| 2TRX |
| ID: | 1446057651 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 108 (105) | ||
| Sequences: | 26678 (18280.8) | ||
| Seq/Len: | 254.076 | ||
| Nf(neff/√len): | 1784.0 |
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: 254.076).
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 |
| 86_V | 89_T | 2.364 | 1.00 |
| 88_A | 102_F | 2.218 | 1.00 |
| 48_E | 100_K | 2.093 | 1.00 |
| 100_K | 104_D | 2.060 | 1.00 |
| 23_I | 54_T | 2.043 | 1.00 |
| 44_E | 96_K | 2.010 | 1.00 |
| 60_I | 67_A | 1.992 | 1.00 |
| 21_G | 54_T | 1.928 | 1.00 |
| 32_C | 35_C | 1.899 | 1.00 |
| 28_W | 57_K | 1.889 | 1.00 |
| 79_L | 89_T | 1.885 | 1.00 |
| 22_A | 82_K | 1.864 | 1.00 |
| 39_A | 57_K | 1.838 | 1.00 |
| 60_I | 75_I | 1.716 | 1.00 |
| 79_L | 86_V | 1.694 | 1.00 |
| 13_D | 69_K | 1.686 | 1.00 |
| 49_Y | 100_K | 1.630 | 1.00 |
| 102_F | 106_N | 1.629 | 1.00 |
| 38_I | 78_L | 1.606 | 1.00 |
| 70_Y | 81_F | 1.559 | 1.00 |
| 95_S | 98_Q | 1.538 | 1.00 |
| 24_L | 78_L | 1.496 | 1.00 |
| 49_Y | 104_D | 1.460 | 1.00 |
| 96_K | 100_K | 1.455 | 1.00 |
| 23_I | 56_A | 1.447 | 1.00 |
| 9_D | 65_G | 1.394 | 0.99 |
| 7_L | 56_A | 1.379 | 0.99 |
| 26_D | 57_K | 1.379 | 0.99 |
| 9_D | 63_N | 1.373 | 0.99 |
| 81_F | 86_V | 1.365 | 0.99 |
| 37_M | 93_A | 1.334 | 0.99 |
| 41_I | 96_K | 1.330 | 0.99 |
| 26_D | 78_L | 1.323 | 0.99 |
| 11_S | 15_D | 1.319 | 0.99 |
| 27_F | 70_Y | 1.318 | 0.99 |
| 8_T | 11_S | 1.317 | 0.99 |
| 90_K | 94_L | 1.315 | 0.99 |
| 48_E | 96_K | 1.295 | 0.99 |
| 41_I | 44_E | 1.280 | 0.99 |
| 102_F | 105_A | 1.279 | 0.99 |
| 22_A | 80_L | 1.276 | 0.99 |
| 30_E | 59_N | 1.266 | 0.99 |
| 9_D | 66_T | 1.261 | 0.99 |
| 94_L | 98_Q | 1.227 | 0.98 |
| 90_K | 102_F | 1.183 | 0.98 |
| 26_D | 39_A | 1.179 | 0.98 |
| 59_N | 62_Q | 1.177 | 0.98 |
| 80_L | 106_N | 1.135 | 0.97 |
| 72_I | 77_T | 1.129 | 0.97 |
| 43_D | 47_D | 1.128 | 0.97 |
| 3_K | 47_D | 1.121 | 0.97 |
| 29_A | 75_I | 1.109 | 0.96 |
| 80_L | 102_F | 1.102 | 0.96 |
| 88_A | 106_N | 1.087 | 0.96 |
| 45_I | 100_K | 1.076 | 0.95 |
| 98_Q | 101_E | 1.073 | 0.95 |
| 25_V | 81_F | 1.056 | 0.95 |
| 27_F | 72_I | 1.049 | 0.94 |
| 24_L | 42_L | 1.039 | 0.94 |
| 27_F | 60_I | 1.024 | 0.93 |
| 77_T | 89_T | 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 | |
| 3f8uA | 2 | 0.9815 | 99.8 | -0.012 | Contact Map |
| 3apoA | 1 | 0.9167 | 99.8 | 0 | Contact Map |
| 2r2jA | 1 | 0.9537 | 99.8 | 0 | Contact Map |
| 2b5eA | 1 | 0.9907 | 99.8 | 0.007 | Contact Map |
| 4kcaA | 2 | 0.9722 | 99.8 | 0.015 | Contact Map |
| 4ekzA | 1 | 0.9907 | 99.7 | 0.036 | Contact Map |
| 3ed3A | 2 | 1 | 99.7 | 0.037 | Contact Map |
| 3dxbA | 8 | 1 | 99.7 | 0.046 | Contact Map |
| 1thxA | 1 | 1 | 99.7 | 0.046 | Contact Map |
| 4kcbA | 2 | 0 | 99.7 | 0.053 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)