| DYSF-1681-1779 |
| ID: | 1480265603 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 99 (98) | ||
| Sequences: | 488 (266.2) | ||
| Seq/Len: | 4.980 | ||
| Nf(neff/√len): | 26.9 |
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: 4.980).
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 |
| 89_P | 99_E | 1.784 | 1.00 |
| 61_P | 85_V | 1.725 | 1.00 |
| 6_V | 36_Y | 1.695 | 0.99 |
| 26_C | 43_F | 1.679 | 0.99 |
| 72_L | 75_L | 1.653 | 0.99 |
| 23_H | 36_Y | 1.627 | 0.99 |
| 24_L | 28_Q | 1.608 | 0.99 |
| 62_H | 65_P | 1.554 | 0.99 |
| 19_S | 36_Y | 1.548 | 0.99 |
| 75_L | 88_R | 1.522 | 0.99 |
| 36_Y | 41_V | 1.517 | 0.99 |
| 26_C | 93_P | 1.487 | 0.98 |
| 64_G | 69_R | 1.473 | 0.98 |
| 16_L | 24_L | 1.426 | 0.98 |
| 50_I | 54_E | 1.404 | 0.97 |
| 27_Q | 33_A | 1.393 | 0.97 |
| 10_N | 20_Q | 1.387 | 0.97 |
| 66_V | 69_R | 1.327 | 0.96 |
| 19_S | 71_A | 1.310 | 0.96 |
| 69_R | 73_H | 1.298 | 0.95 |
| 26_C | 29_H | 1.292 | 0.95 |
| 19_S | 68_E | 1.283 | 0.95 |
| 9_P | 25_F | 1.261 | 0.94 |
| 83_E | 88_R | 1.250 | 0.94 |
| 87_S | 91_Y | 1.220 | 0.93 |
| 41_V | 67_E | 1.206 | 0.92 |
| 25_F | 80_L | 1.204 | 0.92 |
| 3_T | 21_L | 1.193 | 0.92 |
| 67_E | 74_V | 1.184 | 0.91 |
| 45_D | 50_I | 1.167 | 0.91 |
| 15_Q | 29_H | 1.148 | 0.90 |
| 87_S | 98_I | 1.129 | 0.89 |
| 74_V | 97_D | 1.128 | 0.89 |
| 60_N | 63_L | 1.122 | 0.88 |
| 26_C | 30_R | 1.101 | 0.87 |
| 73_H | 77_Q | 1.088 | 0.86 |
| 28_Q | 32_K | 1.083 | 0.86 |
| 75_L | 86_E | 1.074 | 0.85 |
| 2_Q | 76_Q | 1.069 | 0.85 |
| 68_E | 72_L | 1.069 | 0.85 |
| 8_G | 12_W | 1.061 | 0.84 |
| 40_R | 49_S | 1.060 | 0.84 |
| 15_Q | 32_K | 1.055 | 0.84 |
| 26_C | 89_P | 1.040 | 0.83 |
| 17_R | 25_F | 1.038 | 0.82 |
| 8_G | 14_D | 1.034 | 0.82 |
| 78_Q | 92_S | 1.028 | 0.82 |
| 55_A | 85_V | 1.012 | 0.80 |
| 50_I | 53_I | 1.008 | 0.80 |
| 70_L | 87_S | 1.002 | 0.79 |
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 | |
| 3adgA | 1 | 0.6465 | 71.1 | 0.898 | Contact Map |
| 1whnA | 1 | 0.9596 | 67.3 | 0.901 | Contact Map |
| 1di2A | 2 | 0.6465 | 58.7 | 0.906 | Contact Map |
| 3htxA | 2 | 0.5253 | 56.9 | 0.907 | Contact Map |
| 3adjA | 1 | 0.6667 | 49.4 | 0.911 | Contact Map |
| 3adlA | 1 | 0.7172 | 43.5 | 0.914 | Contact Map |
| 3vyyA | 2 | 0.7576 | 36.7 | 0.917 | Contact Map |
| 2db2A | 1 | 0.9596 | 34.1 | 0.919 | Contact Map |
| 3rv0A | 4 | 0.7778 | 31.6 | 0.92 | Contact Map |
| 2khxA | 1 | 0.6869 | 28.2 | 0.922 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)