| 2jxw |
| ID: | 1496033994 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 75 (72) | ||
| Sequences: | 894 (602.7) | ||
| Seq/Len: | 12.417 | ||
| Nf(neff/√len): | 71.0 |
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: 12.417).
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 |
| 62_N | 65_T | 2.750 | 1.00 |
| 6_R | 23_I | 2.542 | 1.00 |
| 11_I | 17_H | 2.535 | 1.00 |
| 47_V | 64_E | 2.365 | 1.00 |
| 50_E | 58_T | 1.890 | 1.00 |
| 46_T | 75_D | 1.868 | 1.00 |
| 21_D | 24_S | 1.838 | 1.00 |
| 52_L | 58_T | 1.832 | 1.00 |
| 9_E | 17_H | 1.801 | 1.00 |
| 33_E | 36_Q | 1.768 | 1.00 |
| 10_G | 27_S | 1.664 | 1.00 |
| 10_G | 51_G | 1.503 | 1.00 |
| 70_W | 73_P | 1.503 | 1.00 |
| 12_T | 53_S | 1.493 | 1.00 |
| 15_G | 18_Y | 1.488 | 1.00 |
| 20_Y | 61_Y | 1.477 | 1.00 |
| 48_W | 73_P | 1.453 | 1.00 |
| 52_L | 56_G | 1.369 | 0.99 |
| 9_E | 31_K | 1.360 | 0.99 |
| 16_Y | 57_F | 1.342 | 0.99 |
| 62_N | 67_E | 1.325 | 0.99 |
| 29_W | 32_P | 1.322 | 0.99 |
| 38_D | 41_K | 1.292 | 0.99 |
| 14_E | 53_S | 1.259 | 0.99 |
| 27_S | 32_P | 1.231 | 0.98 |
| 58_T | 68_S | 1.068 | 0.95 |
| 16_Y | 29_W | 1.047 | 0.94 |
| 21_D | 28_Q | 1.024 | 0.93 |
| 36_Q | 39_L | 1.015 | 0.93 |
| 8_V | 66_G | 1.007 | 0.93 |
| 17_H | 39_L | 1.003 | 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 | |
| 2jxwA | 1 | 1 | 99.7 | 0.168 | Contact Map |
| 2l5fA | 1 | 1 | 99.7 | 0.205 | Contact Map |
| 1o6wA | 1 | 0.96 | 99.6 | 0.216 | Contact Map |
| 4rohA | 1 | 0.9333 | 99.5 | 0.275 | Contact Map |
| 2kxqA | 1 | 1 | 99.5 | 0.281 | Contact Map |
| 1tk7A | 1 | 1 | 99.5 | 0.288 | Contact Map |
| 2dk7A | 1 | 0.7467 | 99 | 0.442 | Contact Map |
| 2dk1A | 1 | 0.6267 | 98.4 | 0.545 | Contact Map |
| 1e0lA | 1 | 0.48 | 98.3 | 0.552 | Contact Map |
| 2ysiA | 1 | 0.4667 | 98.2 | 0.568 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)