| r0 wo gaps |
| ID: | 1425306221 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 21 (21) | ||
| Sequences: | 76 (69.7) | ||
| Seq/Len: | 3.619 | ||
| Nf(neff/√len): | 15.2 |
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: 3.619).
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 |
| 8_I | 12_G | 2.132 | 1.00 |
| 5_V | 10_A | 1.699 | 0.99 |
| 8_I | 16_V | 1.686 | 0.99 |
| 17_H | 21_S | 1.587 | 0.98 |
| 5_V | 18_V | 1.421 | 0.96 |
| 3_N | 17_H | 1.372 | 0.94 |
| 2_A | 15_R | 1.346 | 0.94 |
| 4_Q | 20_N | 1.316 | 0.93 |
| 2_A | 5_V | 1.267 | 0.91 |
| 3_N | 21_S | 1.215 | 0.88 |
| 7_S | 13_Q | 1.150 | 0.84 |
| 10_A | 16_V | 1.148 | 0.84 |
| 1_M | 12_G | 1.120 | 0.82 |
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 | |
| 2kj3A | 3 | 1 | 31.9 | 0.176 | Contact Map |
| 3h09A | 2 | 1 | 1.3 | 0.585 | Contact Map |
| 4aslA | 1 | 1 | 0.8 | 0.631 | Contact Map |
| 3nvnB | 1 | 1 | 0.8 | 0.631 | Contact Map |
| 4ftdA | 1 | 1 | 0.8 | 0.64 | Contact Map |
| 4lhkA | 2 | 1 | 0.8 | 0.64 | Contact Map |
| 3syjA | 1 | 1 | 0.8 | 0.64 | Contact Map |
| 3mujA | 2 | 1 | 0.7 | 0.647 | Contact Map |
| 3tewA | 1 | 1 | 0.7 | 0.65 | Contact Map |
| 2mkiA | 1 | 0.9524 | 0.7 | 0.65 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)