| 3_trees |
| ID: | 1497251881 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 1428 (870.3) | ||
| Seq/Len: | 16.414 | ||
| Nf(neff/√len): | 93.3 |
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: 16.414).
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 |
| 63_I | 81_L | 2.797 | 1.00 |
| 4_Y | 78_I | 2.253 | 1.00 |
| 69_E | 72_D | 2.168 | 1.00 |
| 12_P | 16_D | 1.970 | 1.00 |
| 13_A | 20_E | 1.845 | 1.00 |
| 22_L | 81_L | 1.759 | 1.00 |
| 14_L | 81_L | 1.640 | 1.00 |
| 60_L | 63_I | 1.597 | 1.00 |
| 26_A | 77_L | 1.555 | 1.00 |
| 8_I | 14_L | 1.479 | 1.00 |
| 13_A | 80_T | 1.442 | 1.00 |
| 5_F | 62_L | 1.399 | 0.99 |
| 6_F | 87_A | 1.393 | 0.99 |
| 1_V | 64_L | 1.378 | 0.99 |
| 5_F | 8_I | 1.357 | 0.99 |
| 37_F | 55_L | 1.338 | 0.99 |
| 25_S | 76_T | 1.323 | 0.99 |
| 25_S | 51_S | 1.307 | 0.99 |
| 6_F | 70_A | 1.240 | 0.98 |
| 23_C | 29_Y | 1.237 | 0.98 |
| 50_L | 83_A | 1.231 | 0.98 |
| 58_G | 72_D | 1.213 | 0.98 |
| 9_H | 32_L | 1.203 | 0.98 |
| 13_A | 23_C | 1.180 | 0.98 |
| 33_I | 65_V | 1.160 | 0.97 |
| 32_L | 86_V | 1.142 | 0.97 |
| 28_M | 82_H | 1.140 | 0.97 |
| 58_G | 70_A | 1.133 | 0.97 |
| 7_K | 23_C | 1.132 | 0.97 |
| 12_P | 78_I | 1.130 | 0.97 |
| 22_L | 61_Y | 1.130 | 0.97 |
| 60_L | 70_A | 1.125 | 0.97 |
| 4_Y | 54_S | 1.106 | 0.96 |
| 17_K | 42_F | 1.104 | 0.96 |
| 53_S | 57_L | 1.098 | 0.96 |
| 23_C | 40_R | 1.096 | 0.96 |
| 50_L | 86_V | 1.087 | 0.96 |
| 58_G | 78_I | 1.074 | 0.95 |
| 22_L | 76_T | 1.070 | 0.95 |
| 23_C | 57_L | 1.052 | 0.95 |
| 22_L | 26_A | 1.035 | 0.94 |
| 38_G | 45_F | 1.021 | 0.93 |
| 13_A | 22_L | 1.006 | 0.93 |
| 32_L | 52_S | 1.001 | 0.92 |
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 | |
| 3ccdA | 2 | 0.977 | 94.2 | 0.829 | Contact Map |
| 1ka5A | 1 | 1 | 93.3 | 0.835 | Contact Map |
| 1kklH | 3 | 1 | 93.1 | 0.837 | Contact Map |
| 1ptfA | 1 | 1 | 92.8 | 0.838 | Contact Map |
| 1y51A | 3 | 0.9885 | 92.1 | 0.841 | Contact Map |
| 1sphA | 2 | 0.9885 | 91.9 | 0.842 | Contact Map |
| 3ihsA | 2 | 0.9425 | 91.7 | 0.843 | Contact Map |
| 1pchA | 1 | 0.9885 | 90.1 | 0.849 | Contact Map |
| 3le1A | 2 | 0.9885 | 89.1 | 0.852 | Contact Map |
| 3wpuA | 2 | 0.9655 | 6.9 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)