| 4qhjA |
| ID: | 1491921513 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 108 (98) | ||
| Sequences: | 1754 (1222.7) | ||
| Seq/Len: | 17.898 | ||
| Nf(neff/√len): | 123.5 |
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: 17.898).
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 |
| 10_I | 64_R | 3.778 | 1.00 |
| 54_I | 66_I | 3.106 | 1.00 |
| 76_Y | 79_Y | 2.933 | 1.00 |
| 92_F | 98_I | 2.753 | 1.00 |
| 27_I | 47_T | 2.630 | 1.00 |
| 11_L | 50_I | 2.537 | 1.00 |
| 94_N | 98_I | 2.315 | 1.00 |
| 68_A | 88_L | 2.243 | 1.00 |
| 65_F | 85_E | 2.199 | 1.00 |
| 76_Y | 83_E | 2.185 | 1.00 |
| 58_L | 62_E | 2.121 | 1.00 |
| 89_L | 96_E | 2.004 | 1.00 |
| 72_L | 87_E | 1.942 | 1.00 |
| 85_E | 88_L | 1.807 | 1.00 |
| 61_E | 98_I | 1.691 | 1.00 |
| 34_L | 51_N | 1.601 | 1.00 |
| 46_K | 78_K | 1.600 | 1.00 |
| 76_Y | 87_E | 1.577 | 1.00 |
| 87_E | 90_F | 1.557 | 1.00 |
| 68_A | 92_F | 1.548 | 1.00 |
| 20_L | 75_K | 1.513 | 1.00 |
| 75_K | 87_E | 1.467 | 1.00 |
| 32_K | 49_Y | 1.421 | 1.00 |
| 68_A | 91_L | 1.397 | 0.99 |
| 28_K | 47_T | 1.395 | 0.99 |
| 7_L | 50_I | 1.387 | 0.99 |
| 46_K | 74_L | 1.341 | 0.99 |
| 10_I | 60_D | 1.333 | 0.99 |
| 99_L | 103_I | 1.321 | 0.99 |
| 13_N | 17_E | 1.319 | 0.99 |
| 37_K | 40_S | 1.302 | 0.99 |
| 89_L | 95_K | 1.299 | 0.99 |
| 18_L | 91_L | 1.296 | 0.99 |
| 32_K | 52_K | 1.242 | 0.98 |
| 43_L | 78_K | 1.223 | 0.98 |
| 30_K | 47_T | 1.208 | 0.98 |
| 20_L | 74_L | 1.191 | 0.98 |
| 68_A | 71_L | 1.175 | 0.98 |
| 88_L | 95_K | 1.167 | 0.97 |
| 82_N | 86_E | 1.164 | 0.97 |
| 26_N | 74_L | 1.141 | 0.97 |
| 33_P | 52_K | 1.138 | 0.97 |
| 6_I | 63_I | 1.138 | 0.97 |
| 33_P | 53_N | 1.103 | 0.96 |
| 15_I | 26_N | 1.086 | 0.96 |
| 11_L | 29_I | 1.060 | 0.95 |
| 94_N | 97_A | 1.050 | 0.94 |
| 11_L | 48_I | 1.039 | 0.94 |
| 15_I | 20_L | 1.036 | 0.94 |
| 14_T | 17_E | 1.033 | 0.94 |
| 18_L | 72_L | 1.033 | 0.94 |
| 58_L | 99_L | 1.032 | 0.94 |
| 42_S | 49_Y | 1.019 | 0.93 |
| 50_I | 67_L | 1.008 | 0.93 |
| 18_L | 68_A | 1.005 | 0.93 |
| 41_I | 74_L | 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 | |
| 4qhjA | 2 | 0.9537 | 100 | 0.18 | Contact Map |
| 4jiuA | 1 | 0.9074 | 100 | 0.203 | Contact Map |
| 4jixA | 2 | 0.9444 | 100 | 0.216 | Contact Map |
| 3cqbA | 2 | 0.7593 | 97.9 | 0.755 | Contact Map |
| 4il3A | 2 | 0.9444 | 95.6 | 0.818 | Contact Map |
| 4aw6A | 4 | 0.9352 | 92.8 | 0.841 | Contact Map |
| 3c37A | 2 | 0.9352 | 92.2 | 0.844 | Contact Map |
| 3dteA | 1 | 0.9444 | 81.8 | 0.869 | Contact Map |
| 4jbsA | 2 | 0.9444 | 78.1 | 0.873 | Contact Map |
| 4pj6A | 2 | 0.9259 | 74 | 0.877 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)