| test 1SHF |
| ID: | 1415358822 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 59 (57) | ||
| Sequences: | 4451 (2650.9) | ||
| Seq/Len: | 78.088 | ||
| Nf(neff/√len): | 351.1 |
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: 78.088).
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 |
| 12_A | 19_S | 3.624 | 1.00 |
| 39_A | 50_I | 3.482 | 1.00 |
| 30_N | 38_E | 2.778 | 1.00 |
| 27_Q | 40_R | 2.708 | 1.00 |
| 38_E | 47_T | 2.637 | 1.00 |
| 9_D | 21_H | 2.354 | 1.00 |
| 6_A | 20_F | 2.326 | 1.00 |
| 24_E | 41_S | 2.300 | 1.00 |
| 40_R | 47_T | 2.290 | 1.00 |
| 50_I | 55_V | 2.200 | 1.00 |
| 20_F | 26_F | 1.905 | 1.00 |
| 41_S | 44_T | 1.847 | 1.00 |
| 5_V | 56_A | 1.841 | 1.00 |
| 4_F | 57_P | 1.694 | 1.00 |
| 3_L | 27_Q | 1.678 | 1.00 |
| 26_F | 39_A | 1.523 | 1.00 |
| 5_V | 25_K | 1.505 | 1.00 |
| 37_W | 52_S | 1.448 | 1.00 |
| 41_S | 46_E | 1.442 | 1.00 |
| 3_L | 25_K | 1.441 | 1.00 |
| 9_D | 22_K | 1.340 | 0.99 |
| 4_F | 55_V | 1.334 | 0.99 |
| 2_T | 31_S | 1.303 | 0.99 |
| 31_S | 57_P | 1.217 | 0.98 |
| 21_H | 24_E | 1.169 | 0.97 |
| 4_F | 28_I | 1.105 | 0.96 |
| 38_E | 49_Y | 1.105 | 0.96 |
| 10_Y | 13_R | 1.000 | 0.92 |
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 | |
| 4n78F | 1 | 0 | 99.3 | -0.085 | Contact Map |
| 1fmkA | 1 | 1 | 99.3 | -0.053 | Contact Map |
| 1ri9A | 1 | 0.9492 | 99.3 | -0.046 | Contact Map |
| 1mv3A | 1 | 1 | 99.3 | -0.044 | Contact Map |
| 2de0X | 1 | 1 | 99.3 | -0.043 | Contact Map |
| 2h8hA | 1 | 0.9661 | 99.2 | -0.029 | Contact Map |
| 4mt7A | 1 | 0 | 99.2 | -0.02 | Contact Map |
| 1bb9A | 1 | 1 | 99.2 | -0.014 | Contact Map |
| 3jv3A | 2 | 0.9661 | 99.2 | -0.012 | Contact Map |
| 1k9aA | 6 | 0.9831 | 99.2 | -0.011 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)