| 3a0j |
| ID: | 1511799599 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 73 (68) | ||
| Sequences: | 5177 (2621.6) | ||
| Seq/Len: | 76.132 | ||
| Nf(neff/√len): | 317.9 |
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: 76.132).
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 |
| 28_V | 65_V | 3.214 | 1.00 |
| 50_D | 64_N | 3.067 | 1.00 |
| 52_E | 63_V | 3.067 | 1.00 |
| 45_D | 67_V | 2.386 | 1.00 |
| 7_K | 25_D | 2.300 | 1.00 |
| 48_T | 66_T | 2.147 | 1.00 |
| 20_R | 49_F | 2.112 | 1.00 |
| 3_K | 46_I | 2.076 | 1.00 |
| 3_K | 48_T | 1.973 | 1.00 |
| 5_R | 46_I | 1.782 | 1.00 |
| 53_P | 60_P | 1.733 | 1.00 |
| 48_T | 68_V | 1.612 | 1.00 |
| 2_Q | 20_R | 1.581 | 1.00 |
| 62_A | 65_V | 1.579 | 1.00 |
| 30_Y | 39_R | 1.559 | 1.00 |
| 21_E | 46_I | 1.550 | 1.00 |
| 3_K | 21_E | 1.469 | 1.00 |
| 4_G | 18_I | 1.428 | 1.00 |
| 42_N | 45_D | 1.411 | 1.00 |
| 7_K | 19_E | 1.411 | 1.00 |
| 32_A | 63_V | 1.408 | 1.00 |
| 26_V | 51_V | 1.388 | 0.99 |
| 51_V | 60_P | 1.372 | 0.99 |
| 11_A | 40_T | 1.319 | 0.99 |
| 54_G | 59_G | 1.274 | 0.99 |
| 20_R | 26_V | 1.260 | 0.99 |
| 8_W | 25_D | 1.226 | 0.98 |
| 6_V | 47_V | 1.211 | 0.98 |
| 28_V | 41_L | 1.149 | 0.97 |
| 18_I | 47_V | 1.101 | 0.96 |
| 17_F | 27_F | 1.093 | 0.96 |
| 20_R | 23_D | 1.090 | 0.96 |
| 18_I | 49_F | 1.087 | 0.96 |
| 54_G | 61_Q | 1.085 | 0.96 |
| 34_N | 66_T | 1.076 | 0.95 |
| 20_R | 24_T | 1.014 | 0.93 |
| 32_A | 61_Q | 1.003 | 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 | |
| 3a0jA | 2 | 1 | 99.8 | -0.008 | Contact Map |
| 2lxjA | 1 | 0.9041 | 99.7 | 0.034 | Contact Map |
| 1c9oA | 2 | 0.9041 | 99.7 | 0.038 | Contact Map |
| 3camA | 2 | 0.9041 | 99.7 | 0.053 | Contact Map |
| 3uljA | 2 | 0.9726 | 99.7 | 0.064 | Contact Map |
| 1g6pA | 1 | 0.9041 | 99.7 | 0.065 | Contact Map |
| 3i2zB | 2 | 0.9041 | 99.7 | 0.067 | Contact Map |
| 3ts2A | 2 | 0.9726 | 99.7 | 0.075 | Contact Map |
| 2kcmA | 1 | 0.9589 | 99.7 | 0.075 | Contact Map |
| 2lssA | 1 | 0.9041 | 99.7 | 0.078 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)