| d1x6za1 |
| ID: | 1513364523 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 117 (112) | ||
| Sequences: | 647 (532.3) | ||
| Seq/Len: | 5.777 | ||
| Nf(neff/√len): | 50.3 |
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: 5.777).
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 |
| 103_C | 116_C | 2.858 | 1.00 |
| 10_A | 76_F | 2.658 | 1.00 |
| 105_S | 112_I | 2.426 | 1.00 |
| 11_L | 90_I | 2.181 | 1.00 |
| 75_T | 89_I | 2.159 | 1.00 |
| 23_E | 27_R | 2.142 | 1.00 |
| 4_R | 23_E | 2.077 | 1.00 |
| 56_L | 74_L | 2.065 | 1.00 |
| 112_I | 117_S | 1.858 | 1.00 |
| 6_E | 55_K | 1.795 | 1.00 |
| 4_R | 117_S | 1.679 | 1.00 |
| 93_T | 104_T | 1.673 | 1.00 |
| 107_Q | 112_I | 1.554 | 0.99 |
| 3_A | 111_F | 1.534 | 0.99 |
| 15_N | 18_K | 1.527 | 0.99 |
| 9_S | 13_S | 1.497 | 0.99 |
| 12_A | 15_N | 1.460 | 0.99 |
| 24_A | 30_S | 1.434 | 0.98 |
| 24_A | 28_G | 1.425 | 0.98 |
| 91_T | 104_T | 1.406 | 0.98 |
| 73_T | 91_T | 1.387 | 0.98 |
| 13_S | 76_F | 1.369 | 0.98 |
| 2_F | 5_S | 1.352 | 0.97 |
| 17_L | 49_V | 1.351 | 0.97 |
| 73_T | 89_I | 1.312 | 0.97 |
| 89_I | 106_D | 1.309 | 0.97 |
| 22_E | 94_R | 1.290 | 0.96 |
| 4_R | 70_A | 1.252 | 0.95 |
| 13_S | 56_L | 1.248 | 0.95 |
| 13_S | 74_L | 1.220 | 0.95 |
| 22_E | 99_G | 1.216 | 0.94 |
| 36_G | 40_A | 1.215 | 0.94 |
| 9_S | 74_L | 1.203 | 0.94 |
| 101_W | 116_C | 1.202 | 0.94 |
| 113_P | 116_C | 1.182 | 0.93 |
| 13_S | 53_A | 1.154 | 0.92 |
| 89_I | 112_I | 1.153 | 0.92 |
| 11_L | 92_L | 1.126 | 0.91 |
| 70_A | 94_R | 1.123 | 0.91 |
| 6_E | 16_P | 1.114 | 0.90 |
| 9_S | 56_L | 1.110 | 0.90 |
| 24_A | 29_W | 1.080 | 0.88 |
| 10_A | 13_S | 1.073 | 0.88 |
| 11_L | 74_L | 1.070 | 0.88 |
| 73_T | 93_T | 1.056 | 0.87 |
| 103_C | 113_P | 1.053 | 0.87 |
| 9_S | 55_K | 1.033 | 0.85 |
| 4_R | 59_I | 1.030 | 0.85 |
| 114_K | 117_S | 1.019 | 0.84 |
| 6_E | 79_G | 1.019 | 0.84 |
| 17_L | 53_A | 1.018 | 0.84 |
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 | |
| 1qveA | 2 | 0.9231 | 99.6 | 0.252 | Contact Map |
| 1x6zA | 1 | 0.9829 | 99.6 | 0.259 | Contact Map |
| 3jyzA | 1 | 0.8974 | 99.6 | 0.281 | Contact Map |
| 3sojA | 2 | 0.7692 | 99.3 | 0.387 | Contact Map |
| 1oqwA | 2 | 0.9829 | 99.3 | 0.389 | Contact Map |
| 2hi2A | 1 | 0.906 | 99 | 0.465 | Contact Map |
| 3sokA | 2 | 0.9573 | 99 | 0.468 | Contact Map |
| 4noaA | 1 | 0.8376 | 63 | 0.825 | Contact Map |
| 2m3kA | 1 | 0.906 | 33.3 | 0.853 | Contact Map |
| 2m7gA | 1 | 0.2991 | 6.4 | 0.895 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)