| HPr |
| ID: | 1464770187 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 85 (83) | ||
| Sequences: | 3973 (2621) | ||
| Seq/Len: | 47.867 | ||
| Nf(neff/√len): | 287.7 |
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: 47.867).
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 |
| 5_E | 60_V | 2.855 | 1.00 |
| 3_Q | 62_T | 2.479 | 1.00 |
| 4_Q | 78_V | 2.418 | 1.00 |
| 65_A | 74_V | 2.395 | 1.00 |
| 31_S | 69_D | 2.392 | 1.00 |
| 29_F | 76_H | 2.338 | 1.00 |
| 25_E | 28_G | 2.243 | 1.00 |
| 36_T | 64_S | 2.123 | 1.00 |
| 36_T | 41_S | 1.931 | 1.00 |
| 36_T | 62_T | 1.923 | 1.00 |
| 34_T | 41_S | 1.922 | 1.00 |
| 5_E | 62_T | 1.880 | 1.00 |
| 79_K | 83_E | 1.871 | 1.00 |
| 6_V | 78_V | 1.847 | 1.00 |
| 30_T | 68_E | 1.843 | 1.00 |
| 78_V | 82_A | 1.837 | 1.00 |
| 3_Q | 64_S | 1.813 | 1.00 |
| 25_E | 76_H | 1.689 | 1.00 |
| 37_S | 59_T | 1.687 | 1.00 |
| 22_F | 77_L | 1.683 | 1.00 |
| 2_F | 71_Q | 1.645 | 1.00 |
| 7_T | 60_V | 1.617 | 1.00 |
| 29_F | 73_A | 1.592 | 1.00 |
| 71_Q | 75_E | 1.591 | 1.00 |
| 22_F | 44_A | 1.575 | 1.00 |
| 1_M | 70_E | 1.507 | 1.00 |
| 41_S | 64_S | 1.492 | 1.00 |
| 56_T | 59_T | 1.435 | 1.00 |
| 2_F | 74_V | 1.410 | 1.00 |
| 11_P | 57_Q | 1.339 | 0.99 |
| 4_Q | 75_E | 1.338 | 0.99 |
| 32_E | 66_E | 1.239 | 0.98 |
| 31_S | 65_A | 1.200 | 0.98 |
| 30_T | 69_D | 1.198 | 0.98 |
| 72_K | 76_H | 1.135 | 0.97 |
| 42_A | 53_L | 1.108 | 0.96 |
| 55_L | 61_V | 1.074 | 0.95 |
| 75_E | 79_K | 1.061 | 0.95 |
| 8_I | 55_L | 1.049 | 0.94 |
| 2_F | 70_E | 1.021 | 0.93 |
| 36_T | 39_G | 1.012 | 0.93 |
| 31_S | 73_A | 1.006 | 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 | |
| 3ccdA | 2 | 1 | 99.9 | -0.017 | Contact Map |
| 1ka5A | 1 | 1 | 99.9 | -0.013 | Contact Map |
| 1kklH | 3 | 1 | 99.9 | -0.011 | Contact Map |
| 1ptfA | 1 | 1 | 99.9 | -0.005 | Contact Map |
| 3ihsA | 2 | 0.9647 | 99.9 | -0.005 | Contact Map |
| 1sphA | 2 | 0.9882 | 99.9 | -0.003 | Contact Map |
| 1y51A | 3 | 0.9882 | 99.9 | -0.003 | Contact Map |
| 3le1A | 2 | 1 | 99.9 | 0.002 | Contact Map |
| 1pchA | 1 | 0.9882 | 99.9 | 0.027 | Contact Map |
| 2jpiA | 1 | 0.9059 | 32.5 | 0.858 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)