| melon-160 |
| ID: | 1431641549 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 508 (469) | ||
| Sequences: | 15609 (12164.2) | ||
| Seq/Len: | 33.281 | ||
| Nf(neff/√len): | 561.7 |
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: 33.281).
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 |
| 414_D | 417_S | 4.604 | 1.00 |
| 361_C | 424_E | 4.239 | 1.00 |
| 414_D | 419_R | 4.103 | 1.00 |
| 330_V | 358_Y | 3.485 | 1.00 |
| 332_K | 336_A | 3.268 | 1.00 |
| 320_A | 461_L | 3.266 | 1.00 |
| 336_A | 340_S | 3.246 | 1.00 |
| 265_R | 295_D | 3.092 | 1.00 |
| 384_D | 394_R | 3.085 | 1.00 |
| 320_A | 366_T | 3.069 | 1.00 |
| 334_A | 362_I | 2.995 | 1.00 |
| 323_N | 370_Y | 2.889 | 1.00 |
| 407_R | 416_T | 2.852 | 1.00 |
| 333_K | 421_E | 2.780 | 1.00 |
| 469_D | 499_K | 2.742 | 1.00 |
| 471_K | 499_K | 2.659 | 1.00 |
| 183_L | 460_M | 2.637 | 1.00 |
| 264_H | 277_C | 2.626 | 1.00 |
| 384_D | 391_N | 2.575 | 1.00 |
| 335_R | 339_E | 2.548 | 1.00 |
| 360_R | 458_G | 2.534 | 1.00 |
| 386_S | 391_N | 2.511 | 1.00 |
| 334_A | 465_I | 2.503 | 1.00 |
| 381_S | 392_I | 2.496 | 1.00 |
| 346_K | 352_D | 2.440 | 1.00 |
| 316_T | 457_M | 2.438 | 1.00 |
| 464_L | 470_W | 2.434 | 1.00 |
| 180_V | 321_M | 2.389 | 1.00 |
| 332_K | 469_D | 2.381 | 1.00 |
| 335_R | 469_D | 2.333 | 1.00 |
| 335_R | 501_R | 2.315 | 1.00 |
| 386_S | 389_G | 2.281 | 1.00 |
| 258_Q | 299_K | 2.273 | 1.00 |
| 164_F | 467_C | 2.265 | 1.00 |
| 48_H | 51_L | 2.245 | 1.00 |
| 100_F | 385_C | 2.226 | 1.00 |
| 333_K | 358_Y | 2.214 | 1.00 |
| 320_A | 324_L | 2.202 | 1.00 |
| 61_Q | 65_Q | 2.197 | 1.00 |
| 99_I | 383_A | 2.179 | 1.00 |
| 83_V | 92_C | 2.152 | 1.00 |
| 334_A | 359_L | 2.142 | 1.00 |
| 331_L | 469_D | 2.113 | 1.00 |
| 43_I | 46_I | 2.104 | 1.00 |
| 157_R | 463_T | 2.092 | 1.00 |
| 393_P | 396_T | 2.080 | 1.00 |
| 471_K | 497_L | 2.077 | 1.00 |
| 363_V | 457_M | 2.056 | 1.00 |
| 59_T | 62_T | 1.989 | 1.00 |
| 409_P | 415_P | 1.959 | 1.00 |
| 180_V | 317_I | 1.942 | 1.00 |
| 46_I | 50_H | 1.941 | 1.00 |
| 262_D | 266_R | 1.917 | 1.00 |
| 44_P | 47_G | 1.911 | 1.00 |
| 362_I | 418_F | 1.888 | 1.00 |
| 331_L | 335_R | 1.888 | 1.00 |
| 210_T | 252_R | 1.881 | 1.00 |
| 358_Y | 421_E | 1.877 | 1.00 |
| 320_A | 362_I | 1.861 | 1.00 |
| 323_N | 327_H | 1.854 | 1.00 |
| 164_F | 468_F | 1.844 | 1.00 |
| 70_V | 83_V | 1.840 | 1.00 |
| 369_L | 407_R | 1.835 | 1.00 |
| 74_R | 79_L | 1.830 | 1.00 |
| 89_A | 405_I | 1.828 | 1.00 |
| 262_D | 295_D | 1.823 | 1.00 |
| 361_C | 421_E | 1.817 | 1.00 |
| 332_K | 335_R | 1.814 | 1.00 |
| 470_W | 498_C | 1.806 | 1.00 |
| 338_I | 462_G | 1.805 | 1.00 |
| 325_L | 331_L | 1.784 | 1.00 |
| 154_D | 190_R | 1.767 | 1.00 |
| 251_A | 255_A | 1.762 | 1.00 |
| 81_V | 396_T | 1.762 | 1.00 |
| 62_T | 66_K | 1.749 | 1.00 |
| 69_P | 85_S | 1.729 | 1.00 |
| 72_S | 79_L | 1.725 | 1.00 |
| 362_I | 366_T | 1.719 | 1.00 |
| 339_E | 501_R | 1.715 | 1.00 |
| 88_A | 388_S | 1.693 | 1.00 |
| 164_F | 500_A | 1.688 | 1.00 |
| 323_N | 369_L | 1.686 | 1.00 |
| 317_I | 460_M | 1.683 | 1.00 |
| 321_M | 464_L | 1.682 | 1.00 |
| 217_E | 245_R | 1.678 | 1.00 |
| 258_Q | 262_D | 1.677 | 1.00 |
| 403_W | 407_R | 1.672 | 1.00 |
| 71_L | 82_V | 1.653 | 1.00 |
| 259_G | 263_E | 1.640 | 1.00 |
| 409_P | 416_T | 1.630 | 1.00 |
| 341_Q | 356_L | 1.629 | 1.00 |
| 62_T | 65_Q | 1.624 | 1.00 |
| 42_S | 48_H | 1.622 | 1.00 |
| 39_S | 67_Y | 1.620 | 1.00 |
| 324_L | 334_A | 1.599 | 1.00 |
| 453_A | 457_M | 1.547 | 1.00 |
| 155_E | 190_R | 1.545 | 1.00 |
| 244_K | 248_K | 1.545 | 1.00 |
| 258_Q | 295_D | 1.536 | 1.00 |
| 39_S | 48_H | 1.531 | 1.00 |
| 156_V | 183_L | 1.530 | 1.00 |
| 294_T | 297_I | 1.528 | 1.00 |
| 330_V | 362_I | 1.513 | 1.00 |
| 446_A | 450_T | 1.510 | 1.00 |
| 213_A | 217_E | 1.509 | 1.00 |
| 131_L | 301_L | 1.498 | 1.00 |
| 383_A | 394_R | 1.494 | 1.00 |
| 85_S | 88_A | 1.487 | 1.00 |
| 316_T | 372_A | 1.478 | 1.00 |
| 191_M | 452_M | 1.468 | 1.00 |
| 327_H | 330_V | 1.467 | 1.00 |
| 360_R | 364_L | 1.444 | 1.00 |
| 406_H | 439_A | 1.435 | 1.00 |
| 338_I | 356_L | 1.435 | 1.00 |
| 349_E | 352_D | 1.431 | 1.00 |
| 87_E | 388_S | 1.429 | 1.00 |
| 175_E | 178_P | 1.417 | 1.00 |
| 409_P | 413_E | 1.405 | 0.99 |
| 153_R | 463_T | 1.402 | 0.99 |
| 335_R | 465_I | 1.401 | 0.99 |
| 380_K | 395_D | 1.398 | 0.99 |
| 156_V | 160_V | 1.397 | 0.99 |
| 324_L | 330_V | 1.391 | 0.99 |
| 96_N | 385_C | 1.385 | 0.99 |
| 365_E | 368_R | 1.381 | 0.99 |
| 163_I | 498_C | 1.380 | 0.99 |
| 337_E | 356_L | 1.378 | 0.99 |
| 255_A | 259_G | 1.377 | 0.99 |
| 262_D | 265_R | 1.373 | 0.99 |
| 195_K | 263_E | 1.369 | 0.99 |
| 364_L | 437_M | 1.367 | 0.99 |
| 59_T | 63_L | 1.364 | 0.99 |
| 43_I | 50_H | 1.351 | 0.99 |
| 155_E | 158_R | 1.347 | 0.99 |
| 263_E | 267_G | 1.326 | 0.99 |
| 145_L | 455_R | 1.322 | 0.99 |
| 61_Q | 404_A | 1.310 | 0.99 |
| 254_D | 299_K | 1.309 | 0.99 |
| 189_M | 197_Y | 1.302 | 0.99 |
| 266_R | 270_S | 1.295 | 0.99 |
| 183_L | 187_I | 1.285 | 0.99 |
| 188_T | 309_G | 1.278 | 0.99 |
| 352_D | 355_K | 1.267 | 0.99 |
| 69_P | 410_T | 1.255 | 0.99 |
| 214_I | 252_R | 1.255 | 0.99 |
| 70_V | 88_A | 1.232 | 0.98 |
| 339_E | 466_Q | 1.229 | 0.98 |
| 280_A | 284_K | 1.229 | 0.98 |
| 157_R | 161_K | 1.227 | 0.98 |
| 330_V | 421_E | 1.225 | 0.98 |
| 323_N | 326_N | 1.224 | 0.98 |
| 413_E | 419_R | 1.205 | 0.98 |
| 320_A | 363_V | 1.193 | 0.98 |
| 54_L | 58_R | 1.192 | 0.98 |
| 323_N | 366_T | 1.189 | 0.98 |
| 384_D | 393_P | 1.181 | 0.98 |
| 159_A | 183_L | 1.177 | 0.98 |
| 83_V | 89_A | 1.176 | 0.98 |
| 163_I | 179_L | 1.175 | 0.98 |
| 321_M | 496_A | 1.175 | 0.98 |
| 381_S | 384_D | 1.174 | 0.98 |
| 81_V | 392_I | 1.170 | 0.97 |
| 130_K | 297_I | 1.166 | 0.97 |
| 190_R | 196_R | 1.165 | 0.97 |
| 126_D | 130_K | 1.158 | 0.97 |
| 321_M | 461_L | 1.157 | 0.97 |
| 248_K | 252_R | 1.156 | 0.97 |
| 293_Y | 297_I | 1.151 | 0.97 |
| 329_S | 333_K | 1.147 | 0.97 |
| 126_D | 129_R | 1.147 | 0.97 |
| 338_I | 359_L | 1.142 | 0.97 |
| 153_R | 157_R | 1.140 | 0.97 |
| 89_A | 400_V | 1.136 | 0.97 |
| 65_Q | 409_P | 1.133 | 0.97 |
| 264_H | 280_A | 1.124 | 0.97 |
| 357_S | 361_C | 1.123 | 0.97 |
| 155_E | 196_R | 1.122 | 0.97 |
| 359_L | 362_I | 1.119 | 0.96 |
| 333_K | 336_A | 1.115 | 0.96 |
| 160_V | 463_T | 1.104 | 0.96 |
| 317_I | 457_M | 1.102 | 0.96 |
| 96_N | 99_I | 1.099 | 0.96 |
| 160_V | 468_F | 1.098 | 0.96 |
| 143_S | 146_N | 1.096 | 0.96 |
| 353_L | 458_G | 1.093 | 0.96 |
| 334_A | 358_Y | 1.082 | 0.96 |
| 254_D | 258_Q | 1.079 | 0.95 |
| 162_K | 179_L | 1.078 | 0.95 |
| 185_M | 310_S | 1.075 | 0.95 |
| 84_T | 401_N | 1.075 | 0.95 |
| 217_E | 249_L | 1.073 | 0.95 |
| 367_L | 439_A | 1.072 | 0.95 |
| 188_T | 192_V | 1.069 | 0.95 |
| 155_E | 186_N | 1.066 | 0.95 |
| 364_L | 454_H | 1.065 | 0.95 |
| 406_H | 437_M | 1.059 | 0.95 |
| 263_E | 266_R | 1.051 | 0.94 |
| 324_L | 465_I | 1.050 | 0.94 |
| 90_E | 94_T | 1.050 | 0.94 |
| 392_I | 398_L | 1.049 | 0.94 |
| 402_A | 438_I | 1.048 | 0.94 |
| 160_V | 467_C | 1.047 | 0.94 |
| 322_S | 326_N | 1.044 | 0.94 |
| 63_L | 71_L | 1.040 | 0.94 |
| 158_R | 161_K | 1.039 | 0.94 |
| 324_L | 331_L | 1.036 | 0.94 |
| 157_R | 347_L | 1.036 | 0.94 |
| 261_I | 279_V | 1.034 | 0.94 |
| 260_L | 263_E | 1.034 | 0.94 |
| 98_V | 383_A | 1.032 | 0.94 |
| 450_T | 454_H | 1.029 | 0.94 |
| 152_R | 452_M | 1.027 | 0.94 |
| 102_N | 382_S | 1.024 | 0.93 |
| 481_N | 491_A | 1.022 | 0.93 |
| 316_T | 366_T | 1.015 | 0.93 |
| 325_L | 496_A | 1.014 | 0.93 |
| 367_L | 437_M | 1.008 | 0.93 |
| 295_D | 299_K | 1.003 | 0.93 |
| 414_D | 422_R | 1.002 | 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
- 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 | |
| 3pm0A | 1 | 0.878 | 100 | 0.232 | Contact Map |
| 4r21A | 2 | 0.8268 | 100 | 0.232 | Contact Map |
| 2hi4A | 1 | 0.9134 | 100 | 0.233 | Contact Map |
| 3tbgA | 4 | 0.8937 | 100 | 0.244 | Contact Map |
| 3swzA | 4 | 0.8996 | 100 | 0.252 | Contact Map |
| 4lxjA | 1 | 0.9626 | 100 | 0.255 | Contact Map |
| 3qz1A | 4 | 0.8602 | 100 | 0.255 | Contact Map |
| 1po5A | 1 | 0.8898 | 100 | 0.256 | Contact Map |
| 1r9oA | 1 | 0.8701 | 100 | 0.256 | Contact Map |
| 3k9vA | 2 | 0.8898 | 100 | 0.259 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)