| DYSF-1456-1500 |
| ID: | 1480265969 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 45 (44) | ||
| Sequences: | 150 (93.8) | ||
| Seq/Len: | 3.409 | ||
| Nf(neff/√len): | 14.1 |
Jackhmmer Results: (2016_04)
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: 3.409).
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 |
| 29_S | 36_C | 1.938 | 1.00 |
| 14_I | 44_F | 1.699 | 0.99 |
| 33_R | 41_E | 1.629 | 0.98 |
| 7_D | 41_E | 1.623 | 0.98 |
| 37_G | 40_L | 1.595 | 0.98 |
| 8_K | 32_E | 1.575 | 0.98 |
| 9_E | 12_I | 1.513 | 0.97 |
| 10_P | 13_P | 1.423 | 0.95 |
| 2_L | 9_E | 1.393 | 0.94 |
| 20_I | 34_E | 1.372 | 0.94 |
| 15_Q | 31_G | 1.291 | 0.91 |
| 3_I | 6_D | 1.239 | 0.88 |
| 13_P | 17_E | 1.234 | 0.88 |
| 9_E | 13_P | 1.194 | 0.86 |
| 19_F | 38_S | 1.154 | 0.83 |
| 38_S | 41_E | 1.143 | 0.82 |
| 29_S | 32_E | 1.130 | 0.81 |
| 2_L | 6_D | 1.092 | 0.78 |
| 4_D | 17_E | 1.088 | 0.77 |
| 34_E | 41_E | 1.070 | 0.76 |
| 34_E | 44_F | 1.056 | 0.74 |
| 15_Q | 36_C | 1.051 | 0.74 |
| 17_E | 28_A | 1.049 | 0.74 |
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 | |
| 2p3yA | 2 | 0.8889 | 12 | 0.871 | Contact Map |
| 3hy0A | 2 | 1 | 9 | 0.878 | Contact Map |
| 4e6nA | 2 | 0.8889 | 8.6 | 0.879 | Contact Map |
| 2ygkA | 2 | 0.5111 | 5 | 0.892 | Contact Map |
| 1ea5A | 1 | 0.7333 | 3.8 | 0.897 | Contact Map |
| 1thgA | 1 | 0.6889 | 3.7 | 0.899 | Contact Map |
| 3fy6A | 4 | 0.6 | 3.3 | 0.901 | Contact Map |
| 2g3mA | 6 | 0.8 | 3.2 | 0.902 | Contact Map |
| 1p0iA | 1 | 0.6444 | 3.2 | 0.902 | Contact Map |
| 3hs2A | 8 | 0.4889 | 3.1 | 0.902 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)