| 8061 |
| ID: | 1433386474 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 35 (35) | ||
| Sequences: | 238 (161.4) | ||
| Seq/Len: | 6.800 | ||
| Nf(neff/√len): | 27.3 |
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: 6.800).
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 |
| 10_V | 30_F | 2.033 | 1.00 |
| 10_V | 21_Y | 1.890 | 1.00 |
| 5_N | 8_T | 1.770 | 1.00 |
| 12_D | 16_N | 1.652 | 1.00 |
| 12_D | 18_V | 1.620 | 1.00 |
| 22_V | 33_S | 1.505 | 0.99 |
| 13_P | 21_Y | 1.500 | 0.99 |
| 3_T | 30_F | 1.410 | 0.99 |
| 3_T | 10_V | 1.400 | 0.99 |
| 5_N | 31_A | 1.343 | 0.98 |
| 26_G | 31_A | 1.311 | 0.98 |
| 7_L | 29_R | 1.266 | 0.97 |
| 5_N | 11_Q | 1.234 | 0.96 |
| 27_D | 35_I | 1.205 | 0.96 |
| 7_L | 22_V | 1.070 | 0.90 |
| 7_L | 11_Q | 1.050 | 0.89 |
| 13_P | 30_F | 1.002 | 0.86 |
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 | |
| 3gvoA | 1 | 1 | 98.5 | 0.318 | Contact Map |
| 3k62A | 1 | 1 | 98.3 | 0.362 | Contact Map |
| 3v71A | 1 | 1 | 98.2 | 0.38 | Contact Map |
| 3k49A | 3 | 1 | 98 | 0.399 | Contact Map |
| 4wzrA | 2 | 1 | 98 | 0.402 | Contact Map |
| 3bwtA | 1 | 1 | 97.1 | 0.505 | Contact Map |
| 3mtvA | 1 | 1 | 12.3 | 0.818 | Contact Map |
| 1lvwA | 4 | 0.8 | 6.8 | 0.837 | Contact Map |
| 3isrA | 4 | 1 | 4.4 | 0.851 | Contact Map |
| 1iimA | 2 | 0.6286 | 4.4 | 0.851 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)