| pyy |
| ID: | 1411402004 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 36 (36) | ||
| Sequences: | 56 (24.4) | ||
| Seq/Len: | 1.556 | ||
| Nf(neff/√len): | 4.1 |
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: 1.556).
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 |
| 4_K | 34_Q | 1.889 | 0.97 |
| 29_N | 32_T | 1.784 | 0.96 |
| 15_E | 36_Y | 1.682 | 0.93 |
| 4_K | 16_E | 1.609 | 0.91 |
| 16_E | 34_Q | 1.567 | 0.90 |
| 18_S | 28_L | 1.548 | 0.89 |
| 1_Y | 6_E | 1.421 | 0.83 |
| 12_A | 35_R | 1.333 | 0.77 |
| 25_R | 30_L | 1.239 | 0.69 |
| 15_E | 29_N | 1.233 | 0.68 |
| 14_P | 35_R | 1.230 | 0.68 |
| 20_Y | 25_R | 1.206 | 0.66 |
| 10_E | 26_H | 1.206 | 0.66 |
| 9_G | 12_A | 1.205 | 0.66 |
| 25_R | 36_Y | 1.140 | 0.60 |
| 1_Y | 24_L | 1.095 | 0.55 |
| 9_G | 21_Y | 1.086 | 0.54 |
| 29_N | 36_Y | 1.081 | 0.53 |
| 28_L | 31_V | 1.078 | 0.53 |
| 4_K | 30_L | 1.070 | 0.52 |
| 17_L | 21_Y | 1.061 | 0.51 |
| 21_Y | 24_L | 1.028 | 0.48 |
| 10_E | 19_R | 1.026 | 0.48 |
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 | |
| 1qbfA | 1 | 1 | 99.7 | 0.008 | Contact Map |
| 1bbaA | 1 | 1 | 99.7 | 0.009 | Contact Map |
| 2l60A | 1 | 1 | 99.7 | 0.022 | Contact Map |
| 2bf9A | 1 | 0.9722 | 99.7 | 0.044 | Contact Map |
| 1f8pA | 1 | 1 | 99.5 | 0.131 | Contact Map |
| 1k8vA | 1 | 0.9722 | 84.1 | 0.738 | Contact Map |
| 2iruA | 2 | 1 | 30 | 0.82 | Contact Map |
| 2faoA | 2 | 1 | 28.9 | 0.821 | Contact Map |
| 4c5wA | 1 | 1 | 10.3 | 0.855 | Contact Map |
| 2a26A | 3 | 0.75 | 9.8 | 0.856 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)