| cool002 |
| ID: | 1508841773 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 95 (83) | ||
| Sequences: | 253 (213.9) | ||
| Seq/Len: | 3.048 | ||
| Nf(neff/√len): | 23.5 |
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: 3.048).
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 |
| 70_K | 74_E | 3.090 | 1.00 |
| 19_V | 69_V | 2.981 | 1.00 |
| 46_E | 81_K | 2.937 | 1.00 |
| 40_E | 44_L | 2.439 | 1.00 |
| 64_S | 67_G | 2.254 | 1.00 |
| 74_E | 78_A | 2.181 | 1.00 |
| 40_E | 43_R | 2.046 | 1.00 |
| 12_E | 73_K | 1.993 | 1.00 |
| 42_K | 51_S | 1.890 | 0.99 |
| 61_R | 71_E | 1.819 | 0.99 |
| 49_D | 58_R | 1.751 | 0.99 |
| 63_D | 67_G | 1.558 | 0.97 |
| 17_E | 20_K | 1.510 | 0.96 |
| 23_F | 62_E | 1.466 | 0.95 |
| 78_A | 83_G | 1.460 | 0.95 |
| 78_A | 86_Q | 1.378 | 0.93 |
| 60_D | 64_S | 1.363 | 0.92 |
| 52_D | 56_Y | 1.356 | 0.92 |
| 79_N | 83_G | 1.339 | 0.91 |
| 21_D | 33_L | 1.318 | 0.90 |
| 70_K | 78_A | 1.318 | 0.90 |
| 50_G | 53_L | 1.317 | 0.90 |
| 41_F | 47_H | 1.263 | 0.87 |
| 5_H | 9_D | 1.233 | 0.86 |
| 57_P | 60_D | 1.228 | 0.85 |
| 65_P | 69_V | 1.227 | 0.85 |
| 57_P | 63_D | 1.217 | 0.85 |
| 46_E | 76_R | 1.205 | 0.84 |
| 20_K | 66_E | 1.199 | 0.83 |
| 15_F | 41_F | 1.095 | 0.75 |
| 35_I | 38_V | 1.076 | 0.73 |
| 77_A | 83_G | 1.076 | 0.73 |
| 21_D | 37_L | 1.072 | 0.73 |
| 35_I | 39_L | 1.070 | 0.73 |
| 23_F | 68_I | 1.044 | 0.70 |
| 18_F | 41_F | 1.017 | 0.67 |
| 78_A | 87_G | 1.012 | 0.66 |
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 | |
| 1unkA | 4 | 0.9053 | 100 | 0.106 | Contact Map |
| 4f37A | 2 | 0.9053 | 100 | 0.108 | Contact Map |
| 1fr2A | 1 | 0.8737 | 100 | 0.108 | Contact Map |
| 4uhpB | 4 | 0 | 100 | 0.113 | Contact Map |
| 1gxgA | 1 | 0.8947 | 100 | 0.117 | Contact Map |
| 3u43A | 1 | 0.9684 | 100 | 0.124 | Contact Map |
| 2k0dX | 1 | 0.9053 | 100 | 0.129 | Contact Map |
| 4qkoA | 4 | 0 | 100 | 0.145 | Contact Map |
| 1pjrA | 1 | 0.9053 | 12.8 | 0.921 | Contact Map |
| 4c2tA | 4 | 0.8947 | 12.2 | 0.921 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)