| veg |
| ID: | 1479281098 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 88 (81) | ||
| Sequences: | 418 (233.8) | ||
| Seq/Len: | 5.160 | ||
| Nf(neff/√len): | 26.0 |
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: 5.160).
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 |
| 41_E | 51_K | 3.350 | 1.00 |
| 47_V | 65_S | 2.074 | 1.00 |
| 35_T | 75_K | 1.970 | 1.00 |
| 14_L | 40_L | 1.651 | 0.99 |
| 17_H | 20_K | 1.507 | 0.99 |
| 7_L | 32_Q | 1.480 | 0.98 |
| 43_V | 76_L | 1.410 | 0.98 |
| 23_L | 35_T | 1.402 | 0.98 |
| 25_K | 74_V | 1.401 | 0.98 |
| 11_R | 14_L | 1.388 | 0.97 |
| 15_E | 43_V | 1.382 | 0.97 |
| 33_I | 69_L | 1.358 | 0.97 |
| 24_L | 74_V | 1.352 | 0.97 |
| 63_S | 69_L | 1.277 | 0.95 |
| 10_I | 70_L | 1.258 | 0.95 |
| 11_R | 15_E | 1.234 | 0.94 |
| 10_I | 14_L | 1.232 | 0.94 |
| 54_D | 57_N | 1.229 | 0.94 |
| 12_V | 20_K | 1.217 | 0.93 |
| 21_K | 37_E | 1.209 | 0.93 |
| 3_T | 80_R | 1.208 | 0.93 |
| 5_Q | 9_K | 1.198 | 0.93 |
| 3_T | 56_S | 1.188 | 0.92 |
| 24_L | 46_S | 1.140 | 0.90 |
| 24_L | 67_S | 1.134 | 0.90 |
| 2_A | 79_F | 1.131 | 0.89 |
| 42_K | 56_S | 1.129 | 0.89 |
| 23_L | 37_E | 1.129 | 0.89 |
| 19_G | 29_G | 1.109 | 0.88 |
| 3_T | 79_F | 1.109 | 0.88 |
| 79_F | 82_Q | 1.104 | 0.88 |
| 27_N | 44_Y | 1.080 | 0.86 |
| 9_K | 75_K | 1.073 | 0.86 |
| 7_L | 57_N | 1.072 | 0.86 |
| 13_S | 60_P | 1.071 | 0.86 |
| 34_I | 47_V | 1.049 | 0.84 |
| 36_K | 57_N | 1.047 | 0.84 |
| 8_D | 49_V | 1.045 | 0.84 |
| 52_L | 62_V | 1.031 | 0.83 |
| 3_T | 82_Q | 1.028 | 0.82 |
| 2_A | 82_Q | 1.024 | 0.82 |
| 23_L | 76_L | 1.022 | 0.82 |
| 8_D | 57_N | 1.013 | 0.81 |
| 67_S | 73_N | 1.010 | 0.81 |
| 2_A | 81_D | 1.006 | 0.80 |
| 54_D | 59_Y | 1.005 | 0.80 |
| 42_K | 67_S | 1.001 | 0.80 |
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 | |
| 3fb9A | 2 | 0.9091 | 99.9 | 0.118 | Contact Map |
| 1ib8A | 1 | 0.8636 | 53.2 | 0.866 | Contact Map |
| 2d6fA | 2 | 0.7955 | 21.9 | 0.892 | Contact Map |
| 1zq1A | 2 | 0.8636 | 12.9 | 0.903 | Contact Map |
| 4ioiE | 1 | 0.6023 | 9.8 | 0.908 | Contact Map |
| 3pgwB | 2 | 0.7955 | 8.4 | 0.91 | Contact Map |
| 4f7uA | 2 | 0.8636 | 7.9 | 0.911 | Contact Map |
| 4k17A | 4 | 0.9432 | 6.9 | 0.914 | Contact Map |
| 1y96A | 2 | 0.8977 | 6.4 | 0.915 | Contact Map |
| 3bfmA | 1 | 0.6591 | 6.1 | 0.916 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)