| 1EI0 |
| ID: | 1515666499 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 38 (38) | ||
| Sequences: | 197 (133.4) | ||
| Seq/Len: | 5.184 | ||
| Nf(neff/√len): | 21.6 |
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: 5.184).
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_A | 11_Q | 3.887 | 1.00 |
| 10_I | 21_E | 2.081 | 1.00 |
| 3_C | 7_A | 1.840 | 1.00 |
| 32_K | 38_Y | 1.789 | 1.00 |
| 27_V | 36_A | 1.685 | 1.00 |
| 26_A | 36_A | 1.651 | 0.99 |
| 5_K | 32_K | 1.566 | 0.99 |
| 6_Q | 33_K | 1.345 | 0.97 |
| 28_I | 31_L | 1.294 | 0.96 |
| 1_D | 5_K | 1.242 | 0.94 |
| 16_A | 31_L | 1.183 | 0.92 |
| 30_E | 38_Y | 1.169 | 0.91 |
| 10_I | 18_S | 1.131 | 0.89 |
| 16_A | 30_E | 1.105 | 0.88 |
| 18_S | 21_E | 1.091 | 0.87 |
| 9_E | 21_E | 1.053 | 0.84 |
| 31_L | 38_Y | 1.048 | 0.84 |
| 20_L | 29_Q | 1.017 | 0.82 |
| 1_D | 4_Q | 1.013 | 0.81 |
| 18_S | 36_A | 1.012 | 0.81 |
| 21_E | 25_Q | 1.010 | 0.81 |
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 | |
| 1hp8A | 1 | 1 | 99 | 0.225 | Contact Map |
| 1ei0A | 1 | 1 | 98.6 | 0.342 | Contact Map |
| 2lqtA | 1 | 1 | 94.5 | 0.623 | Contact Map |
| 5aj3m | 1 | 0 | 86.4 | 0.691 | Contact Map |
| 2lqlA | 1 | 1 | 35.7 | 0.786 | Contact Map |
| 3v9mA | 2 | 0.8684 | 2.2 | 0.88 | Contact Map |
| 4ntwC | 1 | 0.8158 | 2.1 | 0.882 | Contact Map |
| 1u96A | 1 | 1 | 2 | 0.882 | Contact Map |
| 3vbzA | 2 | 0.8684 | 1.8 | 0.886 | Contact Map |
| 2l0yB | 1 | 0.4474 | 1.7 | 0.887 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)