0.99 |
| 50_H | 56_H | 1.457 | 0.99 |
| 367_I | 499_S | 1.455 | 0.99 |
| 89_I | 104_I | 1.453 | 0.99 |
| 192_M | 545_M | 1.451 | 0.99 |
| 191_S | 194_E | 1.450 | 0.99 |
| 162_V | 488_N | 1.447 | 0.99 |
| 104_I | 109_L | 1.431 | 0.99 |
| 479_T | 483_Q | 1.428 | 0.99 |
| 148_K | 325_M | 1.426 | 0.99 |
| 205_S | 213_Q | 1.423 | 0.99 |
| 381_N | 384_M | 1.415 | 0.99 |
| 93_D | 100_G | 1.411 | 0.99 |
| 359_V | 362_L | 1.396 | 0.99 |
| 348_L | 352_L | 1.394 | 0.98 |
| 263_H | 324_E | 1.394 | 0.98 |
| 196_V | 345_L | 1.388 | 0.98 |
| 416_T | 422_G | 1.383 | 0.98 |
| 165_M | 291_S | 1.382 | 0.98 |
| 51_S | 58_K | 1.381 | 0.98 |
| 138_M | 481_P | 1.361 | 0.98 |
| 172_E | 206_T | 1.361 | 0.98 |
| 161_H | 165_M | 1.353 | 0.98 |
| 341_S | 490_L | 1.332 | 0.98 |
| 390_Y | 455_P | 1.327 | 0.98 |
| 441_H | 472_V | 1.325 | 0.98 |
| 194_E | 198_K | 1.318 | 0.98 |
| 466_P | 469_Y | 1.313 | 0.98 |
| 204_V | 208_T | 1.307 | 0.97 |
| 169_M | 207_A | 1.307 | 0.97 |
| 173_C | 199_P | 1.302 | 0.97 |
| 352_L | 358_V | 1.289 | 0.97 |
| 348_L | 453_F | 1.287 | 0.97 |
| 177_Q | 500_K | 1.285 | 0.97 |
| 355_A | 358_V | 1.260 | 0.97 |
| 412_P | 427_I | 1.250 | 0.96 |
| 201_Y | 338_H | 1.249 | 0.96 |
| 362_L | 366_H | 1.246 | 0.96 |
| 358_V | 394_V | 1.242 | 0.96 |
| 104_I | 110_M | 1.241 | 0.96 |
| 170_V | 496_M | 1.240 | 0.96 |
| 391_T | 491_K | 1.236 | 0.96 |
| 350_M | 354_K | 1.228 | 0.96 |
| 153_V | 481_P | 1.216 | 0.96 |
| 263_H | 328_S | 1.214 | 0.96 |
| 277_I | 298_R | 1.212 | 0.96 |
| 49_P | 56_H | 1.207 | 0.95 |
| 349_F | 494_M | 1.205 | 0.95 |
| 201_Y | 334_L | 1.198 | 0.95 |
| 228_D | 255_R | 1.195 | 0.95 |
| 174_L | 178_E | 1.178 | 0.95 |
| 447_Y | 450_P | 1.175 | 0.94 |
| 177_Q | 501_Y | 1.174 | 0.94 |
| 136_G | 145_L | 1.170 | 0.94 |
| 522_D | 540_R | 1.168 | 0.94 |
| 146_W | 150_A | 1.166 | 0.94 |
| 476_D | 480_C | 1.165 | 0.94 |
| 348_L | 490_L | 1.153 | 0.94 |
| 438_H | 442_Y | 1.150 | 0.94 |
| 179_K | 198_K | 1.149 | 0.94 |
| 267_R | 271_N | 1.148 | 0.94 |
| 114_S | 471_R | 1.134 | 0.93 |
| 353_S | 545_M | 1.130 | 0.93 |
| 166_T | 492_I | 1.130 | 0.93 |
| 200_V | 340_T | 1.127 | 0.93 |
| 347_F | 446_I | 1.125 | 0.93 |
| 272_K | 276_R | 1.123 | 0.93 |
| 394_V | 398_A | 1.122 | 0.92 |
| 318_I | 325_M | 1.122 | 0.92 |
| 107_P | 443_D | 1.120 | 0.92 |
| 503_F | 547_V | 1.119 | 0.92 |
| 191_S | 544_M | 1.117 | 0.92 |
| 485_M | 489_T | 1.114 | 0.92 |
| 275_E | 279_Q | 1.108 | 0.92 |
| 199_P | 203_I | 1.107 | 0.92 |
| 393_A | 458_W | 1.099 | 0.91 |
| 368_E | 387_K | 1.098 | 0.91 |
| 391_T | 394_V | 1.098 | 0.91 |
| 408_L | 434_T | 1.098 | 0.91 |
| 345_L | 349_F | 1.096 | 0.91 |
| 336_G | 340_T | 1.094 | 0.91 |
| 204_V | 338_H | 1.091 | 0.91 |
| 225_D | 258_I | 1.084 | 0.91 |
| 407_D | 437_A | 1.080 | 0.90 |
| 403_P | 441_H | 1.078 | 0.90 |
| 173_C | 493_V | 1.077 | 0.90 |
| 111_D | 468_D | 1.076 | 0.90 |
| 322_E | 325_M | 1.073 | 0.90 |
| 367_I | 550_K | 1.073 | 0.90 |
| 340_T | 489_T | 1.065 | 0.90 |
| 105_I | 436_S | 1.065 | 0.90 |
| 351_L | 401_L | 1.054 | 0.89 |
| 487_M | 491_K | 1.054 | 0.89 |
| 202_D | 214_H | 1.041 | 0.88 |
| 146_W | 478_R | 1.040 | 0.88 |
| 290_R | 295_L | 1.038 | 0.88 |
| 85_D | 88_E | 1.037 | 0.88 |
| 273_C | 294_D | 1.037 | 0.88 |
| 347_F | 447_Y | 1.036 | 0.88 |
| 157_F | 481_P | 1.035 | 0.88 |
| 447_Y | 458_W | 1.032 | 0.88 |
| 352_L | 394_V | 1.031 | 0.88 |
| 446_I | 469_Y | 1.029 | 0.87 |
| 471_R | 474_G | 1.028 | 0.87 |
| 352_L | 359_V | 1.027 | 0.87 |
| 448_P | 454_R | 1.026 | 0.87 |
| 79_E | 83_L | 1.024 | 0.87 |
| 172_E | 202_D | 1.022 | 0.87 |
| 135_E | 328_S | 1.022 | 0.87 |
| 155_P | 481_P | 1.022 | 0.87 |
| 48_P | 80_L | 1.009 | 0.86 |
| 358_V | 361_K | 1.005 | 0.86 |
| 111_D | 115_L | 1.005 | 0.86 |
| 153_V | 296_L | 1.002 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4lxjA | 1 | 0.8853 | 100 | 0.315 | Contact Map |
| 3nxuA | 2 | 0.7993 | 100 | 0.327 | Contact Map |
| 3k9vA | 2 | 0.8065 | 100 | 0.329 | Contact Map |
| 3czhA | 2 | 0.8172 | 100 | 0.335 | Contact Map |
| 2ij2A | 2 | 0.7993 | 100 | 0.336 | Contact Map |
| 2hi4A | 1 | 0.819 | 100 | 0.338 | Contact Map |
| 3tbgA | 4 | 0.8082 | 100 | 0.34 | Contact Map |
| 2ve3A | 2 | 0.7706 | 100 | 0.342 | Contact Map |
| 3n9yA | 2 | 0.8136 | 100 | 0.343 | Contact Map |
| 3pm0A | 1 | 0.7832 | 100 | 0.343 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)