| d2pija_ |
| ID: | 1450630205 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 59 (58) | ||
| Sequences: | 69 (52.6) | ||
| Seq/Len: | 1.190 | ||
| Nf(neff/√len): | 6.9 |
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: 1.190).
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 |
| 9_Y | 42_I | 2.303 | 0.99 |
| 32_Q | 58_I | 2.230 | 0.99 |
| 33_M | 58_I | 2.173 | 0.98 |
| 25_V | 30_I | 2.022 | 0.97 |
| 25_V | 40_I | 1.976 | 0.96 |
| 10_L | 30_I | 1.656 | 0.89 |
| 25_V | 45_Y | 1.637 | 0.88 |
| 9_Y | 19_L | 1.447 | 0.78 |
| 27_Q | 31_S | 1.431 | 0.77 |
| 1_M | 34_V | 1.403 | 0.75 |
| 13_H | 56_R | 1.366 | 0.72 |
| 34_V | 52_A | 1.339 | 0.70 |
| 19_L | 42_I | 1.325 | 0.68 |
| 19_L | 58_I | 1.316 | 0.68 |
| 10_L | 34_V | 1.311 | 0.67 |
| 10_L | 33_M | 1.298 | 0.66 |
| 19_L | 33_M | 1.277 | 0.64 |
| 23_L | 28_S | 1.202 | 0.57 |
| 7_S | 46_E | 1.177 | 0.55 |
| 23_L | 26_N | 1.107 | 0.48 |
| 18_A | 21_A | 1.096 | 0.47 |
| 30_I | 33_M | 1.075 | 0.45 |
| 3_K | 41_E | 1.075 | 0.45 |
| 9_Y | 26_N | 1.036 | 0.41 |
| 8_K | 23_L | 1.031 | 0.41 |
| 32_Q | 53_N | 1.022 | 0.40 |
| 13_H | 35_R | 1.010 | 0.39 |
| 25_V | 28_S | 1.006 | 0.39 |
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 | |
| 2cw1A | 1 | 0.9831 | 99.6 | 0.382 | Contact Map |
| 2ovgA | 1 | 0.9661 | 98.7 | 0.581 | Contact Map |
| 2pijA | 2 | 1 | 98.4 | 0.623 | Contact Map |
| 2hinA | 2 | 0.9322 | 96.6 | 0.734 | Contact Map |
| 3fzvA | 4 | 0.8814 | 95.1 | 0.765 | Contact Map |
| 1uthA | 1 | 0 | 94.8 | 0.77 | Contact Map |
| 2esnA | 4 | 0.9661 | 94.7 | 0.771 | Contact Map |
| 2h9bA | 2 | 0 | 93.8 | 0.78 | Contact Map |
| 1ixcA | 2 | 0.9661 | 93.5 | 0.783 | Contact Map |
| 3szpA | 2 | 0.9661 | 93.2 | 0.785 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)