| spdl -force run |
| ID: | 1457375358 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 70 (70) | ||
| Sequences: | 58 (22.3) | ||
| Seq/Len: | 0.829 | ||
| Nf(neff/√len): | 2.7 |
Jackhmmer Results: (2015_08)
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: 0.829).
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 |
| 30_L | 37_L | 2.048 | 0.95 |
| 49_M | 61_T | 2.029 | 0.94 |
| 31_V | 45_R | 1.836 | 0.89 |
| 20_R | 32_E | 1.776 | 0.87 |
| 13_L | 34_Q | 1.775 | 0.87 |
| 10_R | 14_K | 1.640 | 0.80 |
| 5_I | 50_T | 1.626 | 0.80 |
| 43_K | 55_Y | 1.523 | 0.73 |
| 26_Y | 64_R | 1.473 | 0.70 |
| 12_R | 29_Q | 1.420 | 0.65 |
| 46_N | 64_R | 1.408 | 0.64 |
| 17_E | 67_E | 1.402 | 0.64 |
| 21_L | 32_E | 1.396 | 0.63 |
| 19_E | 64_R | 1.362 | 0.61 |
| 15_E | 25_Q | 1.296 | 0.55 |
| 48_M | 66_V | 1.280 | 0.54 |
| 19_E | 32_E | 1.277 | 0.53 |
| 52_T | 55_Y | 1.262 | 0.52 |
| 22_K | 67_E | 1.203 | 0.47 |
| 17_E | 38_Q | 1.203 | 0.47 |
| 6_I | 12_R | 1.192 | 0.46 |
| 44_C | 48_M | 1.132 | 0.41 |
| 49_M | 55_Y | 1.123 | 0.40 |
| 26_Y | 29_Q | 1.092 | 0.37 |
| 3_A | 55_Y | 1.092 | 0.37 |
| 26_Y | 52_T | 1.074 | 0.36 |
| 14_K | 22_K | 1.071 | 0.36 |
| 50_T | 54_S | 1.064 | 0.35 |
| 4_D | 50_T | 1.060 | 0.35 |
| 47_E | 65_E | 1.041 | 0.33 |
| 9_L | 65_E | 1.038 | 0.33 |
| 29_Q | 64_R | 1.015 | 0.31 |
| 9_L | 47_E | 1.001 | 0.30 |
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 | |
| 3ghgA | 4 | 0.9143 | 67.6 | 0.846 | Contact Map |
| 2qagB | 1 | 0 | 26.1 | 0.882 | Contact Map |
| 2dfsA | 2 | 1 | 22.8 | 0.885 | Contact Map |
| 2bnxA | 2 | 0.2143 | 16.2 | 0.893 | Contact Map |
| 4hjbC | 4 | 0.3429 | 13.7 | 0.896 | Contact Map |
| 4kv9A | 2 | 0 | 13.6 | 0.896 | Contact Map |
| 4rh7A | 1 | 0.9286 | 10.3 | 0.902 | Contact Map |
| 3vkgA | 2 | 0.8714 | 9.7 | 0.903 | Contact Map |
| 4xa4A | 2 | 0 | 8.5 | 0.905 | Contact Map |
| 4xa6A | 4 | 0 | 8.1 | 0.906 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)