| 2QUP_A |
| ID: | 1414739511 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 145 (144) | ||
| Sequences: | 298 (241.3) | ||
| Seq/Len: | 2.069 | ||
| Nf(neff/√len): | 20.1 |
Jackhmmer Results: (2014_04_16)
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: 2.069).
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 |
| 74_K | 109_D | 2.571 | 1.00 |
| 113_L | 117_D | 1.927 | 0.99 |
| 84_G | 113_L | 1.907 | 0.99 |
| 84_G | 144_Y | 1.832 | 0.98 |
| 88_E | 106_K | 1.626 | 0.95 |
| 134_G | 137_K | 1.583 | 0.94 |
| 109_D | 134_G | 1.558 | 0.93 |
| 123_E | 134_G | 1.543 | 0.93 |
| 111_K | 135_E | 1.519 | 0.92 |
| 113_L | 142_N | 1.498 | 0.92 |
| 130_L | 135_E | 1.490 | 0.91 |
| 84_G | 142_N | 1.488 | 0.91 |
| 130_L | 134_G | 1.481 | 0.91 |
| 31_M | 142_N | 1.467 | 0.90 |
| 58_S | 109_D | 1.458 | 0.90 |
| 108_V | 140_L | 1.431 | 0.89 |
| 104_I | 129_I | 1.427 | 0.89 |
| 54_G | 119_V | 1.418 | 0.88 |
| 62_T | 133_V | 1.414 | 0.88 |
| 118_A | 132_M | 1.411 | 0.88 |
| 111_K | 127_L | 1.340 | 0.84 |
| 70_K | 116_T | 1.337 | 0.84 |
| 65_E | 100_K | 1.336 | 0.84 |
| 70_K | 83_L | 1.313 | 0.82 |
| 62_T | 65_E | 1.296 | 0.81 |
| 125_K | 128_D | 1.255 | 0.78 |
| 53_Q | 63_I | 1.236 | 0.77 |
| 118_A | 121_A | 1.233 | 0.77 |
| 81_V | 106_K | 1.214 | 0.75 |
| 110_R | 114_D | 1.212 | 0.75 |
| 56_L | 74_K | 1.207 | 0.74 |
| 2_D | 5_R | 1.203 | 0.74 |
| 108_V | 143_I | 1.198 | 0.74 |
| 57_L | 89_E | 1.193 | 0.73 |
| 109_D | 140_L | 1.170 | 0.71 |
| 30_V | 134_G | 1.166 | 0.71 |
| 51_D | 55_K | 1.163 | 0.70 |
| 53_Q | 72_L | 1.157 | 0.70 |
| 129_I | 141_I | 1.140 | 0.68 |
| 105_V | 116_T | 1.138 | 0.68 |
| 114_D | 127_L | 1.137 | 0.68 |
| 92_G | 101_I | 1.130 | 0.67 |
| 103_K | 134_G | 1.124 | 0.67 |
| 36_D | 49_K | 1.121 | 0.66 |
| 20_Q | 45_A | 1.108 | 0.65 |
| 2_D | 6_V | 1.108 | 0.65 |
| 92_G | 95_R | 1.105 | 0.65 |
| 111_K | 114_D | 1.092 | 0.63 |
| 43_L | 76_F | 1.086 | 0.63 |
| 34_Q | 124_K | 1.085 | 0.63 |
| 42_R | 50_I | 1.082 | 0.62 |
| 78_G | 102_Y | 1.073 | 0.61 |
| 63_I | 120_L | 1.071 | 0.61 |
| 44_Q | 69_Y | 1.070 | 0.61 |
| 42_R | 56_L | 1.069 | 0.61 |
| 96_R | 108_V | 1.068 | 0.61 |
| 116_T | 119_V | 1.060 | 0.60 |
| 134_G | 142_N | 1.053 | 0.59 |
| 76_F | 108_V | 1.051 | 0.59 |
| 31_M | 70_K | 1.050 | 0.59 |
| 50_I | 72_L | 1.049 | 0.59 |
| 95_R | 98_R | 1.045 | 0.58 |
| 42_R | 79_D | 1.043 | 0.58 |
| 54_G | 133_V | 1.032 | 0.57 |
| 72_L | 79_D | 1.025 | 0.56 |
| 137_K | 140_L | 1.024 | 0.56 |
| 117_D | 133_V | 1.020 | 0.56 |
| 85_L | 144_Y | 1.014 | 0.55 |
| 55_K | 81_V | 1.014 | 0.55 |
| 57_L | 125_K | 1.013 | 0.55 |
| 50_I | 122_K | 1.006 | 0.54 |
| 78_G | 82_E | 1.005 | 0.54 |
| 35_R | 127_L | 1.004 | 0.54 |
| 65_E | 119_V | 1.002 | 0.54 |
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 | |
| 2qupA | 1 | 0.8207 | 100 | 0.106 | Contact Map |
| 2p61A | 1 | 0.7793 | 100 | 0.13 | Contact Map |
| 2hc5A | 1 | 0.7517 | 79.4 | 0.896 | Contact Map |
| 3bghA | 2 | 0.4 | 17.4 | 0.933 | Contact Map |
| 4nsoB | 1 | 0.5862 | 12 | 0.937 | Contact Map |
| 2kw6A | 2 | 0.3862 | 10 | 0.94 | Contact Map |
| 4l6yA | 2 | 0.8138 | 7.6 | 0.943 | Contact Map |
| 4nooB | 2 | 0.5724 | 6.1 | 0.945 | Contact Map |
| 4mzyA | 1 | 0.7793 | 4.4 | 0.949 | Contact Map |
| 2oieA | 4 | 0.5655 | 4.2 | 0.949 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)