| Maher Kassem |
| ID: | 1462287488 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 40 (40) | ||
| Sequences: | 113 (78.4) | ||
| Seq/Len: | 2.825 | ||
| Nf(neff/√len): | 12.4 |
HHblits Results: (2016_02)
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: 2.825).
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_W | 14_W | 2.468 | 1.00 |
| 30_D | 40_L | 2.065 | 1.00 |
| 15_S | 22_I | 1.909 | 0.99 |
| 11_W | 23_P | 1.469 | 0.94 |
| 27_T | 31_T | 1.433 | 0.93 |
| 12_S | 15_S | 1.401 | 0.92 |
| 30_D | 35_I | 1.262 | 0.86 |
| 16_P | 33_V | 1.248 | 0.85 |
| 20_I | 36_S | 1.240 | 0.85 |
| 30_D | 34_W | 1.239 | 0.84 |
| 34_W | 40_L | 1.212 | 0.83 |
| 28_M | 31_T | 1.167 | 0.79 |
| 6_P | 10_Y | 1.134 | 0.77 |
| 15_S | 18_T | 1.130 | 0.76 |
| 14_W | 23_P | 1.116 | 0.75 |
| 7_D | 11_W | 1.085 | 0.72 |
| 9_G | 12_S | 1.071 | 0.71 |
| 26_F | 29_N | 1.063 | 0.70 |
| 29_N | 33_V | 1.036 | 0.67 |
| 20_I | 24_S | 1.035 | 0.67 |
| 6_P | 9_G | 1.012 | 0.64 |
| 5_K | 21_Q | 1.007 | 0.64 |
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 | |
| 3n06B | 1 | 0.65 | 96.7 | 0.589 | Contact Map |
| 1eerB | 2 | 0.55 | 96.3 | 0.607 | Contact Map |
| 3cxeC | 1 | 0.525 | 95.9 | 0.622 | Contact Map |
| 2b5iB | 1 | 0.6 | 94.9 | 0.646 | Contact Map |
| 4nn5B | 1 | 0.625 | 94.8 | 0.647 | Contact Map |
| 4hwbA | 1 | 0.5 | 93.8 | 0.664 | Contact Map |
| 3up1A | 2 | 0.65 | 93.4 | 0.669 | Contact Map |
| 4jzjC | 2 | 0.5 | 93.4 | 0.67 | Contact Map |
| 1cd9B | 2 | 0.6 | 93.1 | 0.673 | Contact Map |
| 1iarB | 1 | 0.525 | 93 | 0.675 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)