| 1DGWX |
| ID: | 1411608651 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 76 (73) | ||
| Sequences: | 1424 (827.8) | ||
| Seq/Len: | 19.507 | ||
| Nf(neff/√len): | 96.9 |
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: 19.507).
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 |
| 52_H | 59_V | 2.425 | 1.00 |
| 54_N | 59_V | 2.350 | 1.00 |
| 63_A | 68_A | 1.923 | 1.00 |
| 5_N | 8_S | 1.863 | 1.00 |
| 24_T | 27_K | 1.830 | 1.00 |
| 4_F | 7_R | 1.790 | 1.00 |
| 43_M | 68_A | 1.740 | 1.00 |
| 23_I | 28_N | 1.630 | 1.00 |
| 6_L | 9_R | 1.576 | 1.00 |
| 63_A | 66_G | 1.566 | 1.00 |
| 6_L | 23_I | 1.494 | 1.00 |
| 41_L | 68_A | 1.461 | 1.00 |
| 50_V | 71_E | 1.449 | 1.00 |
| 4_F | 8_S | 1.407 | 0.99 |
| 52_H | 55_S | 1.374 | 0.99 |
| 31_L | 60_I | 1.287 | 0.99 |
| 4_F | 9_R | 1.272 | 0.99 |
| 30_Q | 33_D | 1.246 | 0.98 |
| 18_G | 49_F | 1.240 | 0.98 |
| 55_S | 59_V | 1.216 | 0.98 |
| 3_P | 7_R | 1.210 | 0.98 |
| 24_T | 73_V | 1.202 | 0.98 |
| 3_P | 6_L | 1.201 | 0.98 |
| 49_F | 53_Y | 1.178 | 0.98 |
| 36_I | 58_T | 1.176 | 0.98 |
| 18_G | 48_L | 1.123 | 0.97 |
| 4_F | 23_I | 1.120 | 0.96 |
| 20_L | 39_N | 1.115 | 0.96 |
| 46_G | 67_R | 1.113 | 0.96 |
| 25_P | 37_L | 1.107 | 0.96 |
| 36_I | 49_F | 1.086 | 0.96 |
| 37_L | 41_L | 1.082 | 0.96 |
| 61_L | 70_V | 1.063 | 0.95 |
| 43_M | 57_A | 1.055 | 0.95 |
| 21_Y | 40_C | 1.045 | 0.94 |
| 48_L | 51_P | 1.026 | 0.94 |
| 38_L | 60_I | 1.022 | 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 | |
| 1dgwX | 1 | 1 | 99.6 | 0.045 | Contact Map |
| 3s7iA | 2 | 1 | 99.4 | 0.118 | Contact Map |
| 4lejA | 1 | 1 | 99.4 | 0.13 | Contact Map |
| 2ea7A | 3 | 1 | 99.4 | 0.14 | Contact Map |
| 2cavA | 1 | 0.9868 | 99.4 | 0.16 | Contact Map |
| 1uijA | 6 | 1 | 99.4 | 0.161 | Contact Map |
| 2e9qA | 1 | 1 | 99.3 | 0.18 | Contact Map |
| 3kscA | 6 | 1 | 99.3 | 0.18 | Contact Map |
| 3kglA | 6 | 1 | 99.3 | 0.184 | Contact Map |
| 3c3vA | 1 | 1 | 99.3 | 0.194 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)