| kaib |
| ID: | 1450063541 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 105 (94) | ||
| Sequences: | 25049 (17651.2) | ||
| Seq/Len: | 266.479 | ||
| Nf(neff/√len): | 1820.6 |
Jackhmmer Results: (2015_08)
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: 266.479).
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 |
| 52_V | 59_V | 2.709 | 1.00 |
| 71_V | 80_V | 2.455 | 1.00 |
| 23_P | 26_Q | 2.241 | 1.00 |
| 35_I | 87_T | 2.173 | 1.00 |
| 91_A | 95_P | 2.051 | 1.00 |
| 12_P | 46_S | 2.019 | 1.00 |
| 52_V | 67_T | 2.010 | 1.00 |
| 79_Q | 93_Q | 2.001 | 1.00 |
| 77_S | 80_V | 1.992 | 1.00 |
| 86_L | 89_Q | 1.965 | 1.00 |
| 14_L | 46_S | 1.847 | 1.00 |
| 71_V | 77_S | 1.845 | 1.00 |
| 30_Q | 49_V | 1.836 | 1.00 |
| 14_L | 48_Q | 1.776 | 1.00 |
| 19_V | 49_V | 1.693 | 1.00 |
| 17_L | 49_V | 1.610 | 1.00 |
| 29_V | 70_L | 1.582 | 1.00 |
| 81_L | 85_D | 1.573 | 1.00 |
| 62_Y | 72_K | 1.555 | 1.00 |
| 32_V | 87_T | 1.518 | 1.00 |
| 32_V | 35_I | 1.507 | 1.00 |
| 87_T | 91_A | 1.507 | 1.00 |
| 41_A | 91_A | 1.406 | 0.99 |
| 18_F | 64_L | 1.375 | 0.99 |
| 41_A | 95_P | 1.372 | 0.99 |
| 17_L | 30_Q | 1.338 | 0.99 |
| 85_D | 89_Q | 1.333 | 0.99 |
| 89_Q | 92_N | 1.312 | 0.99 |
| 18_F | 62_Y | 1.284 | 0.99 |
| 40_E | 91_A | 1.278 | 0.99 |
| 51_N | 54_D | 1.212 | 0.98 |
| 55_Q | 58_L | 1.207 | 0.98 |
| 41_A | 44_P | 1.197 | 0.98 |
| 15_L | 70_L | 1.190 | 0.98 |
| 13_L | 73_I | 1.185 | 0.98 |
| 18_F | 52_V | 1.161 | 0.97 |
| 73_I | 78_R | 1.136 | 0.97 |
| 28_I | 84_I | 1.136 | 0.97 |
| 15_L | 33_K | 1.133 | 0.97 |
| 21_T | 51_N | 1.123 | 0.97 |
| 81_L | 93_Q | 1.116 | 0.96 |
| 93_Q | 97_W | 1.116 | 0.96 |
| 22_R | 53_A | 1.096 | 0.96 |
| 93_Q | 96_Q | 1.080 | 0.95 |
| 57_Q | 61_Y | 1.077 | 0.95 |
| 29_V | 85_D | 1.062 | 0.95 |
| 17_L | 29_V | 1.059 | 0.95 |
| 33_K | 47_L | 1.016 | 0.93 |
| 29_V | 32_V | 1.005 | 0.93 |
| 39_V | 91_A | 1.004 | 0.93 |
| 70_L | 90_L | 1.002 | 0.92 |
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 | |
| 3apoA | 1 | 0.9143 | 99.7 | 0.204 | Contact Map |
| 3f8uA | 2 | 0.9905 | 99.7 | 0.207 | Contact Map |
| 2b5eA | 1 | 0.9905 | 99.7 | 0.216 | Contact Map |
| 2r2jA | 1 | 0.9905 | 99.7 | 0.219 | Contact Map |
| 4ekzA | 1 | 0.9905 | 99.7 | 0.242 | Contact Map |
| 3apqA | 2 | 0.9905 | 99.7 | 0.242 | Contact Map |
| 4xhmA | 2 | 0 | 99.7 | 0.243 | Contact Map |
| 2qgvA | 10 | 0.9333 | 99.7 | 0.246 | Contact Map |
| 4kcaA | 2 | 0.9905 | 99.6 | 0.252 | Contact Map |
| 3gnjA | 4 | 0.9429 | 99.6 | 0.254 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)