| MgrB |
| ID: | 1495567575 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 47 (47) | ||
| Sequences: | 47 (24.6) | ||
| Seq/Len: | 1.000 | ||
| Nf(neff/√len): | 3.6 |
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: 1.000).
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 |
| 16_C | 19_L | 2.281 | 0.98 |
| 10_V | 41_I | 1.662 | 0.86 |
| 1_M | 31_D | 1.635 | 0.84 |
| 10_V | 14_L | 1.561 | 0.81 |
| 19_L | 30_Q | 1.542 | 0.79 |
| 7_V | 13_V | 1.510 | 0.77 |
| 35_F | 43_Q | 1.496 | 0.76 |
| 15_A | 19_L | 1.458 | 0.74 |
| 9_L | 18_L | 1.396 | 0.69 |
| 22_Q | 31_D | 1.357 | 0.66 |
| 26_M | 32_V | 1.306 | 0.62 |
| 19_L | 25_N | 1.289 | 0.60 |
| 21_A | 31_D | 1.252 | 0.57 |
| 24_F | 27_M | 1.197 | 0.52 |
| 11_V | 15_A | 1.156 | 0.48 |
| 1_M | 18_L | 1.152 | 0.48 |
| 5_R | 40_A | 1.138 | 0.46 |
| 5_R | 24_F | 1.137 | 0.46 |
| 13_V | 17_L | 1.122 | 0.45 |
| 21_A | 33_Q | 1.118 | 0.44 |
| 4_F | 7_V | 1.117 | 0.44 |
| 4_F | 13_V | 1.055 | 0.39 |
| 9_L | 15_A | 1.046 | 0.38 |
| 2_K | 21_A | 1.029 | 0.36 |
| 16_C | 30_Q | 1.016 | 0.35 |
| 11_V | 30_Q | 1.004 | 0.34 |
| 23_V | 26_M | 1.004 | 0.34 |
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 | |
| 2cvcA | 1 | 0.4681 | 10.8 | 0.886 | Contact Map |
| 1co7I | 1 | 0.2766 | 9 | 0.89 | Contact Map |
| 3bx4B | 2 | 0.4468 | 6.1 | 0.898 | Contact Map |
| 4xrvA | 2 | 0.234 | 5.8 | 0.899 | Contact Map |
| 2kogA | 1 | 0.5745 | 5.5 | 0.9 | Contact Map |
| 2e84A | 1 | 0.3617 | 5 | 0.902 | Contact Map |
| 2wn4A | 1 | 0 | 4.6 | 0.904 | Contact Map |
| 1z1nX | 1 | 0.383 | 4 | 0.907 | Contact Map |
| 3zhgA | 3 | 0.5106 | 3.9 | 0.907 | Contact Map |
| 2xgrA | 1 | 0.4681 | 3.8 | 0.907 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)