| VTE5 192-302 |
| ID: | 1485971045 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 111 (110) | ||
| Sequences: | 1441 (1035) | ||
| Seq/Len: | 13.100 | ||
| Nf(neff/√len): | 98.7 |
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: 13.100).
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 |
| 43_F | 82_T | 3.264 | 1.00 |
| 39_S | 82_T | 2.567 | 1.00 |
| 24_G | 37_A | 2.533 | 1.00 |
| 11_G | 45_F | 2.491 | 1.00 |
| 84_V | 102_A | 2.471 | 1.00 |
| 77_V | 107_A | 2.171 | 1.00 |
| 26_T | 37_A | 2.171 | 1.00 |
| 12_G | 42_M | 2.137 | 1.00 |
| 25_S | 37_A | 2.106 | 1.00 |
| 39_S | 43_F | 2.074 | 1.00 |
| 8_M | 46_G | 1.977 | 1.00 |
| 15_I | 45_F | 1.932 | 1.00 |
| 81_A | 103_T | 1.871 | 1.00 |
| 9_M | 99_V | 1.741 | 1.00 |
| 45_F | 49_I | 1.736 | 1.00 |
| 19_M | 41_S | 1.732 | 1.00 |
| 96_N | 100_P | 1.594 | 1.00 |
| 43_F | 79_M | 1.539 | 1.00 |
| 15_I | 41_S | 1.501 | 1.00 |
| 42_M | 46_G | 1.481 | 1.00 |
| 16_A | 20_G | 1.434 | 1.00 |
| 47_F | 78_S | 1.371 | 0.99 |
| 19_M | 23_F | 1.350 | 0.99 |
| 28_I | 86_S | 1.321 | 0.99 |
| 47_F | 75_A | 1.280 | 0.99 |
| 5_S | 107_A | 1.253 | 0.99 |
| 17_D | 46_G | 1.204 | 0.98 |
| 38_G | 85_E | 1.203 | 0.98 |
| 20_G | 35_S | 1.200 | 0.98 |
| 17_D | 42_M | 1.147 | 0.97 |
| 95_D | 100_P | 1.145 | 0.97 |
| 9_M | 96_N | 1.109 | 0.96 |
| 41_S | 45_F | 1.095 | 0.96 |
| 12_G | 46_G | 1.091 | 0.96 |
| 8_M | 49_I | 1.090 | 0.96 |
| 8_M | 103_T | 1.082 | 0.96 |
| 97_I | 100_P | 1.075 | 0.95 |
| 50_S | 103_T | 1.056 | 0.95 |
| 39_S | 86_S | 1.051 | 0.94 |
| 14_G | 17_D | 1.051 | 0.94 |
| 94_D | 102_A | 1.046 | 0.94 |
| 11_G | 49_I | 1.044 | 0.94 |
| 13_D | 95_D | 1.030 | 0.94 |
| 11_G | 15_I | 1.029 | 0.94 |
| 13_D | 20_G | 1.022 | 0.93 |
| 44_I | 55_Y | 1.021 | 0.93 |
| 1_I | 5_S | 1.016 | 0.93 |
| 6_L | 35_S | 1.007 | 0.93 |
| 23_F | 49_I | 1.000 | 0.92 |
| 60_L | 65_M | 1.000 | 0.92 |
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 | |
| 4q2eA | 2 | 0.991 | 97.5 | 0.692 | Contact Map |
| 2mofA | 1 | 0.1892 | 4.6 | 0.913 | Contact Map |
| 2cfqA | 1 | 0.8919 | 2.9 | 0.921 | Contact Map |
| 3w4tA | 1 | 0.964 | 2.9 | 0.921 | Contact Map |
| 4gc0A | 1 | 0.9279 | 2.8 | 0.922 | Contact Map |
| 4humA | 1 | 0.964 | 2.2 | 0.926 | Contact Map |
| 3mktA | 2 | 0.964 | 2.1 | 0.927 | Contact Map |
| 3w5aC | 1 | 0.2342 | 2 | 0.928 | Contact Map |
| 4pypA | 1 | 0.8468 | 1.9 | 0.928 | Contact Map |
| 4ldsA | 2 | 0.8468 | 1.8 | 0.929 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)