| d3rnsa2 |
| ID: | 1448766206 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (87) | ||
| Sequences: | 8844 (5572.6) | ||
| Seq/Len: | 101.655 | ||
| Nf(neff/√len): | 597.4 |
HHblits Results: (2015_06)
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: 101.655).
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 |
| 59_K | 66_P | 3.662 | 1.00 |
| 59_K | 89_T | 2.880 | 1.00 |
| 59_K | 68_I | 2.845 | 1.00 |
| 59_K | 86_E | 2.636 | 1.00 |
| 57_E | 70_K | 2.585 | 1.00 |
| 55_D | 93_K | 2.565 | 1.00 |
| 57_E | 68_I | 2.553 | 1.00 |
| 58_G | 92_F | 2.230 | 1.00 |
| 61_Y | 84_A | 2.217 | 1.00 |
| 61_Y | 66_P | 2.201 | 1.00 |
| 63_D | 82_P | 2.161 | 1.00 |
| 55_D | 71_K | 2.071 | 1.00 |
| 86_E | 89_T | 2.034 | 1.00 |
| 61_Y | 86_E | 1.818 | 1.00 |
| 63_D | 81_I | 1.792 | 1.00 |
| 70_K | 73_E | 1.740 | 1.00 |
| 87_A | 90_E | 1.739 | 1.00 |
| 39_S | 86_E | 1.640 | 1.00 |
| 33_S | 93_K | 1.622 | 1.00 |
| 42_P | 82_P | 1.600 | 1.00 |
| 45_A | 83_H | 1.544 | 1.00 |
| 44_K | 82_P | 1.541 | 1.00 |
| 31_I | 93_K | 1.501 | 1.00 |
| 57_E | 90_E | 1.501 | 1.00 |
| 51_V | 75_A | 1.356 | 0.99 |
| 45_A | 49_A | 1.307 | 0.99 |
| 29_M | 50_L | 1.295 | 0.99 |
| 68_I | 89_T | 1.291 | 0.99 |
| 52_T | 74_S | 1.207 | 0.98 |
| 39_S | 84_A | 1.183 | 0.98 |
| 18_S | 30_T | 1.175 | 0.98 |
| 57_E | 89_T | 1.173 | 0.98 |
| 53_V | 69_V | 1.172 | 0.98 |
| 54_L | 95_L | 1.158 | 0.97 |
| 19_K | 31_I | 1.154 | 0.97 |
| 62_V | 65_K | 1.137 | 0.97 |
| 46_P | 80_N | 1.066 | 0.95 |
| 36_K | 90_E | 1.055 | 0.95 |
| 48_D | 76_V | 1.045 | 0.94 |
| 48_D | 79_A | 1.025 | 0.93 |
| 20_N | 28_V | 1.011 | 0.93 |
| 62_V | 81_I | 1.008 | 0.93 |
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 | |
| 2ozjA | 2 | 0.99 | 99.5 | 0.207 | Contact Map |
| 1v70A | 1 | 0.99 | 99.4 | 0.212 | Contact Map |
| 3rnsA | 1 | 0.99 | 99.4 | 0.227 | Contact Map |
| 1yhfA | 1 | 0.99 | 99.4 | 0.232 | Contact Map |
| 2q30A | 8 | 0.99 | 99.4 | 0.246 | Contact Map |
| 3h8uA | 2 | 0.99 | 99.4 | 0.248 | Contact Map |
| 2vpvA | 2 | 0.86 | 99.3 | 0.255 | Contact Map |
| 3fjsA | 4 | 0.99 | 99.3 | 0.262 | Contact Map |
| 2b8mA | 1 | 0.95 | 99.3 | 0.276 | Contact Map |
| 4bifA | 8 | 0.99 | 99.3 | 0.28 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)