| 1pw4 |
| ID: | 1408398807 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 447 (405) | ||
| Sequences: | 64254 (47582.9) | ||
| Seq/Len: | 158.652 | ||
| Nf(neff/√len): | 2364.4 |
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: 158.652).
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 |
| 114_S | 118_V | 3.970 | 1.00 |
| 98_L | 129_F | 3.535 | 1.00 |
| 105_F | 122_L | 3.358 | 1.00 |
| 102_V | 122_L | 3.218 | 1.00 |
| 107_G | 187_Y | 3.180 | 1.00 |
| 151_G | 310_D | 3.138 | 1.00 |
| 88_P | 143_H | 3.046 | 1.00 |
| 100_A | 193_A | 3.011 | 1.00 |
| 117_A | 121_V | 2.968 | 1.00 |
| 71_A | 124_F | 2.938 | 1.00 |
| 115_S | 118_V | 2.776 | 1.00 |
| 372_A | 380_A | 2.716 | 1.00 |
| 116_I | 120_F | 2.654 | 1.00 |
| 79_M | 132_M | 2.645 | 1.00 |
| 84_D | 378_G | 2.577 | 1.00 |
| 283_A | 286_K | 2.518 | 1.00 |
| 102_V | 129_F | 2.493 | 1.00 |
| 145_W | 153_I | 2.464 | 1.00 |
| 57_S | 60_D | 2.447 | 1.00 |
| 95_G | 132_M | 2.429 | 1.00 |
| 263_L | 396_A | 2.379 | 1.00 |
| 75_S | 128_W | 2.265 | 1.00 |
| 149_E | 152_G | 2.206 | 1.00 |
| 259_V | 392_G | 2.126 | 1.00 |
| 102_V | 125_L | 2.121 | 1.00 |
| 146_S | 149_E | 2.100 | 1.00 |
| 215_P | 218_E | 2.091 | 1.00 |
| 297_A | 351_I | 2.044 | 1.00 |
| 75_S | 131_G | 2.030 | 1.00 |
| 243_Q | 247_P | 2.026 | 1.00 |
| 316_N | 370_E | 2.021 | 1.00 |
| 80_G | 84_D | 2.012 | 1.00 |
| 306_G | 310_D | 2.005 | 1.00 |
| 373_P | 376_A | 1.996 | 1.00 |
| 113_T | 118_V | 1.959 | 1.00 |
| 93_P | 197_A | 1.941 | 1.00 |
| 180_N | 184_A | 1.924 | 1.00 |
| 104_L | 190_A | 1.891 | 1.00 |
| 71_A | 75_S | 1.883 | 1.00 |
| 89_R | 93_P | 1.874 | 1.00 |
| 414_M | 418_G | 1.867 | 1.00 |
| 113_T | 122_L | 1.867 | 1.00 |
| 83_S | 136_P | 1.839 | 1.00 |
| 329_T | 424_V | 1.829 | 1.00 |
| 301_G | 355_F | 1.765 | 1.00 |
| 67_G | 120_F | 1.763 | 1.00 |
| 60_D | 116_I | 1.761 | 1.00 |
| 100_A | 197_A | 1.757 | 1.00 |
| 334_V | 349_C | 1.730 | 1.00 |
| 81_S | 85_R | 1.713 | 1.00 |
| 64_A | 119_M | 1.711 | 1.00 |
| 102_V | 126_C | 1.690 | 1.00 |
| 214_P | 217_E | 1.689 | 1.00 |
| 67_G | 124_F | 1.685 | 1.00 |
| 106_M | 122_L | 1.677 | 1.00 |
| 105_F | 108_F | 1.663 | 1.00 |
| 327_L | 356_L | 1.658 | 1.00 |
| 218_E | 221_N | 1.627 | 1.00 |
| 56_F | 116_I | 1.620 | 1.00 |
| 267_G | 400_V | 1.614 | 1.00 |
| 331_A | 349_C | 1.601 | 1.00 |
| 181_D | 184_A | 1.595 | 1.00 |
| 93_P | 201_F | 1.588 | 1.00 |
| 97_I | 197_A | 1.580 | 1.00 |
| 331_A | 356_L | 1.580 | 1.00 |
| 307_W | 311_K | 1.578 | 1.00 |
| 82_V | 91_F | 1.577 | 1.00 |
| 100_A | 190_A | 1.556 | 1.00 |
| 329_T | 421_I | 1.548 | 1.00 |
| 198_L | 202_A | 1.534 | 1.00 |
| 95_G | 129_F | 1.526 | 1.00 |
| 344_T | 348_I | 1.505 | 1.00 |
| 297_A | 301_G | 1.502 | 1.00 |
| 56_F | 60_D | 1.494 | 1.00 |
| 87_N | 90_V | 1.490 | 1.00 |
| 86_S | 91_F | 1.482 | 1.00 |
| 106_M | 119_M | 1.468 | 1.00 |
| 187_Y | 191_F | 1.451 | 1.00 |
| 324_F | 359_G | 1.428 | 1.00 |
| 82_V | 86_S | 1.425 | 1.00 |
| 31_F | 160_A | 1.422 | 1.00 |
| 236_T | 239_Q | 1.405 | 0.99 |
| 173_L | 176_M | 1.379 | 0.99 |
| 23_R | 149_E | 1.363 | 0.99 |
| 255_A | 387_F | 1.362 | 0.99 |
| 392_G | 396_A | 1.361 | 0.99 |
| 104_L | 108_F | 1.361 | 0.99 |
| 244_Y | 247_P | 1.360 | 0.99 |
| 84_D | 88_P | 1.356 | 0.99 |
| 329_T | 417_I | 1.353 | 0.99 |
| 35_A | 164_G | 1.350 | 0.99 |
| 147_Q | 150_R | 1.346 | 0.99 |
| 143_H | 377_A | 1.344 | 0.99 |
| 94_A | 98_L | 1.343 | 0.99 |
| 80_G | 378_G | 1.342 | 0.99 |
| 118_V | 122_L | 1.336 | 0.99 |
| 90_V | 94_A | 1.334 | 0.99 |
| 75_S | 78_I | 1.330 | 0.99 |
| 98_L | 102_V | 1.326 | 0.99 |
| 282_F | 286_K | 1.320 | 0.99 |
| 71_A | 127_G | 1.318 | 0.99 |
| 152_G | 310_D | 1.306 | 0.99 |
| 68_I | 72_Y | 1.303 | 0.99 |
| 107_G | 190_A | 1.300 | 0.99 |
| 266_Y | 393_S | 1.298 | 0.99 |
| 142_V | 150_R | 1.295 | 0.99 |
| 121_V | 125_L | 1.293 | 0.99 |
| 70_I | 394_V | 1.291 | 0.99 |
| 58_R | 405_D | 1.280 | 0.99 |
| 294_Y | 354_G | 1.276 | 0.99 |
| 333_I | 417_I | 1.274 | 0.99 |
| 401_G | 405_D | 1.271 | 0.99 |
| 84_D | 379_T | 1.263 | 0.99 |
| 277_K | 287_S | 1.262 | 0.99 |
| 329_T | 333_I | 1.260 | 0.99 |
| 150_R | 370_E | 1.252 | 0.99 |
| 326_T | 330_I | 1.249 | 0.99 |
| 83_S | 88_P | 1.242 | 0.98 |
| 244_Y | 376_A | 1.240 | 0.98 |
| 35_A | 167_I | 1.238 | 0.98 |
| 38_Y | 161_H | 1.237 | 0.98 |
| 326_T | 424_V | 1.230 | 0.98 |
| 107_G | 183_H | 1.225 | 0.98 |
| 59_G | 405_D | 1.222 | 0.98 |
| 87_N | 91_F | 1.221 | 0.98 |
| 54_Q | 183_H | 1.216 | 0.98 |
| 304_L | 307_W | 1.215 | 0.98 |
| 199_F | 203_M | 1.211 | 0.98 |
| 141_M | 157_W | 1.203 | 0.98 |
| 91_F | 94_A | 1.196 | 0.98 |
| 170_L | 292_F | 1.194 | 0.98 |
| 296_Y | 300_P | 1.194 | 0.98 |
| 200_A | 204_M | 1.193 | 0.98 |
| 418_G | 422_L | 1.192 | 0.98 |
| 308_M | 312_V | 1.190 | 0.98 |
| 66_S | 394_V | 1.180 | 0.98 |
| 100_A | 194_I | 1.176 | 0.98 |
| 212_G | 219_Y | 1.173 | 0.98 |
| 275_Y | 280_K | 1.165 | 0.97 |
| 101_A | 105_F | 1.163 | 0.97 |
| 214_P | 218_E | 1.161 | 0.97 |
| 286_K | 289_W | 1.156 | 0.97 |
| 90_V | 206_D | 1.154 | 0.97 |
| 251_L | 255_A | 1.148 | 0.97 |
| 191_F | 195_L | 1.146 | 0.97 |
| 264_L | 420_S | 1.140 | 0.97 |
| 194_I | 198_L | 1.138 | 0.97 |
| 277_K | 284_L | 1.138 | 0.97 |
| 301_G | 304_L | 1.136 | 0.97 |
| 217_E | 221_N | 1.134 | 0.97 |
| 90_V | 93_P | 1.133 | 0.97 |
| 184_A | 187_Y | 1.129 | 0.97 |
| 50_Y | 53_E | 1.118 | 0.96 |
| 421_I | 425_I | 1.114 | 0.96 |
| 47_A | 177_A | 1.112 | 0.96 |
| 68_I | 123_L | 1.105 | 0.96 |
| 105_F | 118_V | 1.103 | 0.96 |
| 78_I | 81_S | 1.102 | 0.96 |
| 73_G | 386_L | 1.102 | 0.96 |
| 140_T | 204_M | 1.101 | 0.96 |
| 117_A | 120_F | 1.101 | 0.96 |
| 64_A | 116_I | 1.096 | 0.96 |
| 151_G | 306_G | 1.093 | 0.96 |
| 276_L | 282_F | 1.089 | 0.96 |
| 309_S | 363_L | 1.087 | 0.96 |
| 48_M | 61_L | 1.075 | 0.95 |
| 114_S | 183_H | 1.070 | 0.95 |
| 39_L | 168_P | 1.069 | 0.95 |
| 68_I | 130_Q | 1.069 | 0.95 |
| 348_I | 352_V | 1.066 | 0.95 |
| 88_P | 206_D | 1.065 | 0.95 |
| 52_V | 61_L | 1.063 | 0.95 |
| 402_Y | 406_F | 1.059 | 0.95 |
| 77_F | 81_S | 1.058 | 0.95 |
| 246_L | 252_W | 1.056 | 0.95 |
| 123_L | 127_G | 1.053 | 0.95 |
| 342_N | 345_V | 1.048 | 0.94 |
| 47_A | 185_A | 1.048 | 0.94 |
| 93_P | 97_I | 1.047 | 0.94 |
| 252_W | 256_I | 1.044 | 0.94 |
| 336_W | 417_I | 1.036 | 0.94 |
| 108_F | 187_Y | 1.036 | 0.94 |
| 51_L | 182_W | 1.034 | 0.94 |
| 313_F | 318_G | 1.034 | 0.94 |
| 212_G | 215_P | 1.033 | 0.94 |
| 322_V | 424_V | 1.033 | 0.94 |
| 165_G | 295_E | 1.031 | 0.94 |
| 104_L | 187_Y | 1.029 | 0.94 |
| 152_G | 156_V | 1.024 | 0.93 |
| 141_M | 153_I | 1.023 | 0.93 |
| 305_C | 359_G | 1.020 | 0.93 |
| 411_G | 415_V | 1.018 | 0.93 |
| 190_A | 194_I | 1.014 | 0.93 |
| 86_S | 90_V | 1.011 | 0.93 |
| 344_T | 347_M | 1.008 | 0.93 |
| 411_G | 414_M | 1.005 | 0.93 |
| 87_N | 206_D | 1.003 | 0.93 |
| 63_F | 398_A | 1.001 | 0.92 |
| 118_V | 121_V | 1.000 | 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
- 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 | 0.9664 | 100 | 0.219 | Contact Map |
| 4j05A | 2 | 0.8412 | 100 | 0.333 | Contact Map |
| 4gc0A | 1 | 0.9351 | 100 | 0.363 | Contact Map |
| 4d2bA | 1 | 0.8479 | 100 | 0.373 | Contact Map |
| 4pypA | 1 | 0.8926 | 100 | 0.373 | Contact Map |
| 4jr9A | 1 | 0.8143 | 100 | 0.397 | Contact Map |
| 4ikvA | 1 | 0.9485 | 100 | 0.406 | Contact Map |
| 4oh3A | 2 | 0.962 | 100 | 0.41 | Contact Map |
| 4ldsA | 2 | 0.8926 | 100 | 0.412 | Contact Map |
| 4tphA | 2 | 0.8456 | 100 | 0.42 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)