| 3oss |
| ID: | 1501759049 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 65 (61) | ||
| Sequences: | 477 (470) | ||
| Seq/Len: | 7.820 | ||
| Nf(neff/√len): | 60.2 |
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: 7.820).
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 |
| 43_I | 46_I | 2.752 | 1.00 |
| 8_L | 19_A | 2.498 | 1.00 |
| 43_I | 51_V | 2.176 | 1.00 |
| 44_E | 54_R | 2.140 | 1.00 |
| 10_G | 20_V | 1.894 | 1.00 |
| 4_L | 60_E | 1.867 | 1.00 |
| 50_H | 61_R | 1.821 | 1.00 |
| 7_V | 22_E | 1.729 | 1.00 |
| 8_L | 11_I | 1.684 | 1.00 |
| 41_A | 51_V | 1.551 | 1.00 |
| 46_I | 51_V | 1.452 | 0.99 |
| 40_N | 55_Y | 1.439 | 0.99 |
| 47_N | 50_H | 1.327 | 0.98 |
| 11_I | 19_A | 1.217 | 0.97 |
| 55_Y | 60_E | 1.215 | 0.97 |
| 29_V | 41_A | 1.189 | 0.96 |
| 12_A | 64_L | 1.172 | 0.96 |
| 10_G | 13_F | 1.150 | 0.95 |
| 42_V | 57_G | 1.126 | 0.95 |
| 37_D | 40_N | 1.094 | 0.93 |
| 35_R | 42_V | 1.085 | 0.93 |
| 28_Q | 31_L | 1.063 | 0.92 |
| 5_N | 47_N | 1.050 | 0.92 |
| 35_R | 61_R | 1.042 | 0.91 |
| 43_I | 53_L | 1.039 | 0.91 |
| 5_N | 45_E | 1.034 | 0.91 |
| 45_E | 52_M | 1.017 | 0.90 |
| 54_R | 59_I | 1.001 | 0.89 |
| 48_R | 64_L | 1.001 | 0.89 |
| 6_V | 57_G | 1.001 | 0.89 |
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 | 98.9 | 0.089 | Contact Map |
| 2lnvA | 1 | 1 | 98.8 | 0.116 | Contact Map |
| 4av2M | 12 | 1 | 97 | 0.429 | Contact Map |
| 2lc4A | 1 | 1 | 95.1 | 0.52 | Contact Map |
| 2ivwA | 1 | 1 | 95.1 | 0.521 | Contact Map |
| 2y4xA | 2 | 0.9846 | 94.9 | 0.527 | Contact Map |
| 1vw4N | 1 | 0.8769 | 22.1 | 0.762 | Contact Map |
| 2zjrO | 1 | 0.6308 | 14.4 | 0.782 | Contact Map |
| 4rb6V | 1 | 0.6615 | 13.7 | 0.785 | Contact Map |
| 3j3wR | 1 | 0.6769 | 13.3 | 0.786 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)