| 3oss_bakerMSA |
| ID: | 1502277653 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 61 (61) | ||
| Sequences: | 568 (500.8) | ||
| Seq/Len: | 9.311 | ||
| Nf(neff/√len): | 64.1 |
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: 9.311).
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 |
| 41_E | 51_R | 2.821 | 1.00 |
| 5_L | 16_A | 2.719 | 1.00 |
| 40_I | 43_I | 2.337 | 1.00 |
| 44_N | 47_H | 2.211 | 1.00 |
| 43_I | 48_V | 2.156 | 1.00 |
| 47_H | 58_R | 1.964 | 1.00 |
| 5_L | 59_L | 1.962 | 1.00 |
| 5_L | 8_I | 1.860 | 1.00 |
| 7_G | 17_V | 1.800 | 1.00 |
| 1_L | 57_E | 1.646 | 1.00 |
| 40_I | 48_V | 1.610 | 1.00 |
| 14_P | 29_Q | 1.586 | 1.00 |
| 41_E | 56_I | 1.552 | 1.00 |
| 10_F | 14_P | 1.506 | 1.00 |
| 51_R | 54_G | 1.440 | 1.00 |
| 27_Y | 33_L | 1.402 | 0.99 |
| 8_I | 61_L | 1.344 | 0.99 |
| 27_Y | 40_I | 1.243 | 0.98 |
| 4_V | 59_L | 1.180 | 0.97 |
| 19_E | 23_K | 1.133 | 0.96 |
| 1_L | 16_A | 1.068 | 0.94 |
| 39_V | 51_R | 1.066 | 0.94 |
| 5_L | 48_V | 1.014 | 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 | |
| 3ossC | 1 | 1 | 98.8 | 0.083 | Contact Map |
| 2lnvA | 1 | 1 | 98.8 | 0.085 | Contact Map |
| 4av2M | 12 | 1 | 96.8 | 0.427 | Contact Map |
| 2ivwA | 1 | 1 | 93.1 | 0.545 | Contact Map |
| 2lc4A | 1 | 1 | 92.9 | 0.548 | Contact Map |
| 2y4xA | 2 | 1 | 92.6 | 0.552 | Contact Map |
| 1vw4N | 1 | 0.9508 | 18.2 | 0.763 | Contact Map |
| 4rb6V | 1 | 0.6885 | 10.5 | 0.787 | Contact Map |
| 2zjrO | 1 | 0.623 | 10.4 | 0.787 | Contact Map |
| 2arzA | 2 | 0.9016 | 10.2 | 0.788 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)