| lyt |
| ID: | 1429224398 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 62 (61) | ||
| Sequences: | 2367 (1652.9) | ||
| Seq/Len: | 38.803 | ||
| Nf(neff/√len): | 211.6 |
HHblits Results: (2013_03)
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: 38.803).
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 |
| 29_I | 44_I | 4.210 | 1.00 |
| 7_P | 59_A | 3.132 | 1.00 |
| 56_Y | 59_A | 3.049 | 1.00 |
| 12_F | 25_M | 2.467 | 1.00 |
| 22_P | 57_L | 2.057 | 1.00 |
| 36_H | 45_S | 2.004 | 1.00 |
| 26_G | 34_F | 1.958 | 1.00 |
| 4_I | 7_P | 1.895 | 1.00 |
| 28_Y | 32_N | 1.847 | 1.00 |
| 38_G | 43_Q | 1.803 | 1.00 |
| 33_S | 46_S | 1.785 | 1.00 |
| 17_T | 23_S | 1.782 | 1.00 |
| 24_H | 36_H | 1.768 | 1.00 |
| 15_F | 34_F | 1.743 | 1.00 |
| 14_F | 25_M | 1.618 | 1.00 |
| 15_F | 26_G | 1.599 | 1.00 |
| 32_N | 48_N | 1.458 | 1.00 |
| 16_T | 23_S | 1.396 | 0.99 |
| 35_I | 44_I | 1.367 | 0.99 |
| 12_F | 27_I | 1.344 | 0.99 |
| 3_S | 6_S | 1.340 | 0.99 |
| 13_V | 59_A | 1.213 | 0.98 |
| 29_I | 35_I | 1.177 | 0.98 |
| 33_S | 44_I | 1.126 | 0.97 |
| 16_T | 22_P | 1.108 | 0.96 |
| 13_V | 26_G | 1.078 | 0.95 |
| 7_P | 28_Y | 1.059 | 0.95 |
| 34_F | 47_L | 1.048 | 0.94 |
| 28_Y | 31_N | 1.021 | 0.93 |
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 | |
| 4hpeA | 6 | 0.9839 | 99.7 | 0.143 | Contact Map |
| 4fdyA | 2 | 0.9839 | 99.7 | 0.156 | Contact Map |
| 3npfA | 2 | 0.9839 | 99.6 | 0.168 | Contact Map |
| 2k1gA | 1 | 0.9839 | 99.6 | 0.168 | Contact Map |
| 3h41A | 1 | 1 | 99.6 | 0.171 | Contact Map |
| 4xcmA | 2 | 1 | 99.6 | 0.172 | Contact Map |
| 2hbwA | 1 | 0.9839 | 99.6 | 0.175 | Contact Map |
| 4q4gX | 1 | 0.9194 | 99.5 | 0.229 | Contact Map |
| 4eyzA | 2 | 1 | 99.5 | 0.232 | Contact Map |
| 3pbiA | 1 | 0.9194 | 99.4 | 0.293 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)