| sesB |
| ID: | 1490086019 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 42 (38) | ||
| Sequences: | 54 (51) | ||
| Seq/Len: | 1.421 | ||
| Nf(neff/√len): | 8.3 |
HHblits Results: (2016_02)
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: 1.421).
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_Q | 29_E | 2.100 | 0.99 |
| 7_N | 30_V | 1.881 | 0.96 |
| 32_G | 37_G | 1.839 | 0.96 |
| 19_G | 27_G | 1.643 | 0.91 |
| 23_I | 29_E | 1.619 | 0.90 |
| 14_F | 21_Q | 1.618 | 0.90 |
| 34_N | 37_G | 1.509 | 0.86 |
| 28_N | 32_G | 1.478 | 0.84 |
| 12_D | 25_K | 1.427 | 0.81 |
| 20_T | 33_G | 1.285 | 0.70 |
| 8_L | 17_P | 1.278 | 0.70 |
| 20_T | 36_Y | 1.218 | 0.64 |
| 27_G | 30_V | 1.192 | 0.62 |
| 17_P | 31_S | 1.180 | 0.61 |
| 4_S | 7_N | 1.159 | 0.59 |
| 6_N | 12_D | 1.117 | 0.54 |
| 10_S | 25_K | 1.102 | 0.53 |
| 5_F | 13_Q | 1.082 | 0.51 |
| 32_G | 35_F | 1.046 | 0.47 |
| 11_G | 14_F | 1.042 | 0.47 |
| 14_F | 25_K | 1.035 | 0.46 |
| 30_V | 34_N | 1.024 | 0.45 |
| 7_N | 39_V | 1.004 | 0.43 |
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 | |
| 3rlfF | 1 | 1 | 0.9 | 0.877 | Contact Map |
| 3t41A | 2 | 1 | 0.8 | 0.885 | Contact Map |
| 4c7lA | 2 | 0.6905 | 0.7 | 0.888 | Contact Map |
| 3cl5A | 1 | 0.6905 | 0.7 | 0.888 | Contact Map |
| 1flcA | 3 | 0.6905 | 0.7 | 0.889 | Contact Map |
| 2b6nA | 1 | 1 | 0.6 | 0.891 | Contact Map |
| 2wq4A | 3 | 0.1667 | 0.6 | 0.891 | Contact Map |
| 3kogA | 1 | 0.1905 | 0.6 | 0.894 | Contact Map |
| 4q0jA | 1 | 0.1905 | 0.6 | 0.895 | Contact Map |
| 1to2E | 1 | 1 | 0.5 | 0.898 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)