| pora |
| ID: | 1450871474 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 424 (421) | ||
| Sequences: | 2470 (1731.2) | ||
| Seq/Len: | 5.867 | ||
| Nf(neff/√len): | 84.4 |
Jackhmmer Results: (2015_08)
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: 5.867).
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 |
| 121_V | 155_S | 3.207 | 1.00 |
| 32_V | 72_F | 2.848 | 1.00 |
| 280_S | 287_D | 2.804 | 1.00 |
| 123_T | 153_N | 2.782 | 1.00 |
| 40_Y | 64_H | 2.781 | 1.00 |
| 25_L | 28_A | 2.682 | 1.00 |
| 80_F | 83_F | 2.677 | 1.00 |
| 394_A | 416_V | 2.645 | 1.00 |
| 88_Y | 91_A | 2.501 | 1.00 |
| 87_D | 90_A | 2.441 | 1.00 |
| 127_A | 149_V | 2.427 | 1.00 |
| 89_N | 92_D | 2.425 | 1.00 |
| 165_A | 202_Y | 2.420 | 1.00 |
| 274_L | 295_Y | 2.412 | 1.00 |
| 247_I | 281_I | 2.375 | 1.00 |
| 98_N | 101_K | 2.353 | 1.00 |
| 87_D | 91_A | 2.278 | 1.00 |
| 100_I | 103_D | 2.141 | 1.00 |
| 161_L | 206_A | 2.126 | 1.00 |
| 250_T | 280_S | 2.028 | 1.00 |
| 317_A | 320_E | 2.028 | 1.00 |
| 392_F | 420_A | 2.009 | 1.00 |
| 111_Q | 170_M | 1.982 | 1.00 |
| 355_A | 380_A | 1.957 | 1.00 |
| 39_R | 141_I | 1.934 | 1.00 |
| 85_Q | 91_A | 1.933 | 1.00 |
| 210_Y | 219_P | 1.932 | 1.00 |
| 103_D | 107_L | 1.914 | 1.00 |
| 99_G | 103_D | 1.900 | 1.00 |
| 98_N | 103_D | 1.894 | 1.00 |
| 88_Y | 92_D | 1.866 | 1.00 |
| 219_P | 237_A | 1.859 | 1.00 |
| 317_A | 322_F | 1.831 | 1.00 |
| 87_D | 92_D | 1.824 | 1.00 |
| 27_E | 30_K | 1.801 | 1.00 |
| 223_L | 233_Y | 1.795 | 1.00 |
| 100_I | 104_Q | 1.781 | 1.00 |
| 221_L | 233_Y | 1.780 | 1.00 |
| 316_L | 319_E | 1.778 | 1.00 |
| 212_L | 215_G | 1.774 | 1.00 |
| 255_Y | 273_N | 1.771 | 1.00 |
| 251_L | 279_G | 1.758 | 1.00 |
| 85_Q | 88_Y | 1.758 | 1.00 |
| 22_A | 25_L | 1.751 | 1.00 |
| 104_Q | 107_L | 1.742 | 1.00 |
| 394_A | 418_L | 1.726 | 1.00 |
| 156_I | 159_L | 1.710 | 1.00 |
| 123_T | 151_V | 1.703 | 1.00 |
| 159_L | 208_G | 1.700 | 1.00 |
| 98_N | 104_Q | 1.682 | 1.00 |
| 91_A | 94_G | 1.676 | 1.00 |
| 34_V | 72_F | 1.662 | 1.00 |
| 320_E | 323_Y | 1.656 | 1.00 |
| 317_A | 324_T | 1.651 | 1.00 |
| 316_L | 320_E | 1.645 | 1.00 |
| 94_G | 97_A | 1.637 | 1.00 |
| 398_Y | 414_S | 1.635 | 1.00 |
| 105_K | 108_F | 1.625 | 1.00 |
| 305_V | 309_Q | 1.625 | 1.00 |
| 45_G | 415_T | 1.624 | 1.00 |
| 257_G | 273_N | 1.623 | 0.99 |
| 385_K | 391_N | 1.605 | 0.99 |
| 129_K | 147_T | 1.593 | 0.99 |
| 240_S | 248_N | 1.591 | 0.99 |
| 319_E | 324_T | 1.580 | 0.99 |
| 307_E | 310_G | 1.536 | 0.99 |
| 85_Q | 89_N | 1.533 | 0.99 |
| 22_A | 26_E | 1.528 | 0.99 |
| 101_K | 104_Q | 1.518 | 0.99 |
| 308_D | 311_N | 1.512 | 0.99 |
| 283_V | 288_A | 1.508 | 0.99 |
| 76_I | 124_S | 1.487 | 0.99 |
| 239_Y | 251_L | 1.481 | 0.99 |
| 278_K | 289_S | 1.478 | 0.99 |
| 122_A | 155_S | 1.466 | 0.99 |
| 89_N | 94_G | 1.465 | 0.99 |
| 294_Y | 337_I | 1.463 | 0.99 |
| 99_G | 104_Q | 1.460 | 0.99 |
| 24_P | 28_A | 1.454 | 0.99 |
| 315_L | 320_E | 1.452 | 0.99 |
| 319_E | 322_F | 1.434 | 0.98 |
| 74_A | 77_A | 1.433 | 0.98 |
| 318_G | 322_F | 1.431 | 0.98 |
| 38_L | 68_A | 1.430 | 0.98 |
| 253_G | 277_L | 1.425 | 0.98 |
| 10_A | 13_A | 1.418 | 0.98 |
| 306_I | 310_G | 1.417 | 0.98 |
| 323_Y | 326_G | 1.408 | 0.98 |
| 336_N | 346_T | 1.393 | 0.98 |
| 12_L | 15_G | 1.392 | 0.98 |
| 320_E | 325_T | 1.378 | 0.98 |
| 319_E | 323_Y | 1.375 | 0.98 |
| 22_A | 28_A | 1.375 | 0.98 |
| 152_V | 160_T | 1.369 | 0.98 |
| 150_K | 162_A | 1.368 | 0.98 |
| 40_Y | 66_Y | 1.367 | 0.98 |
| 220_Q | 236_D | 1.364 | 0.98 |
| 335_R | 338_F | 1.364 | 0.98 |
| 130_Q | 150_K | 1.354 | 0.98 |
| 305_V | 310_G | 1.345 | 0.97 |
| 123_T | 155_S | 1.344 | 0.97 |
| 86_F | 91_A | 1.334 | 0.97 |
| 304_V | 308_D | 1.331 | 0.97 |
| 9_V | 13_A | 1.330 | 0.97 |
| 396_Y | 416_V | 1.330 | 0.97 |
| 306_I | 312_L | 1.329 | 0.97 |
| 241_T | 251_L | 1.326 | 0.97 |
| 374_K | 402_D | 1.325 | 0.97 |
| 304_V | 310_G | 1.325 | 0.97 |
| 87_D | 94_G | 1.323 | 0.97 |
| 100_I | 105_K | 1.319 | 0.97 |
| 250_T | 282_E | 1.316 | 0.97 |
| 319_E | 326_G | 1.313 | 0.97 |
| 165_A | 200_N | 1.308 | 0.97 |
| 315_L | 318_G | 1.303 | 0.97 |
| 38_L | 66_Y | 1.301 | 0.97 |
| 15_G | 18_S | 1.296 | 0.97 |
| 317_A | 323_Y | 1.293 | 0.97 |
| 302_S | 306_I | 1.291 | 0.96 |
| 247_I | 283_V | 1.290 | 0.96 |
| 147_T | 167_D | 1.280 | 0.96 |
| 381_R | 393_S | 1.273 | 0.96 |
| 86_F | 90_A | 1.269 | 0.96 |
| 336_N | 343_G | 1.256 | 0.96 |
| 306_I | 309_Q | 1.255 | 0.96 |
| 70_V | 74_A | 1.254 | 0.96 |
| 164_F | 203_G | 1.253 | 0.96 |
| 113_Y | 129_K | 1.250 | 0.96 |
| 338_F | 343_G | 1.248 | 0.96 |
| 9_V | 12_L | 1.244 | 0.95 |
| 44_T | 62_Q | 1.230 | 0.95 |
| 83_F | 118_N | 1.226 | 0.95 |
| 103_D | 106_G | 1.226 | 0.95 |
| 24_P | 27_E | 1.216 | 0.95 |
| 159_L | 206_A | 1.215 | 0.95 |
| 336_N | 347_F | 1.213 | 0.95 |
| 260_L | 263_E | 1.210 | 0.94 |
| 122_A | 153_N | 1.201 | 0.94 |
| 261_D | 265_D | 1.197 | 0.94 |
| 122_A | 157_D | 1.196 | 0.94 |
| 304_V | 307_E | 1.194 | 0.94 |
| 386_Y | 392_F | 1.192 | 0.94 |
| 131_Q | 139_N | 1.186 | 0.94 |
| 42_Y | 62_Q | 1.183 | 0.94 |
| 64_H | 74_A | 1.183 | 0.94 |
| 101_K | 107_L | 1.179 | 0.93 |
| 248_N | 282_E | 1.176 | 0.93 |
| 41_R | 419_Q | 1.169 | 0.93 |
| 74_A | 82_A | 1.169 | 0.93 |
| 217_F | 239_Y | 1.167 | 0.93 |
| 388_P | 391_N | 1.166 | 0.93 |
| 115_T | 126_I | 1.165 | 0.93 |
| 48_D | 414_S | 1.163 | 0.93 |
| 338_F | 346_T | 1.163 | 0.93 |
| 11_A | 14_A | 1.155 | 0.92 |
| 318_G | 323_Y | 1.150 | 0.92 |
| 285_G | 349_E | 1.148 | 0.92 |
| 150_K | 203_G | 1.145 | 0.92 |
| 322_F | 325_T | 1.144 | 0.92 |
| 90_A | 94_G | 1.132 | 0.91 |
| 379_V | 397_S | 1.127 | 0.91 |
| 309_Q | 312_L | 1.123 | 0.91 |
| 8_L | 12_L | 1.116 | 0.91 |
| 318_G | 321_I | 1.116 | 0.91 |
| 338_F | 348_N | 1.112 | 0.90 |
| 225_Y | 231_F | 1.110 | 0.90 |
| 316_L | 323_Y | 1.107 | 0.90 |
| 135_I | 234_A | 1.102 | 0.90 |
| 86_F | 89_N | 1.100 | 0.90 |
| 388_P | 392_F | 1.096 | 0.90 |
| 23_T | 26_E | 1.095 | 0.90 |
| 87_D | 110_R | 1.093 | 0.89 |
| 306_I | 311_N | 1.090 | 0.89 |
| 334_G | 339_G | 1.090 | 0.89 |
| 312_L | 315_L | 1.090 | 0.89 |
| 338_F | 342_T | 1.084 | 0.89 |
| 286_W | 343_G | 1.080 | 0.89 |
| 345_Y | 349_E | 1.080 | 0.89 |
| 336_N | 348_N | 1.077 | 0.88 |
| 345_Y | 350_T | 1.077 | 0.88 |
| 341_V | 346_T | 1.073 | 0.88 |
| 85_Q | 90_A | 1.071 | 0.88 |
| 280_S | 289_S | 1.066 | 0.88 |
| 317_A | 321_I | 1.066 | 0.88 |
| 332_D | 338_F | 1.064 | 0.88 |
| 383_D | 391_N | 1.059 | 0.87 |
| 390_L | 422_Y | 1.058 | 0.87 |
| 308_D | 312_L | 1.054 | 0.87 |
| 285_G | 345_Y | 1.054 | 0.87 |
| 391_N | 421_L | 1.051 | 0.87 |
| 22_A | 27_E | 1.050 | 0.87 |
| 147_T | 168_S | 1.050 | 0.87 |
| 278_K | 291_G | 1.050 | 0.87 |
| 14_A | 19_A | 1.050 | 0.87 |
| 231_F | 273_N | 1.050 | 0.87 |
| 343_G | 348_N | 1.048 | 0.87 |
| 19_A | 22_A | 1.043 | 0.86 |
| 336_N | 339_G | 1.042 | 0.86 |
| 123_T | 156_I | 1.038 | 0.86 |
| 381_R | 395_F | 1.036 | 0.86 |
| 207_V | 218_N | 1.033 | 0.86 |
| 338_F | 341_V | 1.033 | 0.86 |
| 98_N | 107_L | 1.031 | 0.85 |
| 16_A | 19_A | 1.031 | 0.85 |
| 354_G | 381_R | 1.028 | 0.85 |
| 37_V | 423_K | 1.027 | 0.85 |
| 317_A | 326_G | 1.027 | 0.85 |
| 207_V | 220_Q | 1.025 | 0.85 |
| 316_L | 321_I | 1.024 | 0.85 |
| 353_V | 382_V | 1.021 | 0.85 |
| 216_Q | 242_T | 1.018 | 0.84 |
| 236_D | 252_E | 1.018 | 0.84 |
| 302_S | 305_V | 1.017 | 0.84 |
| 343_G | 346_T | 1.015 | 0.84 |
| 320_E | 324_T | 1.014 | 0.84 |
| 289_S | 342_T | 1.012 | 0.84 |
| 343_G | 355_A | 1.008 | 0.84 |
| 225_Y | 262_S | 1.007 | 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 | |
| 3sybA | 1 | 0.875 | 100 | 0.33 | Contact Map |
| 2y0lA | 1 | 0.8066 | 100 | 0.368 | Contact Map |
| 3sy7A | 1 | 0.8255 | 100 | 0.369 | Contact Map |
| 2y0hA | 1 | 0.809 | 100 | 0.371 | Contact Map |
| 3t24A | 3 | 0.842 | 100 | 0.372 | Contact Map |
| 3szdB | 2 | 0.8255 | 100 | 0.373 | Contact Map |
| 3szvA | 1 | 0.816 | 100 | 0.376 | Contact Map |
| 4fspA | 1 | 0.8137 | 100 | 0.38 | Contact Map |
| 3sy9A | 4 | 0.7972 | 100 | 0.38 | Contact Map |
| 4ft6A | 1 | 0.8514 | 100 | 0.381 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)