| test-gremlin-vh3 |
| ID: | 1502208276 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 108 (102) | ||
| Sequences: | 6842 (3866.1) | ||
| Seq/Len: | 67.078 | ||
| Nf(neff/√len): | 382.8 |
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: 67.078).
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 | 86_L | 3.260 | 1.00 |
| 13_Q | 16_G | 2.779 | 1.00 |
| 39_Q | 45_L | 2.307 | 1.00 |
| 49_S | 70_I | 2.251 | 1.00 |
| 62_D | 65_K | 2.104 | 1.00 |
| 68_F | 83_M | 2.011 | 1.00 |
| 12_V | 16_G | 2.001 | 1.00 |
| 38_R | 92_A | 1.891 | 1.00 |
| 24_A | 34_M | 1.871 | 1.00 |
| 48_V | 68_F | 1.831 | 1.00 |
| 19_R | 82_Q | 1.752 | 1.00 |
| 19_R | 80_Y | 1.720 | 1.00 |
| 38_R | 46_E | 1.713 | 1.00 |
| 23_A | 78_T | 1.675 | 1.00 |
| 37_V | 47_W | 1.614 | 1.00 |
| 36_W | 81_L | 1.595 | 1.00 |
| 12_V | 18_L | 1.525 | 1.00 |
| 50_A | 59_Y | 1.452 | 1.00 |
| 35_S | 47_W | 1.450 | 1.00 |
| 94_Y | 97_A | 1.427 | 1.00 |
| 40_A | 43_K | 1.425 | 1.00 |
| 90_D | 94_Y | 1.407 | 0.99 |
| 34_M | 79_L | 1.377 | 0.99 |
| 10_G | 18_L | 1.357 | 0.99 |
| 24_A | 29_F | 1.334 | 0.99 |
| 33_A | 50_A | 1.331 | 0.99 |
| 47_W | 61_A | 1.321 | 0.99 |
| 60_Y | 66_G | 1.290 | 0.99 |
| 35_S | 97_A | 1.287 | 0.99 |
| 43_K | 46_E | 1.285 | 0.99 |
| 33_A | 52_S | 1.264 | 0.99 |
| 61_A | 64_V | 1.261 | 0.99 |
| 35_S | 50_A | 1.230 | 0.98 |
| 5_V | 8_G | 1.211 | 0.98 |
| 73_D | 76_K | 1.207 | 0.98 |
| 48_V | 64_V | 1.202 | 0.98 |
| 54_S | 57_S | 1.167 | 0.97 |
| 35_S | 99_G | 1.144 | 0.97 |
| 60_Y | 64_V | 1.142 | 0.97 |
| 67_R | 90_D | 1.121 | 0.97 |
| 2_V | 5_V | 1.108 | 0.96 |
| 51_I | 59_Y | 1.098 | 0.96 |
| 51_I | 79_L | 1.091 | 0.96 |
| 53_G | 56_G | 1.078 | 0.95 |
| 22_C | 38_R | 1.075 | 0.95 |
| 7_S | 10_G | 1.072 | 0.95 |
| 59_Y | 65_K | 1.039 | 0.94 |
| 60_Y | 63_S | 1.034 | 0.94 |
| 3_Q | 6_E | 1.034 | 0.94 |
| 6_E | 9_G | 1.025 | 0.93 |
| 66_G | 85_S | 1.002 | 0.92 |
| 15_G | 22_C | 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 | |
| 4ut7H | 1 | 0.9907 | 99.7 | 0.208 | Contact Map |
| 4pfeA | 2 | 0 | 99.7 | 0.21 | Contact Map |
| 1dqtA | 4 | 0.9444 | 99.7 | 0.241 | Contact Map |
| 4qo1A | 1 | 0.9907 | 99.7 | 0.259 | Contact Map |
| 2vyrE | 8 | 1 | 99.7 | 0.263 | Contact Map |
| 1yjdC | 1 | 0.963 | 99.7 | 0.263 | Contact Map |
| 3k3qA | 1 | 1 | 99.7 | 0.265 | Contact Map |
| 3qycA | 2 | 0.9907 | 99.7 | 0.269 | Contact Map |
| 4qgyA | 2 | 1 | 99.7 | 0.272 | Contact Map |
| 1jtpA | 2 | 1 | 99.6 | 0.276 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)