| gas protein low filter 8 iterations |
| ID: | 1424791476 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 70 (60) | ||
| Sequences: | 211 (98.6) | ||
| Seq/Len: | 3.517 | ||
| Nf(neff/√len): | 12.7 |
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: 3.517).
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 |
| 36_I | 41_I | 2.513 | 1.00 |
| 15_I | 18_I | 2.348 | 1.00 |
| 31_V | 39_L | 1.998 | 1.00 |
| 9_S | 23_I | 1.697 | 0.99 |
| 57_A | 61_G | 1.554 | 0.98 |
| 20_D | 51_E | 1.554 | 0.98 |
| 30_R | 36_I | 1.391 | 0.95 |
| 31_V | 52_T | 1.336 | 0.93 |
| 8_S | 18_I | 1.275 | 0.90 |
| 33_L | 47_I | 1.247 | 0.89 |
| 26_D | 48_A | 1.240 | 0.89 |
| 31_V | 37_E | 1.205 | 0.87 |
| 13_E | 54_L | 1.201 | 0.87 |
| 32_S | 63_T | 1.191 | 0.86 |
| 12_A | 47_I | 1.181 | 0.85 |
| 7_S | 11_L | 1.179 | 0.85 |
| 36_I | 43_A | 1.168 | 0.84 |
| 12_A | 20_D | 1.146 | 0.83 |
| 4_K | 15_I | 1.140 | 0.82 |
| 4_K | 13_E | 1.140 | 0.82 |
| 41_I | 45_I | 1.116 | 0.81 |
| 29_V | 58_E | 1.115 | 0.80 |
| 10_S | 62_L | 1.104 | 0.80 |
| 29_V | 42_E | 1.100 | 0.79 |
| 27_A | 55_K | 1.096 | 0.79 |
| 37_E | 49_S | 1.094 | 0.79 |
| 29_V | 54_L | 1.083 | 0.78 |
| 35_G | 49_S | 1.071 | 0.77 |
| 25_I | 52_T | 1.069 | 0.76 |
| 46_V | 50_V | 1.062 | 0.76 |
| 41_I | 47_I | 1.053 | 0.75 |
| 26_D | 36_I | 1.043 | 0.74 |
| 17_R | 56_Y | 1.041 | 0.74 |
| 46_V | 52_T | 1.031 | 0.73 |
| 9_S | 18_I | 1.017 | 0.71 |
| 12_A | 24_V | 1.012 | 0.71 |
| 25_I | 44_R | 1.005 | 0.70 |
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 | |
| 3cq5A | 3 | 0.7286 | 18.8 | 0.887 | Contact Map |
| 4lp7A | 4 | 0.8 | 8 | 0.904 | Contact Map |
| 2wnsA | 2 | 0.8714 | 7.7 | 0.905 | Contact Map |
| 3g79A | 2 | 1 | 7.6 | 0.905 | Contact Map |
| 2lnaA | 1 | 0.9429 | 7.1 | 0.906 | Contact Map |
| 4n0vA | 2 | 0.8143 | 6.7 | 0.907 | Contact Map |
| 4wbtA | 3 | 0.7714 | 6.3 | 0.908 | Contact Map |
| 3getA | 2 | 0.7 | 6.3 | 0.909 | Contact Map |
| 2yrrA | 2 | 0.7714 | 6.3 | 0.909 | Contact Map |
| 1ax4A | 4 | 1 | 6.1 | 0.909 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)