| MSA |
| ID: | 1518194222 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 73 (73) | ||
| Sequences: | 1133 (816.6) | ||
| Seq/Len: | 15.521 | ||
| Nf(neff/√len): | 95.6 |
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: 15.521).
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 |
| 28_K | 47_L | 2.941 | 1.00 |
| 15_G | 18_D | 2.078 | 1.00 |
| 33_K | 43_V | 2.058 | 1.00 |
| 34_T | 40_V | 2.057 | 1.00 |
| 64_K | 67_E | 2.012 | 1.00 |
| 41_N | 60_H | 1.969 | 1.00 |
| 62_W | 69_F | 1.863 | 1.00 |
| 64_K | 69_F | 1.799 | 1.00 |
| 9_A | 26_P | 1.725 | 1.00 |
| 16_I | 59_V | 1.700 | 1.00 |
| 41_N | 73_N | 1.684 | 1.00 |
| 11_K | 72_F | 1.658 | 1.00 |
| 4_E | 63_E | 1.645 | 1.00 |
| 31_N | 45_E | 1.618 | 1.00 |
| 15_G | 72_F | 1.602 | 1.00 |
| 26_P | 46_V | 1.571 | 1.00 |
| 32_A | 44_F | 1.531 | 1.00 |
| 24_M | 57_Y | 1.512 | 1.00 |
| 27_V | 49_G | 1.397 | 0.99 |
| 30_L | 56_I | 1.394 | 0.99 |
| 46_V | 59_V | 1.378 | 0.99 |
| 9_A | 44_F | 1.377 | 0.99 |
| 16_I | 20_N | 1.354 | 0.99 |
| 38_A | 64_K | 1.353 | 0.99 |
| 41_N | 62_W | 1.348 | 0.99 |
| 5_Y | 32_A | 1.315 | 0.99 |
| 48_F | 57_Y | 1.305 | 0.99 |
| 48_F | 59_V | 1.220 | 0.98 |
| 2_D | 6_M | 1.201 | 0.98 |
| 63_E | 70_E | 1.170 | 0.97 |
| 22_G | 50_E | 1.157 | 0.97 |
| 40_V | 65_P | 1.153 | 0.97 |
| 24_M | 48_F | 1.144 | 0.97 |
| 9_A | 46_V | 1.129 | 0.97 |
| 13_A | 48_F | 1.066 | 0.95 |
| 39_G | 66_W | 1.038 | 0.94 |
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 | |
| 2l4vA | 1 | 1 | 99.7 | 0.04 | Contact Map |
| 3ul5A | 4 | 1 | 99.7 | 0.051 | Contact Map |
| 3imaB | 2 | 0.9863 | 99.7 | 0.053 | Contact Map |
| 1eqkA | 1 | 1 | 99.7 | 0.064 | Contact Map |
| 4n6tA | 1 | 1 | 99.7 | 0.068 | Contact Map |
| 4lziA | 1 | 1 | 99.7 | 0.079 | Contact Map |
| 5a0oB | 2 | 0 | 99.6 | 0.121 | Contact Map |
| 3gaxA | 2 | 1 | 99.6 | 0.146 | Contact Map |
| 4n6oB | 1 | 1 | 99.6 | 0.146 | Contact Map |
| 2ch9A | 1 | 1 | 99.6 | 0.147 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)