| DYSF-1535-1680 |
| ID: | 1480268172 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 146 (99) | ||
| Sequences: | 14369 (8969.5) | ||
| Seq/Len: | 145.141 | ||
| Nf(neff/√len): | 901.5 |
Jackhmmer Results: (2016_04)
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: 145.141).
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 |
| 83_N | 95_K | 3.280 | 1.00 |
| 52_R | 92_V | 2.710 | 1.00 |
| 53_A | 93_F | 2.604 | 1.00 |
| 108_D | 129_V | 2.456 | 1.00 |
| 58_P | 62_N | 2.330 | 1.00 |
| 114_Y | 124_K | 2.289 | 1.00 |
| 117_D | 123_E | 2.093 | 1.00 |
| 65_C | 125_I | 2.063 | 1.00 |
| 50_I | 82_D | 2.058 | 1.00 |
| 110_K | 129_V | 2.049 | 1.00 |
| 49_Y | 96_M | 2.040 | 1.00 |
| 69_I | 111_I | 2.022 | 1.00 |
| 85_I | 88_T | 2.000 | 1.00 |
| 47_R | 98_E | 1.991 | 1.00 |
| 69_I | 113_L | 1.917 | 1.00 |
| 124_K | 127_E | 1.808 | 1.00 |
| 110_K | 127_E | 1.746 | 1.00 |
| 53_A | 56_L | 1.693 | 1.00 |
| 59_K | 125_I | 1.691 | 1.00 |
| 84_Y | 116_Y | 1.680 | 1.00 |
| 70_K | 112_T | 1.644 | 1.00 |
| 112_T | 127_E | 1.620 | 1.00 |
| 50_I | 69_I | 1.594 | 1.00 |
| 69_I | 82_D | 1.587 | 1.00 |
| 71_I | 97_F | 1.572 | 1.00 |
| 45_L | 100_T | 1.554 | 1.00 |
| 71_I | 111_I | 1.546 | 1.00 |
| 68_Y | 122_D | 1.443 | 1.00 |
| 51_V | 94_G | 1.443 | 1.00 |
| 56_L | 113_L | 1.420 | 1.00 |
| 47_R | 96_M | 1.392 | 0.99 |
| 131_D | 134_N | 1.370 | 0.99 |
| 108_D | 131_D | 1.350 | 0.99 |
| 72_S | 112_T | 1.340 | 0.99 |
| 50_I | 71_I | 1.314 | 0.99 |
| 49_Y | 94_G | 1.306 | 0.99 |
| 112_T | 124_K | 1.292 | 0.99 |
| 65_C | 89_L | 1.282 | 0.99 |
| 68_Y | 114_Y | 1.281 | 0.99 |
| 45_L | 98_E | 1.229 | 0.98 |
| 58_P | 64_K | 1.213 | 0.98 |
| 53_A | 91_P | 1.207 | 0.98 |
| 70_K | 114_Y | 1.172 | 0.98 |
| 72_S | 110_K | 1.168 | 0.97 |
| 67_P | 93_F | 1.131 | 0.97 |
| 85_I | 93_F | 1.095 | 0.96 |
| 69_I | 93_F | 1.086 | 0.96 |
| 80_D | 97_F | 1.082 | 0.96 |
| 67_P | 115_D | 1.072 | 0.95 |
| 86_P | 116_Y | 1.072 | 0.95 |
| 64_K | 89_L | 1.068 | 0.95 |
| 58_P | 65_C | 1.065 | 0.95 |
| 68_Y | 116_Y | 1.036 | 0.94 |
| 54_F | 92_V | 1.009 | 0.93 |
| 59_K | 65_C | 1.001 | 0.92 |
| 80_D | 99_L | 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 | |
| 3jzyA | 1 | 0.6986 | 99.8 | 0.44 | Contact Map |
| 2r83A | 2 | 0.8151 | 99.8 | 0.445 | Contact Map |
| 3m7fB | 1 | 0.6644 | 99.8 | 0.455 | Contact Map |
| 1cjyA | 2 | 0.7329 | 99.8 | 0.458 | Contact Map |
| 4npjA | 2 | 0.8356 | 99.7 | 0.461 | Contact Map |
| 1rsyA | 1 | 0.8767 | 99.7 | 0.462 | Contact Map |
| 1dqvA | 1 | 0.8219 | 99.7 | 0.463 | Contact Map |
| 3fdwA | 2 | 0.8082 | 99.7 | 0.463 | Contact Map |
| 2cm5A | 1 | 0.863 | 99.7 | 0.465 | Contact Map |
| 4iqhA | 3 | 0.7055 | 99.7 | 0.466 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)