| lingu |
| ID: | 1421687076 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (85) | ||
| Sequences: | 415 (356.7) | ||
| Seq/Len: | 4.882 | ||
| Nf(neff/√len): | 38.7 |
Jackhmmer Results: (2014_04_16)
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: 4.882).
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 |
| 10_R | 86_G | 2.189 | 1.00 |
| 22_T | 74_L | 1.939 | 1.00 |
| 33_G | 59_L | 1.834 | 1.00 |
| 82_W | 86_G | 1.680 | 0.99 |
| 25_G | 28_L | 1.579 | 0.99 |
| 18_A | 78_L | 1.555 | 0.99 |
| 14_T | 17_Y | 1.513 | 0.99 |
| 20_F | 24_A | 1.475 | 0.98 |
| 73_L | 81_G | 1.471 | 0.98 |
| 73_L | 77_G | 1.471 | 0.98 |
| 7_L | 11_L | 1.463 | 0.98 |
| 28_L | 85_A | 1.359 | 0.97 |
| 23_L | 72_F | 1.332 | 0.96 |
| 17_Y | 81_G | 1.316 | 0.96 |
| 73_L | 86_G | 1.303 | 0.95 |
| 21_L | 77_G | 1.294 | 0.95 |
| 16_S | 80_G | 1.289 | 0.95 |
| 25_G | 29_L | 1.273 | 0.94 |
| 71_A | 75_V | 1.269 | 0.94 |
| 21_L | 80_G | 1.230 | 0.93 |
| 31_A | 69_V | 1.218 | 0.93 |
| 28_L | 35_F | 1.210 | 0.92 |
| 29_L | 69_V | 1.207 | 0.92 |
| 32_V | 73_L | 1.200 | 0.92 |
| 66_A | 73_L | 1.187 | 0.91 |
| 3_R | 7_L | 1.177 | 0.91 |
| 60_R | 68_W | 1.158 | 0.90 |
| 43_L | 75_V | 1.145 | 0.89 |
| 14_T | 27_L | 1.142 | 0.89 |
| 32_V | 35_F | 1.139 | 0.89 |
| 12_K | 76_F | 1.134 | 0.89 |
| 19_G | 26_V | 1.127 | 0.88 |
| 12_K | 23_L | 1.107 | 0.87 |
| 19_G | 30_V | 1.105 | 0.87 |
| 71_A | 82_W | 1.085 | 0.86 |
| 13_L | 24_A | 1.069 | 0.84 |
| 9_V | 17_Y | 1.059 | 0.84 |
| 7_L | 20_F | 1.029 | 0.81 |
| 18_A | 53_T | 1.029 | 0.81 |
| 27_L | 30_V | 1.027 | 0.81 |
| 19_G | 22_T | 1.021 | 0.80 |
| 18_A | 74_L | 1.016 | 0.80 |
| 40_G | 49_A | 1.014 | 0.80 |
| 54_P | 57_V | 1.000 | 0.78 |
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 | 90.6 | 0.76 | Contact Map |
| 4gycB | 1 | 0.7011 | 65.9 | 0.815 | Contact Map |
| 2f95B | 1 | 0.6092 | 52.6 | 0.829 | Contact Map |
| 3e4oA | 2 | 0.5287 | 34.1 | 0.848 | Contact Map |
| 2onkC | 4 | 0.908 | 17.9 | 0.867 | Contact Map |
| 4i5sA | 2 | 0.1034 | 12.6 | 0.876 | Contact Map |
| 3d31C | 2 | 0.8391 | 11.2 | 0.879 | Contact Map |
| 3rlfG | 1 | 0.8736 | 8.9 | 0.884 | Contact Map |
| 2yevC | 2 | 0.6897 | 8.2 | 0.885 | Contact Map |
| 1z1nX | 1 | 0 | 5.5 | 0.894 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)