| 2RQL |
| ID: | 1447168060 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 107 (104) | ||
| Sequences: | 1323 (988.6) | ||
| Seq/Len: | 12.721 | ||
| Nf(neff/√len): | 96.9 |
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: 12.721).
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 |
| 18_T | 37_Y | 3.993 | 1.00 |
| 17_I | 40_G | 2.651 | 1.00 |
| 42_V | 96_I | 2.474 | 1.00 |
| 65_D | 69_I | 2.073 | 1.00 |
| 11_A | 55_V | 1.882 | 1.00 |
| 45_A | 53_S | 1.838 | 1.00 |
| 103_V | 107_A | 1.707 | 1.00 |
| 31_A | 34_V | 1.671 | 1.00 |
| 18_T | 67_F | 1.660 | 1.00 |
| 13_L | 40_G | 1.527 | 1.00 |
| 35_M | 92_V | 1.517 | 1.00 |
| 79_D | 82_Y | 1.442 | 1.00 |
| 77_V | 83_L | 1.420 | 1.00 |
| 24_W | 72_R | 1.364 | 0.99 |
| 65_D | 71_P | 1.339 | 0.99 |
| 62_V | 75_L | 1.335 | 0.99 |
| 85_T | 89_M | 1.314 | 0.99 |
| 35_M | 89_M | 1.304 | 0.99 |
| 9_V | 47_F | 1.277 | 0.99 |
| 4_I | 8_V | 1.269 | 0.99 |
| 69_I | 96_I | 1.242 | 0.98 |
| 77_V | 86_F | 1.239 | 0.98 |
| 32_N | 85_T | 1.237 | 0.98 |
| 22_M | 68_F | 1.223 | 0.98 |
| 50_R | 98_N | 1.216 | 0.98 |
| 50_R | 54_V | 1.211 | 0.98 |
| 35_M | 38_L | 1.202 | 0.98 |
| 32_N | 82_Y | 1.199 | 0.98 |
| 15_A | 19_L | 1.148 | 0.97 |
| 17_I | 21_A | 1.147 | 0.97 |
| 66_L | 75_L | 1.134 | 0.97 |
| 69_I | 82_Y | 1.132 | 0.97 |
| 46_L | 104_R | 1.127 | 0.97 |
| 82_Y | 86_F | 1.118 | 0.96 |
| 54_V | 90_L | 1.113 | 0.96 |
| 13_L | 44_V | 1.095 | 0.96 |
| 102_G | 106_Q | 1.089 | 0.96 |
| 32_N | 35_M | 1.088 | 0.96 |
| 16_V | 20_I | 1.087 | 0.96 |
| 22_M | 73_G | 1.084 | 0.96 |
| 65_D | 68_F | 1.083 | 0.96 |
| 61_V | 82_Y | 1.072 | 0.95 |
| 14_S | 60_N | 1.067 | 0.95 |
| 57_T | 93_G | 1.061 | 0.95 |
| 7_S | 51_W | 1.059 | 0.95 |
| 37_Y | 68_F | 1.055 | 0.95 |
| 61_V | 86_F | 1.051 | 0.94 |
| 94_L | 103_V | 1.048 | 0.94 |
| 33_L | 95_V | 1.044 | 0.94 |
| 69_I | 77_V | 1.039 | 0.94 |
| 61_V | 89_M | 1.036 | 0.94 |
| 69_I | 89_M | 1.034 | 0.94 |
| 5_Q | 12_A | 1.016 | 0.93 |
| 34_V | 64_F | 1.015 | 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 | |
| 2ksfA | 1 | 1 | 99.9 | 0.016 | Contact Map |
| 4dveA | 3 | 0.9065 | 41.5 | 0.847 | Contact Map |
| 4hzuS | 1 | 0.9159 | 28.5 | 0.86 | Contact Map |
| 4tkrA | 2 | 0.9252 | 25 | 0.863 | Contact Map |
| 4rfsS | 1 | 0.9626 | 19.3 | 0.871 | Contact Map |
| 3rlbA | 2 | 0.9159 | 18.2 | 0.872 | Contact Map |
| 3p5nA | 2 | 0.9159 | 13.7 | 0.879 | Contact Map |
| 4z7fA | 6 | 0 | 12.2 | 0.882 | Contact Map |
| 4huqS | 1 | 0.8598 | 6.3 | 0.896 | Contact Map |
| 3nd0A | 2 | 0.9626 | 5.3 | 0.9 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)