| xavi12 |
| ID: | 1445220491 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 58 (56) | ||
| Sequences: | 3252 (2519.3) | ||
| Seq/Len: | 58.071 | ||
| Nf(neff/√len): | 336.7 |
HHblits Results: (2015_06)
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: 58.071).
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 |
| 14_C | 38_C | 5.160 | 1.00 |
| 9_P | 22_F | 3.006 | 1.00 |
| 48_A | 52_M | 2.927 | 1.00 |
| 24_N | 31_Q | 2.771 | 1.00 |
| 20_R | 44_N | 2.734 | 1.00 |
| 27_A | 31_Q | 2.404 | 1.00 |
| 52_M | 56_G | 2.052 | 1.00 |
| 4_F | 54_T | 2.049 | 1.00 |
| 17_R | 34_V | 2.023 | 1.00 |
| 20_R | 46_K | 1.991 | 1.00 |
| 21_Y | 48_A | 1.936 | 1.00 |
| 51_C | 55_C | 1.918 | 1.00 |
| 47_S | 50_D | 1.774 | 1.00 |
| 22_F | 31_Q | 1.545 | 1.00 |
| 13_P | 39_R | 1.472 | 1.00 |
| 19_I | 32_T | 1.255 | 0.99 |
| 7_E | 42_R | 1.253 | 0.99 |
| 4_F | 42_R | 1.248 | 0.99 |
| 6_L | 25_A | 1.220 | 0.98 |
| 7_E | 45_F | 1.205 | 0.98 |
| 19_I | 34_V | 1.195 | 0.98 |
| 10_Y | 40_A | 1.194 | 0.98 |
| 13_P | 36_G | 1.173 | 0.98 |
| 12_G | 40_A | 1.082 | 0.96 |
| 46_K | 50_D | 1.060 | 0.95 |
| 17_R | 36_G | 1.054 | 0.95 |
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 | |
| 2ddiA | 1 | 1 | 99.4 | -0.092 | Contact Map |
| 3aubA | 2 | 1 | 99.4 | -0.08 | Contact Map |
| 1g6xA | 1 | 1 | 99.4 | -0.078 | Contact Map |
| 1y62A | 6 | 0.9655 | 99.4 | -0.075 | Contact Map |
| 1co7I | 1 | 0.7069 | 99.4 | -0.072 | Contact Map |
| 3augA | 2 | 1 | 99.4 | -0.07 | Contact Map |
| 1yc0I | 1 | 1 | 99.4 | -0.068 | Contact Map |
| 2m99A | 1 | 0.9828 | 99.4 | -0.065 | Contact Map |
| 4bqdA | 2 | 1 | 99.4 | -0.064 | Contact Map |
| 1bunB | 1 | 1 | 99.4 | -0.062 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)