| VgrG 520-580 |
| ID: | 1490184619 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 61 (60) | ||
| Sequences: | 875 (477.9) | ||
| Seq/Len: | 14.583 | ||
| Nf(neff/√len): | 61.7 |
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: 14.583).
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 |
| 25_A | 33_I | 3.794 | 1.00 |
| 48_Q | 60_E | 3.128 | 1.00 |
| 3_G | 31_D | 2.857 | 1.00 |
| 37_G | 41_I | 2.544 | 1.00 |
| 8_L | 27_L | 2.430 | 1.00 |
| 15_D | 19_E | 2.171 | 1.00 |
| 2_Y | 23_E | 1.972 | 1.00 |
| 58_M | 61_A | 1.919 | 1.00 |
| 13_N | 55_M | 1.734 | 1.00 |
| 31_D | 39_K | 1.549 | 1.00 |
| 1_E | 5_K | 1.438 | 1.00 |
| 33_I | 37_G | 1.398 | 0.99 |
| 14_V | 20_L | 1.372 | 0.99 |
| 37_G | 40_G | 1.338 | 0.99 |
| 1_E | 19_E | 1.292 | 0.99 |
| 3_G | 6_T | 1.282 | 0.99 |
| 29_T | 33_I | 1.280 | 0.99 |
| 46_D | 60_E | 1.264 | 0.99 |
| 42_F | 46_D | 1.254 | 0.99 |
| 53_G | 57_D | 1.229 | 0.98 |
| 44_S | 61_A | 1.208 | 0.98 |
| 46_D | 61_A | 1.192 | 0.98 |
| 21_R | 26_E | 1.190 | 0.98 |
| 38_G | 47_M | 1.151 | 0.97 |
| 57_D | 60_E | 1.145 | 0.97 |
| 42_F | 45_A | 1.102 | 0.96 |
| 45_A | 57_D | 1.014 | 0.93 |
| 6_T | 10_L | 1.012 | 0.93 |
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 | |
| 3dgpB | 1 | 0.4426 | 4.4 | 0.901 | Contact Map |
| 2o14A | 1 | 0.9836 | 3 | 0.908 | Contact Map |
| 4kkrA | 2 | 0.9672 | 1.7 | 0.92 | Contact Map |
| 2c3fA | 1 | 0.9508 | 1.6 | 0.921 | Contact Map |
| 1knxA | 6 | 0.8361 | 1.4 | 0.924 | Contact Map |
| 3izoF | 3 | 0 | 1.3 | 0.926 | Contact Map |
| 2ozvA | 2 | 0.3934 | 1.2 | 0.927 | Contact Map |
| 4pabA | 2 | 0.9836 | 1.2 | 0.927 | Contact Map |
| 4o9xA | 1 | 0.8689 | 1.1 | 0.928 | Contact Map |
| 1e8gA | 2 | 0.4098 | 1 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)