| hp36 |
| ID: | 1482013632 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 36 (36) | ||
| Sequences: | 547 (310.2) | ||
| Seq/Len: | 15.194 | ||
| Nf(neff/√len): | 51.7 |
HHblits Results: (2016_02)
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: 15.194).
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 |
| 28_N | 32_E | 2.488 | 1.00 |
| 23_L | 26_Q | 2.321 | 1.00 |
| 4_D | 15_R | 1.890 | 1.00 |
| 21_L | 29_L | 1.672 | 1.00 |
| 2_L | 7_F | 1.662 | 1.00 |
| 19_A | 26_Q | 1.657 | 1.00 |
| 23_L | 27_Q | 1.501 | 1.00 |
| 13_M | 21_L | 1.399 | 0.99 |
| 22_P | 34_G | 1.349 | 0.99 |
| 3_S | 7_F | 1.215 | 0.98 |
| 4_D | 8_K | 1.185 | 0.98 |
| 6_D | 26_Q | 1.176 | 0.98 |
| 31_K | 34_G | 1.163 | 0.97 |
| 9_A | 12_G | 1.158 | 0.97 |
| 7_F | 18_F | 1.151 | 0.97 |
| 18_F | 21_L | 1.062 | 0.95 |
| 4_D | 23_L | 1.013 | 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 | |
| 1ujsA | 1 | 1 | 99.3 | -0.103 | Contact Map |
| 1yu8X | 1 | 1 | 99.3 | -0.094 | Contact Map |
| 2k6mS | 1 | 1 | 99.3 | -0.087 | Contact Map |
| 1qzpA | 1 | 1 | 99.3 | -0.086 | Contact Map |
| 1undA | 1 | 1 | 99.2 | -0.068 | Contact Map |
| 1wy3A | 1 | 0.9444 | 99.1 | -0.019 | Contact Map |
| 2pnwA | 1 | 0.7222 | 13.6 | 0.779 | Contact Map |
| 4jrbA | 1 | 0.9444 | 8.5 | 0.797 | Contact Map |
| 3edyA | 1 | 1 | 7.9 | 0.801 | Contact Map |
| 1t1eA | 1 | 1 | 7.8 | 0.802 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)