| VTE6_195_333 |
| ID: | 1490531489 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 139 (131) | ||
| Sequences: | 933 (671.9) | ||
| Seq/Len: | 7.122 | ||
| Nf(neff/√len): | 58.7 |
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: 7.122).
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 |
| 21_S | 57_G | 2.913 | 1.00 |
| 14_T | 122_G | 2.688 | 1.00 |
| 15_K | 119_I | 2.456 | 1.00 |
| 41_V | 45_T | 2.342 | 1.00 |
| 65_A | 82_C | 2.289 | 1.00 |
| 14_T | 118_N | 2.123 | 1.00 |
| 62_F | 83_V | 2.084 | 1.00 |
| 101_Q | 111_N | 2.075 | 1.00 |
| 31_T | 40_I | 2.028 | 1.00 |
| 109_L | 114_V | 1.914 | 1.00 |
| 57_G | 90_N | 1.815 | 1.00 |
| 20_V | 60_A | 1.788 | 1.00 |
| 16_V | 20_V | 1.721 | 1.00 |
| 92_G | 121_L | 1.698 | 1.00 |
| 34_L | 41_V | 1.692 | 1.00 |
| 54_T | 91_L | 1.680 | 1.00 |
| 49_M | 54_T | 1.636 | 1.00 |
| 9_V | 82_C | 1.544 | 1.00 |
| 24_I | 56_A | 1.534 | 0.99 |
| 7_G | 127_I | 1.525 | 0.99 |
| 17_S | 61_S | 1.485 | 0.99 |
| 35_A | 98_A | 1.439 | 0.99 |
| 11_S | 15_K | 1.403 | 0.99 |
| 118_N | 122_G | 1.374 | 0.99 |
| 89_A | 93_E | 1.362 | 0.98 |
| 20_V | 63_F | 1.344 | 0.98 |
| 119_I | 123_S | 1.337 | 0.98 |
| 61_S | 82_C | 1.329 | 0.98 |
| 61_S | 65_A | 1.329 | 0.98 |
| 24_I | 52_E | 1.327 | 0.98 |
| 48_A | 94_S | 1.323 | 0.98 |
| 58_L | 87_Q | 1.314 | 0.98 |
| 33_Y | 40_I | 1.296 | 0.98 |
| 42_P | 45_T | 1.287 | 0.98 |
| 46_E | 102_D | 1.282 | 0.98 |
| 50_S | 54_T | 1.281 | 0.97 |
| 58_L | 84_L | 1.274 | 0.97 |
| 36_T | 98_A | 1.258 | 0.97 |
| 12_F | 15_K | 1.257 | 0.97 |
| 81_V | 85_A | 1.251 | 0.97 |
| 10_S | 122_G | 1.248 | 0.97 |
| 36_T | 94_S | 1.239 | 0.97 |
| 10_S | 126_A | 1.234 | 0.97 |
| 51_L | 55_L | 1.189 | 0.96 |
| 101_Q | 105_G | 1.175 | 0.95 |
| 17_S | 90_N | 1.174 | 0.95 |
| 29_G | 52_E | 1.174 | 0.95 |
| 20_V | 46_E | 1.167 | 0.95 |
| 21_S | 90_N | 1.144 | 0.94 |
| 22_S | 112_D | 1.110 | 0.93 |
| 57_G | 91_L | 1.110 | 0.93 |
| 9_V | 86_S | 1.108 | 0.93 |
| 117_I | 120_S | 1.106 | 0.93 |
| 14_T | 82_C | 1.103 | 0.93 |
| 116_V | 120_S | 1.097 | 0.92 |
| 109_L | 113_V | 1.081 | 0.92 |
| 66_S | 79_A | 1.079 | 0.92 |
| 10_S | 85_A | 1.032 | 0.89 |
| 28_Y | 52_E | 1.022 | 0.88 |
| 41_V | 48_A | 1.021 | 0.88 |
| 11_S | 123_S | 1.015 | 0.88 |
| 2_Q | 69_C | 1.001 | 0.87 |
| 93_E | 97_G | 1.000 | 0.87 |
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 | 0.9137 | 34.3 | 0.928 | Contact Map |
| 1ciiA | 1 | 0.705 | 3.8 | 0.954 | Contact Map |
| 2i88A | 1 | 0.7194 | 2.6 | 0.957 | Contact Map |
| 1skhA | 1 | 0.1727 | 2.5 | 0.958 | Contact Map |
| 2micA | 2 | 0.2518 | 2.5 | 0.958 | Contact Map |
| 2bs2C | 2 | 0.3453 | 2 | 0.96 | Contact Map |
| 3votA | 2 | 0.2806 | 1.7 | 0.962 | Contact Map |
| 3orgA | 4 | 0.5036 | 1.7 | 0.962 | Contact Map |
| 1ji6A | 1 | 0.6115 | 1.6 | 0.962 | Contact Map |
| 4j05A | 2 | 0.8849 | 1.4 | 0.964 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)