| lingu |
| ID: | 1421651664 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 164 (126.3) | ||
| Seq/Len: | 1.885 | ||
| Nf(neff/√len): | 13.5 |
HHblits Results: (2013_03)
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: 1.885).
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 |
| 30_V | 82_W | 2.085 | 0.99 |
| 73_L | 77_G | 2.007 | 0.99 |
| 24_A | 77_G | 1.905 | 0.98 |
| 25_G | 81_G | 1.870 | 0.98 |
| 21_L | 77_G | 1.717 | 0.96 |
| 77_G | 80_G | 1.512 | 0.91 |
| 79_V | 83_F | 1.510 | 0.91 |
| 20_F | 80_G | 1.504 | 0.90 |
| 17_Y | 81_G | 1.499 | 0.90 |
| 12_K | 23_L | 1.420 | 0.87 |
| 21_L | 29_L | 1.415 | 0.86 |
| 11_L | 14_T | 1.385 | 0.85 |
| 17_Y | 25_G | 1.345 | 0.82 |
| 31_A | 69_V | 1.315 | 0.80 |
| 22_T | 74_L | 1.302 | 0.79 |
| 34_V | 75_V | 1.297 | 0.79 |
| 50_V | 75_V | 1.270 | 0.77 |
| 63_A | 87_R | 1.268 | 0.77 |
| 24_A | 73_L | 1.259 | 0.76 |
| 21_L | 81_G | 1.259 | 0.76 |
| 31_A | 61_S | 1.255 | 0.76 |
| 9_V | 84_L | 1.240 | 0.75 |
| 38_D | 56_T | 1.229 | 0.74 |
| 41_W | 45_N | 1.207 | 0.72 |
| 26_V | 75_V | 1.204 | 0.71 |
| 12_K | 76_F | 1.189 | 0.70 |
| 47_R | 57_V | 1.156 | 0.67 |
| 10_R | 14_T | 1.151 | 0.67 |
| 1_M | 6_G | 1.149 | 0.66 |
| 32_V | 82_W | 1.148 | 0.66 |
| 66_A | 73_L | 1.131 | 0.65 |
| 7_L | 59_L | 1.126 | 0.64 |
| 33_G | 59_L | 1.112 | 0.63 |
| 28_L | 35_F | 1.106 | 0.62 |
| 23_L | 84_L | 1.091 | 0.60 |
| 7_L | 11_L | 1.089 | 0.60 |
| 68_W | 72_F | 1.082 | 0.59 |
| 50_V | 69_V | 1.081 | 0.59 |
| 78_L | 83_F | 1.064 | 0.58 |
| 14_T | 69_V | 1.062 | 0.57 |
| 21_L | 80_G | 1.061 | 0.57 |
| 8_S | 84_L | 1.058 | 0.57 |
| 8_S | 19_G | 1.056 | 0.57 |
| 37_L | 80_G | 1.052 | 0.56 |
| 26_V | 49_A | 1.051 | 0.56 |
| 18_A | 78_L | 1.050 | 0.56 |
| 34_V | 47_R | 1.030 | 0.54 |
| 51_R | 75_V | 1.029 | 0.54 |
| 47_R | 51_R | 1.019 | 0.53 |
| 15_L | 84_L | 1.013 | 0.52 |
| 18_A | 67_A | 1.012 | 0.52 |
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 | |
| 2kseA | 1 | 0.4483 | 46 | 0.842 | Contact Map |
| 4gycB | 1 | 0.7011 | 33.7 | 0.853 | Contact Map |
| 2f95B | 1 | 0.6092 | 27.8 | 0.859 | Contact Map |
| 2f93B | 1 | 0.5862 | 11.4 | 0.882 | Contact Map |
| 2l6wA | 2 | 0.4483 | 5.6 | 0.898 | Contact Map |
| 4i5sA | 2 | 0.1034 | 5.2 | 0.899 | Contact Map |
| 3ayfA | 1 | 0.9655 | 3.1 | 0.91 | Contact Map |
| 1z1nX | 1 | 0 | 2.6 | 0.913 | Contact Map |
| 4p02B | 1 | 0.4483 | 2.3 | 0.915 | Contact Map |
| 3d31C | 2 | 0.8506 | 2.3 | 0.916 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)