| VH |
| ID: | 1472053263 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 132 (119) | ||
| Sequences: | 2889 (1736) | ||
| Seq/Len: | 24.277 | ||
| Nf(neff/√len): | 159.1 |
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: 24.277).
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 |
| 122_L | 125_R | 2.800 | 1.00 |
| 120_F | 128_F | 2.589 | 1.00 |
| 121_D | 128_F | 2.355 | 1.00 |
| 124_G | 127_T | 2.326 | 1.00 |
| 52_M | 72_V | 2.289 | 1.00 |
| 72_V | 87_L | 2.208 | 1.00 |
| 119_K | 128_F | 2.137 | 1.00 |
| 122_L | 128_F | 2.017 | 1.00 |
| 38_M | 83_L | 1.979 | 1.00 |
| 12_S | 15_S | 1.808 | 1.00 |
| 126_G | 129_V | 1.745 | 1.00 |
| 116_L | 119_K | 1.700 | 1.00 |
| 11_K | 15_S | 1.697 | 1.00 |
| 119_K | 122_L | 1.659 | 1.00 |
| 17_L | 129_V | 1.648 | 1.00 |
| 54_G | 63_T | 1.536 | 1.00 |
| 66_H | 69_R | 1.518 | 1.00 |
| 123_W | 129_V | 1.498 | 1.00 |
| 37_F | 54_G | 1.498 | 1.00 |
| 43_Q | 49_L | 1.436 | 1.00 |
| 18_T | 84_S | 1.434 | 1.00 |
| 41_V | 51_Y | 1.419 | 1.00 |
| 11_K | 90_L | 1.373 | 0.99 |
| 124_G | 129_V | 1.348 | 0.99 |
| 42_R | 96_A | 1.332 | 0.99 |
| 29_G | 32_H | 1.325 | 0.99 |
| 126_G | 131_V | 1.324 | 0.99 |
| 127_T | 131_V | 1.320 | 0.99 |
| 23_V | 38_M | 1.291 | 0.99 |
| 41_V | 49_L | 1.278 | 0.99 |
| 14_G | 18_T | 1.266 | 0.99 |
| 123_W | 126_G | 1.262 | 0.99 |
| 18_T | 86_A | 1.247 | 0.99 |
| 87_L | 91_T | 1.247 | 0.99 |
| 58_S | 61_T | 1.227 | 0.98 |
| 9_A | 17_L | 1.204 | 0.98 |
| 16_S | 90_L | 1.187 | 0.98 |
| 9_A | 18_T | 1.186 | 0.98 |
| 53_G | 74_I | 1.175 | 0.98 |
| 50_E | 53_G | 1.170 | 0.97 |
| 56_L | 76_A | 1.170 | 0.97 |
| 59_T | 63_T | 1.168 | 0.97 |
| 129_V | 132_S | 1.165 | 0.97 |
| 63_T | 66_H | 1.139 | 0.97 |
| 71_R | 87_L | 1.135 | 0.97 |
| 123_W | 132_S | 1.113 | 0.96 |
| 39_I | 54_G | 1.109 | 0.96 |
| 105_G | 117_E | 1.101 | 0.96 |
| 64_Y | 68_F | 1.085 | 0.96 |
| 37_F | 63_T | 1.082 | 0.96 |
| 42_R | 50_E | 1.078 | 0.95 |
| 119_K | 125_R | 1.073 | 0.95 |
| 68_F | 72_V | 1.067 | 0.95 |
| 6_P | 9_A | 1.028 | 0.94 |
| 74_I | 78_G | 1.018 | 0.93 |
| 58_S | 63_T | 1.017 | 0.93 |
| 14_G | 82_V | 1.015 | 0.93 |
| 56_L | 59_T | 1.012 | 0.93 |
| 55_I | 74_I | 1.004 | 0.93 |
| 14_G | 70_G | 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 | 0.9621 | 99.9 | 0.225 | Contact Map |
| 4pfeA | 2 | 0 | 99.9 | 0.227 | Contact Map |
| 4qgyA | 2 | 0.9621 | 99.8 | 0.266 | Contact Map |
| 1dqtA | 4 | 0.8636 | 99.8 | 0.267 | Contact Map |
| 4i13B | 1 | 0.947 | 99.8 | 0.282 | Contact Map |
| 3g9aB | 1 | 0.9545 | 99.8 | 0.283 | Contact Map |
| 1yjdC | 1 | 0.8712 | 99.8 | 0.284 | Contact Map |
| 4qo1A | 1 | 0.9167 | 99.8 | 0.29 | Contact Map |
| 3k3qA | 1 | 0.9545 | 99.8 | 0.291 | Contact Map |
| 2vyrE | 8 | 0.9242 | 99.8 | 0.291 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)