| T0809 |
| ID: | 1402086345 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 62 (60) | ||
| Sequences: | 585 (505.3) | ||
| Seq/Len: | 9.750 | ||
| Nf(neff/√len): | 65.2 |
Jackhmmer Results: (2014_04_16)
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: 9.750).
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_V | 37_Y | 4.424 | 1.00 |
| 47_K | 50_D | 3.986 | 1.00 |
| 15_D | 55_K | 2.328 | 1.00 |
| 49_L | 59_V | 2.148 | 1.00 |
| 5_Y | 45_D | 2.092 | 1.00 |
| 11_E | 16_Q | 2.083 | 1.00 |
| 12_V | 17_V | 1.832 | 1.00 |
| 4_D | 7_T | 1.812 | 1.00 |
| 13_N | 51_N | 1.745 | 1.00 |
| 19_E | 58_K | 1.665 | 1.00 |
| 53_L | 59_V | 1.581 | 1.00 |
| 19_E | 60_V | 1.493 | 1.00 |
| 27_I | 37_Y | 1.472 | 1.00 |
| 41_I | 49_L | 1.457 | 1.00 |
| 41_I | 61_G | 1.379 | 0.99 |
| 7_T | 11_E | 1.368 | 0.99 |
| 4_D | 58_K | 1.309 | 0.99 |
| 30_T | 36_R | 1.270 | 0.99 |
| 17_V | 31_K | 1.264 | 0.99 |
| 50_D | 53_L | 1.219 | 0.98 |
| 50_D | 54_T | 1.212 | 0.98 |
| 27_I | 41_I | 1.174 | 0.97 |
| 27_I | 39_T | 1.152 | 0.97 |
| 25_R | 40_Y | 1.144 | 0.97 |
| 23_N | 26_E | 1.049 | 0.94 |
| 41_I | 44_Q | 1.036 | 0.94 |
| 20_A | 59_V | 1.026 | 0.93 |
| 11_E | 31_K | 1.019 | 0.93 |
| 51_N | 55_K | 1.006 | 0.92 |
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 | |
| 2lnaA | 1 | 0.9839 | 45.5 | 0.841 | Contact Map |
| 3pm6A | 2 | 0.7742 | 17.5 | 0.871 | Contact Map |
| 2wlbA | 2 | 0.6129 | 14.7 | 0.876 | Contact Map |
| 3q94A | 2 | 0.8387 | 11.8 | 0.881 | Contact Map |
| 2y5cA | 2 | 0.6129 | 10.5 | 0.883 | Contact Map |
| 3if4A | 4 | 0.7742 | 9.8 | 0.885 | Contact Map |
| 2iswA | 2 | 0.8387 | 9.7 | 0.885 | Contact Map |
| 3n9rA | 8 | 0.8387 | 9.6 | 0.885 | Contact Map |
| 1l5pA | 3 | 0.5806 | 9.2 | 0.886 | Contact Map |
| 1qoaA | 2 | 0.5968 | 8.3 | 0.889 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)