| VH-biotin |
| ID: | 1495279423 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 120 (117) | ||
| Sequences: | 6203 (3396.9) | ||
| Seq/Len: | 53.017 | ||
| Nf(neff/√len): | 314.0 |
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: 53.017).
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_K | 86_L | 2.734 | 1.00 |
| 111_G | 114_T | 2.490 | 1.00 |
| 13_K | 16_S | 2.301 | 1.00 |
| 62_Q | 65_Q | 2.169 | 1.00 |
| 12_K | 16_S | 2.061 | 1.00 |
| 38_R | 92_A | 1.949 | 1.00 |
| 68_V | 83_L | 1.909 | 1.00 |
| 39_Q | 45_L | 1.780 | 1.00 |
| 48_M | 68_V | 1.754 | 1.00 |
| 110_W | 113_G | 1.733 | 1.00 |
| 113_G | 116_V | 1.696 | 1.00 |
| 49_G | 70_I | 1.685 | 1.00 |
| 37_V | 47_W | 1.656 | 1.00 |
| 36_W | 81_M | 1.574 | 1.00 |
| 19_K | 80_Y | 1.556 | 1.00 |
| 106_W | 109_Y | 1.527 | 1.00 |
| 24_S | 34_F | 1.522 | 1.00 |
| 48_M | 64_F | 1.500 | 1.00 |
| 114_T | 118_V | 1.500 | 1.00 |
| 34_F | 79_A | 1.489 | 1.00 |
| 12_K | 18_V | 1.480 | 1.00 |
| 90_D | 94_Y | 1.463 | 1.00 |
| 38_R | 46_E | 1.428 | 1.00 |
| 110_W | 114_T | 1.417 | 1.00 |
| 110_W | 115_L | 1.406 | 0.99 |
| 35_Q | 47_W | 1.404 | 0.99 |
| 33_F | 50_R | 1.397 | 0.99 |
| 107_F | 110_W | 1.384 | 0.99 |
| 19_K | 82_E | 1.367 | 0.99 |
| 110_W | 116_V | 1.328 | 0.99 |
| 108_A | 117_T | 1.319 | 0.99 |
| 108_A | 115_L | 1.304 | 0.99 |
| 10_E | 18_V | 1.300 | 0.99 |
| 35_Q | 97_A | 1.294 | 0.99 |
| 109_Y | 112_Q | 1.264 | 0.99 |
| 106_W | 110_W | 1.259 | 0.99 |
| 112_Q | 117_T | 1.249 | 0.99 |
| 108_A | 112_Q | 1.245 | 0.98 |
| 73_D | 76_T | 1.236 | 0.98 |
| 94_Y | 97_A | 1.229 | 0.98 |
| 115_L | 118_V | 1.219 | 0.98 |
| 113_G | 118_V | 1.214 | 0.98 |
| 111_G | 115_L | 1.197 | 0.98 |
| 54_A | 57_F | 1.197 | 0.98 |
| 107_F | 115_L | 1.189 | 0.98 |
| 61_A | 64_F | 1.159 | 0.97 |
| 106_W | 112_Q | 1.150 | 0.97 |
| 33_F | 52_D | 1.148 | 0.97 |
| 67_R | 90_D | 1.143 | 0.97 |
| 50_R | 59_K | 1.109 | 0.96 |
| 111_G | 116_V | 1.093 | 0.96 |
| 51_I | 79_A | 1.086 | 0.96 |
| 115_L | 119_S | 1.076 | 0.95 |
| 18_V | 116_V | 1.062 | 0.95 |
| 109_Y | 117_T | 1.061 | 0.95 |
| 60_Y | 64_F | 1.059 | 0.95 |
| 47_W | 61_A | 1.057 | 0.95 |
| 53_P | 56_G | 1.053 | 0.95 |
| 23_K | 78_T | 1.050 | 0.94 |
| 100_D | 103_G | 1.049 | 0.94 |
| 110_W | 119_S | 1.049 | 0.94 |
| 43_Q | 46_E | 1.048 | 0.94 |
| 69_T | 82_E | 1.045 | 0.94 |
| 67_R | 83_L | 1.045 | 0.94 |
| 17_S | 82_E | 1.036 | 0.94 |
| 112_Q | 115_L | 1.035 | 0.94 |
| 60_Y | 66_G | 1.029 | 0.94 |
| 24_S | 29_N | 1.022 | 0.93 |
| 109_Y | 115_L | 1.011 | 0.93 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | 0.9917 | 99.8 | 0.148 | Contact Map |
| 4pfeA | 2 | 0 | 99.8 | 0.151 | Contact Map |
| 4qgyA | 2 | 1 | 99.8 | 0.185 | Contact Map |
| 4i13B | 1 | 1 | 99.8 | 0.205 | Contact Map |
| 1dqtA | 4 | 0.9583 | 99.8 | 0.207 | Contact Map |
| 3g9aB | 1 | 0.975 | 99.8 | 0.208 | Contact Map |
| 3k3qA | 1 | 1 | 99.8 | 0.208 | Contact Map |
| 3j697 | 1 | 1 | 99.8 | 0.21 | Contact Map |
| 3lh2H | 4 | 0.9917 | 99.8 | 0.21 | Contact Map |
| 1yjdC | 1 | 0.9583 | 99.8 | 0.216 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)