| 2TRX |
| ID: | 1515789910 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 108 (105) | ||
| Sequences: | 19813 (13161.7) | ||
| Seq/Len: | 188.695 | ||
| Nf(neff/√len): | 1284.5 |
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: 188.695).
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 | 2.269 | 1.00 |
| 60_I | 67_A | 2.207 | 1.00 |
| 79_L | 89_T | 2.133 | 1.00 |
| 48_E | 100_K | 2.065 | 1.00 |
| 44_E | 96_K | 1.991 | 1.00 |
| 13_D | 69_K | 1.972 | 1.00 |
| 88_A | 102_F | 1.971 | 1.00 |
| 100_K | 104_D | 1.945 | 1.00 |
| 9_D | 65_G | 1.875 | 1.00 |
| 70_Y | 81_F | 1.866 | 1.00 |
| 21_G | 54_T | 1.852 | 1.00 |
| 38_I | 78_L | 1.826 | 1.00 |
| 7_L | 56_A | 1.799 | 1.00 |
| 79_L | 86_V | 1.762 | 1.00 |
| 60_I | 75_I | 1.722 | 1.00 |
| 32_C | 35_C | 1.712 | 1.00 |
| 95_S | 98_Q | 1.684 | 1.00 |
| 23_I | 54_T | 1.665 | 1.00 |
| 9_D | 66_T | 1.647 | 1.00 |
| 49_Y | 104_D | 1.645 | 1.00 |
| 26_D | 57_K | 1.619 | 1.00 |
| 41_I | 44_E | 1.568 | 1.00 |
| 11_S | 15_D | 1.523 | 1.00 |
| 22_A | 82_K | 1.487 | 1.00 |
| 49_Y | 100_K | 1.485 | 1.00 |
| 27_F | 72_I | 1.424 | 1.00 |
| 48_E | 96_K | 1.421 | 1.00 |
| 59_N | 62_Q | 1.402 | 0.99 |
| 102_F | 106_N | 1.396 | 0.99 |
| 80_L | 106_N | 1.391 | 0.99 |
| 8_T | 11_S | 1.357 | 0.99 |
| 98_Q | 101_E | 1.309 | 0.99 |
| 41_I | 96_K | 1.283 | 0.99 |
| 25_V | 81_F | 1.283 | 0.99 |
| 9_D | 63_N | 1.280 | 0.99 |
| 39_A | 57_K | 1.279 | 0.99 |
| 15_D | 54_T | 1.247 | 0.99 |
| 24_L | 78_L | 1.241 | 0.98 |
| 22_A | 80_L | 1.232 | 0.98 |
| 23_I | 56_A | 1.212 | 0.98 |
| 27_F | 70_Y | 1.207 | 0.98 |
| 90_K | 94_L | 1.201 | 0.98 |
| 24_L | 42_L | 1.201 | 0.98 |
| 80_L | 102_F | 1.171 | 0.98 |
| 26_D | 39_A | 1.153 | 0.97 |
| 96_K | 100_K | 1.151 | 0.97 |
| 42_L | 55_V | 1.139 | 0.97 |
| 30_E | 59_N | 1.138 | 0.97 |
| 94_L | 98_Q | 1.135 | 0.97 |
| 45_I | 100_K | 1.111 | 0.96 |
| 28_W | 57_K | 1.107 | 0.96 |
| 45_I | 96_K | 1.104 | 0.96 |
| 88_A | 106_N | 1.103 | 0.96 |
| 81_F | 86_V | 1.103 | 0.96 |
| 31_W | 61_D | 1.095 | 0.96 |
| 37_M | 93_A | 1.089 | 0.96 |
| 27_F | 60_I | 1.087 | 0.96 |
| 26_D | 38_I | 1.068 | 0.95 |
| 3_K | 47_D | 1.064 | 0.95 |
| 39_A | 43_D | 1.045 | 0.94 |
| 13_D | 18_K | 1.020 | 0.93 |
| 7_L | 15_D | 1.014 | 0.93 |
| 102_F | 105_A | 1.012 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | -0.014 | Contact Map |
| 2r2jA | 1 | 0.9537 | 99.8 | 0.002 | Contact Map |
| 3apoA | 1 | 0.9167 | 99.8 | 0.005 | Contact Map |
| 2b5eA | 1 | 0.9907 | 99.8 | 0.011 | Contact Map |
| 4kcaA | 2 | 0.9722 | 99.8 | 0.038 | Contact Map |
| 4ekzA | 1 | 0.9907 | 99.8 | 0.043 | Contact Map |
| 3ed3A | 2 | 1 | 99.8 | 0.045 | Contact Map |
| 1sjiA | 2 | 0.9815 | 99.7 | 0.061 | Contact Map |
| 3us3A | 1 | 0.9815 | 99.7 | 0.067 | Contact Map |
| 3t58A | 4 | 1 | 99.7 | 0.076 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)