| pte |
| ID: | 1451209258 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 59 (53) | ||
| Sequences: | 566 (413.9) | ||
| Seq/Len: | 10.679 | ||
| Nf(neff/√len): | 56.9 |
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: 10.679).
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 |
| 46_R | 52_Q | 3.316 | 1.00 |
| 23_N | 57_V | 2.592 | 1.00 |
| 22_L | 57_V | 2.302 | 1.00 |
| 51_S | 54_D | 2.155 | 1.00 |
| 15_A | 19_R | 2.092 | 1.00 |
| 31_I | 34_Y | 1.811 | 1.00 |
| 15_A | 18_D | 1.753 | 1.00 |
| 52_Q | 56_D | 1.714 | 1.00 |
| 17_R | 58_M | 1.676 | 1.00 |
| 27_L | 58_M | 1.631 | 1.00 |
| 35_D | 39_T | 1.592 | 1.00 |
| 29_M | 32_Y | 1.472 | 1.00 |
| 45_L | 50_F | 1.349 | 0.99 |
| 17_R | 22_L | 1.324 | 0.99 |
| 36_Y | 41_F | 1.269 | 0.99 |
| 26_M | 34_Y | 1.233 | 0.98 |
| 42_I | 46_R | 1.181 | 0.98 |
| 21_L | 25_V | 1.142 | 0.97 |
| 14_H | 17_R | 1.087 | 0.96 |
| 38_L | 42_I | 1.080 | 0.95 |
| 14_H | 18_D | 1.060 | 0.95 |
| 32_Y | 36_Y | 1.055 | 0.95 |
| 16_L | 25_V | 1.035 | 0.94 |
| 17_R | 54_D | 1.024 | 0.93 |
| 22_L | 54_D | 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 | |
| 3k2gA | 4 | 1 | 98.2 | 0.529 | Contact Map |
| 3rhgA | 1 | 1 | 98.1 | 0.544 | Contact Map |
| 3ovgA | 6 | 1 | 96.4 | 0.657 | Contact Map |
| 3pnzA | 6 | 1 | 96.4 | 0.658 | Contact Map |
| 3gtxA | 1 | 1 | 96.4 | 0.659 | Contact Map |
| 4if2A | 1 | 1 | 96.2 | 0.664 | Contact Map |
| 3tn4A | 2 | 1 | 96 | 0.669 | Contact Map |
| 4kezA | 4 | 1 | 95.9 | 0.674 | Contact Map |
| 1bf6A | 2 | 1 | 95.4 | 0.686 | Contact Map |
| 4rdzA | 2 | 1 | 94.7 | 0.698 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)