| nonnot5 |
| ID: | 1501785004 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 23 (23) | ||
| Sequences: | 13515 (10659.7) | ||
| Seq/Len: | 587.609 | ||
| Nf(neff/√len): | 2222.7 |
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: 587.609).
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 |
| 2_H | 9_N | 2.587 | 1.00 |
| 12_T | 15_G | 2.242 | 1.00 |
| 17_R | 20_L | 2.135 | 1.00 |
| 13_K | 17_R | 2.056 | 1.00 |
| 5_E | 20_L | 1.996 | 1.00 |
| 4_S | 20_L | 1.967 | 1.00 |
| 11_N | 15_G | 1.739 | 1.00 |
| 4_S | 9_N | 1.699 | 1.00 |
| 15_G | 18_R | 1.616 | 1.00 |
| 3_C | 6_C | 1.578 | 1.00 |
| 6_C | 19_H | 1.489 | 1.00 |
| 14_L | 18_R | 1.257 | 0.99 |
| 3_C | 19_H | 1.212 | 0.98 |
| 2_H | 7_G | 1.197 | 0.98 |
| 18_R | 21_A | 1.087 | 0.96 |
| 2_H | 5_E | 1.085 | 0.96 |
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 | |
| 1ej6B | 2 | 1 | 91.2 | -0.29 | Contact Map |
| 1zr9A | 1 | 1 | 88.3 | -0.245 | Contact Map |
| 2eluA | 1 | 1 | 87.9 | -0.242 | Contact Map |
| 4ijdA | 2 | 1 | 84.6 | -0.204 | Contact Map |
| 2eppA | 1 | 1 | 81.7 | -0.177 | Contact Map |
| 2lvuA | 1 | 1 | 76.4 | -0.135 | Contact Map |
| 3rayA | 1 | 0 | 76.1 | -0.133 | Contact Map |
| 2elvA | 1 | 1 | 75.6 | -0.13 | Contact Map |
| 2en3A | 1 | 1 | 75.4 | -0.128 | Contact Map |
| 1rimA | 1 | 1 | 74.5 | -0.122 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)