| d3glxa1 |
| ID: | 1449072417 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 59 (59) | ||
| Sequences: | 2040 (1356.5) | ||
| Seq/Len: | 34.576 | ||
| Nf(neff/√len): | 176.6 |
HHblits Results: (2015_06)
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: 34.576).
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 |
| 3_T | 46_D | 2.966 | 1.00 |
| 38_Q | 42_R | 2.226 | 1.00 |
| 2_T | 35_T | 2.060 | 1.00 |
| 50_V | 58_Q | 2.037 | 1.00 |
| 31_Q | 36_V | 1.971 | 1.00 |
| 4_E | 8_R | 1.963 | 1.00 |
| 5_M | 8_R | 1.896 | 1.00 |
| 22_R | 36_V | 1.855 | 1.00 |
| 44_E | 51_V | 1.819 | 1.00 |
| 25_I | 40_V | 1.769 | 1.00 |
| 12_E | 28_R | 1.667 | 1.00 |
| 10_I | 49_V | 1.644 | 1.00 |
| 9_T | 28_R | 1.622 | 1.00 |
| 35_T | 39_T | 1.615 | 1.00 |
| 9_T | 25_I | 1.453 | 1.00 |
| 1_D | 5_M | 1.375 | 0.99 |
| 40_V | 49_V | 1.359 | 0.99 |
| 3_T | 8_R | 1.228 | 0.98 |
| 5_M | 38_Q | 1.228 | 0.98 |
| 23_A | 33_G | 1.213 | 0.98 |
| 16_E | 28_R | 1.196 | 0.98 |
| 51_V | 54_D | 1.178 | 0.98 |
| 22_R | 37_S | 1.100 | 0.96 |
| 40_V | 57_L | 1.094 | 0.96 |
| 3_T | 39_T | 1.071 | 0.95 |
| 23_A | 55_R | 1.059 | 0.95 |
| 22_R | 40_V | 1.048 | 0.94 |
| 14_E | 20_P | 1.023 | 0.93 |
| 17_G | 54_D | 1.022 | 0.93 |
| 43_M | 48_L | 1.017 | 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 | |
| 3hrsA | 2 | 1 | 98.9 | 0.309 | Contact Map |
| 2p8tA | 1 | 0.8983 | 98.9 | 0.313 | Contact Map |
| 4o5vA | 1 | 1 | 98.8 | 0.317 | Contact Map |
| 1fx7A | 4 | 1 | 98.8 | 0.323 | Contact Map |
| 2qq9A | 1 | 1 | 98.8 | 0.325 | Contact Map |
| 1on2A | 2 | 1 | 98.6 | 0.374 | Contact Map |
| 2h09A | 1 | 1 | 98.3 | 0.42 | Contact Map |
| 2x4hA | 4 | 0.9831 | 98.2 | 0.439 | Contact Map |
| 2qvoA | 1 | 1 | 97.6 | 0.512 | Contact Map |
| 1mkmA | 2 | 1 | 97.6 | 0.514 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)