| IS-efficient |
| ID: | 1488088021 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 40 (40) | ||
| Sequences: | 1402 (1401) | ||
| Seq/Len: | 35.050 | ||
| Nf(neff/√len): | 221.5 |
HHblits Results: (2016_02)
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: 35.050).
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 |
| 31_C | 34_T | 2.030 | 1.00 |
| 2_A | 28_T | 1.824 | 1.00 |
| 22_T | 26_A | 1.770 | 1.00 |
| 13_G | 29_A | 1.739 | 1.00 |
| 13_G | 28_T | 1.693 | 1.00 |
| 12_C | 15_C | 1.654 | 1.00 |
| 11_A | 20_T | 1.455 | 1.00 |
| 34_T | 37_C | 1.365 | 0.99 |
| 34_T | 40_C | 1.234 | 0.98 |
| 27_A | 31_C | 1.209 | 0.98 |
| 11_A | 28_T | 1.207 | 0.98 |
| 1_G | 25_C | 1.198 | 0.98 |
| 5_T | 17_T | 1.196 | 0.98 |
| 8_G | 11_A | 1.195 | 0.98 |
| 2_A | 23_T | 1.191 | 0.98 |
| 6_T | 23_T | 1.166 | 0.97 |
| 4_T | 38_T | 1.120 | 0.96 |
| 25_C | 40_C | 1.108 | 0.96 |
| 36_A | 39_G | 1.102 | 0.96 |
| 37_C | 40_C | 1.086 | 0.96 |
| 18_G | 24_A | 1.086 | 0.96 |
| 6_T | 10_T | 1.077 | 0.95 |
| 9_G | 12_C | 1.042 | 0.94 |
| 7_G | 13_G | 1.022 | 0.93 |
| 17_T | 35_A | 1.001 | 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 | |
| 2pk2A | 4 | 0 | 0.6 | 0.427 | Contact Map |
| 4kblA | 2 | 0 | 0.5 | 0.46 | Contact Map |
| 2wolA | 1 | 0.25 | 0.1 | 0.702 | Contact Map |
| 1cn3F | 1 | 0.275 | 0.1 | 0.725 | Contact Map |
| 2aanA | 1 | 0 | 0.1 | 0.741 | Contact Map |
| 1s58A | 1 | 0.125 | 0.1 | 0.769 | Contact Map |
| 4aenA | 1 | 0 | 0.1 | 0.785 | Contact Map |
| 4ladB | 1 | 0.075 | 0.1 | 0.791 | Contact Map |
| 1x0gA | 4 | 0.4 | 0.1 | 0.829 | Contact Map |
| 1t2yA | 1 | 0.4 | 0.1 | 0.829 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)