| 4nbi |
| ID: | 1477915531 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 164 (151) | ||
| Sequences: | 2993 (1719.1) | ||
| Seq/Len: | 19.821 | ||
| Nf(neff/√len): | 139.9 |
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: 19.821).
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 |
| 53_L | 122_E | 3.119 | 1.00 |
| 120_I | 134_I | 3.052 | 1.00 |
| 49_W | 118_K | 2.908 | 1.00 |
| 61_N | 99_N | 2.691 | 1.00 |
| 113_L | 117_N | 2.549 | 1.00 |
| 38_I | 145_V | 2.498 | 1.00 |
| 75_N | 78_D | 2.416 | 1.00 |
| 37_L | 64_L | 2.411 | 1.00 |
| 44_H | 92_F | 2.330 | 1.00 |
| 85_I | 120_I | 2.326 | 1.00 |
| 83_L | 123_F | 2.274 | 1.00 |
| 31_S | 133_K | 2.129 | 1.00 |
| 72_W | 151_V | 2.090 | 1.00 |
| 111_E | 114_I | 2.086 | 1.00 |
| 85_I | 119_I | 2.058 | 1.00 |
| 48_T | 51_D | 2.024 | 1.00 |
| 56_I | 123_F | 1.948 | 1.00 |
| 37_L | 76_V | 1.874 | 1.00 |
| 51_D | 157_T | 1.785 | 1.00 |
| 57_R | 61_N | 1.779 | 1.00 |
| 67_N | 73_D | 1.750 | 1.00 |
| 14_S | 144_D | 1.722 | 1.00 |
| 85_I | 123_F | 1.715 | 1.00 |
| 45_K | 105_L | 1.702 | 1.00 |
| 53_L | 118_K | 1.670 | 1.00 |
| 76_V | 83_L | 1.650 | 1.00 |
| 71_T | 103_F | 1.641 | 1.00 |
| 39_C | 59_C | 1.636 | 1.00 |
| 142_N | 146_T | 1.623 | 1.00 |
| 76_V | 81_Y | 1.601 | 1.00 |
| 41_L | 119_I | 1.597 | 1.00 |
| 82_E | 131_K | 1.561 | 1.00 |
| 40_F | 145_V | 1.554 | 1.00 |
| 122_E | 125_K | 1.550 | 1.00 |
| 12_I | 144_D | 1.496 | 1.00 |
| 13_L | 143_I | 1.485 | 1.00 |
| 34_K | 82_E | 1.472 | 1.00 |
| 93_G | 153_I | 1.440 | 1.00 |
| 68_D | 74_K | 1.425 | 1.00 |
| 61_N | 77_K | 1.421 | 1.00 |
| 142_N | 148_D | 1.400 | 0.99 |
| 45_K | 108_E | 1.371 | 0.99 |
| 51_D | 158_H | 1.366 | 0.99 |
| 124_K | 134_I | 1.364 | 0.99 |
| 87_S | 116_Y | 1.363 | 0.99 |
| 108_E | 111_E | 1.360 | 0.99 |
| 107_K | 111_E | 1.350 | 0.99 |
| 85_I | 116_Y | 1.346 | 0.99 |
| 45_K | 107_K | 1.343 | 0.99 |
| 56_I | 122_E | 1.341 | 0.99 |
| 118_K | 122_E | 1.336 | 0.99 |
| 60_L | 123_F | 1.330 | 0.99 |
| 49_W | 53_L | 1.327 | 0.99 |
| 46_N | 158_H | 1.327 | 0.99 |
| 121_D | 125_K | 1.325 | 0.99 |
| 59_C | 119_I | 1.305 | 0.99 |
| 121_D | 124_K | 1.286 | 0.99 |
| 82_E | 133_K | 1.267 | 0.99 |
| 60_L | 83_L | 1.257 | 0.99 |
| 66_N | 70_K | 1.237 | 0.98 |
| 94_N | 105_L | 1.221 | 0.98 |
| 38_I | 86_V | 1.208 | 0.98 |
| 95_T | 155_I | 1.188 | 0.98 |
| 88_Q | 91_L | 1.170 | 0.97 |
| 41_L | 85_I | 1.169 | 0.97 |
| 31_S | 84_L | 1.168 | 0.97 |
| 49_W | 114_I | 1.165 | 0.97 |
| 113_L | 136_K | 1.158 | 0.97 |
| 51_D | 54_Y | 1.145 | 0.97 |
| 143_I | 147_N | 1.143 | 0.97 |
| 74_K | 77_K | 1.142 | 0.97 |
| 117_N | 121_D | 1.137 | 0.97 |
| 66_N | 71_T | 1.128 | 0.97 |
| 44_H | 105_L | 1.115 | 0.96 |
| 117_N | 134_I | 1.110 | 0.96 |
| 46_N | 111_E | 1.101 | 0.96 |
| 12_I | 32_E | 1.098 | 0.96 |
| 43_I | 55_I | 1.096 | 0.96 |
| 53_L | 56_I | 1.084 | 0.96 |
| 122_E | 126_Q | 1.083 | 0.96 |
| 118_K | 121_D | 1.075 | 0.95 |
| 39_C | 85_I | 1.073 | 0.95 |
| 57_R | 127_Y | 1.067 | 0.95 |
| 66_N | 103_F | 1.043 | 0.94 |
| 28_E | 136_K | 1.030 | 0.94 |
| 56_I | 60_L | 1.013 | 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 | |
| 4nbiA | 2 | 0.9939 | 100 | 0.031 | Contact Map |
| 2okvA | 4 | 0.9085 | 100 | 0.052 | Contact Map |
| 2dboA | 1 | 0.9024 | 100 | 0.053 | Contact Map |
| 1jkeA | 4 | 0.8841 | 100 | 0.06 | Contact Map |
| 1j7gA | 1 | 0.878 | 100 | 0.063 | Contact Map |
| 1tc5A | 4 | 0.8841 | 100 | 0.13 | Contact Map |
| 4rriA | 1 | 0 | 86.7 | 0.913 | Contact Map |
| 4rrfA | 6 | 0 | 82.6 | 0.918 | Contact Map |
| 4rrqA | 2 | 0 | 71.4 | 0.926 | Contact Map |
| 2g5xA | 1 | 0.372 | 20.6 | 0.947 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)