| Pfam PF13900 v27 |
| ID: | 1429155527 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 43 (43) | ||
| Sequences: | 589 (265.7) | ||
| Seq/Len: | 13.698 | ||
| Nf(neff/√len): | 40.5 |
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: 13.698).
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 |
| 11_L | 17_E | 3.098 | 1.00 |
| 35_P | 38_G | 1.946 | 1.00 |
| 6_L | 12_P | 1.819 | 1.00 |
| 16_F | 21_C | 1.803 | 1.00 |
| 11_L | 18_G | 1.719 | 1.00 |
| 34_P | 38_G | 1.542 | 1.00 |
| 16_F | 19_S | 1.537 | 1.00 |
| 35_P | 39_N | 1.498 | 1.00 |
| 4_C | 7_G | 1.444 | 1.00 |
| 14_P | 31_R | 1.399 | 0.99 |
| 34_P | 40_F | 1.367 | 0.99 |
| 27_S | 30_Y | 1.315 | 0.99 |
| 2_Q | 5_D | 1.278 | 0.99 |
| 21_C | 31_R | 1.268 | 0.99 |
| 28_W | 31_R | 1.258 | 0.99 |
| 13_P | 16_F | 1.246 | 0.98 |
| 34_P | 37_P | 1.233 | 0.98 |
| 9_L | 23_S | 1.058 | 0.95 |
| 27_S | 32_R | 1.052 | 0.95 |
| 2_Q | 25_P | 1.028 | 0.94 |
| 4_C | 11_L | 1.026 | 0.94 |
| 15_G | 27_S | 1.018 | 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 | |
| 2bivA | 3 | 0.3953 | 3.8 | 0.89 | Contact Map |
| 3f6nA | 4 | 0 | 2.3 | 0.902 | Contact Map |
| 3abhA | 2 | 0.3953 | 2.1 | 0.904 | Contact Map |
| 1tz7A | 2 | 0.6977 | 1.9 | 0.906 | Contact Map |
| 3zdsA | 12 | 0.8372 | 1.8 | 0.908 | Contact Map |
| 4c5iA | 2 | 0.3256 | 1.6 | 0.91 | Contact Map |
| 3wtsA | 2 | 0.8372 | 1.6 | 0.91 | Contact Map |
| 4m5dA | 1 | 0.9302 | 1.5 | 0.912 | Contact Map |
| 4g59C | 2 | 0 | 1.5 | 0.912 | Contact Map |
| 1oz2A | 1 | 0.5349 | 1.3 | 0.914 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)