| Witold Dyrka -force run |
| ID: | 1504789081 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 166 (151) | ||
| Sequences: | 67 (39.5) | ||
| Seq/Len: | 0.444 | ||
| Nf(neff/√len): | 3.2 |
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: 0.444).
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 |
| 14_E | 131_E | 2.257 | 0.91 |
| 38_K | 44_G | 1.808 | 0.74 |
| 115_R | 118_S | 1.686 | 0.66 |
| 30_C | 43_L | 1.651 | 0.64 |
| 110_F | 156_D | 1.613 | 0.61 |
| 124_L | 127_L | 1.546 | 0.56 |
| 32_E | 103_A | 1.495 | 0.52 |
| 38_K | 155_E | 1.493 | 0.52 |
| 88_I | 155_E | 1.473 | 0.51 |
| 30_C | 66_P | 1.456 | 0.49 |
| 34_K | 132_Q | 1.431 | 0.47 |
| 30_C | 154_D | 1.401 | 0.45 |
| 37_K | 122_K | 1.391 | 0.45 |
| 28_K | 32_E | 1.382 | 0.44 |
| 149_D | 156_D | 1.369 | 0.43 |
| 55_E | 70_L | 1.352 | 0.42 |
| 13_L | 122_K | 1.345 | 0.41 |
| 131_E | 154_D | 1.330 | 0.40 |
| 40_C | 136_V | 1.327 | 0.40 |
| 51_I | 57_L | 1.326 | 0.40 |
| 99_R | 119_D | 1.323 | 0.40 |
| 42_R | 110_F | 1.315 | 0.39 |
| 15_N | 112_D | 1.314 | 0.39 |
| 37_K | 99_R | 1.312 | 0.39 |
| 31_E | 113_V | 1.298 | 0.38 |
| 36_C | 76_R | 1.291 | 0.37 |
| 70_L | 99_R | 1.280 | 0.37 |
| 131_E | 161_Q | 1.280 | 0.37 |
| 36_C | 39_Q | 1.276 | 0.36 |
| 20_I | 90_K | 1.257 | 0.35 |
| 43_L | 51_I | 1.229 | 0.33 |
| 33_M | 77_F | 1.222 | 0.33 |
| 28_K | 41_R | 1.219 | 0.32 |
| 14_E | 154_D | 1.197 | 0.31 |
| 80_A | 120_V | 1.196 | 0.31 |
| 29_R | 36_C | 1.183 | 0.30 |
| 52_K | 104_S | 1.181 | 0.30 |
| 50_L | 114_N | 1.180 | 0.30 |
| 52_K | 118_S | 1.178 | 0.30 |
| 51_I | 83_E | 1.158 | 0.29 |
| 34_K | 47_V | 1.157 | 0.29 |
| 114_N | 129_Q | 1.151 | 0.28 |
| 84_A | 155_E | 1.151 | 0.28 |
| 36_C | 57_L | 1.150 | 0.28 |
| 53_P | 141_Q | 1.147 | 0.28 |
| 151_Q | 155_E | 1.142 | 0.28 |
| 103_A | 139_I | 1.136 | 0.27 |
| 78_K | 85_N | 1.135 | 0.27 |
| 108_I | 140_S | 1.135 | 0.27 |
| 103_A | 134_M | 1.133 | 0.27 |
| 75_N | 160_F | 1.123 | 0.26 |
| 141_Q | 144_S | 1.123 | 0.26 |
| 97_I | 141_Q | 1.122 | 0.26 |
| 84_A | 101_L | 1.107 | 0.26 |
| 34_K | 77_F | 1.102 | 0.25 |
| 110_F | 149_D | 1.094 | 0.25 |
| 66_P | 76_R | 1.092 | 0.25 |
| 33_M | 115_R | 1.088 | 0.25 |
| 33_M | 145_W | 1.083 | 0.24 |
| 19_I | 122_K | 1.073 | 0.24 |
| 82_E | 101_L | 1.068 | 0.23 |
| 78_K | 99_R | 1.066 | 0.23 |
| 88_I | 163_L | 1.060 | 0.23 |
| 47_V | 97_I | 1.059 | 0.23 |
| 19_I | 61_G | 1.055 | 0.23 |
| 83_E | 130_V | 1.051 | 0.23 |
| 76_R | 136_V | 1.045 | 0.22 |
| 41_R | 47_V | 1.040 | 0.22 |
| 19_I | 32_E | 1.039 | 0.22 |
| 113_V | 137_S | 1.032 | 0.22 |
| 23_G | 121_W | 1.017 | 0.21 |
| 53_P | 58_Q | 1.016 | 0.21 |
| 85_N | 136_V | 1.016 | 0.21 |
| 116_K | 148_E | 1.009 | 0.20 |
| 35_Y | 47_V | 1.007 | 0.20 |
| 49_G | 150_Q | 1.001 | 0.20 |
| 29_R | 76_R | 1.000 | 0.20 |
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 | |
| 2msvA | 1 | 0.9277 | 100 | 0.372 | Contact Map |
| 4btfA | 1 | 0.753 | 100 | 0.585 | Contact Map |
| 4dgwA | 1 | 0.741 | 93.4 | 0.914 | Contact Map |
| 3rfyA | 1 | 0.7349 | 93.2 | 0.914 | Contact Map |
| 1y9jA | 1 | 0.6807 | 90.1 | 0.921 | Contact Map |
| 1vptA | 1 | 0.7771 | 89.1 | 0.923 | Contact Map |
| 1u60A | 4 | 0.3373 | 71.3 | 0.936 | Contact Map |
| 2wvqA | 2 | 0.8313 | 41 | 0.947 | Contact Map |
| 4bqmA | 2 | 0.3072 | 31.3 | 0.95 | Contact Map |
| 4bex1 | 1 | 0.6566 | 27.5 | 0.952 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)