| sesB yet again |
| ID: | 1489765613 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 42 (39) | ||
| Sequences: | 56 (51) | ||
| Seq/Len: | 1.436 | ||
| Nf(neff/√len): | 8.2 |
Jackhmmer Results: (2016_04)
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: 1.436).
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 |
| 21_Q | 29_E | 2.645 | 1.00 |
| 18_G | 23_I | 2.386 | 1.00 |
| 7_N | 35_F | 1.873 | 0.96 |
| 25_K | 40_Q | 1.631 | 0.91 |
| 3_S | 31_S | 1.562 | 0.88 |
| 22_N | 28_N | 1.543 | 0.87 |
| 8_L | 29_E | 1.481 | 0.84 |
| 28_N | 32_G | 1.386 | 0.78 |
| 5_F | 35_F | 1.384 | 0.78 |
| 21_Q | 24_N | 1.306 | 0.72 |
| 5_F | 13_Q | 1.228 | 0.66 |
| 22_N | 26_G | 1.196 | 0.63 |
| 24_N | 34_N | 1.192 | 0.62 |
| 12_D | 28_N | 1.171 | 0.60 |
| 17_P | 24_N | 1.161 | 0.59 |
| 16_T | 39_V | 1.151 | 0.58 |
| 13_Q | 18_G | 1.145 | 0.58 |
| 5_F | 15_N | 1.144 | 0.57 |
| 32_G | 37_G | 1.114 | 0.54 |
| 11_G | 29_E | 1.103 | 0.53 |
| 4_S | 7_N | 1.095 | 0.53 |
| 14_F | 36_Y | 1.049 | 0.48 |
| 15_N | 37_G | 1.032 | 0.46 |
| 17_P | 31_S | 1.007 | 0.44 |
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 | |
| 3kogA | 1 | 0.1905 | 1.2 | 0.911 | Contact Map |
| 4j94A | 1 | 1 | 1.1 | 0.913 | Contact Map |
| 2iy9A | 1 | 1 | 1 | 0.916 | Contact Map |
| 4h6xA | 2 | 1 | 0.9 | 0.916 | Contact Map |
| 3n6yA | 2 | 0.3571 | 0.9 | 0.917 | Contact Map |
| 1gciA | 1 | 1 | 0.9 | 0.917 | Contact Map |
| 4dztA | 1 | 1 | 0.9 | 0.917 | Contact Map |
| 1to2E | 1 | 1 | 0.9 | 0.918 | Contact Map |
| 2b6nA | 1 | 1 | 0.9 | 0.918 | Contact Map |
| 3nb2A | 4 | 0.4286 | 0.8 | 0.92 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)