| V2EDE2 |
| ID: | 1514007283 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 219 (77.2) | ||
| Seq/Len: | 2.517 | ||
| 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: 2.517).
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 |
| 28_V | 31_A | 2.731 | 1.00 |
| 46_A | 81_V | 1.796 | 0.98 |
| 12_Y | 18_G | 1.643 | 0.97 |
| 3_A | 7_L | 1.636 | 0.97 |
| 74_A | 79_Q | 1.629 | 0.97 |
| 42_N | 45_H | 1.564 | 0.95 |
| 9_V | 17_L | 1.540 | 0.95 |
| 21_L | 44_F | 1.523 | 0.95 |
| 73_Q | 76_V | 1.486 | 0.94 |
| 27_S | 31_A | 1.485 | 0.94 |
| 72_D | 77_E | 1.429 | 0.92 |
| 42_N | 71_M | 1.426 | 0.92 |
| 9_V | 85_Q | 1.419 | 0.91 |
| 55_L | 63_C | 1.384 | 0.90 |
| 59_I | 62_C | 1.351 | 0.89 |
| 4_V | 8_Q | 1.333 | 0.88 |
| 43_H | 49_E | 1.302 | 0.86 |
| 63_C | 66_C | 1.301 | 0.86 |
| 66_C | 69_H | 1.294 | 0.85 |
| 24_D | 68_R | 1.272 | 0.84 |
| 15_D | 19_Y | 1.267 | 0.84 |
| 27_S | 81_V | 1.213 | 0.80 |
| 13_S | 19_Y | 1.195 | 0.79 |
| 45_H | 48_L | 1.187 | 0.78 |
| 16_T | 24_D | 1.158 | 0.76 |
| 51_T | 54_E | 1.152 | 0.75 |
| 40_R | 47_R | 1.125 | 0.72 |
| 11_T | 15_D | 1.124 | 0.72 |
| 5_K | 84_V | 1.119 | 0.72 |
| 4_V | 76_V | 1.106 | 0.71 |
| 57_Q | 67_P | 1.098 | 0.70 |
| 61_C | 64_P | 1.092 | 0.69 |
| 65_H | 68_R | 1.083 | 0.68 |
| 78_A | 86_K | 1.073 | 0.67 |
| 42_N | 81_V | 1.068 | 0.67 |
| 63_C | 69_H | 1.048 | 0.65 |
| 39_R | 42_N | 1.031 | 0.63 |
| 36_E | 60_P | 1.030 | 0.63 |
| 4_V | 39_R | 1.022 | 0.62 |
| 11_T | 51_T | 1.018 | 0.61 |
| 31_A | 39_R | 1.016 | 0.61 |
| 33_N | 54_E | 1.012 | 0.61 |
| 42_N | 76_V | 1.005 | 0.60 |
| 76_V | 87_P | 1.004 | 0.60 |
| 33_N | 39_R | 1.002 | 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 | |
| 4wwsA | 5 | 0.7356 | 13.9 | 0.942 | Contact Map |
| 2wnfA | 1 | 0.3218 | 11.3 | 0.944 | Contact Map |
| 1vdhA | 5 | 0.7356 | 10.1 | 0.945 | Contact Map |
| 1t0tV | 5 | 0.7356 | 7.4 | 0.949 | Contact Map |
| 3nsjA | 1 | 1 | 6.3 | 0.95 | Contact Map |
| 4rbnA | 4 | 0 | 4.8 | 0.953 | Contact Map |
| 3ibyA | 4 | 0.5862 | 4.7 | 0.953 | Contact Map |
| 2xocA | 2 | 0.1954 | 4.2 | 0.954 | Contact Map |
| 1m45B | 1 | 0.2644 | 4.1 | 0.954 | Contact Map |
| 4q9aA | 2 | 0.3678 | 4.1 | 0.954 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)