| 3oss |
| ID: | 1500381927 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 65 (65) | ||
| Sequences: | 220 (144.7) | ||
| Seq/Len: | 3.385 | ||
| Nf(neff/√len): | 17.9 |
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: 3.385).
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 |
| 43_I | 46_I | 4.106 | 1.00 |
| 21_I | 51_V | 2.010 | 1.00 |
| 27_Q | 64_L | 1.860 | 0.99 |
| 2_T | 62_L | 1.807 | 0.99 |
| 2_T | 53_L | 1.786 | 0.99 |
| 21_I | 62_L | 1.651 | 0.98 |
| 50_H | 61_R | 1.601 | 0.98 |
| 53_L | 62_L | 1.382 | 0.94 |
| 8_L | 11_I | 1.347 | 0.93 |
| 61_R | 65_A | 1.342 | 0.93 |
| 2_T | 8_L | 1.341 | 0.93 |
| 18_G | 29_V | 1.307 | 0.91 |
| 9_R | 12_A | 1.273 | 0.90 |
| 42_V | 54_R | 1.252 | 0.89 |
| 2_T | 51_V | 1.250 | 0.89 |
| 39_H | 63_S | 1.243 | 0.88 |
| 41_A | 55_Y | 1.235 | 0.88 |
| 41_A | 64_L | 1.234 | 0.88 |
| 29_V | 39_H | 1.211 | 0.86 |
| 11_I | 26_K | 1.194 | 0.85 |
| 52_M | 61_R | 1.175 | 0.84 |
| 18_G | 34_E | 1.166 | 0.83 |
| 13_F | 21_I | 1.136 | 0.81 |
| 8_L | 21_I | 1.120 | 0.80 |
| 43_I | 51_V | 1.111 | 0.79 |
| 14_G | 34_E | 1.104 | 0.79 |
| 21_I | 60_E | 1.102 | 0.78 |
| 7_V | 31_L | 1.092 | 0.78 |
| 14_G | 50_H | 1.091 | 0.77 |
| 28_Q | 37_D | 1.070 | 0.76 |
| 1_E | 42_V | 1.065 | 0.75 |
| 22_E | 42_V | 1.045 | 0.73 |
| 42_V | 45_E | 1.036 | 0.72 |
| 3_R | 45_E | 1.035 | 0.72 |
| 50_H | 63_S | 1.024 | 0.71 |
| 42_V | 53_L | 1.006 | 0.69 |
| 48_R | 58_K | 1.003 | 0.69 |
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 | |
| 3ossC | 1 | 1 | 99.7 | 0.185 | Contact Map |
| 2lnvA | 1 | 1 | 99.7 | 0.204 | Contact Map |
| 4av2M | 12 | 1 | 79.2 | 0.796 | Contact Map |
| 2ivwA | 1 | 1 | 49 | 0.834 | Contact Map |
| 2lc4A | 1 | 1 | 48 | 0.835 | Contact Map |
| 2y4xA | 2 | 0.9846 | 38 | 0.845 | Contact Map |
| 2f5tX | 1 | 0.8462 | 14.2 | 0.874 | Contact Map |
| 3qphA | 1 | 0.8308 | 11.4 | 0.879 | Contact Map |
| 2fauA | 1 | 0.8154 | 6.9 | 0.89 | Contact Map |
| 4toiA | 1 | 0.5538 | 5.8 | 0.894 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)