| rv1616 |
| ID: | 1447735483 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 132 (114) | ||
| Sequences: | 367 (297.3) | ||
| Seq/Len: | 3.219 | ||
| Nf(neff/√len): | 27.8 |
HHblits Results: (2015_06)
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: 3.219).
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 |
| 32_H | 62_D | 2.790 | 1.00 |
| 67_E | 70_A | 2.689 | 1.00 |
| 59_M | 79_L | 2.494 | 1.00 |
| 72_I | 76_V | 2.272 | 1.00 |
| 44_K | 50_N | 1.969 | 1.00 |
| 43_F | 47_T | 1.894 | 0.99 |
| 78_L | 83_P | 1.879 | 0.99 |
| 43_F | 49_W | 1.842 | 0.99 |
| 63_L | 68_L | 1.756 | 0.99 |
| 27_G | 64_L | 1.743 | 0.99 |
| 22_A | 26_I | 1.724 | 0.99 |
| 56_G | 78_L | 1.677 | 0.98 |
| 77_F | 111_A | 1.633 | 0.98 |
| 57_L | 61_H | 1.628 | 0.98 |
| 22_A | 57_L | 1.525 | 0.97 |
| 40_P | 57_L | 1.522 | 0.97 |
| 85_L | 125_P | 1.392 | 0.94 |
| 37_L | 88_W | 1.350 | 0.92 |
| 43_F | 116_T | 1.348 | 0.92 |
| 40_P | 44_K | 1.343 | 0.92 |
| 31_P | 61_H | 1.338 | 0.92 |
| 86_A | 109_A | 1.252 | 0.88 |
| 67_E | 121_L | 1.244 | 0.87 |
| 69_A | 118_L | 1.240 | 0.87 |
| 71_S | 83_P | 1.228 | 0.86 |
| 50_N | 128_P | 1.201 | 0.85 |
| 49_W | 84_V | 1.192 | 0.84 |
| 81_G | 108_V | 1.188 | 0.84 |
| 50_N | 120_N | 1.173 | 0.83 |
| 110_V | 114_A | 1.172 | 0.83 |
| 66_G | 70_A | 1.169 | 0.83 |
| 62_D | 70_A | 1.164 | 0.82 |
| 31_P | 42_L | 1.162 | 0.82 |
| 73_N | 127_V | 1.153 | 0.81 |
| 61_H | 120_N | 1.125 | 0.79 |
| 69_A | 72_I | 1.121 | 0.79 |
| 21_G | 80_V | 1.104 | 0.77 |
| 83_P | 120_N | 1.094 | 0.76 |
| 30_D | 34_S | 1.093 | 0.76 |
| 83_P | 87_S | 1.083 | 0.75 |
| 56_G | 60_I | 1.079 | 0.75 |
| 40_P | 121_L | 1.065 | 0.74 |
| 87_S | 91_L | 1.055 | 0.73 |
| 77_F | 115_W | 1.052 | 0.72 |
| 19_L | 106_I | 1.051 | 0.72 |
| 74_D | 115_W | 1.051 | 0.72 |
| 84_V | 111_A | 1.050 | 0.72 |
| 18_L | 21_G | 1.034 | 0.70 |
| 75_N | 120_N | 1.032 | 0.70 |
| 75_N | 119_R | 1.019 | 0.69 |
| 38_Y | 57_L | 1.009 | 0.68 |
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 | |
| 1k82A | 4 | 0.5303 | 8.2 | 0.937 | Contact Map |
| 2jwaA | 2 | 0.3333 | 7.8 | 0.938 | Contact Map |
| 3u6pA | 1 | 0.447 | 6.4 | 0.94 | Contact Map |
| 1k3xA | 1 | 0.4924 | 5.9 | 0.941 | Contact Map |
| 1ee8A | 2 | 0.5985 | 5.5 | 0.942 | Contact Map |
| 3wajA | 1 | 0.6894 | 5.2 | 0.943 | Contact Map |
| 1h7bA | 1 | 0.3182 | 4.9 | 0.943 | Contact Map |
| 4mb7A | 1 | 0.5152 | 4.4 | 0.944 | Contact Map |
| 2ks1B | 1 | 0.3333 | 3.6 | 0.947 | Contact Map |
| 4pd2A | 1 | 0.5833 | 2.9 | 0.949 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)