| Pfam PF13900 v27 |
| ID: | 1429155422 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 48 (48) | ||
| Sequences: | 638 (291.7) | ||
| Seq/Len: | 13.292 | ||
| Nf(neff/√len): | 42.1 |
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: 13.292).
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 |
| 16_P | 22_K | 2.737 | 1.00 |
| 11_L | 17_P | 2.614 | 1.00 |
| 21_F | 26_C | 2.291 | 1.00 |
| 21_F | 24_F | 2.248 | 1.00 |
| 40_P | 43_A | 2.055 | 1.00 |
| 4_A | 7_Q | 1.974 | 1.00 |
| 40_P | 44_N | 1.793 | 1.00 |
| 16_P | 23_Q | 1.773 | 1.00 |
| 3_Q | 7_Q | 1.444 | 1.00 |
| 32_S | 35_Y | 1.371 | 0.99 |
| 19_P | 36_R | 1.353 | 0.99 |
| 26_C | 36_R | 1.345 | 0.99 |
| 11_L | 24_F | 1.335 | 0.99 |
| 39_P | 43_A | 1.241 | 0.98 |
| 18_P | 24_F | 1.223 | 0.98 |
| 1_V | 4_A | 1.208 | 0.98 |
| 3_Q | 6_V | 1.186 | 0.98 |
| 15_Q | 18_P | 1.185 | 0.98 |
| 18_P | 21_F | 1.161 | 0.97 |
| 17_P | 24_F | 1.114 | 0.96 |
| 2_A | 5_G | 1.088 | 0.96 |
| 34_D | 37_H | 1.044 | 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 | |
| 2qh5A | 2 | 0.2083 | 2.3 | 0.912 | Contact Map |
| 4agiA | 4 | 0.3958 | 2 | 0.914 | Contact Map |
| 3vthA | 2 | 0.3542 | 2 | 0.915 | Contact Map |
| 1tz7A | 2 | 0.625 | 1.4 | 0.921 | Contact Map |
| 4g59C | 2 | 0 | 1.3 | 0.923 | Contact Map |
| 3wtsA | 2 | 0.75 | 1.3 | 0.923 | Contact Map |
| 4m5dA | 1 | 0.875 | 1.3 | 0.923 | Contact Map |
| 1pbyC | 1 | 0.3958 | 1.2 | 0.925 | Contact Map |
| 1jmxG | 1 | 0.3958 | 1.2 | 0.925 | Contact Map |
| 2bivA | 3 | 0.4167 | 1.1 | 0.926 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)