| pum2 |
| ID: | 1433422581 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 35 (35) | ||
| Sequences: | 197 (108.4) | ||
| Seq/Len: | 5.629 | ||
| Nf(neff/√len): | 18.3 |
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: 5.629).
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 |
| 1_E | 24_E | 1.701 | 1.00 |
| 1_E | 13_Q | 1.635 | 0.99 |
| 7_L | 11_K | 1.456 | 0.99 |
| 19_V | 24_E | 1.456 | 0.99 |
| 9_C | 24_E | 1.453 | 0.98 |
| 1_E | 23_I | 1.405 | 0.98 |
| 5_H | 21_K | 1.373 | 0.98 |
| 13_Q | 24_E | 1.321 | 0.97 |
| 19_V | 26_V | 1.292 | 0.96 |
| 23_I | 35_I | 1.257 | 0.95 |
| 10_V | 25_C | 1.249 | 0.95 |
| 2_L | 27_Q | 1.240 | 0.95 |
| 27_Q | 31_L | 1.188 | 0.93 |
| 16_N | 33_F | 1.163 | 0.92 |
| 14_N | 23_I | 1.158 | 0.92 |
| 13_Q | 23_I | 1.111 | 0.90 |
| 9_C | 35_I | 1.098 | 0.89 |
| 25_C | 32_Q | 1.085 | 0.88 |
| 18_V | 24_E | 1.084 | 0.88 |
| 21_K | 31_L | 1.042 | 0.85 |
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 | 98.4 | 0.396 | Contact Map |
| 3v71A | 1 | 1 | 98.3 | 0.4 | Contact Map |
| 3k62A | 1 | 1 | 98.3 | 0.403 | Contact Map |
| 3k49A | 3 | 1 | 98.3 | 0.409 | Contact Map |
| 4wzrA | 2 | 1 | 97.4 | 0.517 | Contact Map |
| 3bwtA | 1 | 1 | 94.8 | 0.626 | Contact Map |
| 3er9B | 1 | 0.9429 | 33.7 | 0.794 | Contact Map |
| 2vchA | 1 | 0.3714 | 7.7 | 0.847 | Contact Map |
| 1rw2A | 1 | 0.9714 | 6.2 | 0.853 | Contact Map |
| 4c5sA | 4 | 0.4 | 5.8 | 0.856 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)