| msmeg_1981 |
| ID: | 1491267922 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 136 (129) | ||
| Sequences: | 1797 (1098.6) | ||
| Seq/Len: | 13.930 | ||
| Nf(neff/√len): | 96.7 |
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: 13.930).
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 |
| 63_V | 74_V | 3.926 | 1.00 |
| 62_R | 133_R | 2.839 | 1.00 |
| 77_L | 131_V | 2.621 | 1.00 |
| 77_L | 129_R | 2.421 | 1.00 |
| 13_L | 26_E | 2.258 | 1.00 |
| 62_R | 75_T | 2.257 | 1.00 |
| 44_A | 54_Y | 2.223 | 1.00 |
| 58_L | 78_P | 2.181 | 1.00 |
| 19_R | 55_R | 2.061 | 1.00 |
| 64_T | 71_T | 2.029 | 1.00 |
| 62_R | 73_A | 2.013 | 1.00 |
| 17_I | 60_E | 2.005 | 1.00 |
| 79_L | 87_I | 2.002 | 1.00 |
| 79_L | 129_R | 1.854 | 1.00 |
| 77_L | 83_E | 1.816 | 1.00 |
| 54_Y | 128_I | 1.803 | 1.00 |
| 70_R | 132_P | 1.800 | 1.00 |
| 54_Y | 78_P | 1.779 | 1.00 |
| 41_Y | 87_I | 1.712 | 1.00 |
| 90_R | 93_V | 1.656 | 1.00 |
| 17_I | 24_N | 1.654 | 1.00 |
| 72_I | 132_P | 1.648 | 1.00 |
| 54_Y | 58_L | 1.615 | 1.00 |
| 78_P | 128_I | 1.608 | 1.00 |
| 57_V | 63_V | 1.606 | 1.00 |
| 84_G | 124_Q | 1.596 | 1.00 |
| 42_T | 130_F | 1.578 | 1.00 |
| 19_R | 60_E | 1.574 | 1.00 |
| 75_T | 131_V | 1.572 | 1.00 |
| 73_A | 133_R | 1.543 | 1.00 |
| 12_L | 31_V | 1.539 | 1.00 |
| 13_L | 28_V | 1.513 | 1.00 |
| 75_T | 133_R | 1.453 | 1.00 |
| 117_D | 120_A | 1.387 | 0.99 |
| 61_P | 76_A | 1.385 | 0.99 |
| 39_G | 131_V | 1.385 | 0.99 |
| 12_L | 130_F | 1.318 | 0.99 |
| 74_V | 130_F | 1.260 | 0.99 |
| 64_T | 73_A | 1.254 | 0.99 |
| 33_E | 38_T | 1.218 | 0.98 |
| 66_Q | 71_T | 1.217 | 0.98 |
| 43_V | 91_Y | 1.208 | 0.98 |
| 44_A | 128_I | 1.192 | 0.98 |
| 50_K | 126_P | 1.189 | 0.98 |
| 15_H | 26_E | 1.189 | 0.98 |
| 76_A | 130_F | 1.176 | 0.98 |
| 107_M | 114_S | 1.175 | 0.98 |
| 50_K | 54_Y | 1.172 | 0.98 |
| 15_H | 64_T | 1.170 | 0.97 |
| 65_I | 74_V | 1.168 | 0.97 |
| 31_V | 67_V | 1.157 | 0.97 |
| 4_G | 7_F | 1.153 | 0.97 |
| 54_Y | 126_P | 1.138 | 0.97 |
| 46_G | 52_A | 1.110 | 0.96 |
| 39_G | 129_R | 1.099 | 0.96 |
| 100_R | 104_P | 1.098 | 0.96 |
| 81_Q | 84_G | 1.091 | 0.96 |
| 15_H | 24_N | 1.088 | 0.96 |
| 12_L | 65_I | 1.084 | 0.96 |
| 80_D | 83_E | 1.069 | 0.95 |
| 114_S | 117_D | 1.064 | 0.95 |
| 90_R | 94_R | 1.055 | 0.95 |
| 52_A | 55_R | 1.047 | 0.94 |
| 18_G | 56_N | 1.033 | 0.94 |
| 35_D | 38_T | 1.029 | 0.94 |
| 65_I | 72_I | 1.024 | 0.93 |
| 34_H | 129_R | 1.023 | 0.93 |
| 28_V | 66_Q | 1.017 | 0.93 |
| 19_R | 61_P | 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 | |
| 3h96A | 4 | 0.8603 | 100 | 0.245 | Contact Map |
| 3r5zA | 2 | 0.8456 | 99.9 | 0.273 | Contact Map |
| 3r5yA | 4 | 0.8456 | 99.9 | 0.273 | Contact Map |
| 3r5lA | 1 | 0.8309 | 99.9 | 0.372 | Contact Map |
| 3f7eA | 2 | 0.8382 | 98.6 | 0.703 | Contact Map |
| 2iabA | 2 | 0.8235 | 98.4 | 0.722 | Contact Map |
| 1rfeA | 1 | 0.8603 | 98.3 | 0.724 | Contact Map |
| 2htiA | 1 | 0.7721 | 98.3 | 0.725 | Contact Map |
| 3gasA | 6 | 0.8309 | 98.3 | 0.726 | Contact Map |
| 2fg9A | 1 | 0.8382 | 98.1 | 0.741 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)