| test-gremling-vh4 |
| ID: | 1502208222 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 107 (105) | ||
| Sequences: | 6681 (3724.5) | ||
| Seq/Len: | 63.629 | ||
| Nf(neff/√len): | 363.5 |
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: 63.629).
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 |
| 12_V | 85_V | 2.933 | 1.00 |
| 13_K | 16_E | 2.654 | 1.00 |
| 98_G | 101_T | 2.247 | 1.00 |
| 67_V | 82_L | 2.132 | 1.00 |
| 38_R | 91_A | 2.040 | 1.00 |
| 61_P | 64_K | 1.949 | 1.00 |
| 12_V | 16_E | 1.921 | 1.00 |
| 39_Q | 45_L | 1.863 | 1.00 |
| 24_V | 34_W | 1.853 | 1.00 |
| 49_G | 69_I | 1.852 | 1.00 |
| 97_W | 100_G | 1.843 | 1.00 |
| 36_W | 80_L | 1.615 | 1.00 |
| 48_I | 67_V | 1.597 | 1.00 |
| 37_I | 47_W | 1.595 | 1.00 |
| 12_V | 18_L | 1.570 | 1.00 |
| 38_R | 46_E | 1.537 | 1.00 |
| 100_G | 103_V | 1.536 | 1.00 |
| 99_Q | 104_T | 1.518 | 1.00 |
| 35_S | 47_W | 1.486 | 1.00 |
| 19_S | 79_S | 1.482 | 1.00 |
| 48_I | 63_L | 1.480 | 1.00 |
| 19_S | 81_K | 1.478 | 1.00 |
| 97_W | 103_V | 1.452 | 1.00 |
| 101_T | 105_V | 1.449 | 1.00 |
| 34_W | 78_F | 1.431 | 1.00 |
| 35_S | 96_A | 1.407 | 0.99 |
| 5_Q | 8_G | 1.397 | 0.99 |
| 23_T | 77_Q | 1.372 | 0.99 |
| 10_G | 18_L | 1.354 | 0.99 |
| 102_L | 105_V | 1.350 | 0.99 |
| 66_R | 89_D | 1.315 | 0.99 |
| 33_Y | 50_Y | 1.283 | 0.99 |
| 97_W | 102_L | 1.280 | 0.99 |
| 18_L | 103_V | 1.232 | 0.98 |
| 93_Y | 96_A | 1.193 | 0.98 |
| 6_E | 9_P | 1.190 | 0.98 |
| 15_S | 22_C | 1.173 | 0.98 |
| 66_R | 82_L | 1.165 | 0.97 |
| 98_G | 102_L | 1.158 | 0.97 |
| 72_D | 75_K | 1.148 | 0.97 |
| 51_I | 78_F | 1.137 | 0.97 |
| 50_Y | 58_N | 1.134 | 0.97 |
| 60_N | 63_L | 1.130 | 0.97 |
| 65_S | 84_S | 1.114 | 0.96 |
| 89_D | 93_Y | 1.108 | 0.96 |
| 33_Y | 52_Y | 1.104 | 0.96 |
| 98_G | 103_V | 1.078 | 0.95 |
| 43_K | 46_E | 1.068 | 0.95 |
| 2_V | 5_Q | 1.066 | 0.95 |
| 99_Q | 102_L | 1.036 | 0.94 |
| 7_S | 10_G | 1.016 | 0.93 |
| 99_Q | 103_V | 1.005 | 0.93 |
| 100_G | 105_V | 1.005 | 0.93 |
| 73_T | 76_N | 1.001 | 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 | |
| 4pfeA | 2 | 0 | 99.8 | 0.189 | Contact Map |
| 4ut7H | 1 | 0.9907 | 99.8 | 0.207 | Contact Map |
| 1yjdC | 1 | 0.9626 | 99.8 | 0.237 | Contact Map |
| 1dqtA | 4 | 0.9533 | 99.8 | 0.244 | Contact Map |
| 3g9aB | 1 | 0.9813 | 99.7 | 0.254 | Contact Map |
| 4qgyA | 2 | 1 | 99.7 | 0.255 | Contact Map |
| 3k3qA | 1 | 1 | 99.7 | 0.261 | Contact Map |
| 4qo1A | 1 | 0.9907 | 99.7 | 0.262 | Contact Map |
| 4wemB | 1 | 1 | 99.7 | 0.263 | Contact Map |
| 4n8pA | 1 | 0.9346 | 99.7 | 0.265 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)