| adayTest |
| ID: | 1452210012 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 117 (116) | ||
| Sequences: | 6261 (3265.1) | ||
| Seq/Len: | 53.974 | ||
| Nf(neff/√len): | 303.2 |
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: 53.974).
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 |
| 12_K | 86_L | 2.977 | 1.00 |
| 62_P | 65_Q | 2.317 | 1.00 |
| 108_G | 111_T | 2.221 | 1.00 |
| 68_V | 83_W | 2.041 | 1.00 |
| 38_R | 92_A | 1.938 | 1.00 |
| 49_G | 70_I | 1.908 | 1.00 |
| 39_Q | 45_L | 1.900 | 1.00 |
| 13_K | 16_E | 1.881 | 1.00 |
| 37_V | 47_S | 1.807 | 1.00 |
| 12_K | 18_L | 1.786 | 1.00 |
| 34_I | 79_A | 1.752 | 1.00 |
| 111_T | 115_V | 1.717 | 1.00 |
| 38_R | 46_E | 1.672 | 1.00 |
| 107_W | 110_G | 1.610 | 1.00 |
| 19_K | 82_Q | 1.552 | 1.00 |
| 24_G | 34_I | 1.528 | 1.00 |
| 12_K | 16_E | 1.516 | 1.00 |
| 104_F | 112_L | 1.503 | 1.00 |
| 106_Y | 116_S | 1.499 | 1.00 |
| 110_G | 113_V | 1.487 | 1.00 |
| 112_L | 116_S | 1.477 | 1.00 |
| 106_Y | 109_R | 1.473 | 1.00 |
| 103_G | 112_L | 1.463 | 1.00 |
| 105_D | 112_L | 1.462 | 1.00 |
| 14_P | 88_A | 1.385 | 0.99 |
| 104_F | 113_V | 1.357 | 0.99 |
| 18_L | 113_V | 1.357 | 0.99 |
| 103_G | 106_Y | 1.275 | 0.99 |
| 67_Q | 83_W | 1.273 | 0.99 |
| 19_K | 80_Y | 1.272 | 0.99 |
| 107_W | 112_L | 1.259 | 0.99 |
| 105_D | 114_T | 1.232 | 0.98 |
| 33_W | 50_I | 1.228 | 0.98 |
| 33_W | 52_Y | 1.226 | 0.98 |
| 106_Y | 112_L | 1.221 | 0.98 |
| 22_C | 36_W | 1.214 | 0.98 |
| 110_G | 115_V | 1.206 | 0.98 |
| 106_Y | 114_T | 1.203 | 0.98 |
| 35_A | 50_I | 1.197 | 0.98 |
| 108_G | 112_L | 1.178 | 0.98 |
| 109_R | 116_S | 1.178 | 0.98 |
| 48_M | 68_V | 1.159 | 0.97 |
| 105_D | 109_R | 1.158 | 0.97 |
| 67_Q | 90_D | 1.150 | 0.97 |
| 109_R | 112_L | 1.139 | 0.97 |
| 17_S | 82_Q | 1.138 | 0.97 |
| 36_W | 81_L | 1.132 | 0.97 |
| 104_F | 114_T | 1.121 | 0.97 |
| 73_D | 76_I | 1.121 | 0.97 |
| 60_Y | 64_F | 1.115 | 0.96 |
| 23_K | 78_T | 1.106 | 0.96 |
| 104_F | 109_R | 1.102 | 0.96 |
| 48_M | 64_F | 1.096 | 0.96 |
| 101_I | 108_G | 1.094 | 0.96 |
| 43_K | 46_E | 1.086 | 0.96 |
| 69_T | 82_Q | 1.067 | 0.95 |
| 105_D | 116_S | 1.061 | 0.95 |
| 35_A | 47_S | 1.041 | 0.94 |
| 51_I | 72_A | 1.040 | 0.94 |
| 71_S | 80_Y | 1.018 | 0.93 |
| 109_R | 113_V | 1.018 | 0.93 |
| 40_M | 43_K | 1.008 | 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 | |
| 4pfeA | 2 | 0 | 99.9 | 0.163 | Contact Map |
| 4ut7H | 1 | 0.9915 | 99.9 | 0.167 | Contact Map |
| 3k3qA | 1 | 1 | 99.8 | 0.207 | Contact Map |
| 1dqtA | 4 | 0.9487 | 99.8 | 0.209 | Contact Map |
| 4qgyA | 2 | 1 | 99.8 | 0.21 | Contact Map |
| 4i13B | 1 | 1 | 99.8 | 0.218 | Contact Map |
| 1zvyA | 1 | 0.9829 | 99.8 | 0.218 | Contact Map |
| 3lh2H | 4 | 0.9915 | 99.8 | 0.219 | Contact Map |
| 3qycA | 2 | 0.9915 | 99.8 | 0.223 | Contact Map |
| 3g9aB | 1 | 0.9744 | 99.8 | 0.226 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)