| hGR Question Mark Increase Iter |
| ID: | 1478536026 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 56 (55) | ||
| Sequences: | 61 (44.4) | ||
| Seq/Len: | 1.109 | ||
| Nf(neff/√len): | 6.0 |
Jackhmmer Results: (2016_04)
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: 1.109).
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 |
| 25_A | 51_Q | 2.347 | 0.99 |
| 8_C | 13_I | 1.811 | 0.93 |
| 6_E | 13_I | 1.727 | 0.90 |
| 22_Y | 38_S | 1.726 | 0.90 |
| 3_D | 34_G | 1.548 | 0.82 |
| 42_V | 47_T | 1.406 | 0.73 |
| 13_I | 31_N | 1.394 | 0.72 |
| 42_V | 46_S | 1.354 | 0.69 |
| 41_S | 54_H | 1.353 | 0.69 |
| 11_G | 50_G | 1.347 | 0.68 |
| 2_E | 22_Y | 1.298 | 0.64 |
| 20_T | 25_A | 1.292 | 0.64 |
| 13_I | 42_V | 1.277 | 0.62 |
| 15_Q | 54_H | 1.226 | 0.58 |
| 5_I | 12_V | 1.202 | 0.55 |
| 28_P | 32_I | 1.201 | 0.55 |
| 41_S | 50_G | 1.196 | 0.55 |
| 40_I | 48_S | 1.185 | 0.54 |
| 5_I | 30_A | 1.163 | 0.52 |
| 17_K | 54_H | 1.120 | 0.47 |
| 3_D | 22_Y | 1.116 | 0.47 |
| 4_F | 17_K | 1.114 | 0.47 |
| 38_S | 41_S | 1.109 | 0.46 |
| 6_E | 43_H | 1.083 | 0.44 |
| 20_T | 51_Q | 1.046 | 0.41 |
| 7_L | 22_Y | 1.034 | 0.39 |
| 15_Q | 41_S | 1.028 | 0.39 |
| 46_S | 55_Y | 1.026 | 0.39 |
| 17_K | 26_S | 1.011 | 0.37 |
| 10_P | 54_H | 1.006 | 0.37 |
| 42_V | 48_S | 1.001 | 0.36 |
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 | |
| 2jv3A | 1 | 0.3393 | 6 | 0.914 | Contact Map |
| 4g1gA | 2 | 0.8393 | 3 | 0.926 | Contact Map |
| 2z84A | 1 | 0.2143 | 2.8 | 0.928 | Contact Map |
| 1ityA | 1 | 0.3393 | 2.7 | 0.928 | Contact Map |
| 1x66A | 1 | 0.5536 | 2.4 | 0.929 | Contact Map |
| 4oj5A | 3 | 0.8571 | 2.4 | 0.93 | Contact Map |
| 2ff6H | 1 | 0.1786 | 2.3 | 0.931 | Contact Map |
| 1jegB | 1 | 0.1607 | 2.1 | 0.932 | Contact Map |
| 2j3tD | 1 | 0.3393 | 2.1 | 0.932 | Contact Map |
| 1sv0A | 2 | 0.3393 | 2 | 0.933 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)