| heca |
| ID: | 1431622460 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 35 (35) | ||
| Sequences: | 11766 (10828.3) | ||
| Seq/Len: | 336.171 | ||
| Nf(neff/√len): | 1830.3 |
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: 336.171).
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 |
| 12_A | 30_T | 2.988 | 1.00 |
| 9_F | 27_T | 2.774 | 1.00 |
| 3_E | 21_K | 2.668 | 1.00 |
| 26_M | 35_F | 2.306 | 1.00 |
| 5_N | 22_G | 1.876 | 1.00 |
| 1_G | 8_L | 1.793 | 1.00 |
| 14_N | 31_G | 1.764 | 1.00 |
| 7_L | 25_I | 1.648 | 1.00 |
| 9_F | 29_G | 1.545 | 1.00 |
| 19_G | 26_M | 1.488 | 1.00 |
| 2_G | 6_D | 1.486 | 1.00 |
| 8_L | 17_L | 1.468 | 1.00 |
| 16_L | 34_T | 1.363 | 0.99 |
| 27_T | 35_F | 1.338 | 0.99 |
| 2_G | 20_G | 1.317 | 0.99 |
| 5_N | 23_N | 1.292 | 0.99 |
| 11_G | 15_D | 1.282 | 0.99 |
| 7_L | 27_T | 1.234 | 0.98 |
| 11_G | 29_G | 1.220 | 0.98 |
| 14_N | 32_A | 1.062 | 0.95 |
| 19_G | 24_D | 1.058 | 0.95 |
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 | |
| 1k7iA | 1 | 1 | 98.2 | -0.014 | Contact Map |
| 1g9kA | 1 | 1 | 98.2 | -0.01 | Contact Map |
| 2ml3A | 1 | 1 | 98.1 | -0.005 | Contact Map |
| 4i35A | 1 | 1 | 98.1 | -0.003 | Contact Map |
| 1kapP | 1 | 1 | 98.1 | 0 | Contact Map |
| 2agmA | 1 | 1 | 98.1 | 0.008 | Contact Map |
| 2ml1A | 1 | 1 | 98.1 | 0.01 | Contact Map |
| 2z8xA | 1 | 1 | 97.8 | 0.071 | Contact Map |
| 2qubA | 6 | 1 | 97.8 | 0.085 | Contact Map |
| 3p4gA | 4 | 1 | 97.2 | 0.176 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)