| TEST123 |
| ID: | 1397561199 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 118 (112) | ||
| Sequences: | 981 (870.7) | ||
| Seq/Len: | 8.759 | ||
| Nf(neff/√len): | 82.3 |
HHblits Results: (2013_03)
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: 8.759).
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 |
| 24_E | 57_H | 5.235 | 1.00 |
| 12_E | 15_R | 3.178 | 1.00 |
| 63_D | 70_V | 2.886 | 1.00 |
| 10_W | 15_R | 2.231 | 1.00 |
| 76_M | 110_T | 2.214 | 1.00 |
| 11_D | 14_F | 1.935 | 1.00 |
| 74_K | 78_K | 1.860 | 1.00 |
| 31_G | 46_T | 1.845 | 1.00 |
| 62_M | 70_V | 1.800 | 1.00 |
| 68_S | 117_K | 1.760 | 1.00 |
| 52_T | 81_L | 1.700 | 1.00 |
| 16_V | 115_K | 1.660 | 1.00 |
| 62_M | 114_Y | 1.659 | 1.00 |
| 20_Q | 57_H | 1.657 | 1.00 |
| 69_E | 113_K | 1.645 | 1.00 |
| 25_H | 54_H | 1.626 | 1.00 |
| 112_F | 115_K | 1.593 | 1.00 |
| 34_D | 46_T | 1.588 | 1.00 |
| 53_N | 57_H | 1.553 | 1.00 |
| 50_V | 102_W | 1.529 | 1.00 |
| 27_K | 30_K | 1.498 | 1.00 |
| 69_E | 72_P | 1.483 | 1.00 |
| 19_E | 23_E | 1.469 | 1.00 |
| 60_A | 64_A | 1.432 | 0.99 |
| 70_V | 74_K | 1.395 | 0.99 |
| 28_I | 103_L | 1.355 | 0.99 |
| 33_F | 36_I | 1.331 | 0.99 |
| 70_V | 78_K | 1.323 | 0.99 |
| 82_E | 86_G | 1.298 | 0.99 |
| 48_V | 88_S | 1.281 | 0.98 |
| 21_L | 61_M | 1.274 | 0.98 |
| 78_K | 81_L | 1.236 | 0.98 |
| 26_K | 30_K | 1.216 | 0.98 |
| 83_K | 98_Y | 1.213 | 0.98 |
| 81_L | 85_G | 1.211 | 0.97 |
| 16_V | 21_L | 1.206 | 0.97 |
| 63_D | 74_K | 1.201 | 0.97 |
| 104_V | 108_K | 1.175 | 0.97 |
| 76_M | 79_D | 1.160 | 0.96 |
| 27_K | 46_T | 1.160 | 0.96 |
| 103_L | 107_I | 1.147 | 0.96 |
| 45_A | 88_S | 1.131 | 0.96 |
| 77_H | 111_D | 1.131 | 0.96 |
| 23_E | 26_K | 1.117 | 0.95 |
| 67_Y | 73_H | 1.108 | 0.95 |
| 67_Y | 114_Y | 1.095 | 0.95 |
| 51_T | 74_K | 1.083 | 0.94 |
| 24_E | 54_H | 1.081 | 0.94 |
| 28_I | 47_L | 1.079 | 0.94 |
| 90_P | 94_K | 1.079 | 0.94 |
| 32_I | 103_L | 1.061 | 0.93 |
| 59_E | 74_K | 1.050 | 0.93 |
| 10_W | 26_K | 1.045 | 0.93 |
| 50_V | 107_I | 1.022 | 0.92 |
| 48_V | 84_I | 1.022 | 0.92 |
| 15_R | 29_F | 1.009 | 0.91 |
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
- 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 | |
| 2mhrA | 1 | 1 | 100 | 0.033 | Contact Map |
| 2hmqA | 4 | 0.9576 | 100 | 0.087 | Contact Map |
| 3agtA | 2 | 0.9576 | 100 | 0.172 | Contact Map |
| 2p0nA | 2 | 0.8898 | 90.6 | 0.843 | Contact Map |
| 3caxA | 1 | 0.8898 | 84.9 | 0.857 | Contact Map |
| 2l74A | 1 | 0.4915 | 7.5 | 0.926 | Contact Map |
| 3tfgA | 2 | 0.678 | 4.6 | 0.933 | Contact Map |
| 1xgkA | 1 | 0.3305 | 4.5 | 0.934 | Contact Map |
| 3tj1A | 2 | 0.9915 | 3.7 | 0.936 | Contact Map |
| 2rdeA | 2 | 0.3814 | 3.7 | 0.936 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)