| YJDL_POTS |
| ID: | 1432741557 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 485 (451) | ||
| Sequences: | 16564 (11263.1) | ||
| Seq/Len: | 36.727 | ||
| Nf(neff/√len): | 530.4 |
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: 36.727).
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 |
| 100_F | 104_L | 4.101 | 1.00 |
| 96_T | 101_S | 3.798 | 1.00 |
| 93_G | 171_A | 3.678 | 1.00 |
| 84_L | 112_G | 3.534 | 1.00 |
| 88_G | 105_A | 3.249 | 1.00 |
| 74_N | 126_E | 3.219 | 1.00 |
| 99_T | 103_Y | 3.069 | 1.00 |
| 206_K | 211_V | 2.951 | 1.00 |
| 86_T | 177_M | 2.859 | 1.00 |
| 42_D | 45_H | 2.855 | 1.00 |
| 60_T | 114_G | 2.779 | 1.00 |
| 81_G | 115_L | 2.770 | 1.00 |
| 88_G | 112_G | 2.730 | 1.00 |
| 91_V | 105_A | 2.689 | 1.00 |
| 351_L | 387_A | 2.671 | 1.00 |
| 136_D | 330_S | 2.643 | 1.00 |
| 403_K | 408_L | 2.639 | 1.00 |
| 98_S | 101_S | 2.628 | 1.00 |
| 64_G | 115_L | 2.567 | 1.00 |
| 449_S | 453_E | 2.495 | 1.00 |
| 128_Y | 138_G | 2.485 | 1.00 |
| 56_L | 107_A | 2.472 | 1.00 |
| 375_G | 379_S | 2.388 | 1.00 |
| 69_D | 406_G | 2.320 | 1.00 |
| 353_A | 459_V | 2.289 | 1.00 |
| 355_G | 380_G | 2.280 | 1.00 |
| 355_G | 387_A | 2.256 | 1.00 |
| 353_A | 456_L | 2.216 | 1.00 |
| 321_A | 386_F | 2.207 | 1.00 |
| 88_G | 108_I | 2.138 | 1.00 |
| 131_N | 134_R | 2.047 | 1.00 |
| 88_G | 109_I | 1.987 | 1.00 |
| 68_A | 119_N | 1.978 | 1.00 |
| 95_D | 101_S | 1.963 | 1.00 |
| 317_A | 382_A | 1.909 | 1.00 |
| 67_L | 77_A | 1.909 | 1.00 |
| 95_D | 105_A | 1.907 | 1.00 |
| 65_G | 69_D | 1.891 | 1.00 |
| 360_A | 452_G | 1.882 | 1.00 |
| 86_T | 174_G | 1.873 | 1.00 |
| 134_R | 137_G | 1.858 | 1.00 |
| 60_T | 111_C | 1.848 | 1.00 |
| 164_Y | 168_V | 1.838 | 1.00 |
| 360_A | 449_S | 1.816 | 1.00 |
| 73_G | 76_T | 1.815 | 1.00 |
| 90_V | 174_G | 1.802 | 1.00 |
| 334_R | 401_R | 1.799 | 1.00 |
| 165_G | 168_V | 1.798 | 1.00 |
| 93_G | 174_G | 1.794 | 1.00 |
| 65_G | 406_G | 1.792 | 1.00 |
| 350_L | 459_V | 1.783 | 1.00 |
| 75_R | 79_I | 1.764 | 1.00 |
| 79_I | 181_L | 1.722 | 1.00 |
| 86_T | 181_L | 1.717 | 1.00 |
| 326_A | 330_S | 1.711 | 1.00 |
| 52_A | 107_A | 1.701 | 1.00 |
| 358_L | 380_G | 1.691 | 1.00 |
| 207_F | 213_S | 1.690 | 1.00 |
| 86_T | 178_F | 1.679 | 1.00 |
| 353_A | 452_G | 1.667 | 1.00 |
| 357_M | 452_G | 1.667 | 1.00 |
| 327_W | 331_P | 1.660 | 1.00 |
| 45_H | 99_T | 1.622 | 1.00 |
| 52_A | 103_Y | 1.606 | 1.00 |
| 43_D | 294_R | 1.599 | 1.00 |
| 129_D | 134_R | 1.599 | 1.00 |
| 91_V | 94_I | 1.588 | 1.00 |
| 348_G | 390_F | 1.584 | 1.00 |
| 76_T | 80_A | 1.584 | 1.00 |
| 83_L | 181_L | 1.558 | 1.00 |
| 66_W | 70_R | 1.540 | 1.00 |
| 80_A | 84_L | 1.535 | 1.00 |
| 92_L | 105_A | 1.530 | 1.00 |
| 55_S | 422_W | 1.529 | 1.00 |
| 445_Q | 449_S | 1.518 | 1.00 |
| 168_V | 172_L | 1.499 | 1.00 |
| 87_L | 91_V | 1.492 | 1.00 |
| 171_A | 175_G | 1.481 | 1.00 |
| 56_L | 60_T | 1.481 | 1.00 |
| 373_S | 376_V | 1.472 | 1.00 |
| 346_A | 459_V | 1.467 | 1.00 |
| 314_N | 385_G | 1.466 | 1.00 |
| 49_L | 102_L | 1.463 | 1.00 |
| 155_I | 312_S | 1.462 | 1.00 |
| 90_V | 94_I | 1.450 | 1.00 |
| 317_A | 321_A | 1.449 | 1.00 |
| 453_E | 457_A | 1.434 | 1.00 |
| 139_F | 400_T | 1.424 | 1.00 |
| 347_F | 351_L | 1.412 | 1.00 |
| 168_V | 171_A | 1.399 | 0.99 |
| 353_A | 357_M | 1.390 | 0.99 |
| 60_T | 63_L | 1.368 | 0.99 |
| 156_A | 159_L | 1.366 | 0.99 |
| 69_D | 407_V | 1.363 | 0.99 |
| 348_G | 387_A | 1.361 | 0.99 |
| 83_L | 87_L | 1.358 | 0.99 |
| 53_Y | 57_V | 1.355 | 0.99 |
| 456_L | 460_A | 1.354 | 0.99 |
| 18_I | 145_A | 1.351 | 0.99 |
| 350_L | 354_C | 1.348 | 0.99 |
| 357_M | 361_F | 1.341 | 0.99 |
| 299_Q | 306_P | 1.333 | 0.99 |
| 41_F | 45_H | 1.329 | 0.99 |
| 69_D | 74_N | 1.329 | 0.99 |
| 452_G | 456_L | 1.327 | 0.99 |
| 282_Q | 421_N | 1.303 | 0.99 |
| 92_L | 102_L | 1.300 | 0.99 |
| 306_P | 309_L | 1.299 | 0.99 |
| 74_N | 193_S | 1.292 | 0.99 |
| 68_A | 74_N | 1.291 | 0.99 |
| 144_A | 319_M | 1.285 | 0.99 |
| 79_I | 185_L | 1.267 | 0.99 |
| 91_V | 101_S | 1.265 | 0.99 |
| 279_V | 424_A | 1.265 | 0.99 |
| 324_V | 327_W | 1.259 | 0.99 |
| 125_G | 135_R | 1.256 | 0.99 |
| 275_T | 420_A | 1.248 | 0.99 |
| 293_D | 307_T | 1.235 | 0.98 |
| 446_R | 449_S | 1.229 | 0.98 |
| 460_A | 464_V | 1.223 | 0.98 |
| 316_I | 320_L | 1.222 | 0.98 |
| 82_A | 180_G | 1.219 | 0.98 |
| 150_S | 315_A | 1.216 | 0.98 |
| 114_G | 118_S | 1.212 | 0.98 |
| 41_F | 99_T | 1.206 | 0.98 |
| 436_I | 443_A | 1.203 | 0.98 |
| 124_L | 138_G | 1.203 | 0.98 |
| 19_W | 23_S | 1.199 | 0.98 |
| 446_R | 450_Q | 1.198 | 0.98 |
| 121_S | 142_L | 1.197 | 0.98 |
| 84_L | 88_G | 1.195 | 0.98 |
| 36_T | 46_A | 1.179 | 0.98 |
| 78_V | 120_I | 1.178 | 0.98 |
| 355_G | 384_M | 1.178 | 0.98 |
| 160_A | 168_V | 1.170 | 0.97 |
| 76_T | 79_I | 1.170 | 0.97 |
| 333_S | 343_L | 1.168 | 0.97 |
| 346_A | 350_L | 1.167 | 0.97 |
| 431_T | 436_I | 1.166 | 0.97 |
| 160_A | 172_L | 1.165 | 0.97 |
| 48_S | 426_V | 1.163 | 0.97 |
| 291_F | 296_V | 1.151 | 0.97 |
| 8_R | 12_Y | 1.148 | 0.97 |
| 210_P | 213_S | 1.146 | 0.97 |
| 427_V | 430_Q | 1.146 | 0.97 |
| 106_L | 110_I | 1.146 | 0.97 |
| 82_A | 181_L | 1.146 | 0.97 |
| 38_Q | 167_H | 1.144 | 0.97 |
| 160_A | 164_Y | 1.143 | 0.97 |
| 14_V | 145_A | 1.130 | 0.97 |
| 352_M | 455_T | 1.130 | 0.97 |
| 159_L | 163_W | 1.130 | 0.97 |
| 48_S | 52_A | 1.130 | 0.97 |
| 348_G | 391_I | 1.127 | 0.97 |
| 157_C | 169_G | 1.127 | 0.97 |
| 23_S | 89_H | 1.123 | 0.97 |
| 81_G | 112_G | 1.120 | 0.96 |
| 349_L | 459_V | 1.118 | 0.96 |
| 85_M | 113_Y | 1.113 | 0.96 |
| 136_D | 326_A | 1.111 | 0.96 |
| 168_V | 175_G | 1.108 | 0.96 |
| 329_A | 394_V | 1.108 | 0.96 |
| 49_L | 99_T | 1.108 | 0.96 |
| 321_A | 324_V | 1.106 | 0.96 |
| 343_L | 347_F | 1.105 | 0.96 |
| 346_A | 463_V | 1.104 | 0.96 |
| 74_N | 122_C | 1.103 | 0.96 |
| 72_L | 77_A | 1.102 | 0.96 |
| 135_R | 400_T | 1.100 | 0.96 |
| 328_L | 344_K | 1.097 | 0.96 |
| 154_P | 312_S | 1.095 | 0.96 |
| 355_G | 383_L | 1.094 | 0.96 |
| 178_F | 182_L | 1.094 | 0.96 |
| 86_T | 90_V | 1.090 | 0.96 |
| 17_Q | 21_Y | 1.085 | 0.96 |
| 71_L | 77_A | 1.083 | 0.96 |
| 73_G | 77_A | 1.079 | 0.95 |
| 292_I | 377_M | 1.077 | 0.95 |
| 73_G | 193_S | 1.073 | 0.95 |
| 420_A | 424_A | 1.072 | 0.95 |
| 419_V | 423_L | 1.070 | 0.95 |
| 360_A | 445_Q | 1.070 | 0.95 |
| 291_F | 295_F | 1.065 | 0.95 |
| 438_G | 443_A | 1.065 | 0.95 |
| 147_N | 150_S | 1.065 | 0.95 |
| 51_S | 422_W | 1.059 | 0.95 |
| 80_A | 83_L | 1.059 | 0.95 |
| 175_G | 178_F | 1.058 | 0.95 |
| 48_S | 51_S | 1.058 | 0.95 |
| 332_E | 344_K | 1.056 | 0.95 |
| 85_M | 116_F | 1.052 | 0.95 |
| 89_H | 109_I | 1.047 | 0.94 |
| 54_A | 421_N | 1.045 | 0.94 |
| 48_S | 103_Y | 1.043 | 0.94 |
| 379_S | 383_L | 1.042 | 0.94 |
| 329_A | 333_S | 1.036 | 0.94 |
| 283_Q | 428_A | 1.036 | 0.94 |
| 79_I | 184_F | 1.035 | 0.94 |
| 137_G | 330_S | 1.034 | 0.94 |
| 96_T | 167_H | 1.033 | 0.94 |
| 251_A | 260_H | 1.031 | 0.94 |
| 271_M | 415_A | 1.030 | 0.94 |
| 167_H | 171_A | 1.028 | 0.94 |
| 354_C | 358_L | 1.027 | 0.94 |
| 286_S | 289_S | 1.027 | 0.94 |
| 343_L | 346_A | 1.026 | 0.94 |
| 35_L | 39_L | 1.025 | 0.93 |
| 375_G | 378_I | 1.023 | 0.93 |
| 350_L | 353_A | 1.023 | 0.93 |
| 64_G | 118_S | 1.021 | 0.93 |
| 85_M | 112_G | 1.018 | 0.93 |
| 118_S | 122_C | 1.016 | 0.93 |
| 139_F | 397_A | 1.012 | 0.93 |
| 53_Y | 106_L | 1.010 | 0.93 |
| 378_I | 382_A | 1.008 | 0.93 |
| 58_Y | 422_W | 1.008 | 0.93 |
| 29_A | 32_I | 1.008 | 0.93 |
| 76_T | 193_S | 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 | |
| 1pw4A | 1 | 0.8351 | 100 | 0.37 | Contact Map |
| 4q65A | 1 | 0.8804 | 100 | 0.373 | Contact Map |
| 3wdoA | 1 | 0.8268 | 100 | 0.377 | Contact Map |
| 4j05A | 2 | 0.8 | 100 | 0.391 | Contact Map |
| 4ikvA | 1 | 0.9361 | 100 | 0.392 | Contact Map |
| 4pypA | 1 | 0.8639 | 100 | 0.401 | Contact Map |
| 2cfqA | 1 | 0.8247 | 100 | 0.41 | Contact Map |
| 2gfpA | 2 | 0.7691 | 100 | 0.414 | Contact Map |
| 3o7qA | 1 | 0.7876 | 100 | 0.415 | Contact Map |
| 4ldsA | 2 | 0.8557 | 100 | 0.42 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)