| 4euu gremlin |
| ID: | 1516522185 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 306 (289) | ||
| Sequences: | 13301 (7774.7) | ||
| Seq/Len: | 46.024 | ||
| Nf(neff/√len): | 457.3 |
HHblits Results: (2016_02)
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 |
| 116_L | 211_F | 4.657 | 1.00 |
| 286_E | 291_K | 4.039 | 1.00 |
| 142_M | 156_T | 3.974 | 1.00 |
| 13_D | 25_R | 3.579 | 1.00 |
| 25_R | 34_L | 3.545 | 1.00 |
| 283_N | 293_W | 3.238 | 1.00 |
| 123_M | 207_I | 3.187 | 1.00 |
| 26_G | 35_F | 3.142 | 1.00 |
| 26_G | 37_I | 2.998 | 1.00 |
| 28_H | 31_T | 2.959 | 1.00 |
| 63_N | 69_K | 2.919 | 1.00 |
| 122_G | 155_L | 2.913 | 1.00 |
| 136_I | 210_T | 2.760 | 1.00 |
| 204_L | 284_I | 2.740 | 1.00 |
| 120_V | 207_I | 2.698 | 1.00 |
| 288_D | 291_K | 2.683 | 1.00 |
| 37_I | 85_I | 2.612 | 1.00 |
| 87_E | 154_K | 2.598 | 1.00 |
| 14_I | 22_N | 2.579 | 1.00 |
| 124_N | 128_E | 2.573 | 1.00 |
| 95_Y | 139_G | 2.431 | 1.00 |
| 27_R | 34_L | 2.306 | 1.00 |
| 116_L | 207_I | 2.291 | 1.00 |
| 14_I | 17_Q | 2.272 | 1.00 |
| 64_H | 125_H | 2.233 | 1.00 |
| 112_F | 215_A | 2.114 | 1.00 |
| 25_R | 88_F | 2.095 | 1.00 |
| 137_K | 176_T | 2.083 | 1.00 |
| 71_F | 87_E | 2.075 | 1.00 |
| 33_D | 71_F | 2.071 | 1.00 |
| 141_I | 153_Y | 2.065 | 1.00 |
| 12_S | 27_R | 2.011 | 1.00 |
| 14_I | 24_F | 1.976 | 1.00 |
| 175_G | 180_L | 1.919 | 1.00 |
| 141_I | 210_T | 1.902 | 1.00 |
| 135_D | 140_N | 1.873 | 1.00 |
| 181_H | 202_V | 1.800 | 1.00 |
| 27_R | 32_G | 1.787 | 1.00 |
| 118_D | 153_Y | 1.782 | 1.00 |
| 69_K | 87_E | 1.777 | 1.00 |
| 108_P | 111_E | 1.771 | 1.00 |
| 23_V | 36_A | 1.767 | 1.00 |
| 109_E | 270_S | 1.729 | 1.00 |
| 211_F | 280_V | 1.727 | 1.00 |
| 117_R | 121_G | 1.717 | 1.00 |
| 10_L | 29_K | 1.705 | 1.00 |
| 66_N | 121_G | 1.695 | 1.00 |
| 213_H | 219_L | 1.679 | 1.00 |
| 179_Y | 213_H | 1.640 | 1.00 |
| 93_S | 96_T | 1.634 | 1.00 |
| 119_V | 141_I | 1.632 | 1.00 |
| 24_F | 39_V | 1.614 | 1.00 |
| 115_V | 153_Y | 1.586 | 1.00 |
| 233_V | 237_I | 1.580 | 1.00 |
| 70_L | 84_L | 1.576 | 1.00 |
| 279_P | 283_N | 1.564 | 1.00 |
| 283_N | 286_E | 1.556 | 1.00 |
| 181_H | 184_M | 1.532 | 1.00 |
| 131_I | 161_A | 1.528 | 1.00 |
| 61_K | 163_E | 1.510 | 1.00 |
| 123_M | 136_I | 1.509 | 1.00 |
| 138_P | 179_Y | 1.490 | 1.00 |
| 124_N | 296_D | 1.488 | 1.00 |
| 58_V | 161_A | 1.483 | 1.00 |
| 136_I | 155_L | 1.478 | 1.00 |
| 109_E | 274_Q | 1.462 | 1.00 |
| 119_V | 153_Y | 1.462 | 1.00 |
| 201_T | 294_G | 1.451 | 1.00 |
| 198_Y | 202_V | 1.434 | 1.00 |
| 35_F | 71_F | 1.430 | 1.00 |
| 68_V | 86_M | 1.425 | 1.00 |
| 89_C | 154_K | 1.414 | 1.00 |
| 28_H | 33_D | 1.401 | 0.99 |
| 125_H | 129_N | 1.390 | 0.99 |
| 12_S | 25_R | 1.371 | 0.99 |
| 135_D | 159_G | 1.371 | 0.99 |
| 10_L | 27_R | 1.369 | 0.99 |
| 35_F | 85_I | 1.358 | 0.99 |
| 212_Y | 216_T | 1.350 | 0.99 |
| 137_K | 140_N | 1.326 | 0.99 |
| 215_A | 273_L | 1.318 | 0.99 |
| 209_V | 219_L | 1.309 | 0.99 |
| 67_I | 126_L | 1.304 | 0.99 |
| 112_F | 214_A | 1.295 | 0.99 |
| 280_V | 284_I | 1.293 | 0.99 |
| 208_G | 284_I | 1.282 | 0.99 |
| 134_R | 174_Y | 1.280 | 0.99 |
| 118_D | 150_Q | 1.277 | 0.99 |
| 11_L | 24_F | 1.273 | 0.99 |
| 95_Y | 99_E | 1.270 | 0.99 |
| 39_V | 83_V | 1.270 | 0.99 |
| 89_C | 142_M | 1.263 | 0.99 |
| 204_L | 295_F | 1.249 | 0.99 |
| 59_L | 70_L | 1.213 | 0.98 |
| 90_P | 147_E | 1.211 | 0.98 |
| 68_V | 89_C | 1.198 | 0.98 |
| 61_K | 129_N | 1.197 | 0.98 |
| 42_N | 75_E | 1.192 | 0.98 |
| 97_V | 107_L | 1.186 | 0.98 |
| 62_L | 125_H | 1.186 | 0.98 |
| 62_L | 126_L | 1.184 | 0.98 |
| 98_L | 213_H | 1.179 | 0.98 |
| 121_G | 124_N | 1.156 | 0.97 |
| 59_L | 86_M | 1.148 | 0.97 |
| 130_G | 200_A | 1.145 | 0.97 |
| 114_I | 118_D | 1.143 | 0.97 |
| 18_G | 21_A | 1.140 | 0.97 |
| 16_G | 23_V | 1.136 | 0.97 |
| 34_L | 88_F | 1.133 | 0.97 |
| 293_W | 297_Q | 1.131 | 0.97 |
| 95_Y | 213_H | 1.125 | 0.97 |
| 26_G | 85_I | 1.121 | 0.97 |
| 93_S | 139_G | 1.119 | 0.96 |
| 119_V | 210_T | 1.099 | 0.96 |
| 34_L | 90_P | 1.096 | 0.96 |
| 74_E | 85_I | 1.096 | 0.96 |
| 68_V | 156_T | 1.094 | 0.96 |
| 37_I | 83_V | 1.093 | 0.96 |
| 294_G | 297_Q | 1.087 | 0.96 |
| 65_K | 121_G | 1.087 | 0.96 |
| 270_S | 274_Q | 1.081 | 0.95 |
| 110_S | 113_L | 1.066 | 0.95 |
| 123_M | 127_R | 1.061 | 0.95 |
| 119_V | 122_G | 1.048 | 0.94 |
| 64_H | 67_I | 1.042 | 0.94 |
| 109_E | 112_F | 1.042 | 0.94 |
| 284_I | 293_W | 1.042 | 0.94 |
| 146_G | 150_Q | 1.039 | 0.94 |
| 283_N | 297_Q | 1.025 | 0.93 |
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 | |
| 4im0A | 1 | 0.915 | 100 | 0.076 | Contact Map |
| 4euuA | 2 | 0.9967 | 100 | 0.098 | Contact Map |
| 4kikA | 2 | 0.9412 | 100 | 0.192 | Contact Map |
| 4ic7A | 2 | 0.9248 | 100 | 0.224 | Contact Map |
| 3utoA | 2 | 0.8693 | 100 | 0.228 | Contact Map |
| 4aojA | 3 | 0.8203 | 100 | 0.236 | Contact Map |
| 4aszA | 1 | 0.8464 | 100 | 0.236 | Contact Map |
| 3zonA | 1 | 0.8268 | 100 | 0.236 | Contact Map |
| 5a46A | 2 | 0 | 100 | 0.236 | Contact Map |
| 4qoxA | 1 | 0.8529 | 100 | 0.237 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)