| fivRT |
| ID: | 1494000175 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 558 (394) | ||
| Sequences: | 9204 (7142.8) | ||
| Seq/Len: | 23.360 | ||
| Nf(neff/√len): | 359.8 |
HHblits Results: (2016_02)
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: 23.360).
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 |
| 299_R | 303_Q | 3.809 | 1.00 |
| 295_T | 298_A | 3.588 | 1.00 |
| 48_K | 144_V | 3.089 | 1.00 |
| 48_K | 146_C | 3.013 | 1.00 |
| 249_E | 299_R | 2.856 | 1.00 |
| 193_S | 196_E | 2.755 | 1.00 |
| 39_E | 43_R | 2.723 | 1.00 |
| 124_A | 146_C | 2.632 | 1.00 |
| 190_S | 200_K | 2.599 | 1.00 |
| 263_I | 273_L | 2.526 | 1.00 |
| 85_K | 153_I | 2.425 | 1.00 |
| 123_Y | 126_Y | 2.329 | 1.00 |
| 294_W | 299_R | 2.325 | 1.00 |
| 61_F | 73_L | 2.292 | 1.00 |
| 78_E | 81_K | 2.172 | 1.00 |
| 169_P | 207_L | 2.166 | 1.00 |
| 318_Y | 324_L | 2.129 | 1.00 |
| 125_P | 144_V | 2.123 | 1.00 |
| 48_K | 124_A | 2.114 | 1.00 |
| 178_D | 200_K | 2.110 | 1.00 |
| 37_I | 40_R | 2.082 | 1.00 |
| 319_D | 322_K | 2.081 | 1.00 |
| 42_E | 47_V | 2.020 | 1.00 |
| 304_K | 308_A | 1.986 | 1.00 |
| 252_T | 255_E | 1.984 | 1.00 |
| 40_R | 44_E | 1.963 | 1.00 |
| 120_D | 123_Y | 1.927 | 1.00 |
| 32_E | 36_E | 1.908 | 1.00 |
| 347_K | 350_W | 1.898 | 1.00 |
| 362_E | 370_R | 1.897 | 1.00 |
| 353_K | 359_K | 1.892 | 1.00 |
| 227_T | 232_E | 1.883 | 1.00 |
| 206_K | 210_W | 1.753 | 1.00 |
| 33_A | 37_I | 1.751 | 1.00 |
| 45_G | 146_C | 1.744 | 1.00 |
| 190_S | 197_H | 1.717 | 1.00 |
| 33_A | 36_E | 1.699 | 1.00 |
| 333_P | 367_I | 1.691 | 1.00 |
| 225_P | 232_E | 1.682 | 1.00 |
| 327_K | 341_Y | 1.681 | 1.00 |
| 119_L | 127_T | 1.674 | 1.00 |
| 251_P | 255_E | 1.668 | 1.00 |
| 26_L | 34_L | 1.662 | 1.00 |
| 336_I | 355_S | 1.653 | 1.00 |
| 357_Q | 360_K | 1.646 | 1.00 |
| 234_H | 237_T | 1.636 | 1.00 |
| 27_T | 30_K | 1.607 | 1.00 |
| 86_G | 161_S | 1.600 | 1.00 |
| 296_K | 300_L | 1.558 | 1.00 |
| 191_N | 196_E | 1.548 | 1.00 |
| 106_T | 197_H | 1.528 | 1.00 |
| 9_K | 120_D | 1.526 | 1.00 |
| 202_E | 206_K | 1.510 | 1.00 |
| 35_T | 140_G | 1.510 | 1.00 |
| 102_K | 189_G | 1.504 | 1.00 |
| 196_E | 200_K | 1.496 | 1.00 |
| 124_A | 144_V | 1.492 | 1.00 |
| 113_A | 159_Y | 1.491 | 1.00 |
| 91_L | 164_D | 1.480 | 1.00 |
| 276_K | 280_N | 1.476 | 1.00 |
| 414_E | 417_Y | 1.473 | 1.00 |
| 8_V | 158_I | 1.459 | 1.00 |
| 359_K | 362_E | 1.453 | 1.00 |
| 320_P | 324_L | 1.452 | 1.00 |
| 300_L | 304_K | 1.451 | 1.00 |
| 201_V | 205_R | 1.436 | 1.00 |
| 234_H | 239_T | 1.408 | 1.00 |
| 42_E | 49_R | 1.395 | 0.99 |
| 322_K | 343_K | 1.395 | 0.99 |
| 167_I | 179_I | 1.391 | 0.99 |
| 148_L | 158_I | 1.389 | 0.99 |
| 357_Q | 361_A | 1.388 | 0.99 |
| 259_L | 263_I | 1.386 | 0.99 |
| 152_W | 155_S | 1.378 | 0.99 |
| 148_L | 155_S | 1.371 | 0.99 |
| 253_L | 257_Q | 1.363 | 0.99 |
| 326_A | 329_S | 1.356 | 0.99 |
| 243_K | 246_D | 1.352 | 0.99 |
| 225_P | 234_H | 1.340 | 0.99 |
| 132_P | 140_G | 1.322 | 0.99 |
| 166_I | 211_W | 1.316 | 0.99 |
| 121_P | 124_A | 1.315 | 0.99 |
| 225_P | 239_T | 1.314 | 0.99 |
| 170_F | 207_L | 1.314 | 0.99 |
| 280_N | 297_E | 1.311 | 0.99 |
| 303_Q | 306_K | 1.310 | 0.99 |
| 160_Q | 164_D | 1.310 | 0.99 |
| 47_V | 129_F | 1.309 | 0.99 |
| 73_L | 150_Q | 1.301 | 0.99 |
| 364_T | 367_I | 1.300 | 0.99 |
| 227_T | 243_K | 1.300 | 0.99 |
| 60_V | 72_M | 1.294 | 0.99 |
| 356_R | 359_K | 1.288 | 0.99 |
| 264_N | 273_L | 1.280 | 0.99 |
| 358_K | 361_A | 1.275 | 0.99 |
| 115_F | 145_W | 1.274 | 0.99 |
| 194_K | 198_K | 1.274 | 0.99 |
| 62_A | 70_W | 1.272 | 0.99 |
| 307_K | 311_E | 1.268 | 0.99 |
| 49_R | 141_R | 1.266 | 0.99 |
| 280_N | 283_R | 1.264 | 0.99 |
| 131_L | 141_R | 1.260 | 0.99 |
| 241_Q | 244_Q | 1.259 | 0.99 |
| 199_E | 203_E | 1.257 | 0.99 |
| 358_K | 362_E | 1.254 | 0.99 |
| 304_K | 307_K | 1.252 | 0.99 |
| 59_P | 78_E | 1.247 | 0.99 |
| 115_F | 150_Q | 1.245 | 0.98 |
| 37_I | 41_L | 1.244 | 0.98 |
| 42_E | 143_F | 1.232 | 0.98 |
| 208_L | 215_T | 1.232 | 0.98 |
| 64_K | 70_W | 1.230 | 0.98 |
| 154_L | 157_L | 1.218 | 0.98 |
| 163_L | 181_Q | 1.210 | 0.98 |
| 254_N | 257_Q | 1.201 | 0.98 |
| 180_Y | 189_G | 1.198 | 0.98 |
| 227_T | 241_Q | 1.191 | 0.98 |
| 257_Q | 261_G | 1.190 | 0.98 |
| 101_I | 191_N | 1.189 | 0.98 |
| 216_P | 219_K | 1.183 | 0.98 |
| 298_A | 301_E | 1.176 | 0.98 |
| 264_N | 267_S | 1.176 | 0.98 |
| 107_V | 221_Q | 1.166 | 0.97 |
| 108_L | 215_T | 1.166 | 0.97 |
| 119_L | 124_A | 1.165 | 0.97 |
| 224_P | 235_P | 1.164 | 0.97 |
| 46_K | 147_S | 1.154 | 0.97 |
| 131_L | 140_G | 1.153 | 0.97 |
| 323_E | 343_K | 1.153 | 0.97 |
| 252_T | 292_R | 1.152 | 0.97 |
| 279_T | 282_M | 1.137 | 0.97 |
| 302_V | 306_K | 1.133 | 0.97 |
| 203_E | 206_K | 1.132 | 0.97 |
| 292_R | 298_A | 1.130 | 0.97 |
| 57_N | 130_T | 1.129 | 0.97 |
| 277_A | 301_E | 1.129 | 0.97 |
| 167_I | 204_L | 1.128 | 0.97 |
| 360_K | 367_I | 1.126 | 0.97 |
| 63_I | 73_L | 1.125 | 0.97 |
| 76_F | 79_L | 1.125 | 0.97 |
| 35_T | 39_E | 1.124 | 0.97 |
| 119_L | 123_Y | 1.124 | 0.97 |
| 401_N | 405_S | 1.123 | 0.97 |
| 127_T | 145_W | 1.122 | 0.97 |
| 112_D | 115_F | 1.120 | 0.96 |
| 181_Q | 186_I | 1.118 | 0.96 |
| 362_E | 366_D | 1.116 | 0.96 |
| 104_Q | 194_K | 1.115 | 0.96 |
| 336_I | 353_K | 1.114 | 0.96 |
| 353_K | 356_R | 1.106 | 0.96 |
| 281_M | 285_N | 1.104 | 0.96 |
| 281_M | 298_A | 1.104 | 0.96 |
| 75_D | 80_N | 1.103 | 0.96 |
| 374_K | 378_E | 1.101 | 0.96 |
| 368_A | 371_A | 1.100 | 0.96 |
| 366_D | 369_L | 1.095 | 0.96 |
| 232_E | 242_Q | 1.093 | 0.96 |
| 127_T | 152_W | 1.092 | 0.96 |
| 363_N | 366_D | 1.092 | 0.96 |
| 163_L | 167_I | 1.092 | 0.96 |
| 128_A | 142_R | 1.088 | 0.96 |
| 279_T | 283_R | 1.085 | 0.96 |
| 351_Y | 378_E | 1.084 | 0.96 |
| 110_I | 116_T | 1.080 | 0.95 |
| 382_R | 387_P | 1.076 | 0.95 |
| 379_S | 383_I | 1.073 | 0.95 |
| 196_E | 199_E | 1.071 | 0.95 |
| 386_E | 406_P | 1.069 | 0.95 |
| 364_T | 368_A | 1.068 | 0.95 |
| 170_F | 178_D | 1.068 | 0.95 |
| 128_A | 144_V | 1.063 | 0.95 |
| 30_K | 70_W | 1.060 | 0.95 |
| 270_I | 273_L | 1.060 | 0.95 |
| 338_Y | 374_K | 1.054 | 0.95 |
| 275_I | 279_T | 1.053 | 0.95 |
| 109_D | 114_Y | 1.051 | 0.94 |
| 40_R | 43_R | 1.046 | 0.94 |
| 178_D | 203_E | 1.045 | 0.94 |
| 31_I | 35_T | 1.044 | 0.94 |
| 41_L | 145_W | 1.040 | 0.94 |
| 46_K | 145_W | 1.040 | 0.94 |
| 55_P | 125_P | 1.038 | 0.94 |
| 259_L | 302_V | 1.030 | 0.94 |
| 275_I | 305_A | 1.025 | 0.93 |
| 167_I | 181_Q | 1.024 | 0.93 |
| 83_T | 154_L | 1.023 | 0.93 |
| 78_E | 82_L | 1.021 | 0.93 |
| 207_L | 210_W | 1.020 | 0.93 |
| 255_E | 258_K | 1.019 | 0.93 |
| 326_A | 382_R | 1.018 | 0.93 |
| 33_A | 70_W | 1.016 | 0.93 |
| 34_L | 60_V | 1.015 | 0.93 |
| 331_V | 335_Q | 1.015 | 0.93 |
| 197_H | 201_V | 1.010 | 0.93 |
| 114_Y | 156_P | 1.009 | 0.93 |
| 41_L | 46_K | 1.005 | 0.93 |
| 373_Y | 376_R | 1.002 | 0.92 |
| 329_S | 337_S | 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 | |
| 1mu2A | 1 | 0.948 | 100 | 0.163 | Contact Map |
| 4g1qA | 1 | 0.9713 | 100 | 0.175 | Contact Map |
| 4mh8A | 1 | 0.7276 | 100 | 0.214 | Contact Map |
| 4g1qB | 1 | 0.733 | 100 | 0.345 | Contact Map |
| 4ol8A | 4 | 0.7097 | 100 | 0.397 | Contact Map |
| 4xpcA | 1 | 0 | 100 | 0.606 | Contact Map |
| 3qioA | 1 | 0.2294 | 99.9 | 0.812 | Contact Map |
| 3p1gA | 1 | 0.2455 | 99.9 | 0.818 | Contact Map |
| 2e4lA | 1 | 0.2168 | 99.9 | 0.824 | Contact Map |
| 1rilA | 1 | 0.2168 | 99.8 | 0.824 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)