| pumdrome |
| ID: | 1433422879 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 35 (35) | ||
| Sequences: | 217 (126.3) | ||
| Seq/Len: | 6.200 | ||
| Nf(neff/√len): | 21.3 |
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: 6.200).
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 |
| 5_Q | 8_S | 1.766 | 1.00 |
| 14_Y | 17_R | 1.654 | 1.00 |
| 14_Y | 24_E | 1.587 | 0.99 |
| 26_C | 30_Q | 1.583 | 0.99 |
| 17_R | 24_E | 1.486 | 0.99 |
| 27_T | 30_Q | 1.310 | 0.97 |
| 3_K | 33_P | 1.292 | 0.97 |
| 9_L | 17_R | 1.285 | 0.97 |
| 19_I | 23_L | 1.254 | 0.96 |
| 25_H | 29_E | 1.201 | 0.95 |
| 14_Y | 18_V | 1.199 | 0.95 |
| 10_S | 23_L | 1.198 | 0.95 |
| 29_E | 33_P | 1.189 | 0.94 |
| 1_A | 29_E | 1.168 | 0.94 |
| 6_V | 19_I | 1.152 | 0.93 |
| 27_T | 32_T | 1.121 | 0.92 |
| 16_C | 21_R | 1.108 | 0.91 |
| 9_L | 13_P | 1.096 | 0.90 |
| 8_S | 22_I | 1.063 | 0.89 |
| 18_V | 21_R | 1.051 | 0.88 |
| 20_Q | 24_E | 1.048 | 0.88 |
| 7_Y | 29_E | 1.004 | 0.84 |
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 | |
| 3k49A | 3 | 1 | 98.3 | 0.37 | Contact Map |
| 3gvoA | 1 | 1 | 98.3 | 0.374 | Contact Map |
| 4wzrA | 2 | 1 | 97.7 | 0.454 | Contact Map |
| 3v71A | 1 | 1 | 97.7 | 0.455 | Contact Map |
| 3k62A | 1 | 1 | 97.7 | 0.457 | Contact Map |
| 3bwtA | 1 | 1 | 97 | 0.517 | Contact Map |
| 4n0aH | 3 | 1 | 6.3 | 0.843 | Contact Map |
| 2xesA | 2 | 1 | 6.1 | 0.844 | Contact Map |
| 3hlzA | 2 | 0.8 | 5.7 | 0.847 | Contact Map |
| 4ogpA | 2 | 1 | 5.7 | 0.847 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)