| 2VXF |
| ID: | 1515674961 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 88 (83) | ||
| Sequences: | 322 (191.5) | ||
| Seq/Len: | 3.880 | ||
| Nf(neff/√len): | 21.0 |
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: 3.880).
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 |
| 33_D | 36_N | 2.777 | 1.00 |
| 22_E | 76_K | 2.726 | 1.00 |
| 51_D | 54_T | 2.159 | 1.00 |
| 26_E | 75_I | 2.091 | 1.00 |
| 49_T | 52_R | 1.486 | 0.97 |
| 67_Y | 73_S | 1.466 | 0.97 |
| 12_G | 17_L | 1.454 | 0.97 |
| 40_A | 69_I | 1.438 | 0.96 |
| 45_R | 64_T | 1.389 | 0.95 |
| 15_I | 78_L | 1.365 | 0.95 |
| 65_F | 68_I | 1.359 | 0.95 |
| 39_V | 81_C | 1.347 | 0.94 |
| 42_A | 61_R | 1.341 | 0.94 |
| 68_I | 74_D | 1.311 | 0.93 |
| 44_V | 48_G | 1.294 | 0.93 |
| 29_L | 77_D | 1.231 | 0.90 |
| 39_V | 78_L | 1.230 | 0.90 |
| 62_D | 66_E | 1.196 | 0.88 |
| 51_D | 57_P | 1.180 | 0.87 |
| 48_G | 52_R | 1.158 | 0.86 |
| 42_A | 66_E | 1.139 | 0.85 |
| 44_V | 50_E | 1.134 | 0.84 |
| 9_P | 34_T | 1.127 | 0.84 |
| 16_S | 23_I | 1.108 | 0.82 |
| 43_K | 53_P | 1.108 | 0.82 |
| 39_V | 79_T | 1.106 | 0.82 |
| 37_S | 65_F | 1.105 | 0.82 |
| 18_I | 23_I | 1.095 | 0.81 |
| 12_G | 24_R | 1.090 | 0.81 |
| 46_S | 60_P | 1.089 | 0.81 |
| 19_S | 24_R | 1.070 | 0.79 |
| 23_I | 46_S | 1.066 | 0.79 |
| 21_A | 71_R | 1.061 | 0.78 |
| 46_S | 71_R | 1.061 | 0.78 |
| 75_I | 81_C | 1.056 | 0.78 |
| 40_A | 67_Y | 1.052 | 0.77 |
| 38_T | 41_L | 1.042 | 0.77 |
| 66_E | 74_D | 1.029 | 0.75 |
| 9_P | 80_V | 1.018 | 0.74 |
| 30_Y | 81_C | 1.014 | 0.74 |
| 15_I | 24_R | 1.004 | 0.73 |
| 30_Y | 69_I | 1.003 | 0.73 |
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 | |
| 2fb7A | 1 | 0.9091 | 100 | 0.019 | Contact Map |
| 2vxeA | 1 | 0.9886 | 100 | 0.069 | Contact Map |
| 4a53A | 1 | 0.7727 | 99.6 | 0.539 | Contact Map |
| 2vc8A | 1 | 0.7841 | 99.2 | 0.639 | Contact Map |
| 2rm4A | 1 | 0.8636 | 97 | 0.798 | Contact Map |
| 3pgwB | 2 | 0.9659 | 95.7 | 0.822 | Contact Map |
| 1y96A | 2 | 0.8295 | 95.1 | 0.83 | Contact Map |
| 3pggA | 2 | 0.8636 | 93 | 0.845 | Contact Map |
| 4emkA | 1 | 0.8068 | 92.5 | 0.847 | Contact Map |
| 4c92E | 1 | 0.9318 | 92.1 | 0.85 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)