| 10006_6 |
| ID: | 1433410266 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 68 (68) | ||
| Sequences: | 266 (194.6) | ||
| Seq/Len: | 3.912 | ||
| Nf(neff/√len): | 23.6 |
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: 3.912).
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 |
| 19_V | 43_L | 2.259 | 1.00 |
| 12_H | 34_H | 1.963 | 1.00 |
| 20_D | 46_S | 1.930 | 1.00 |
| 16_F | 42_H | 1.906 | 1.00 |
| 58_G | 62_W | 1.891 | 1.00 |
| 12_H | 42_H | 1.760 | 0.99 |
| 35_Q | 54_T | 1.712 | 0.99 |
| 15_L | 50_Y | 1.563 | 0.98 |
| 11_R | 34_H | 1.547 | 0.98 |
| 35_Q | 57_A | 1.444 | 0.97 |
| 11_R | 14_V | 1.389 | 0.95 |
| 29_Q | 63_R | 1.380 | 0.95 |
| 37_E | 45_D | 1.369 | 0.95 |
| 27_N | 65_R | 1.351 | 0.95 |
| 3_I | 14_V | 1.340 | 0.94 |
| 41_A | 45_D | 1.306 | 0.93 |
| 8_R | 64_Y | 1.299 | 0.93 |
| 43_L | 50_Y | 1.266 | 0.92 |
| 14_V | 18_A | 1.229 | 0.90 |
| 40_F | 44_Q | 1.217 | 0.89 |
| 27_N | 67_T | 1.216 | 0.89 |
| 31_C | 61_D | 1.206 | 0.89 |
| 56_E | 63_R | 1.166 | 0.86 |
| 56_E | 61_D | 1.163 | 0.86 |
| 37_E | 41_A | 1.163 | 0.86 |
| 31_C | 65_R | 1.143 | 0.85 |
| 34_H | 38_P | 1.126 | 0.84 |
| 55_L | 63_R | 1.122 | 0.83 |
| 41_A | 64_Y | 1.107 | 0.82 |
| 37_E | 40_F | 1.101 | 0.82 |
| 23_P | 26_E | 1.098 | 0.82 |
| 15_L | 22_L | 1.092 | 0.81 |
| 1_L | 30_I | 1.058 | 0.78 |
| 16_F | 66_I | 1.055 | 0.78 |
| 47_T | 66_I | 1.025 | 0.75 |
| 30_I | 48_Q | 1.004 | 0.73 |
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 | |
| 1pavA | 1 | 0.9706 | 97.4 | 0.718 | Contact Map |
| 1jdqA | 1 | 0.9706 | 96.7 | 0.746 | Contact Map |
| 3hz7A | 1 | 0.9706 | 96.2 | 0.76 | Contact Map |
| 3lvjC | 2 | 0.9706 | 96.1 | 0.761 | Contact Map |
| 1je3A | 1 | 0.9559 | 95.4 | 0.775 | Contact Map |
| 2lxrA | 1 | 0.9559 | 91.3 | 0.808 | Contact Map |
| 1okgA | 1 | 0.6471 | 44.8 | 0.872 | Contact Map |
| 3sluA | 2 | 0.9853 | 17.9 | 0.895 | Contact Map |
| 1rqpA | 3 | 0.9118 | 12.6 | 0.902 | Contact Map |
| 3hnrA | 1 | 0.9706 | 10.1 | 0.906 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)