| T0829 |
| ID: | 1403547195 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 70 (70) | ||
| Sequences: | 266 (212.7) | ||
| Seq/Len: | 3.800 | ||
| Nf(neff/√len): | 25.4 |
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: 3.800).
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 |
| 3_R | 24_E | 3.217 | 1.00 |
| 45_N | 55_F | 2.350 | 1.00 |
| 42_A | 55_F | 2.187 | 1.00 |
| 3_R | 13_S | 2.048 | 1.00 |
| 24_E | 34_Q | 1.937 | 1.00 |
| 56_F | 61_K | 1.847 | 1.00 |
| 8_S | 53_G | 1.520 | 0.98 |
| 23_L | 60_I | 1.477 | 0.97 |
| 37_G | 65_L | 1.407 | 0.96 |
| 42_A | 64_F | 1.355 | 0.94 |
| 53_G | 61_K | 1.311 | 0.93 |
| 3_R | 26_Q | 1.289 | 0.92 |
| 27_F | 53_G | 1.283 | 0.92 |
| 23_L | 35_Y | 1.275 | 0.92 |
| 14_I | 46_F | 1.259 | 0.91 |
| 23_L | 36_L | 1.258 | 0.91 |
| 26_Q | 34_Q | 1.257 | 0.91 |
| 43_H | 47_M | 1.256 | 0.91 |
| 14_I | 63_K | 1.225 | 0.89 |
| 57_D | 61_K | 1.191 | 0.87 |
| 39_P | 42_A | 1.184 | 0.87 |
| 22_M | 48_S | 1.181 | 0.87 |
| 6_V | 15_G | 1.177 | 0.87 |
| 6_V | 14_I | 1.162 | 0.86 |
| 53_G | 57_D | 1.162 | 0.86 |
| 15_G | 26_Q | 1.146 | 0.85 |
| 16_Y | 42_A | 1.135 | 0.84 |
| 25_I | 68_K | 1.114 | 0.82 |
| 36_L | 67_R | 1.110 | 0.82 |
| 37_G | 67_R | 1.089 | 0.80 |
| 11_I | 56_F | 1.073 | 0.79 |
| 34_Q | 67_R | 1.032 | 0.75 |
| 25_I | 37_G | 1.016 | 0.73 |
| 13_S | 24_E | 1.005 | 0.72 |
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 | |
| 3k8rA | 2 | 0.8571 | 18.9 | 0.884 | Contact Map |
| 2x8nA | 1 | 0.9429 | 17.1 | 0.886 | Contact Map |
| 3nv7A | 1 | 0.5143 | 15.6 | 0.888 | Contact Map |
| 1f9aA | 6 | 0.6143 | 10.1 | 0.897 | Contact Map |
| 1n9wA | 2 | 0.4286 | 9.8 | 0.898 | Contact Map |
| 2ji4A | 1 | 0.8429 | 9 | 0.899 | Contact Map |
| 4j15A | 2 | 0.5143 | 8.5 | 0.9 | Contact Map |
| 4f3rA | 3 | 0.5 | 8.1 | 0.901 | Contact Map |
| 2qmeI | 1 | 0.3429 | 8.1 | 0.901 | Contact Map |
| 1wydA | 2 | 0.9286 | 7.8 | 0.902 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)