| VC1917 |
| ID: | 1403873851 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 103 (97) | ||
| Sequences: | 1104 (998.8) | ||
| Seq/Len: | 11.381 | ||
| Nf(neff/√len): | 101.4 |
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: 11.381).
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 |
| 48_S | 51_E | 4.561 | 1.00 |
| 82_D | 85_N | 4.017 | 1.00 |
| 63_K | 66_A | 3.930 | 1.00 |
| 65_Q | 69_D | 3.249 | 1.00 |
| 84_T | 94_V | 3.036 | 1.00 |
| 49_A | 65_Q | 2.414 | 1.00 |
| 78_T | 82_D | 2.167 | 1.00 |
| 84_T | 91_E | 2.152 | 1.00 |
| 63_K | 93_T | 2.053 | 1.00 |
| 49_A | 53_A | 2.018 | 1.00 |
| 62_K | 65_Q | 1.938 | 1.00 |
| 70_Y | 85_N | 1.760 | 1.00 |
| 53_A | 61_L | 1.695 | 1.00 |
| 80_I | 94_V | 1.622 | 1.00 |
| 57_K | 100_R | 1.581 | 1.00 |
| 56_L | 100_R | 1.505 | 1.00 |
| 43_N | 46_T | 1.490 | 1.00 |
| 69_D | 72_E | 1.457 | 1.00 |
| 69_D | 73_A | 1.444 | 1.00 |
| 95_R | 98_A | 1.392 | 0.99 |
| 44_I | 101_I | 1.364 | 0.99 |
| 81_D | 98_A | 1.310 | 0.99 |
| 62_K | 66_A | 1.283 | 0.99 |
| 89_I | 94_V | 1.281 | 0.99 |
| 59_I | 63_K | 1.268 | 0.99 |
| 79_H | 82_D | 1.251 | 0.99 |
| 49_A | 68_V | 1.246 | 0.98 |
| 93_T | 96_N | 1.207 | 0.98 |
| 83_L | 94_V | 1.205 | 0.98 |
| 56_L | 101_I | 1.179 | 0.98 |
| 49_A | 61_L | 1.169 | 0.97 |
| 97_N | 100_R | 1.156 | 0.97 |
| 91_E | 95_R | 1.140 | 0.97 |
| 81_D | 94_V | 1.132 | 0.97 |
| 43_N | 102_L | 1.087 | 0.96 |
| 43_N | 103_L | 1.083 | 0.96 |
| 57_K | 97_N | 1.070 | 0.95 |
| 77_F | 86_V | 1.067 | 0.95 |
| 93_T | 97_N | 1.065 | 0.95 |
| 44_I | 97_N | 1.056 | 0.95 |
| 86_V | 90_G | 1.023 | 0.93 |
| 61_L | 65_Q | 1.009 | 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 | |
| 3psiA | 1 | 0.9903 | 99.7 | 0.377 | Contact Map |
| 3psfA | 1 | 0.9903 | 99.6 | 0.41 | Contact Map |
| 1s5lU | 2 | 0.7379 | 99.6 | 0.418 | Contact Map |
| 3bzcA | 1 | 0.9903 | 99.5 | 0.451 | Contact Map |
| 2i5hA | 1 | 0.8738 | 99.4 | 0.479 | Contact Map |
| 3arcU | 2 | 0.7184 | 99.4 | 0.495 | Contact Map |
| 2eduA | 1 | 0.8641 | 99.3 | 0.502 | Contact Map |
| 3ci0K | 1 | 0.7476 | 99.3 | 0.504 | Contact Map |
| 2duyA | 1 | 0.6311 | 99.3 | 0.522 | Contact Map |
| 2bcqA | 1 | 0.932 | 98.8 | 0.607 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)