| icb |
| ID: | 1493152026 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 75 (68) | ||
| Sequences: | 24116 (16457.8) | ||
| Seq/Len: | 354.647 | ||
| Nf(neff/√len): | 1995.8 |
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: 354.647).
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 |
| 22_Q | 60_E | 3.921 | 1.00 |
| 7_K | 63_F | 2.970 | 1.00 |
| 25_K | 47_D | 2.298 | 1.00 |
| 7_K | 11_E | 2.134 | 1.00 |
| 13_Y | 31_L | 1.955 | 1.00 |
| 19_D | 27_E | 1.787 | 1.00 |
| 29_K | 43_P | 1.777 | 1.00 |
| 3_P | 67_Q | 1.682 | 1.00 |
| 19_D | 22_Q | 1.627 | 1.00 |
| 63_F | 67_Q | 1.578 | 1.00 |
| 53_L | 69_L | 1.564 | 1.00 |
| 14_A | 19_D | 1.535 | 1.00 |
| 58_D | 65_E | 1.471 | 1.00 |
| 16_K | 30_L | 1.452 | 1.00 |
| 14_A | 21_N | 1.405 | 0.99 |
| 25_K | 50_F | 1.384 | 0.99 |
| 14_A | 17_E | 1.322 | 0.99 |
| 11_E | 18_G | 1.321 | 0.99 |
| 11_E | 63_F | 1.317 | 0.99 |
| 62_S | 65_E | 1.317 | 0.99 |
| 29_K | 46_L | 1.285 | 0.99 |
| 53_L | 61_V | 1.265 | 0.99 |
| 58_D | 62_S | 1.265 | 0.99 |
| 9_I | 12_K | 1.248 | 0.99 |
| 56_N | 65_E | 1.202 | 0.98 |
| 54_D | 57_G | 1.201 | 0.98 |
| 17_E | 27_E | 1.199 | 0.98 |
| 22_Q | 62_S | 1.190 | 0.98 |
| 19_D | 24_S | 1.185 | 0.98 |
| 8_G | 12_K | 1.177 | 0.98 |
| 56_N | 62_S | 1.135 | 0.97 |
| 47_D | 51_E | 1.116 | 0.96 |
| 24_S | 27_E | 1.078 | 0.95 |
| 54_D | 59_G | 1.065 | 0.95 |
| 25_K | 29_K | 1.054 | 0.95 |
| 12_K | 34_T | 1.048 | 0.94 |
| 29_K | 33_Q | 1.045 | 0.94 |
| 46_L | 50_F | 1.031 | 0.94 |
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 | |
| 3mwuA | 1 | 0.68 | 99 | 0.169 | Contact Map |
| 4d1eA | 1 | 0.9467 | 99 | 0.184 | Contact Map |
| 4mvfA | 1 | 0.8933 | 98.9 | 0.203 | Contact Map |
| 3q5iA | 1 | 0.9067 | 98.9 | 0.204 | Contact Map |
| 2m97A | 1 | 0.92 | 98.9 | 0.206 | Contact Map |
| 1nubA | 2 | 0.92 | 98.9 | 0.209 | Contact Map |
| 4qoxA | 1 | 0.92 | 98.9 | 0.21 | Contact Map |
| 4oy4A | 1 | 0.36 | 98.9 | 0.213 | Contact Map |
| 4c0kA | 1 | 0.9333 | 98.9 | 0.217 | Contact Map |
| 3a4uB | 1 | 0.7867 | 98.9 | 0.217 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)