| 3E7R |
| ID: | 1427310003 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 40 (36) | ||
| Sequences: | 40 (26.2) | ||
| Seq/Len: | 1.111 | ||
| Nf(neff/√len): | 4.4 |
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: 1.111).
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 |
| 12_D | 34_G | 2.878 | 1.00 |
| 27_G | 40_Y | 2.660 | 1.00 |
| 1_G | 29_Y | 1.806 | 0.93 |
| 32_K | 36_V | 1.645 | 0.87 |
| 8_W | 16_H | 1.632 | 0.86 |
| 22_I | 38_K | 1.382 | 0.71 |
| 2_F | 9_D | 1.369 | 0.70 |
| 31_A | 40_Y | 1.354 | 0.69 |
| 8_W | 31_A | 1.300 | 0.64 |
| 3_G | 13_M | 1.287 | 0.63 |
| 1_G | 28_G | 1.286 | 0.63 |
| 1_G | 9_D | 1.205 | 0.56 |
| 25_Y | 36_V | 1.163 | 0.52 |
| 16_H | 26_K | 1.115 | 0.47 |
| 25_Y | 31_A | 1.104 | 0.46 |
| 17_N | 22_I | 1.103 | 0.46 |
| 14_Q | 27_G | 1.022 | 0.38 |
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 | |
| 1zfuA | 1 | 1 | 99.2 | 0.26 | Contact Map |
| 2lt8A | 1 | 0.9 | 99.1 | 0.289 | Contact Map |
| 2b68A | 1 | 0.875 | 98.9 | 0.332 | Contact Map |
| 2lr5A | 1 | 0.875 | 98.9 | 0.346 | Contact Map |
| 1fjnA | 1 | 0.875 | 98.8 | 0.357 | Contact Map |
| 2ru0A | 1 | 0.875 | 98.4 | 0.443 | Contact Map |
| 2rtyA | 1 | 0.75 | 97.5 | 0.546 | Contact Map |
| 1icaA | 1 | 0.8 | 97.3 | 0.563 | Contact Map |
| 2ln4A | 1 | 0.825 | 97.2 | 0.574 | Contact Map |
| 2kozA | 1 | 0.725 | 96.5 | 0.608 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)