| V2EDE3 |
| ID: | 1514007978 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 84 (84) | ||
| Sequences: | 204 (75.9) | ||
| Seq/Len: | 2.429 | ||
| Nf(neff/√len): | 8.3 |
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: 2.429).
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 |
| 26_V | 29_A | 2.870 | 1.00 |
| 3_A | 7_L | 1.873 | 0.99 |
| 43_A | 78_V | 1.814 | 0.98 |
| 10_Y | 16_G | 1.761 | 0.98 |
| 71_A | 76_Q | 1.613 | 0.96 |
| 19_L | 41_F | 1.594 | 0.96 |
| 4_V | 8_Q | 1.594 | 0.96 |
| 70_Q | 73_V | 1.584 | 0.96 |
| 4_V | 73_V | 1.473 | 0.93 |
| 25_S | 29_A | 1.460 | 0.92 |
| 56_I | 59_C | 1.389 | 0.90 |
| 60_C | 63_C | 1.370 | 0.89 |
| 52_L | 60_C | 1.365 | 0.89 |
| 42_H | 45_L | 1.350 | 0.88 |
| 40_H | 46_E | 1.336 | 0.87 |
| 63_C | 66_H | 1.315 | 0.86 |
| 9_T | 48_T | 1.312 | 0.86 |
| 11_S | 17_Y | 1.260 | 0.83 |
| 22_D | 65_R | 1.247 | 0.82 |
| 75_A | 83_K | 1.232 | 0.81 |
| 48_T | 51_E | 1.225 | 0.80 |
| 29_A | 48_T | 1.140 | 0.73 |
| 13_D | 48_T | 1.138 | 0.73 |
| 5_K | 81_V | 1.138 | 0.73 |
| 14_T | 22_D | 1.136 | 0.73 |
| 25_S | 78_V | 1.133 | 0.72 |
| 9_T | 13_D | 1.130 | 0.72 |
| 13_D | 17_Y | 1.100 | 0.69 |
| 38_R | 44_R | 1.086 | 0.68 |
| 54_Q | 64_P | 1.065 | 0.65 |
| 2_L | 6_Y | 1.064 | 0.65 |
| 73_V | 84_P | 1.058 | 0.65 |
| 75_A | 82_Q | 1.057 | 0.65 |
| 29_A | 37_R | 1.051 | 0.64 |
| 69_D | 74_E | 1.049 | 0.64 |
| 58_C | 61_P | 1.046 | 0.63 |
| 78_V | 83_K | 1.046 | 0.63 |
| 7_L | 69_D | 1.045 | 0.63 |
| 47_G | 54_Q | 1.038 | 0.62 |
| 10_Y | 14_T | 1.035 | 0.62 |
| 62_H | 65_R | 1.028 | 0.61 |
| 68_M | 81_V | 1.025 | 0.61 |
| 59_C | 70_Q | 1.023 | 0.61 |
| 8_Q | 68_M | 1.022 | 0.61 |
| 31_N | 37_R | 1.021 | 0.61 |
| 15_L | 27_I | 1.013 | 0.60 |
| 60_C | 66_H | 1.005 | 0.59 |
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 | |
| 2wnfA | 1 | 0.3333 | 12.2 | 0.942 | Contact Map |
| 3czuB | 1 | 0.5595 | 6.4 | 0.949 | Contact Map |
| 2p9xA | 4 | 0.3929 | 5.8 | 0.95 | Contact Map |
| 3heiB | 8 | 0.5595 | 5.8 | 0.95 | Contact Map |
| 4g0dW | 4 | 0.1667 | 5.7 | 0.95 | Contact Map |
| 2xocA | 2 | 0.1786 | 5.6 | 0.95 | Contact Map |
| 3ucaA | 2 | 0.3452 | 4.6 | 0.952 | Contact Map |
| 1m45B | 1 | 0.2738 | 4.4 | 0.952 | Contact Map |
| 4rbnA | 4 | 0 | 3.8 | 0.954 | Contact Map |
| 1i1qB | 1 | 0.3571 | 3.8 | 0.954 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)