| endorphin |
| ID: | 1434356072 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 31 (31) | ||
| Sequences: | 49 (28.6) | ||
| Seq/Len: | 1.581 | ||
| Nf(neff/√len): | 5.1 |
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: 1.581).
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 |
| 21_A | 25_N | 1.795 | 0.96 |
| 18_F | 22_I | 1.675 | 0.93 |
| 1_Y | 13_P | 1.557 | 0.90 |
| 6_T | 21_A | 1.515 | 0.88 |
| 2_G | 8_E | 1.467 | 0.86 |
| 2_G | 16_T | 1.393 | 0.81 |
| 1_Y | 5_M | 1.331 | 0.77 |
| 28_K | 31_E | 1.278 | 0.73 |
| 11_Q | 18_F | 1.268 | 0.72 |
| 10_S | 23_I | 1.209 | 0.67 |
| 27_Y | 30_G | 1.187 | 0.65 |
| 7_S | 15_V | 1.167 | 0.63 |
| 10_S | 19_K | 1.163 | 0.62 |
| 20_N | 24_K | 1.158 | 0.62 |
| 13_P | 16_T | 1.135 | 0.60 |
| 15_V | 21_A | 1.115 | 0.57 |
| 6_T | 19_K | 1.078 | 0.54 |
| 15_V | 26_A | 1.059 | 0.52 |
| 12_T | 26_A | 1.034 | 0.49 |
| 8_E | 16_T | 1.033 | 0.49 |
| 3_G | 13_P | 1.000 | 0.46 |
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 | |
| 3renA | 2 | 0.8065 | 9.5 | 0.81 | Contact Map |
| 4b0yA | 1 | 0.9677 | 6.6 | 0.823 | Contact Map |
| 3r8jA | 2 | 0.9677 | 6.5 | 0.823 | Contact Map |
| 3c2qA | 2 | 0.9677 | 6.3 | 0.824 | Contact Map |
| 2govA | 1 | 0.9677 | 6.1 | 0.826 | Contact Map |
| 2qyfB | 2 | 0.9032 | 4 | 0.84 | Contact Map |
| 1zjcA | 1 | 0.7742 | 3.7 | 0.843 | Contact Map |
| 2qxfA | 1 | 0.9355 | 3.5 | 0.844 | Contact Map |
| 2xvsA | 1 | 0.8065 | 3.4 | 0.845 | Contact Map |
| 3vkgA | 2 | 1 | 3.4 | 0.845 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)