| yjdlleastfilt |
| ID: | 1399398546 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 485 (465) | ||
| Sequences: | 2907 (2024.5) | ||
| Seq/Len: | 6.252 | ||
| Nf(neff/√len): | 93.9 |
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: 6.252).
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 |
| 74_N | 126_E | 2.703 | 1.00 |
| 81_G | 115_L | 2.508 | 1.00 |
| 42_D | 45_H | 2.328 | 1.00 |
| 72_L | 77_A | 2.281 | 1.00 |
| 395_A | 412_Y | 2.258 | 1.00 |
| 160_A | 172_L | 2.255 | 1.00 |
| 406_G | 410_G | 2.171 | 1.00 |
| 14_V | 145_A | 2.139 | 1.00 |
| 93_G | 171_A | 2.132 | 1.00 |
| 65_G | 406_G | 2.111 | 1.00 |
| 314_N | 385_G | 2.081 | 1.00 |
| 43_D | 294_R | 2.066 | 1.00 |
| 165_G | 168_V | 2.064 | 1.00 |
| 310_F | 374_M | 2.017 | 1.00 |
| 452_G | 456_L | 2.009 | 1.00 |
| 87_L | 108_I | 1.999 | 1.00 |
| 320_L | 324_V | 1.986 | 1.00 |
| 23_S | 89_H | 1.980 | 1.00 |
| 35_L | 39_L | 1.976 | 1.00 |
| 93_G | 174_G | 1.937 | 1.00 |
| 331_P | 335_G | 1.935 | 1.00 |
| 100_F | 104_L | 1.920 | 1.00 |
| 17_Q | 21_Y | 1.916 | 1.00 |
| 277_F | 387_A | 1.911 | 1.00 |
| 314_N | 388_E | 1.887 | 1.00 |
| 168_V | 171_A | 1.849 | 1.00 |
| 92_L | 105_A | 1.836 | 1.00 |
| 142_L | 146_G | 1.832 | 1.00 |
| 88_G | 112_G | 1.827 | 1.00 |
| 84_L | 112_G | 1.825 | 1.00 |
| 143_Y | 388_E | 1.822 | 1.00 |
| 26_G | 157_C | 1.813 | 1.00 |
| 20_E | 117_K | 1.786 | 1.00 |
| 192_Q | 195_R | 1.770 | 1.00 |
| 147_N | 314_N | 1.761 | 1.00 |
| 21_Y | 146_G | 1.758 | 1.00 |
| 88_G | 109_I | 1.751 | 1.00 |
| 90_V | 174_G | 1.741 | 1.00 |
| 298_R | 304_E | 1.739 | 1.00 |
| 91_V | 105_A | 1.732 | 1.00 |
| 17_Q | 20_E | 1.728 | 1.00 |
| 446_R | 449_S | 1.727 | 1.00 |
| 91_V | 108_I | 1.718 | 1.00 |
| 453_E | 457_A | 1.714 | 1.00 |
| 86_T | 178_F | 1.696 | 1.00 |
| 331_P | 334_R | 1.687 | 1.00 |
| 314_N | 318_V | 1.683 | 1.00 |
| 67_L | 72_L | 1.678 | 1.00 |
| 21_Y | 117_K | 1.672 | 1.00 |
| 161_A | 308_A | 1.671 | 1.00 |
| 171_A | 175_G | 1.666 | 1.00 |
| 88_G | 105_A | 1.634 | 1.00 |
| 60_T | 63_L | 1.623 | 1.00 |
| 156_A | 159_L | 1.594 | 0.99 |
| 317_A | 382_A | 1.585 | 0.99 |
| 33_L | 289_S | 1.574 | 0.99 |
| 87_L | 91_V | 1.548 | 0.99 |
| 65_G | 410_G | 1.544 | 0.99 |
| 67_L | 71_L | 1.528 | 0.99 |
| 318_V | 388_E | 1.511 | 0.99 |
| 139_F | 400_T | 1.508 | 0.99 |
| 85_M | 113_Y | 1.484 | 0.99 |
| 86_T | 174_G | 1.483 | 0.99 |
| 20_E | 24_F | 1.475 | 0.99 |
| 360_A | 449_S | 1.466 | 0.99 |
| 128_Y | 138_G | 1.460 | 0.99 |
| 17_Q | 117_K | 1.458 | 0.99 |
| 74_N | 405_S | 1.451 | 0.99 |
| 238_L | 242_V | 1.451 | 0.99 |
| 278_W | 392_D | 1.438 | 0.99 |
| 147_N | 388_E | 1.423 | 0.99 |
| 86_T | 90_V | 1.421 | 0.99 |
| 6_Q | 9_A | 1.414 | 0.99 |
| 158_G | 308_A | 1.410 | 0.98 |
| 322_G | 326_A | 1.406 | 0.98 |
| 347_F | 390_F | 1.402 | 0.98 |
| 75_R | 192_Q | 1.401 | 0.98 |
| 456_L | 460_A | 1.391 | 0.98 |
| 160_A | 164_Y | 1.388 | 0.98 |
| 28_R | 282_Q | 1.385 | 0.98 |
| 21_Y | 24_F | 1.366 | 0.98 |
| 24_F | 54_A | 1.360 | 0.98 |
| 58_Y | 117_K | 1.358 | 0.98 |
| 6_Q | 10_I | 1.355 | 0.98 |
| 24_F | 117_K | 1.354 | 0.98 |
| 350_L | 459_V | 1.350 | 0.98 |
| 20_E | 25_Y | 1.349 | 0.98 |
| 397_A | 401_R | 1.348 | 0.98 |
| 259_E | 262_R | 1.347 | 0.98 |
| 52_A | 422_W | 1.331 | 0.98 |
| 50_F | 285_G | 1.329 | 0.98 |
| 373_S | 376_V | 1.322 | 0.97 |
| 143_Y | 318_V | 1.317 | 0.97 |
| 19_W | 176_G | 1.312 | 0.97 |
| 348_G | 391_I | 1.305 | 0.97 |
| 60_T | 110_I | 1.305 | 0.97 |
| 17_Q | 142_L | 1.300 | 0.97 |
| 326_A | 330_S | 1.300 | 0.97 |
| 151_I | 319_M | 1.292 | 0.97 |
| 332_E | 337_S | 1.282 | 0.97 |
| 67_L | 77_A | 1.281 | 0.97 |
| 164_Y | 168_V | 1.279 | 0.97 |
| 121_S | 142_L | 1.276 | 0.97 |
| 124_L | 138_G | 1.276 | 0.97 |
| 143_Y | 147_N | 1.276 | 0.97 |
| 346_A | 459_V | 1.273 | 0.97 |
| 87_L | 172_L | 1.263 | 0.96 |
| 288_I | 380_G | 1.257 | 0.96 |
| 353_A | 459_V | 1.254 | 0.96 |
| 331_P | 336_N | 1.245 | 0.96 |
| 355_G | 384_M | 1.241 | 0.96 |
| 59_V | 414_L | 1.238 | 0.96 |
| 351_L | 386_F | 1.237 | 0.96 |
| 61_P | 68_A | 1.235 | 0.96 |
| 281_A | 318_V | 1.229 | 0.96 |
| 85_M | 116_F | 1.225 | 0.95 |
| 47_I | 429_Q | 1.224 | 0.95 |
| 126_E | 405_S | 1.221 | 0.95 |
| 21_Y | 25_Y | 1.218 | 0.95 |
| 372_A | 376_V | 1.212 | 0.95 |
| 18_I | 145_A | 1.210 | 0.95 |
| 51_S | 425_G | 1.210 | 0.95 |
| 449_S | 453_E | 1.204 | 0.95 |
| 286_S | 428_A | 1.204 | 0.95 |
| 281_A | 284_G | 1.203 | 0.95 |
| 457_A | 461_I | 1.202 | 0.95 |
| 288_I | 381_L | 1.200 | 0.95 |
| 144_A | 322_G | 1.198 | 0.95 |
| 232_N | 235_S | 1.188 | 0.94 |
| 77_A | 115_L | 1.185 | 0.94 |
| 125_G | 400_T | 1.184 | 0.94 |
| 306_P | 309_L | 1.181 | 0.94 |
| 348_G | 387_A | 1.179 | 0.94 |
| 426_V | 430_Q | 1.178 | 0.94 |
| 459_V | 463_V | 1.177 | 0.94 |
| 340_R | 343_L | 1.173 | 0.94 |
| 17_Q | 413_M | 1.172 | 0.94 |
| 216_V | 219_L | 1.167 | 0.94 |
| 316_I | 320_L | 1.166 | 0.94 |
| 148_I | 318_V | 1.165 | 0.94 |
| 303_I | 309_L | 1.161 | 0.93 |
| 173_A | 176_G | 1.159 | 0.93 |
| 28_R | 50_F | 1.153 | 0.93 |
| 392_D | 396_I | 1.153 | 0.93 |
| 80_A | 83_L | 1.152 | 0.93 |
| 18_I | 148_I | 1.147 | 0.93 |
| 296_V | 377_M | 1.144 | 0.93 |
| 427_V | 430_Q | 1.143 | 0.93 |
| 274_G | 416_T | 1.138 | 0.93 |
| 276_L | 458_C | 1.138 | 0.93 |
| 63_L | 71_L | 1.134 | 0.92 |
| 124_L | 142_L | 1.132 | 0.92 |
| 136_D | 397_A | 1.131 | 0.92 |
| 78_V | 120_I | 1.130 | 0.92 |
| 68_A | 119_N | 1.128 | 0.92 |
| 447_F | 451_M | 1.127 | 0.92 |
| 353_A | 357_M | 1.123 | 0.92 |
| 313_V | 378_I | 1.121 | 0.92 |
| 357_M | 361_F | 1.119 | 0.92 |
| 425_G | 429_Q | 1.118 | 0.92 |
| 292_I | 377_M | 1.117 | 0.92 |
| 121_S | 396_I | 1.113 | 0.91 |
| 325_L | 390_F | 1.111 | 0.91 |
| 358_L | 383_L | 1.108 | 0.91 |
| 156_A | 172_L | 1.104 | 0.91 |
| 43_D | 290_L | 1.103 | 0.91 |
| 238_L | 249_I | 1.099 | 0.91 |
| 155_I | 312_S | 1.099 | 0.91 |
| 50_F | 286_S | 1.096 | 0.91 |
| 20_E | 177_M | 1.093 | 0.90 |
| 231_E | 234_W | 1.086 | 0.90 |
| 72_L | 80_A | 1.085 | 0.90 |
| 63_L | 67_L | 1.085 | 0.90 |
| 95_D | 101_S | 1.078 | 0.90 |
| 317_A | 385_G | 1.076 | 0.89 |
| 33_L | 307_T | 1.074 | 0.89 |
| 147_N | 150_S | 1.073 | 0.89 |
| 56_L | 107_A | 1.071 | 0.89 |
| 271_M | 411_I | 1.070 | 0.89 |
| 221_L | 226_F | 1.067 | 0.89 |
| 20_E | 26_G | 1.066 | 0.89 |
| 339_L | 347_F | 1.066 | 0.89 |
| 19_W | 22_F | 1.064 | 0.89 |
| 392_D | 395_A | 1.064 | 0.89 |
| 325_L | 328_L | 1.061 | 0.89 |
| 64_G | 114_G | 1.058 | 0.88 |
| 385_G | 389_L | 1.058 | 0.88 |
| 188_H | 193_S | 1.054 | 0.88 |
| 74_N | 122_C | 1.053 | 0.88 |
| 145_A | 149_G | 1.047 | 0.88 |
| 146_G | 413_M | 1.045 | 0.88 |
| 467_F | 471_F | 1.045 | 0.88 |
| 223_P | 226_F | 1.045 | 0.88 |
| 332_E | 335_G | 1.044 | 0.88 |
| 90_V | 171_A | 1.043 | 0.87 |
| 143_Y | 314_N | 1.040 | 0.87 |
| 85_M | 109_I | 1.040 | 0.87 |
| 75_R | 411_I | 1.039 | 0.87 |
| 98_S | 101_S | 1.038 | 0.87 |
| 299_Q | 304_E | 1.038 | 0.87 |
| 151_I | 316_I | 1.034 | 0.87 |
| 23_S | 27_M | 1.034 | 0.87 |
| 277_F | 314_N | 1.034 | 0.87 |
| 396_I | 413_M | 1.033 | 0.87 |
| 359_L | 380_G | 1.033 | 0.87 |
| 58_Y | 68_A | 1.032 | 0.87 |
| 284_G | 384_M | 1.027 | 0.86 |
| 345_F | 348_G | 1.026 | 0.86 |
| 48_S | 52_A | 1.026 | 0.86 |
| 156_A | 182_L | 1.025 | 0.86 |
| 159_L | 163_W | 1.025 | 0.86 |
| 283_Q | 287_T | 1.024 | 0.86 |
| 236_G | 239_L | 1.023 | 0.86 |
| 275_T | 420_A | 1.021 | 0.86 |
| 431_T | 443_A | 1.021 | 0.86 |
| 158_G | 309_L | 1.020 | 0.86 |
| 148_I | 152_A | 1.014 | 0.85 |
| 311_Q | 314_N | 1.013 | 0.85 |
| 353_A | 456_L | 1.011 | 0.85 |
| 166_W | 289_S | 1.011 | 0.85 |
| 91_V | 94_I | 1.010 | 0.85 |
| 218_M | 221_L | 1.009 | 0.85 |
| 117_K | 413_M | 1.008 | 0.85 |
| 28_R | 285_G | 1.002 | 0.84 |
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 | |
| 4lepA | 2 | 0.9113 | 100 | 0.512 | Contact Map |
| 4apsA | 2 | 0.8763 | 100 | 0.517 | Contact Map |
| 4ikvA | 1 | 0.9464 | 100 | 0.531 | Contact Map |
| 2xutA | 3 | 0.866 | 100 | 0.543 | Contact Map |
| 4oh3A | 2 | 0.934 | 100 | 0.548 | Contact Map |
| 1pw4A | 1 | 0.8371 | 100 | 0.596 | Contact Map |
| 4j05A | 2 | 0.7959 | 100 | 0.6 | Contact Map |
| 4gc0A | 1 | 0.8742 | 100 | 0.619 | Contact Map |
| 4jr9A | 1 | 0.7423 | 100 | 0.627 | Contact Map |
| 4ldsA | 2 | 0.8557 | 100 | 0.628 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)