| pengfei tian |
| ID: | 1447259026 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 56 (56) | ||
| Sequences: | 2537 (2537) | ||
| Seq/Len: | 45.304 | ||
| Nf(neff/√len): | 339.0 |
HHblits Results: (2015_06)
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: 45.304).
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 |
| 23_Q | 48_L | 1.811 | 1.00 |
| 14_V | 18_T | 1.605 | 1.00 |
| 28_A | 32_I | 1.564 | 1.00 |
| 18_T | 50_L | 1.471 | 1.00 |
| 17_M | 26_S | 1.413 | 1.00 |
| 33_W | 54_F | 1.387 | 0.99 |
| 2_A | 28_A | 1.372 | 0.99 |
| 36_Q | 50_L | 1.324 | 0.99 |
| 42_P | 50_L | 1.318 | 0.99 |
| 11_Y | 44_D | 1.291 | 0.99 |
| 2_A | 29_G | 1.247 | 0.99 |
| 24_P | 28_A | 1.242 | 0.98 |
| 15_P | 45_I | 1.235 | 0.98 |
| 11_Y | 46_W | 1.219 | 0.98 |
| 25_N | 29_G | 1.210 | 0.98 |
| 4_E | 21_Y | 1.185 | 0.98 |
| 38_I | 51_Q | 1.166 | 0.97 |
| 10_L | 34_N | 1.158 | 0.97 |
| 16_I | 34_N | 1.146 | 0.97 |
| 8_L | 29_G | 1.133 | 0.97 |
| 9_E | 50_L | 1.130 | 0.97 |
| 9_E | 38_I | 1.106 | 0.96 |
| 20_D | 47_K | 1.101 | 0.96 |
| 40_V | 54_F | 1.101 | 0.96 |
| 12_I | 27_A | 1.084 | 0.96 |
| 24_P | 42_P | 1.078 | 0.95 |
| 15_P | 46_W | 1.028 | 0.94 |
| 12_I | 44_D | 1.005 | 0.93 |
| 23_Q | 47_K | 1.001 | 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 | |
| 2jwsA | 1 | 1 | 91.7 | 0.296 | Contact Map |
| 1pgxA | 1 | 1 | 81.7 | 0.4 | Contact Map |
| 1pn5A | 1 | 0 | 81.3 | 0.403 | Contact Map |
| 1igdA | 1 | 1 | 77 | 0.425 | Contact Map |
| 2rpvA | 1 | 1 | 75.7 | 0.432 | Contact Map |
| 2khuA | 1 | 0 | 74.9 | 0.435 | Contact Map |
| 3ui3A | 2 | 0.8214 | 69.9 | 0.456 | Contact Map |
| 3filA | 1 | 0.9821 | 67.8 | 0.464 | Contact Map |
| 2fs1A | 1 | 1 | 58.1 | 0.497 | Contact Map |
| 2mbbA | 1 | 0 | 56.2 | 0.502 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)