| cgtY-TAYHGYWARDFKKTNPAYGTIADFQNLIAA 10-4-8i |
| ID: | 1510738952 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 30 (29) | ||
| Sequences: | 14645 (6641.2) | ||
| Seq/Len: | 505.000 | ||
| Nf(neff/√len): | 1233.2 |
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: 505.000).
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 |
| 20_T | 23_D | 3.426 | 1.00 |
| 26_N | 30_A | 2.467 | 1.00 |
| 13_K | 21_I | 2.438 | 1.00 |
| 2_A | 7_W | 1.921 | 1.00 |
| 8_A | 11_F | 1.909 | 1.00 |
| 24_F | 28_I | 1.775 | 1.00 |
| 5_G | 17_A | 1.773 | 1.00 |
| 23_D | 26_N | 1.597 | 1.00 |
| 21_I | 25_Q | 1.594 | 1.00 |
| 22_A | 25_Q | 1.550 | 1.00 |
| 14_T | 24_F | 1.352 | 0.99 |
| 5_G | 18_Y | 1.307 | 0.99 |
| 15_N | 18_Y | 1.280 | 0.99 |
| 25_Q | 28_I | 1.132 | 0.97 |
| 25_Q | 29_A | 1.109 | 0.96 |
| 22_A | 26_N | 1.032 | 0.94 |
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 | |
| 3edfA | 2 | 1 | 97.3 | -0.108 | Contact Map |
| 1d3cA | 1 | 1 | 97.3 | -0.108 | Contact Map |
| 4jclA | 1 | 1 | 97.3 | -0.107 | Contact Map |
| 1qhoA | 1 | 1 | 97.3 | -0.102 | Contact Map |
| 4jcmA | 1 | 1 | 97.3 | -0.101 | Contact Map |
| 1iv8A | 1 | 1 | 97.2 | -0.096 | Contact Map |
| 3bmvA | 1 | 1 | 97.2 | -0.094 | Contact Map |
| 1cygA | 1 | 1 | 97.2 | -0.093 | Contact Map |
| 1ji1A | 2 | 1 | 97.2 | -0.093 | Contact Map |
| 3hjeA | 1 | 1 | 97.2 | -0.086 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)