| VTE6_194_298 |
| ID: | 1490537524 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 105 (102) | ||
| Sequences: | 944 (651.6) | ||
| Seq/Len: | 9.255 | ||
| Nf(neff/√len): | 64.5 |
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: 9.255).
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 |
| 22_S | 58_G | 2.971 | 1.00 |
| 66_A | 83_C | 2.427 | 1.00 |
| 63_F | 84_V | 2.296 | 1.00 |
| 42_V | 46_T | 2.215 | 1.00 |
| 55_T | 92_L | 2.006 | 1.00 |
| 21_V | 61_A | 1.971 | 1.00 |
| 32_T | 41_I | 1.926 | 1.00 |
| 17_V | 21_V | 1.910 | 1.00 |
| 12_S | 16_K | 1.828 | 1.00 |
| 58_G | 91_N | 1.804 | 1.00 |
| 35_L | 42_V | 1.761 | 1.00 |
| 13_F | 16_K | 1.607 | 1.00 |
| 25_I | 57_A | 1.596 | 1.00 |
| 59_L | 88_Q | 1.550 | 1.00 |
| 10_V | 83_C | 1.537 | 1.00 |
| 18_S | 62_S | 1.521 | 1.00 |
| 21_V | 47_E | 1.520 | 1.00 |
| 34_Y | 41_I | 1.497 | 1.00 |
| 50_M | 55_T | 1.478 | 1.00 |
| 90_A | 94_E | 1.399 | 0.99 |
| 94_E | 98_G | 1.361 | 0.99 |
| 36_A | 99_A | 1.355 | 0.99 |
| 47_E | 103_D | 1.341 | 0.99 |
| 43_P | 46_T | 1.322 | 0.99 |
| 11_S | 86_A | 1.319 | 0.99 |
| 62_S | 83_C | 1.315 | 0.99 |
| 18_S | 91_N | 1.288 | 0.99 |
| 59_L | 85_L | 1.275 | 0.99 |
| 21_V | 64_F | 1.264 | 0.98 |
| 49_A | 95_S | 1.246 | 0.98 |
| 62_S | 66_A | 1.231 | 0.98 |
| 21_V | 102_Q | 1.229 | 0.98 |
| 8_G | 36_A | 1.223 | 0.98 |
| 82_V | 86_A | 1.207 | 0.98 |
| 25_I | 53_E | 1.198 | 0.98 |
| 33_T | 49_A | 1.186 | 0.97 |
| 10_V | 87_S | 1.170 | 0.97 |
| 29_Y | 53_E | 1.169 | 0.97 |
| 3_Q | 70_C | 1.154 | 0.97 |
| 58_G | 92_L | 1.154 | 0.97 |
| 91_N | 102_Q | 1.144 | 0.97 |
| 15_T | 83_C | 1.142 | 0.96 |
| 51_S | 55_T | 1.135 | 0.96 |
| 97_I | 101_F | 1.118 | 0.96 |
| 52_L | 56_L | 1.116 | 0.96 |
| 42_V | 49_A | 1.113 | 0.96 |
| 47_E | 102_Q | 1.057 | 0.94 |
| 37_T | 95_S | 1.056 | 0.94 |
| 22_S | 91_N | 1.045 | 0.93 |
| 16_K | 23_S | 1.043 | 0.93 |
| 7_L | 11_S | 1.041 | 0.93 |
| 16_K | 58_G | 1.018 | 0.92 |
| 66_A | 79_E | 1.001 | 0.91 |
| 53_E | 56_L | 1.000 | 0.91 |
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 | 0.9048 | 69.8 | 0.879 | Contact Map |
| 3fewX | 1 | 0.9238 | 8.6 | 0.926 | Contact Map |
| 1ciiA | 1 | 0.9333 | 4.9 | 0.934 | Contact Map |
| 1colA | 2 | 0.9524 | 3.9 | 0.937 | Contact Map |
| 3nd0A | 2 | 0.9714 | 3.1 | 0.94 | Contact Map |
| 1rh1A | 1 | 0.9143 | 3.1 | 0.94 | Contact Map |
| 2i88A | 1 | 0.8857 | 2.9 | 0.941 | Contact Map |
| 4eneA | 2 | 0.9714 | 2.3 | 0.944 | Contact Map |
| 1a87A | 1 | 0.9524 | 2 | 0.946 | Contact Map |
| 3votA | 2 | 0.381 | 2 | 0.946 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)