| VTE5 171-304 |
| ID: | 1486639668 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 134 (132) | ||
| Sequences: | 1274 (936.4) | ||
| Seq/Len: | 9.652 | ||
| Nf(neff/√len): | 81.5 |
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: 9.652).
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 |
| 64_F | 103_T | 3.095 | 1.00 |
| 60_S | 103_T | 2.580 | 1.00 |
| 45_G | 58_A | 2.472 | 1.00 |
| 105_V | 123_A | 2.268 | 1.00 |
| 98_V | 128_A | 2.181 | 1.00 |
| 8_A | 12_S | 2.170 | 1.00 |
| 47_T | 58_A | 2.086 | 1.00 |
| 33_G | 63_M | 2.057 | 1.00 |
| 32_G | 66_F | 2.008 | 1.00 |
| 46_S | 58_A | 1.976 | 1.00 |
| 60_S | 64_F | 1.945 | 1.00 |
| 29_M | 67_G | 1.914 | 1.00 |
| 36_I | 66_F | 1.902 | 1.00 |
| 40_M | 62_S | 1.761 | 1.00 |
| 66_F | 70_I | 1.699 | 1.00 |
| 16_F | 125_I | 1.652 | 1.00 |
| 64_F | 100_M | 1.592 | 1.00 |
| 102_A | 124_T | 1.585 | 1.00 |
| 22_I | 26_S | 1.559 | 1.00 |
| 40_M | 44_F | 1.478 | 1.00 |
| 117_N | 121_P | 1.476 | 1.00 |
| 36_I | 62_S | 1.445 | 1.00 |
| 37_A | 41_G | 1.438 | 1.00 |
| 5_Y | 35_G | 1.435 | 1.00 |
| 63_M | 67_G | 1.379 | 0.99 |
| 30_M | 120_V | 1.378 | 0.99 |
| 9_L | 27_L | 1.352 | 0.99 |
| 101_V | 123_A | 1.348 | 0.99 |
| 49_I | 107_S | 1.327 | 0.99 |
| 72_I | 77_Y | 1.315 | 0.99 |
| 12_S | 125_I | 1.303 | 0.99 |
| 59_G | 106_E | 1.302 | 0.99 |
| 5_Y | 30_M | 1.300 | 0.99 |
| 116_D | 121_P | 1.269 | 0.99 |
| 41_G | 56_S | 1.257 | 0.98 |
| 57_W | 61_I | 1.248 | 0.98 |
| 2_P | 35_G | 1.212 | 0.98 |
| 123_A | 127_A | 1.203 | 0.98 |
| 8_A | 120_V | 1.188 | 0.98 |
| 26_S | 128_A | 1.183 | 0.98 |
| 25_I | 71_S | 1.180 | 0.97 |
| 2_P | 115_D | 1.169 | 0.97 |
| 2_P | 5_Y | 1.165 | 0.97 |
| 85_H | 90_T | 1.152 | 0.97 |
| 34_D | 41_G | 1.129 | 0.96 |
| 32_G | 70_I | 1.128 | 0.96 |
| 101_V | 127_A | 1.116 | 0.96 |
| 68_F | 99_S | 1.107 | 0.96 |
| 17_W | 63_M | 1.095 | 0.96 |
| 62_S | 66_F | 1.087 | 0.95 |
| 40_M | 43_K | 1.085 | 0.95 |
| 12_S | 26_S | 1.084 | 0.95 |
| 41_G | 59_G | 1.078 | 0.95 |
| 60_S | 107_S | 1.077 | 0.95 |
| 6_V | 9_L | 1.075 | 0.95 |
| 68_F | 96_A | 1.064 | 0.95 |
| 33_G | 67_G | 1.062 | 0.95 |
| 29_M | 124_T | 1.046 | 0.94 |
| 5_Y | 31_C | 1.046 | 0.94 |
| 28_A | 70_I | 1.045 | 0.94 |
| 126_L | 130_L | 1.042 | 0.94 |
| 37_A | 106_E | 1.042 | 0.94 |
| 118_I | 121_P | 1.034 | 0.93 |
| 17_W | 35_G | 1.026 | 0.93 |
| 63_M | 103_T | 1.013 | 0.93 |
| 37_A | 63_M | 1.006 | 0.92 |
| 56_S | 59_G | 1.003 | 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 | 0.9925 | 97.8 | 0.716 | Contact Map |
| 4p6vB | 1 | 0.3955 | 5.3 | 0.924 | Contact Map |
| 4n7wA | 2 | 0.3881 | 3.1 | 0.932 | Contact Map |
| 3w5aC | 1 | 0.209 | 3 | 0.932 | Contact Map |
| 2mofA | 1 | 0.1716 | 2.2 | 0.937 | Contact Map |
| 2micA | 2 | 0.1791 | 1.8 | 0.94 | Contact Map |
| 2wswA | 1 | 0.5821 | 1.6 | 0.941 | Contact Map |
| 3s0xA | 2 | 0.5373 | 1.5 | 0.942 | Contact Map |
| 4humA | 1 | 0.9552 | 1.3 | 0.944 | Contact Map |
| 3zuxA | 1 | 0.3582 | 1.1 | 0.947 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)