| mouse VH |
| ID: | 1512638784 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 121 (121) | ||
| Sequences: | 260 (205) | ||
| Seq/Len: | 2.149 | ||
| Nf(neff/√len): | 18.6 |
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: 2.149).
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 |
| 108_M | 116_S | 2.364 | 1.00 |
| 110_Y | 116_S | 2.107 | 0.99 |
| 112_G | 119_V | 2.078 | 0.99 |
| 114_G | 117_V | 2.015 | 0.99 |
| 112_G | 117_V | 1.989 | 0.99 |
| 109_D | 121_S | 1.948 | 0.99 |
| 110_Y | 113_Q | 1.792 | 0.98 |
| 117_V | 120_S | 1.637 | 0.96 |
| 38_K | 67_K | 1.598 | 0.95 |
| 40_R | 91_S | 1.577 | 0.94 |
| 114_G | 120_S | 1.571 | 0.94 |
| 114_G | 119_V | 1.538 | 0.93 |
| 107_A | 116_S | 1.505 | 0.92 |
| 68_A | 83_L | 1.494 | 0.92 |
| 111_W | 117_V | 1.460 | 0.91 |
| 116_S | 121_S | 1.426 | 0.89 |
| 118_T | 121_S | 1.415 | 0.89 |
| 40_R | 67_K | 1.394 | 0.88 |
| 12_A | 87_T | 1.387 | 0.87 |
| 111_W | 119_V | 1.375 | 0.87 |
| 63_K | 81_M | 1.374 | 0.87 |
| 27_Y | 30_T | 1.374 | 0.87 |
| 111_W | 120_S | 1.365 | 0.86 |
| 68_A | 82_Q | 1.343 | 0.85 |
| 71_T | 81_M | 1.337 | 0.85 |
| 112_G | 121_S | 1.308 | 0.83 |
| 6_Q | 10_E | 1.298 | 0.82 |
| 113_Q | 120_S | 1.287 | 0.82 |
| 5_Q | 87_T | 1.271 | 0.80 |
| 112_G | 115_T | 1.270 | 0.80 |
| 61_N | 91_S | 1.267 | 0.80 |
| 6_Q | 9_A | 1.253 | 0.79 |
| 111_W | 115_T | 1.245 | 0.78 |
| 32_Y | 98_R | 1.242 | 0.78 |
| 31_T | 100_R | 1.237 | 0.78 |
| 10_E | 18_V | 1.230 | 0.77 |
| 19_K | 80_S | 1.227 | 0.77 |
| 115_T | 118_T | 1.222 | 0.77 |
| 111_W | 114_G | 1.204 | 0.75 |
| 10_E | 13_R | 1.201 | 0.75 |
| 3_Q | 49_G | 1.199 | 0.75 |
| 12_A | 76_S | 1.196 | 0.74 |
| 107_A | 110_Y | 1.190 | 0.74 |
| 48_I | 76_S | 1.176 | 0.73 |
| 112_G | 120_S | 1.176 | 0.73 |
| 115_T | 119_V | 1.162 | 0.71 |
| 106_Y | 110_Y | 1.160 | 0.71 |
| 43_Q | 81_M | 1.157 | 0.71 |
| 115_T | 120_S | 1.149 | 0.70 |
| 64_F | 74_K | 1.138 | 0.69 |
| 12_A | 20_M | 1.124 | 0.68 |
| 6_Q | 76_S | 1.107 | 0.66 |
| 34_M | 79_A | 1.099 | 0.65 |
| 5_Q | 9_A | 1.092 | 0.65 |
| 113_Q | 118_T | 1.089 | 0.64 |
| 29_F | 34_M | 1.079 | 0.63 |
| 61_N | 65_K | 1.079 | 0.63 |
| 40_R | 44_G | 1.068 | 0.62 |
| 48_I | 72_A | 1.035 | 0.58 |
| 15_G | 21_S | 1.033 | 0.58 |
| 17_S | 66_D | 1.015 | 0.56 |
| 113_Q | 117_V | 1.012 | 0.56 |
| 109_D | 114_G | 1.003 | 0.55 |
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 | 0.9917 | 99.9 | 0.511 | Contact Map |
| 4pfeA | 2 | 0 | 99.9 | 0.558 | Contact Map |
| 3g9aB | 1 | 0.9752 | 99.9 | 0.56 | Contact Map |
| 4qgyA | 2 | 1 | 99.9 | 0.575 | Contact Map |
| 4qo1A | 1 | 0.9917 | 99.9 | 0.585 | Contact Map |
| 2vyrE | 8 | 1 | 99.9 | 0.585 | Contact Map |
| 1yjdC | 1 | 0.9421 | 99.9 | 0.587 | Contact Map |
| 4i13B | 1 | 1 | 99.9 | 0.598 | Contact Map |
| 1dqtA | 4 | 0.9504 | 99.8 | 0.609 | Contact Map |
| 1zvhA | 1 | 0.9917 | 99.8 | 0.61 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)