| 2kxq |
| ID: | 1496038389 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 90 (84) | ||
| Sequences: | 1504 (971.2) | ||
| Seq/Len: | 17.905 | ||
| Nf(neff/√len): | 106.0 |
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: 17.905).
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 |
| 10_L | 13_G | 2.468 | 1.00 |
| 18_T | 24_V | 2.216 | 1.00 |
| 56_L | 59_G | 2.166 | 1.00 |
| 28_H | 35_T | 2.044 | 1.00 |
| 64_N | 70_V | 1.944 | 1.00 |
| 15_E | 29_T | 1.778 | 1.00 |
| 74_D | 77_N | 1.739 | 1.00 |
| 17_R | 27_L | 1.704 | 1.00 |
| 59_G | 76_N | 1.668 | 1.00 |
| 61_E | 75_H | 1.631 | 1.00 |
| 16_Q | 24_V | 1.565 | 1.00 |
| 62_I | 70_V | 1.539 | 1.00 |
| 83_T | 88_S | 1.522 | 1.00 |
| 72_F | 84_D | 1.458 | 1.00 |
| 28_H | 31_T | 1.447 | 1.00 |
| 23_Q | 69_R | 1.414 | 1.00 |
| 63_R | 69_R | 1.406 | 0.99 |
| 17_R | 63_R | 1.405 | 0.99 |
| 57_P | 60_W | 1.381 | 0.99 |
| 64_N | 68_G | 1.303 | 0.99 |
| 65_T | 69_R | 1.291 | 0.99 |
| 63_R | 73_V | 1.289 | 0.99 |
| 14_Y | 26_F | 1.283 | 0.99 |
| 25_Y | 36_W | 1.276 | 0.99 |
| 29_T | 33_V | 1.263 | 0.99 |
| 26_F | 39_P | 1.247 | 0.99 |
| 19_T | 23_Q | 1.225 | 0.98 |
| 13_G | 30_Q | 1.194 | 0.98 |
| 27_L | 34_S | 1.187 | 0.98 |
| 46_S | 49_N | 1.173 | 0.98 |
| 26_F | 38_D | 1.152 | 0.97 |
| 80_T | 85_P | 1.124 | 0.97 |
| 65_T | 71_Y | 1.105 | 0.96 |
| 11_P | 14_Y | 1.076 | 0.95 |
| 28_H | 33_V | 1.060 | 0.95 |
| 25_Y | 71_Y | 1.053 | 0.95 |
| 81_Q | 85_P | 1.045 | 0.94 |
| 62_I | 72_F | 1.041 | 0.94 |
| 71_Y | 82_F | 1.034 | 0.94 |
| 75_H | 80_T | 1.028 | 0.94 |
| 21_Q | 37_H | 1.027 | 0.94 |
| 78_R | 85_P | 1.015 | 0.93 |
| 56_L | 86_R | 1.008 | 0.93 |
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 | |
| 2kxqA | 1 | 1 | 99.8 | 0.082 | Contact Map |
| 1tk7A | 1 | 0.9444 | 99.8 | 0.14 | Contact Map |
| 4rohA | 1 | 0.8111 | 99.8 | 0.144 | Contact Map |
| 2l5fA | 1 | 0.9444 | 99.7 | 0.182 | Contact Map |
| 2jxwA | 1 | 0.8333 | 99.7 | 0.211 | Contact Map |
| 1o6wA | 1 | 0.8333 | 99.6 | 0.252 | Contact Map |
| 3l4hA | 1 | 0.7889 | 99.2 | 0.394 | Contact Map |
| 2dwvA | 2 | 0.5333 | 98.8 | 0.493 | Contact Map |
| 2ysdA | 1 | 0.5778 | 98.7 | 0.497 | Contact Map |
| 1eg3A | 1 | 0.5 | 98.7 | 0.511 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)