| 2kqf |
| ID: | 1468858335 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 96 (93) | ||
| Sequences: | 380 (202.7) | ||
| Seq/Len: | 4.086 | ||
| 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: 4.086).
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 |
| 23_A | 73_H | 1.863 | 1.00 |
| 43_V | 52_A | 1.787 | 0.99 |
| 73_H | 77_V | 1.702 | 0.99 |
| 62_H | 81_L | 1.601 | 0.99 |
| 62_H | 90_S | 1.581 | 0.98 |
| 68_V | 76_V | 1.565 | 0.98 |
| 62_H | 88_A | 1.564 | 0.98 |
| 8_I | 46_G | 1.557 | 0.98 |
| 12_R | 91_T | 1.536 | 0.98 |
| 23_A | 38_H | 1.490 | 0.98 |
| 23_A | 76_V | 1.486 | 0.97 |
| 58_D | 63_V | 1.440 | 0.97 |
| 8_I | 60_I | 1.436 | 0.97 |
| 43_V | 49_A | 1.416 | 0.96 |
| 65_G | 78_E | 1.414 | 0.96 |
| 21_L | 24_I | 1.350 | 0.95 |
| 19_F | 22_R | 1.348 | 0.95 |
| 43_V | 73_H | 1.298 | 0.93 |
| 67_P | 71_L | 1.281 | 0.93 |
| 76_V | 79_L | 1.264 | 0.92 |
| 46_G | 50_S | 1.249 | 0.92 |
| 13_A | 16_K | 1.210 | 0.90 |
| 57_G | 80_I | 1.199 | 0.89 |
| 60_I | 65_G | 1.197 | 0.89 |
| 63_V | 87_V | 1.191 | 0.89 |
| 51_E | 82_K | 1.172 | 0.88 |
| 42_H | 45_D | 1.161 | 0.87 |
| 24_I | 40_V | 1.157 | 0.87 |
| 68_V | 79_L | 1.139 | 0.86 |
| 24_I | 38_H | 1.135 | 0.85 |
| 41_W | 80_I | 1.132 | 0.85 |
| 15_K | 56_Q | 1.116 | 0.84 |
| 3_S | 45_D | 1.115 | 0.84 |
| 13_A | 35_T | 1.111 | 0.84 |
| 29_G | 34_Y | 1.103 | 0.83 |
| 31_S | 36_V | 1.097 | 0.83 |
| 21_L | 40_V | 1.084 | 0.82 |
| 78_E | 84_G | 1.076 | 0.81 |
| 45_D | 48_P | 1.071 | 0.80 |
| 74_T | 91_T | 1.068 | 0.80 |
| 26_V | 35_T | 1.061 | 0.80 |
| 17_Y | 38_H | 1.061 | 0.80 |
| 19_F | 89_I | 1.058 | 0.79 |
| 75_E | 78_E | 1.050 | 0.79 |
| 29_G | 60_I | 1.049 | 0.79 |
| 10_I | 39_M | 1.045 | 0.78 |
| 15_K | 89_I | 1.035 | 0.77 |
| 71_L | 93_P | 1.033 | 0.77 |
| 72_V | 90_S | 1.031 | 0.77 |
| 82_K | 89_I | 1.024 | 0.76 |
| 5_R | 40_V | 1.023 | 0.76 |
| 41_W | 63_V | 1.014 | 0.75 |
| 48_P | 60_I | 1.009 | 0.75 |
| 43_V | 94_L | 1.003 | 0.74 |
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 | |
| 2yuyA | 1 | 1 | 99.7 | 0.403 | Contact Map |
| 2xkxA | 2 | 0.9792 | 99.6 | 0.41 | Contact Map |
| 3khfA | 2 | 0.9583 | 99.6 | 0.423 | Contact Map |
| 2egoA | 2 | 0.9271 | 99.6 | 0.433 | Contact Map |
| 2z17A | 1 | 0.9583 | 99.6 | 0.447 | Contact Map |
| 1z87A | 1 | 0.9271 | 99.5 | 0.45 | Contact Map |
| 1q3oA | 2 | 1 | 99.5 | 0.455 | Contact Map |
| 1uhpA | 1 | 1 | 99.5 | 0.456 | Contact Map |
| 1uewA | 1 | 1 | 99.5 | 0.456 | Contact Map |
| 3l4fD | 1 | 1 | 99.5 | 0.459 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)