| 1a7e |
| ID: | 1453736763 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 118 (114) | ||
| Sequences: | 1477 (1248.7) | ||
| Seq/Len: | 12.956 | ||
| Nf(neff/√len): | 117.0 |
HHblits Results: (2015_06)
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: 12.956).
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 |
| 24_E | 57_H | 5.123 | 1.00 |
| 12_E | 15_R | 3.410 | 1.00 |
| 63_D | 70_V | 2.690 | 1.00 |
| 68_S | 117_K | 2.494 | 1.00 |
| 34_D | 46_T | 2.435 | 1.00 |
| 76_M | 110_T | 2.404 | 1.00 |
| 31_G | 46_T | 1.987 | 1.00 |
| 10_W | 15_R | 1.926 | 1.00 |
| 27_K | 30_K | 1.888 | 1.00 |
| 11_D | 14_F | 1.864 | 1.00 |
| 53_N | 57_H | 1.814 | 1.00 |
| 74_K | 78_K | 1.777 | 1.00 |
| 28_I | 103_N | 1.738 | 1.00 |
| 25_H | 54_H | 1.732 | 1.00 |
| 62_M | 114_Y | 1.729 | 1.00 |
| 65_A | 118_L | 1.727 | 1.00 |
| 112_F | 115_K | 1.691 | 1.00 |
| 52_T | 81_L | 1.645 | 1.00 |
| 63_D | 74_K | 1.613 | 1.00 |
| 60_A | 64_A | 1.610 | 1.00 |
| 20_Q | 57_H | 1.568 | 1.00 |
| 19_E | 23_E | 1.562 | 1.00 |
| 62_M | 70_V | 1.552 | 1.00 |
| 16_V | 115_K | 1.521 | 1.00 |
| 69_E | 113_K | 1.506 | 1.00 |
| 70_V | 78_K | 1.504 | 1.00 |
| 26_K | 30_K | 1.494 | 1.00 |
| 70_V | 74_K | 1.473 | 1.00 |
| 27_K | 46_T | 1.448 | 1.00 |
| 48_V | 88_S | 1.422 | 1.00 |
| 69_E | 72_P | 1.370 | 0.99 |
| 59_E | 74_K | 1.291 | 0.99 |
| 41_A | 91_V | 1.289 | 0.99 |
| 27_K | 31_G | 1.269 | 0.99 |
| 77_H | 111_D | 1.255 | 0.99 |
| 23_E | 26_K | 1.251 | 0.99 |
| 82_E | 86_G | 1.212 | 0.98 |
| 83_K | 86_G | 1.211 | 0.98 |
| 48_V | 85_G | 1.190 | 0.98 |
| 56_T | 60_A | 1.189 | 0.98 |
| 16_V | 21_L | 1.188 | 0.98 |
| 29_F | 33_F | 1.151 | 0.97 |
| 39_N | 93_A | 1.091 | 0.96 |
| 32_I | 103_N | 1.085 | 0.96 |
| 14_F | 108_K | 1.083 | 0.96 |
| 15_R | 29_F | 1.074 | 0.95 |
| 10_W | 26_K | 1.064 | 0.95 |
| 105_N | 109_G | 1.064 | 0.95 |
| 21_L | 57_H | 1.060 | 0.95 |
| 75_K | 79_D | 1.052 | 0.95 |
| 25_H | 58_E | 1.051 | 0.94 |
| 50_V | 107_I | 1.051 | 0.94 |
| 51_T | 80_F | 1.049 | 0.94 |
| 24_E | 54_H | 1.046 | 0.94 |
| 110_T | 113_K | 1.040 | 0.94 |
| 78_K | 81_L | 1.030 | 0.94 |
| 73_H | 77_H | 1.016 | 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 | |
| 2mhrA | 1 | 1 | 100 | 0.026 | Contact Map |
| 2hmqA | 4 | 0.9576 | 100 | 0.048 | Contact Map |
| 4xpxA | 1 | 0 | 100 | 0.11 | Contact Map |
| 3agtA | 2 | 0.9576 | 100 | 0.121 | Contact Map |
| 3caxA | 1 | 0.8898 | 81.3 | 0.851 | Contact Map |
| 2p0nA | 2 | 0.8898 | 71.9 | 0.863 | Contact Map |
| 3cljA | 1 | 0.3644 | 5.6 | 0.925 | Contact Map |
| 1bgfA | 1 | 0.4492 | 4 | 0.93 | Contact Map |
| 4q0cA | 4 | 0.5593 | 4 | 0.93 | Contact Map |
| 3m07A | 1 | 0.9746 | 3.8 | 0.931 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)